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To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages. This file is where this pass\u0027s cyclomatic complexity CONCENTRATES: moments/LD/Matrices.py holds 4 of the 58 methods over the threshold \u2014 including the worst \u2014 and 315 of the 915 points over it (34%), 2.2\u00D7 the next-largest file (moments/Demes/Demes.py at 145). No single row can show this, because each is measured only against the threshold: reducing this one file moves this dimension further than any other file in the repository."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":995}}}],"partialFingerprints":{"codehealthFindingId/v1":"4d031274510471e17f627e8e9a10f7c7893b04abd7f8d0a235c4aa16bddc8b73"}},{"ruleId":"D1","level":"warning","message":{"text":"Matrices.migration_ld (cyclomatic 103): Matrices.migration_ld has cyclomatic complexity 103 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top. 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To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":17}}}],"partialFingerprints":{"codehealthFindingId/v1":"0dcfb5d2397d1f568cd3fa026dc97c42592447d2c85c59665094ca7a9cad96c4"}},{"ruleId":"D1","level":"warning","message":{"text":"Parsing._tally_vcf (cyclomatic 72): Parsing._tally_vcf has cyclomatic complexity 72 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":317}}}],"partialFingerprints":{"codehealthFindingId/v1":"4c1b34d0ec14a629b14dbe15ff95feeff5767fa389f025347b3ce4cb1eb29cf2"}},{"ruleId":"D1","level":"warning","message":{"text":"Parsing._count_types_sparse (cyclomatic 43): Parsing._count_types_sparse has cyclomatic complexity 43 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":549}}}],"partialFingerprints":{"codehealthFindingId/v1":"08c2f9ddc11b573910eb2c83250b38ce999d4b5ac16ba0db5ba8e190336a3316"}},{"ruleId":"D1","level":"warning","message":{"text":"Demes._get_deme_sample_sizes (cyclomatic 40): Demes._get_deme_sample_sizes has cyclomatic complexity 40 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1023}}}],"partialFingerprints":{"codehealthFindingId/v1":"436216fe4b512f915c3724a621087d424b9ea40dcbddc5011a2a8f907540ee68"}},{"ruleId":"D1","level":"warning","message":{"text":"Matrices.drift_ld (cyclomatic 40): Matrices.drift_ld has cyclomatic complexity 40 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline. This file is where this pass\u0027s cyclomatic complexity CONCENTRATES: moments/LD/Matrices.py holds 4 of the 58 methods over the threshold \u2014 including the worst \u2014 and 315 of the 915 points over it (34%), 2.2\u00D7 the next-largest file (moments/Demes/Demes.py at 145). No single row can show this, because each is measured only against the threshold: reducing this one file moves this dimension further than any other file in the repository."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":35}}}],"partialFingerprints":{"codehealthFindingId/v1":"9b922d351ddb8c4e54b3da02e5294bf5fd1784b5b8039cd5d21cf7b7c76267a1"}},{"ruleId":"D1","level":"warning","message":{"text":"Jackknife.closest_ijk_edges (cyclomatic 39): Jackknife.closest_ijk_edges has cyclomatic complexity 39 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":267}}}],"partialFingerprints":{"codehealthFindingId/v1":"b7fed46560375751814b96b9584418012719d4499a0e0ec757fb165fc7df2c46"}},{"ruleId":"D1","level":"warning","message":{"text":"Integration.integrate_nD (cyclomatic 37): Integration.integrate_nD has cyclomatic complexity 37 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":889}}}],"partialFingerprints":{"codehealthFindingId/v1":"e514aaa8b5ca26457b12042fc74bdb9a265fe3b010726da317b987a5964b1741"}},{"ruleId":"D1","level":"warning","message":{"text":"Misc.make_data_dict_vcf (cyclomatic 37): Misc.make_data_dict_vcf has cyclomatic complexity 37 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":409}}}],"partialFingerprints":{"codehealthFindingId/v1":"b5c9d1d05c883b0095d9a60802fff9d77dfaeb047628eac13cfebe209f5df4a4"}},{"ruleId":"D1","level":"warning","message":{"text":"Integration.integrate (cyclomatic 36): Integration.integrate has cyclomatic complexity 36 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Integration.py"},"region":{"startLine":15}}}],"partialFingerprints":{"codehealthFindingId/v1":"66ff0943724041c190aa15446e8f1440e5a9b089e730eba76b3940aa706e8883"}},{"ruleId":"D1","level":"warning","message":{"text":"ModelPlot.plot_model (cyclomatic 34): ModelPlot.plot_model has cyclomatic complexity 34 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/ModelPlot.py"},"region":{"startLine":82}}}],"partialFingerprints":{"codehealthFindingId/v1":"3dc129bb7cf7eeb25aec7e6761dfaf710803fe10e4d7724ea163560a46e78186"}},{"ruleId":"D1","level":"warning","message":{"text":"Plotting.plot_ld_curves_comp (cyclomatic 32): Plotting.plot_ld_curves_comp has cyclomatic complexity 32 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Plotting.py"},"region":{"startLine":120}}}],"partialFingerprints":{"codehealthFindingId/v1":"f88477fd46e338d0986643e83f68e9fd71c8578d604fc44bb776242d9e64ea59"}},{"ruleId":"D1","level":"warning","message":{"text":"Demes.LD (cyclomatic 31): Demes.LD has cyclomatic complexity 31 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":387}}}],"partialFingerprints":{"codehealthFindingId/v1":"57f4a34282daab74c97e2137f1b60db05253cdb871ba79e2afce95badeb60a3d"}},{"ruleId":"D1","level":"warning","message":{"text":"Jackknife.calc_jk (cyclomatic 31): Jackknife.calc_jk has cyclomatic complexity 31 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":887}}}],"partialFingerprints":{"codehealthFindingId/v1":"afb8669a6d80aefa0a21be3154a4414d222deaae93376c4fa705f194deda7502"}},{"ruleId":"D1","level":"warning","message":{"text":"Demes.LDdecay (cyclomatic 27): Demes.LDdecay has cyclomatic complexity 27 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":543}}}],"partialFingerprints":{"codehealthFindingId/v1":"94bf320a7f472d25b8465690309248529506cd122950f0e600fa0304f9ad9da0"}},{"ruleId":"D1","level":"warning","message":{"text":"LDstats.integrate (cyclomatic 27): LDstats.integrate has cyclomatic complexity 27 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":961}}}],"partialFingerprints":{"codehealthFindingId/v1":"86004509efe93f364af6656c4bc0c9e482f95471bf7173197e49982a9ba03694"}},{"ruleId":"D1","level":"warning","message":{"text":"Misc.bootstrap (cyclomatic 27): Misc.bootstrap has cyclomatic complexity 27 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":672}}}],"partialFingerprints":{"codehealthFindingId/v1":"98c4e296947495edb301608b0a972ca7a7e329884beaeb83cec74fd164d3c9b4"}},{"ruleId":"D1","level":"warning","message":{"text":"Jackknife.closest_ijk (cyclomatic 27): Jackknife.closest_ijk has cyclomatic complexity 27 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":51}}}],"partialFingerprints":{"codehealthFindingId/v1":"7a67231b92d057e16888a1d199d8d7ca74871b0dd52652a9d6e8c127680f91e9"}},{"ruleId":"D1","level":"warning","message":{"text":"Demes._get_demographic_events (cyclomatic 26): Demes._get_demographic_events has cyclomatic complexity 26 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":745}}}],"partialFingerprints":{"codehealthFindingId/v1":"81f1952cef730d7017eb84ef06d9d6f3c8f496dda5cf4f7d568c3d473fce6bce"}},{"ruleId":"D1","level":"warning","message":{"text":"Demes._compute_sfs (cyclomatic 26): Demes._compute_sfs has cyclomatic complexity 26 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1165}}}],"partialFingerprints":{"codehealthFindingId/v1":"c6e6ca9a6332b29c2899bf1f25aad7fecc5af59edda33029edac52717cb27f72"}},{"ruleId":"D1","level":"warning","message":{"text":"Integration_nomig.integrate_nomig (cyclomatic 26): Integration_nomig.integrate_nomig has cyclomatic complexity 26 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration_nomig.py"},"region":{"startLine":402}}}],"partialFingerprints":{"codehealthFindingId/v1":"cbfd9cd82d4758a30f0914c07ed306d723113336eec59b34bf602cf4050de8e8"}},{"ruleId":"D1","level":"warning","message":{"text":"Numerics.integrate (cyclomatic 26): Numerics.integrate has cyclomatic complexity 26 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Numerics.py"},"region":{"startLine":192}}}],"partialFingerprints":{"codehealthFindingId/v1":"6e48228f046595a3231207a34ae93085b53f47a3d9dc4678ca2c9f9dc466b347"}},{"ruleId":"D1","level":"warning","message":{"text":"Spectrum.integrate (cyclomatic 26): Spectrum.integrate has cyclomatic complexity 26 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":672}}}],"partialFingerprints":{"codehealthFindingId/v1":"69ddc124676a1aaa1d537e14cff3381dc8a4aacfec27e328c4b04c4035f11967"}},{"ruleId":"D1","level":"warning","message":{"text":"Jackknife.closest_ijk_sides (cyclomatic 25): Jackknife.closest_ijk_sides has cyclomatic complexity 25 (threshold 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":141}}}],"partialFingerprints":{"codehealthFindingId/v1":"6bd5d26fe5d9a3e80a73a1f25b85fec503407f8b69c234af9f76ee5f73851dfe"}},{"ruleId":"D1","level":"warning","message":{"text":"Inference._set_value (cyclomatic 24): Inference._set_value has cyclomatic complexity 24 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":133}}}],"partialFingerprints":{"codehealthFindingId/v1":"ef921fbd8cd9db0693486add0b9ba78d263aafd37c3e73b4cf3a3f8f27345073"}},{"ruleId":"D1","level":"warning","message":{"text":"Numerics.steady_state (cyclomatic 24): Numerics.steady_state has cyclomatic complexity 24 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Numerics.py"},"region":{"startLine":380}}}],"partialFingerprints":{"codehealthFindingId/v1":"fc3f98180316dd7c8ee83698253453ce41800be06c81b6a63f337e97faee6804"}},{"ruleId":"D1","level":"warning","message":{"text":"stats_from_genotype_counts.pi2 (cyclomatic 24): stats_from_genotype_counts.pi2 has cyclomatic complexity 24 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":468}}}],"partialFingerprints":{"codehealthFindingId/v1":"ffd9dd6093dae3bcc1bcd5b8c9b04c88894ffe0a4272ff955c01aba857f84fd5"}},{"ruleId":"D1","level":"warning","message":{"text":"Spectrum.f4 (cyclomatic 24): Spectrum.f4 has cyclomatic complexity 24 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1206}}}],"partialFingerprints":{"codehealthFindingId/v1":"02b461c8aa1ca3cca2335d35fccf9e9e6698d027f0fe9895a56308c1101f9fe0"}},{"ruleId":"D1","level":"warning","message":{"text":"Numerics.drift (cyclomatic 24): Numerics.drift has cyclomatic complexity 24 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":68}}}],"partialFingerprints":{"codehealthFindingId/v1":"a8d39555de5bb8ead349202718adedd8c04a6988f23c12fc8ee397e9e8f99f42"}},{"ruleId":"D1","level":"warning","message":{"text":"Inference._get_value (cyclomatic 23): Inference._get_value has cyclomatic complexity 23 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":60}}}],"partialFingerprints":{"codehealthFindingId/v1":"04e57052090761b1031fc8187cdf4791f2afaf7f3821ee0804789ea4eb4f2ec6"}},{"ruleId":"D1","level":"warning","message":{"text":"Inference._object_func (cyclomatic 23): Inference._object_func has cyclomatic complexity 23 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Inference.py"},"region":{"startLine":295}}}],"partialFingerprints":{"codehealthFindingId/v1":"244bfd7922ed6a8da3b2026be4d04571016100bb85899455814f2bb9003982d6"}},{"ruleId":"D1","level":"warning","message":{"text":"stats_from_haplotype_counts.pi2 (cyclomatic 23): stats_from_haplotype_counts.pi2 has cyclomatic complexity 23 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_haplotype_counts.py"},"region":{"startLine":105}}}],"partialFingerprints":{"codehealthFindingId/v1":"d3d5a6f690ea47a603735feb169ecf664c85b67cd428ad745a5d60402b6eba26"}},{"ruleId":"D1","level":"warning","message":{"text":"Plotting.plot_3d_spectrum (cyclomatic 23): Plotting.plot_3d_spectrum has cyclomatic complexity 23 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":803}}}],"partialFingerprints":{"codehealthFindingId/v1":"353c5a1677e31acf914193858f368f1a6af8758a813f99e9221580ab8c154c6d"}},{"ruleId":"D1","level":"warning","message":{"text":"Plotting.plot_4d_comp_Poisson (cyclomatic 21): Plotting.plot_4d_comp_Poisson has cyclomatic complexity 21 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":997}}}],"partialFingerprints":{"codehealthFindingId/v1":"0ae8869f7185f4db5dabf4d1ddad333f13a73d1fb57c98cfedd554afb801d608"}},{"ruleId":"D1","level":"warning","message":{"text":"Integration.integrate_cn (cyclomatic 21): Integration.integrate_cn has cyclomatic complexity 21 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Integration.py"},"region":{"startLine":29}}}],"partialFingerprints":{"codehealthFindingId/v1":"9501f431c0c3a502b1c87bb0739bf5ba8635d221fd29cddfc0a16c9c97fd8eeb"}},{"ruleId":"D1","level":"warning","message":{"text":"Inference.optimize (cyclomatic 20): Inference.optimize has cyclomatic complexity 20 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":419}}}],"partialFingerprints":{"codehealthFindingId/v1":"9a481beb4b18f9682a0fc13974a81d9823ab3da1c39aff8f49c15c1a3e4d559f"}},{"ruleId":"D1","level":"warning","message":{"text":"Integration_nomig.integrate_neutral (cyclomatic 20): Integration_nomig.integrate_neutral has cyclomatic complexity 20 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration_nomig.py"},"region":{"startLine":644}}}],"partialFingerprints":{"codehealthFindingId/v1":"06111511c3fa4dc324520c60f0f4d3104d61eab2f68975ade9606ddef2020f68"}},{"ruleId":"D1","level":"warning","message":{"text":"Parsing.get_genotypes (cyclomatic 20): Parsing.get_genotypes has cyclomatic complexity 20 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":98}}}],"partialFingerprints":{"codehealthFindingId/v1":"6fa55028e2ef0bc04f56130db5671bc43f17e05f458aabf3edf345eafb05b128"}},{"ruleId":"D1","level":"warning","message":{"text":"Util.rescale_params (cyclomatic 20): Util.rescale_params has cyclomatic complexity 20 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Util.py"},"region":{"startLine":150}}}],"partialFingerprints":{"codehealthFindingId/v1":"e056585526ef3582137da98beb144ba51c506f60b66bf8aa5872a3ee2df97f8c"}},{"ruleId":"D1","level":"warning","message":{"text":"Parsing._parse_filters (cyclomatic 20): Parsing._parse_filters has cyclomatic complexity 20 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":683}}}],"partialFingerprints":{"codehealthFindingId/v1":"f9787402e1e9b37aa364788d417f6b90704675ca05f2c68199a5dc9c71777307"}},{"ruleId":"D1","level":"warning","message":{"text":"Plotting.plot_3d_comp_Poisson (cyclomatic 20): Plotting.plot_3d_comp_Poisson has cyclomatic complexity 20 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":634}}}],"partialFingerprints":{"codehealthFindingId/v1":"47086de59b1b224fd48d0c0f1e4c2dc8b0e5d26c4b11d3864eb36248b971feab"}},{"ruleId":"D1","level":"warning","message":{"text":"Spectrum.__new__ (cyclomatic 20): Spectrum.__new__ has cyclomatic complexity 20 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":78}}}],"partialFingerprints":{"codehealthFindingId/v1":"981c134c0b6caaf32b4329794b4924260a3515810778ab0611ca5ab1ad7dfab4"}},{"ruleId":"D1","level":"warning","message":{"text":"Parsing._call_sgc (cyclomatic 19): Parsing._call_sgc has cyclomatic complexity 19 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":790}}}],"partialFingerprints":{"codehealthFindingId/v1":"7714b9cb9770ab923ae4ff4cba20e6fd5dc283f1c8bcd0a40ea5b43c479ef6d9"}},{"ruleId":"D1","level":"warning","message":{"text":"Spectrum.f3 (cyclomatic 19): Spectrum.f3 has cyclomatic complexity 19 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1134}}}],"partialFingerprints":{"codehealthFindingId/v1":"37a83cb43033cc3d0324181f7265d07dd81763ee49595bedfac31684ab0abddc"}},{"ruleId":"D1","level":"warning","message":{"text":"Demes._augment_with_ancient_samples (cyclomatic 18): Demes._augment_with_ancient_samples has cyclomatic complexity 18 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":683}}}],"partialFingerprints":{"codehealthFindingId/v1":"59631ecb825fa6d5aae7760ae9e10ad4956fc103cb3a1c1f37821ec3bfab52a9"}},{"ruleId":"D1","level":"warning","message":{"text":"LDstats.to_file (cyclomatic 18): LDstats.to_file has cyclomatic complexity 18 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":671}}}],"partialFingerprints":{"codehealthFindingId/v1":"f4e917e13df3226a76e915a9ed97fdc30cf94b2f82d3b4bac7676acd13f2252a"}},{"ruleId":"D1","level":"warning","message":{"text":"Inference.optimize_LD (cyclomatic 17): Inference.optimize_LD has cyclomatic complexity 17 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":1018}}}],"partialFingerprints":{"codehealthFindingId/v1":"fe5bdd55636490dd13846e7fb1a797dd7719966d0f7d96e8998d8315fcdbeaac"}},{"ruleId":"D1","level":"warning","message":{"text":"Util._compute_D (cyclomatic 17): Util._compute_D has cyclomatic complexity 17 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top. This shape REPEATS in the file: 3 other methods here (Util._compute_D2, Util._compute_Dz, Util._compute_pi2) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":125}}}],"partialFingerprints":{"codehealthFindingId/v1":"050fc5146a52fdc1f911402fe1963d8b42e116ad0ef5a21bc6a87299128e8f99"}},{"ruleId":"D1","level":"warning","message":{"text":"Util._compute_D2 (cyclomatic 17): Util._compute_D2 has cyclomatic complexity 17 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top. This shape REPEATS in the file: 3 other methods here (Util._compute_D, Util._compute_Dz, Util._compute_pi2) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":159}}}],"partialFingerprints":{"codehealthFindingId/v1":"ff111bb16ecea57d2992813200ba734c95a42ad0fc89f3cea7861b78eb4f4534"}},{"ruleId":"D1","level":"warning","message":{"text":"Util._compute_Dz (cyclomatic 17): Util._compute_Dz has cyclomatic complexity 17 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top. This shape REPEATS in the file: 3 other methods here (Util._compute_D, Util._compute_D2, Util._compute_pi2) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":222}}}],"partialFingerprints":{"codehealthFindingId/v1":"a3b8f2963b0cc486c38045472b17fe43635a147d028e926130492913c499d594"}},{"ruleId":"D1","level":"warning","message":{"text":"Util._compute_pi2 (cyclomatic 17): Util._compute_pi2 has cyclomatic complexity 17 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top. This shape REPEATS in the file: 3 other methods here (Util._compute_D, Util._compute_D2, Util._compute_Dz) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":321}}}],"partialFingerprints":{"codehealthFindingId/v1":"40c0293c83e43e94fe44c52c889d18a450571503b0fd6a8ba245a25167ff4cc1"}},{"ruleId":"D1","level":"warning","message":{"text":"Matrices.mutation_ld (cyclomatic 16): Matrices.mutation_ld has cyclomatic complexity 16 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top. This file is where this pass\u0027s cyclomatic complexity CONCENTRATES: moments/LD/Matrices.py holds 4 of the 58 methods over the threshold \u2014 including the worst \u2014 and 315 of the 915 points over it (34%), 2.2\u00D7 the next-largest file (moments/Demes/Demes.py at 145). No single row can show this, because each is measured only against the threshold: reducing this one file moves this dimension further than any other file in the repository."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":258}}}],"partialFingerprints":{"codehealthFindingId/v1":"c4a105c2d799fd197143fbf77f599741835a6eb008babeee1200d95e1c87a983"}},{"ruleId":"D1","level":"warning","message":{"text":"Parsing.subset_data (cyclomatic 16): Parsing.subset_data has cyclomatic complexity 16 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":1504}}}],"partialFingerprints":{"codehealthFindingId/v1":"31463260aa2e8e7feea82d66dd5cb5fc85f4fada3bf608d17c27b10cd991b367"}},{"ruleId":"D1","level":"warning","message":{"text":"Plotting.plot_ld_curves (cyclomatic 16): Plotting.plot_ld_curves has cyclomatic complexity 16 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Plotting.py"},"region":{"startLine":23}}}],"partialFingerprints":{"codehealthFindingId/v1":"ab556fb8e3fe75aed937dd043891351a67b2edf991841f4c1750cebd2c47a81c"}},{"ruleId":"D1","level":"warning","message":{"text":"Plotting.plot_2d_comp_Poisson (cyclomatic 16): Plotting.plot_2d_comp_Poisson has cyclomatic complexity 16 (threshold 15). To reduce it, split the body: these branches sit side by side rather than nested inside one another, so extracting each one on its own would leave a function per branch. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":439}}}],"partialFingerprints":{"codehealthFindingId/v1":"3ee6953a279b136376c23d94dd7b0e919b9af29a462086e43e0f7012fffd0b68"}},{"ruleId":"D1","level":"warning","message":{"text":"TriSpectrum.fold_ancestral (cyclomatic 16): TriSpectrum.fold_ancestral has cyclomatic complexity 16 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/TriSpectrum_mod.py"},"region":{"startLine":346}}}],"partialFingerprints":{"codehealthFindingId/v1":"67afe2b5b18c6165a0c5cba0d7357e85a42a93c728b028b1c7c4b2afbdb7aca7"}},{"ruleId":"D1","level":"warning","message":{"text":"Numerics.drift_reversible (cyclomatic 16): Numerics.drift_reversible has cyclomatic complexity 16 (threshold 15). To reduce it, separate the cases: extract each independent branch into its own named function, and where the body has guards that only reject input, fold those into early returns at the top."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":960}}}],"partialFingerprints":{"codehealthFindingId/v1":"f7b3add336c585367ade5291448a2d7ced0f16b9abfd543cef5ce95cc5b60bd9"}},{"ruleId":"D2","level":"warning","message":{"text":"Matrices.migration_ld (cognitive 358): Matrices.migration_ld has cognitive complexity 358 (threshold 15). Drivers by points: if/else 59 (264 pts), loops 25 (92 pts), boolean chains 2 (nesting depth added 272). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":415}}}],"partialFingerprints":{"codehealthFindingId/v1":"8f10ca87ee26916df4e7c8a8982668be1c818828e84138a1e01a5a84dd23010d"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._tally_vcf (cognitive 158): Parsing._tally_vcf has cognitive complexity 158 (threshold 15). Drivers by points: if/else 57 (130 pts), loops 8 (20 pts), boolean chains 8 (nesting depth added 85). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":317}}}],"partialFingerprints":{"codehealthFindingId/v1":"91f1e226de1fcde650806db854aa2fc83779681e8a266e97e520f30bb5817c41"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes.SFS (cognitive 152): Demes.SFS has cognitive complexity 152 (threshold 15). Drivers by points: if/else 65 (113 pts), loops 13 (27 pts), boolean chains 12 (nesting depth added 62). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":17}}}],"partialFingerprints":{"codehealthFindingId/v1":"f0a8cf64880eae8f95ae23210d815904b55c2d7f0266b715da27d99be20db20e"}},{"ruleId":"D2","level":"warning","message":{"text":"Matrices.admix_ld (cognitive 134): Matrices.admix_ld has cognitive complexity 134 (threshold 15). Drivers by points: boolean chains 82, if/else 19 (51 pts), loops 1 (nesting depth added 32). To reduce it, name the conditions: bind each compound test to a well-named local or a small predicate function, so the body reads as a sequence of named decisions rather than a chain of operators."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":995}}}],"partialFingerprints":{"codehealthFindingId/v1":"c2bc2e00cf9b26a5aa65872937ffcf687f346a1c3af5ec76107f5a637dfe5738"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes._get_deme_sample_sizes (cognitive 123): Demes._get_deme_sample_sizes has cognitive complexity 123 (threshold 15). Drivers by points: if/else 13 (65 pts), loops 15 (52 pts), boolean chains 6 (nesting depth added 89). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1023}}}],"partialFingerprints":{"codehealthFindingId/v1":"f53101cd98cfeb86af888ef016e96ce857f3bc6bf814c52ee5a84d6c9fd7d5b1"}},{"ruleId":"D2","level":"warning","message":{"text":"Jackknife.calc_jk (cognitive 112): Jackknife.calc_jk has cognitive complexity 112 (threshold 15). Drivers by points: loops 28 (108 pts), if/else 2 (3 pts), error handling 1 (nesting depth added 81). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":887}}}],"partialFingerprints":{"codehealthFindingId/v1":"bcae1a6eef916052da3340f84a04c6a4a0c1ea607e5ef86d228d33375e5d7f8c"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._count_types_sparse (cognitive 99): Parsing._count_types_sparse has cognitive complexity 99 (threshold 15). Drivers by points: if/else 31 (53 pts), loops 18 (44 pts), error handling 1 (2 pts) (nesting depth added 49). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":549}}}],"partialFingerprints":{"codehealthFindingId/v1":"da2666d1f021a34a2b241a12a842b21ccd67cf649617c127724e2f6a22fa8337"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference._set_value (cognitive 88): Inference._set_value has cognitive complexity 88 (threshold 15). Drivers by points: if/else 13 (48 pts), loops 7 (27 pts), error handling 2 (13 pts) (nesting depth added 66). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. Invert each enclosing check into an early exit (a return, or the language\u0027s equivalent) so the happy path stays at one level, and where a level cannot be exited early, lift the block it encloses into its own named function."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":133}}}],"partialFingerprints":{"codehealthFindingId/v1":"1c113f8127c8427e705dce824ad3c2d5faab47dd6ae6b1d9038e5bda289767e0"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.drift (cognitive 84): Numerics.drift has cognitive complexity 84 (threshold 15). Drivers by points: if/else 16 (75 pts), loops 3 (6 pts), boolean chains 3 (nesting depth added 62). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":68}}}],"partialFingerprints":{"codehealthFindingId/v1":"caa57f580507748f79037b89c8979e6243cfce9a6d9ab0c5453bdbdb646c5325"}},{"ruleId":"D2","level":"warning","message":{"text":"Misc.make_data_dict_vcf (cognitive 81): Misc.make_data_dict_vcf has cognitive complexity 81 (threshold 15). Drivers by points: if/else 24 (63 pts), loops 4 (7 pts), boolean chains 6, ternaries 1 (3 pts), error handling 1 (2 pts) (nesting depth added 45). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":409}}}],"partialFingerprints":{"codehealthFindingId/v1":"a4efa5520baa57c36af8edc8873050e7c90903451a8d50c9e7dd8ac48ea571ed"}},{"ruleId":"D2","level":"warning","message":{"text":"Integration.integrate_nD (cognitive 80): Integration.integrate_nD has cognitive complexity 80 (threshold 15). Drivers by points: if/else 39 (61 pts), loops 5 (17 pts), boolean chains 2 (nesting depth added 34). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":889}}}],"partialFingerprints":{"codehealthFindingId/v1":"c36491b2da559315fbad605b87a30b8c8a556e94793669f3973e9a301ce39673"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference._get_value (cognitive 76): Inference._get_value has cognitive complexity 76 (threshold 15). Drivers by points: if/else 13 (36 pts), loops 7 (27 pts), error handling 2 (13 pts) (nesting depth added 54). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. Invert each enclosing check into an early exit (a return, or the language\u0027s equivalent) so the happy path stays at one level, and where a level cannot be exited early, lift the block it encloses into its own named function."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":60}}}],"partialFingerprints":{"codehealthFindingId/v1":"f610c0c850bf63ef520135ea25e2930871890e8bc309b37a78c83d761159bfad"}},{"ruleId":"D2","level":"warning","message":{"text":"ModelPlot.plot_model (cognitive 71): ModelPlot.plot_model has cognitive complexity 71 (threshold 15). Drivers by points: if/else 25 (40 pts), ternaries 5 (15 pts), loops 6 (13 pts), boolean chains 3 (nesting depth added 32). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/ModelPlot.py"},"region":{"startLine":82}}}],"partialFingerprints":{"codehealthFindingId/v1":"03add7e1d209cb9065d761d306b8019f73b2a0d72eba4f5fe1873e6ea3e4c80d"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes._augment_with_ancient_samples (cognitive 68): Demes._augment_with_ancient_samples has cognitive complexity 68 (threshold 15). Drivers by points: if/else 10 (46 pts), loops 5 (21 pts), boolean chains 1 (nesting depth added 52). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. Invert each enclosing check into an early exit (a return, or the language\u0027s equivalent) so the happy path stays at one level, and where a level cannot be exited early, lift the block it encloses into its own named function."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":683}}}],"partialFingerprints":{"codehealthFindingId/v1":"7aff1f038dfc6dc12e394f5fc67871c382882e4a170d569c52e68fa3c7b4a803"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.integrate (cognitive 65): Numerics.integrate has cognitive complexity 65 (threshold 15). Drivers by points: if/else 30 (61 pts), boolean chains 3, loops 1 (nesting depth added 31). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. Invert each enclosing check into an early exit (a return, or the language\u0027s equivalent) so the happy path stays at one level, and where a level cannot be exited early, lift the block it encloses into its own named function."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Numerics.py"},"region":{"startLine":192}}}],"partialFingerprints":{"codehealthFindingId/v1":"77884e325d561bd01d0abec3754e2c5661a00fccf487bacb12f31b6c4258e55a"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._parse_filters (cognitive 65): Parsing._parse_filters has cognitive complexity 65 (threshold 15). Drivers by points: if/else 17 (53 pts), loops 3 (9 pts), error handling 1 (3 pts) (nesting depth added 44). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":683}}}],"partialFingerprints":{"codehealthFindingId/v1":"0e96d0c6f0e0df75daf5c82be83f55722a89bc581321fad2ba828a2208463997"}},{"ruleId":"D2","level":"warning","message":{"text":"Misc.bootstrap (cognitive 62): Misc.bootstrap has cognitive complexity 62 (threshold 15). Drivers by points: if/else 14 (33 pts), loops 9 (22 pts), ternaries 2 (5 pts), boolean chains 2 (nesting depth added 35). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":672}}}],"partialFingerprints":{"codehealthFindingId/v1":"481d1a39be5276e429541a2c8bc0505b3872696d67431ef8c178640add022435"}},{"ruleId":"D2","level":"warning","message":{"text":"Integration.integrate (cognitive 62): Integration.integrate has cognitive complexity 62 (threshold 15). Drivers by points: if/else 33 (56 pts), boolean chains 5, loops 1 (nesting depth added 23). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Integration.py"},"region":{"startLine":15}}}],"partialFingerprints":{"codehealthFindingId/v1":"ba1f671f29e75f099173feb07e6aae7782d50107d6b6c979bc6af1efb42fd720"}},{"ruleId":"D2","level":"warning","message":{"text":"Matrices.drift_ld (cognitive 61): Matrices.drift_ld has cognitive complexity 61 (threshold 15). Drivers by points: loops 11 (39 pts), if/else 10 (20 pts), boolean chains 2 (nesting depth added 38). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":35}}}],"partialFingerprints":{"codehealthFindingId/v1":"3105f71505f52c814308400d2317346c0a51e212e4d6f610b1303f3e7676d9e3"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes._compute_sfs (cognitive 58): Demes._compute_sfs has cognitive complexity 58 (threshold 15). Drivers by points: if/else 21 (34 pts), loops 5 (15 pts), ternaries 2 (8 pts), boolean chains 1 (nesting depth added 29). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1165}}}],"partialFingerprints":{"codehealthFindingId/v1":"393abe3adec54d36e832c3466676f87aa23379c98bc561ab8dc9d793e079e1ac"}},{"ruleId":"D2","level":"warning","message":{"text":"Integration_nomig.integrate_nomig (cognitive 56): Integration_nomig.integrate_nomig has cognitive complexity 56 (threshold 15). Drivers by points: if/else 28 (47 pts), loops 3 (8 pts), boolean chains 1 (nesting depth added 24). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration_nomig.py"},"region":{"startLine":402}}}],"partialFingerprints":{"codehealthFindingId/v1":"7952bd3c8a5e5c63e533ae7466b2082304689d299b72c64974f80ad2ae9574b1"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_3d_spectrum (cognitive 54): Plotting.plot_3d_spectrum has cognitive complexity 54 (threshold 15). Drivers by points: if/else 20 (42 pts), boolean chains 6, loops 3 (6 pts) (nesting depth added 25). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":803}}}],"partialFingerprints":{"codehealthFindingId/v1":"8890745c737607b006d20ba22ec98dc6fcfe9cf5116805b55fa11a5d42b410f0"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.drift_reversible (cognitive 54): Numerics.drift_reversible has cognitive complexity 54 (threshold 15). Drivers by points: if/else 12 (48 pts), loops 3 (6 pts) (nesting depth added 39). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":960}}}],"partialFingerprints":{"codehealthFindingId/v1":"5857b699c72e321dc5dd61b27ff830b57de2b1780048189e2ce4db0416c8e5fa"}},{"ruleId":"D2","level":"warning","message":{"text":"LinearSystem.calcM_jk3 (cognitive 52): LinearSystem.calcM_jk3 has cognitive complexity 52 (threshold 15). Drivers by points: if/else 10 (45 pts), loops 4 (7 pts) (nesting depth added 38). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LinearSystem.py"},"region":{"startLine":263}}}],"partialFingerprints":{"codehealthFindingId/v1":"8f32db4ac83b445c74f4d02bf4de0995e9c4c0ea3bf326f9cf28c70c72bbe356"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_ld_curves_comp (cognitive 51): Plotting.plot_ld_curves_comp has cognitive complexity 51 (threshold 15). Drivers by points: if/else 22 (34 pts), loops 6 (13 pts), boolean chains 4 (nesting depth added 19). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Plotting.py"},"region":{"startLine":120}}}],"partialFingerprints":{"codehealthFindingId/v1":"c4bad64f8b7be174842833b6c23cf527f2f74357e22f618f8443ad1d54b4f3fe"}},{"ruleId":"D2","level":"warning","message":{"text":"Integration_nomig.integrate_neutral (cognitive 48): Integration_nomig.integrate_neutral has cognitive complexity 48 (threshold 15). Drivers by points: if/else 20 (36 pts), loops 4 (11 pts), boolean chains 1 (nesting depth added 23). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration_nomig.py"},"region":{"startLine":644}}}],"partialFingerprints":{"codehealthFindingId/v1":"8c4b74fbc2fee15be02517563c8c239301ae5305fd4bdc9e84fd3480a2079e99"}},{"ruleId":"D2","level":"warning","message":{"text":"Util._compute_D (cognitive 48): Util._compute_D has cognitive complexity 48 (threshold 15). Drivers by points: if/else 10 (32 pts), loops 4 (11 pts), boolean chains 5 (nesting depth added 29). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: 3 other methods here (Util._compute_D2, Util._compute_Dz, Util._compute_pi2) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":125}}}],"partialFingerprints":{"codehealthFindingId/v1":"aafb0c60f53240b418f2ae16e2e28bd340ac0ca7fcafc650b41e726d53059562"}},{"ruleId":"D2","level":"warning","message":{"text":"Util._compute_D2 (cognitive 48): Util._compute_D2 has cognitive complexity 48 (threshold 15). Drivers by points: if/else 10 (32 pts), loops 4 (11 pts), boolean chains 5 (nesting depth added 29). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: 3 other methods here (Util._compute_D, Util._compute_Dz, Util._compute_pi2) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":159}}}],"partialFingerprints":{"codehealthFindingId/v1":"c167c707690390e9d96eefe740a1b4c05bb1091f906cf04589d9f94989d4229b"}},{"ruleId":"D2","level":"warning","message":{"text":"Util._compute_Dz (cognitive 48): Util._compute_Dz has cognitive complexity 48 (threshold 15). Drivers by points: if/else 10 (32 pts), loops 4 (11 pts), boolean chains 5 (nesting depth added 29). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: 3 other methods here (Util._compute_D, Util._compute_D2, Util._compute_pi2) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":222}}}],"partialFingerprints":{"codehealthFindingId/v1":"4cc1b72a84d066f277648ce4694de671836c6c33d8e25354fd945cf190acc0f7"}},{"ruleId":"D2","level":"warning","message":{"text":"Util._compute_pi2 (cognitive 48): Util._compute_pi2 has cognitive complexity 48 (threshold 15). Drivers by points: if/else 10 (32 pts), loops 4 (11 pts), boolean chains 5 (nesting depth added 29). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: 3 other methods here (Util._compute_D, Util._compute_D2, Util._compute_Dz) have the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written 4 times rather than 4 independent problems. Splitting this body alone leaves the other 3 exactly as they are. Where these are variations on one operation, the change that clears all 4 is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":321}}}],"partialFingerprints":{"codehealthFindingId/v1":"eace6b6e59fcda12491a2c61516faf4b2bca1b5b968a13e0349e1845b6e89abf"}},{"ruleId":"D2","level":"warning","message":{"text":"Integration.integrate_cn (cognitive 46): Integration.integrate_cn has cognitive complexity 46 (threshold 15). Drivers by points: if/else 18 (38 pts), boolean chains 4, loops 2 (4 pts) (nesting depth added 22). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Integration.py"},"region":{"startLine":29}}}],"partialFingerprints":{"codehealthFindingId/v1":"1d78c587b6e64a416c5bc6e61a4693a65fc418b8c4fa66976ab6bc517d18ad07"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes.LD (cognitive 44): Demes.LD has cognitive complexity 44 (threshold 15). Drivers by points: if/else 22 (35 pts), boolean chains 5, loops 4 (nesting depth added 13). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":387}}}],"partialFingerprints":{"codehealthFindingId/v1":"5cc3e6c4a020b4cc8a71bfbe6cb208db5c62a0cc90029cb9089d4e65cc04f61a"}},{"ruleId":"D2","level":"warning","message":{"text":"Jackknife.closest_ijk_edges (cognitive 41): Jackknife.closest_ijk_edges has cognitive complexity 41 (threshold 15). Drivers by points: loops 12 (24 pts), boolean chains 14, if/else 3 (nesting depth added 12). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":267}}}],"partialFingerprints":{"codehealthFindingId/v1":"8af3d0ca69df92824197831db5c1e5424d574357519ddc04079875d02af068a0"}},{"ruleId":"D2","level":"warning","message":{"text":"Matrices.mutation_ld (cognitive 40): Matrices.mutation_ld has cognitive complexity 40 (threshold 15). Drivers by points: if/else 13 (29 pts), loops 4 (10 pts), boolean chains 1 (nesting depth added 22). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":258}}}],"partialFingerprints":{"codehealthFindingId/v1":"8931d739017bc15f64c67b5cdf72a07301caa7a2a70e1b8fa6083f34a382cea1"}},{"ruleId":"D2","level":"warning","message":{"text":"Jackknife.closest_ijk (cognitive 40): Jackknife.closest_ijk has cognitive complexity 40 (threshold 15). Drivers by points: if/else 8 (18 pts), boolean chains 12, loops 6 (10 pts) (nesting depth added 14). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":51}}}],"partialFingerprints":{"codehealthFindingId/v1":"8b393376c877acf0d46bafdfc0101a32023569018336038a531910242bf9368b"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference._object_func (cognitive 39): Inference._object_func has cognitive complexity 39 (threshold 15). Drivers by points: if/else 22 (32 pts), loops 2 (4 pts), boolean chains 3 (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Inference.py"},"region":{"startLine":295}}}],"partialFingerprints":{"codehealthFindingId/v1":"323aabbc3e87868ff0b6686eabbcf9b3acff8601f4099fb688c0f84c88f26898"}},{"ruleId":"D2","level":"warning","message":{"text":"Matrices.migration_h (cognitive 39): Matrices.migration_h has cognitive complexity 39 (threshold 15). Drivers by points: if/else 10 (22 pts), loops 7 (17 pts) (nesting depth added 22). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":367}}}],"partialFingerprints":{"codehealthFindingId/v1":"1d1bf59d439f73d800501644179c5fac2a36ce5601639848a82410a580dc6ed1"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.integrate (cognitive 38): Spectrum.integrate has cognitive complexity 38 (threshold 15). Drivers by points: if/else 21 (29 pts), boolean chains 9 (nesting depth added 8). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":672}}}],"partialFingerprints":{"codehealthFindingId/v1":"bc0c7cdbe66c6cf6df083dd2cd93085be78ac668a0091d280719adaebb41c809"}},{"ruleId":"D2","level":"warning","message":{"text":"Jackknife.closest_ijk_sides (cognitive 38): Jackknife.closest_ijk_sides has cognitive complexity 38 (threshold 15). Drivers by points: loops 12 (28 pts), if/else 6, boolean chains 4 (nesting depth added 16). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":141}}}],"partialFingerprints":{"codehealthFindingId/v1":"673c9f0f712d5f5d1cb19cc301de580cd527659b7a977d1e00418dd3cc028bae"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._call_sgc (cognitive 37): Parsing._call_sgc has cognitive complexity 37 (threshold 15). Drivers by points: if/else 21 (37 pts) (nesting depth added 16). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":790}}}],"partialFingerprints":{"codehealthFindingId/v1":"1d2d1580e127fef048a9e337f64d2e0ed82cd23318b76ff3947a750bfe3afc28"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing.subset_data (cognitive 36): Parsing.subset_data has cognitive complexity 36 (threshold 15). Drivers by points: if/else 13 (31 pts), loops 4 (5 pts) (nesting depth added 19). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":1504}}}],"partialFingerprints":{"codehealthFindingId/v1":"63b1ed37a16d5b1488ea8e70b94e30d4992c89119f34bf5c83c155fae745208f"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes._get_demographic_events (cognitive 35): Demes._get_demographic_events has cognitive complexity 35 (threshold 15). Drivers by points: loops 16 (22 pts), if/else 6 (10 pts), boolean chains 3 (nesting depth added 10). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":745}}}],"partialFingerprints":{"codehealthFindingId/v1":"a8c7e81c9b387690eef40b191758579966bb300f2f152e463eb3ad1aa7ba69cb"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_4d_comp_Poisson (cognitive 35): Plotting.plot_4d_comp_Poisson has cognitive complexity 35 (threshold 15). Drivers by points: if/else 19 (28 pts), loops 3 (6 pts), boolean chains 1 (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":997}}}],"partialFingerprints":{"codehealthFindingId/v1":"85c8242ebb93c90ddeda31dcb90b85260254edf4edb860bdbae1c0b72b67fd4c"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.drift (cognitive 33): Numerics.drift has cognitive complexity 33 (threshold 15). Drivers by points: if/else 7 (26 pts), boolean chains 4, loops 2 (3 pts) (nesting depth added 20). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":57}}}],"partialFingerprints":{"codehealthFindingId/v1":"ae36c1b9452eca25c6b75c7132d94e49f3323ea3c6972b1626ace5519a1ef1e7"}},{"ruleId":"D2","level":"warning","message":{"text":"Util.ld_names (cognitive 31): Util.ld_names has cognitive complexity 31 (threshold 15). Drivers by points: loops 9 (19 pts), if/else 2 (10 pts), boolean chains 2 (nesting depth added 18). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Util.py"},"region":{"startLine":22}}}],"partialFingerprints":{"codehealthFindingId/v1":"70ea9ca06adad3b4be6ed74d9bf38117b7e8ecc78b9e59e024dd5595090d7e6f"}},{"ruleId":"D2","level":"warning","message":{"text":"Util._compute_S (cognitive 31): Util._compute_S has cognitive complexity 31 (threshold 15). Drivers by points: if/else 6 (16 pts), loops 4 (14 pts), boolean chains 1 (nesting depth added 20). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":106}}}],"partialFingerprints":{"codehealthFindingId/v1":"d40fe61109ff1c15d7fbd0409f0a4a5f5d04ee1203ebeadba5e0e089eca970b4"}},{"ruleId":"D2","level":"warning","message":{"text":"DemesUtil.slice (cognitive 30): DemesUtil.slice has cognitive complexity 30 (threshold 15). Drivers by points: if/else 11 (22 pts), loops 3 (8 pts) (nesting depth added 16). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/DemesUtil.py"},"region":{"startLine":6}}}],"partialFingerprints":{"codehealthFindingId/v1":"a08dbd10897bf7a03e76c23804b6717251a490884caaee0963ddd6c9d0fba02e"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.steady_state (cognitive 30): Numerics.steady_state has cognitive complexity 30 (threshold 15). Drivers by points: if/else 14 (20 pts), loops 3 (6 pts), boolean chains 4 (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Numerics.py"},"region":{"startLine":380}}}],"partialFingerprints":{"codehealthFindingId/v1":"dd920be28995b691af6dee9d79261e37cab16cc77f7b8cb052e84960838e2889"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_3d_comp_Poisson (cognitive 30): Plotting.plot_3d_comp_Poisson has cognitive complexity 30 (threshold 15). Drivers by points: if/else 19 (26 pts), loops 2 (3 pts), boolean chains 1 (nesting depth added 8). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":634}}}],"partialFingerprints":{"codehealthFindingId/v1":"0b3a1bf97fd2a6f8d9f149a471159ee33811b90e060c8e95e76284466a4f475c"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes.LDdecay (cognitive 28): Demes.LDdecay has cognitive complexity 28 (threshold 15). Drivers by points: if/else 15 (20 pts), boolean chains 4, loops 2 (4 pts) (nesting depth added 7). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":543}}}],"partialFingerprints":{"codehealthFindingId/v1":"379c55b07f84abbc6241ac3fc6a8f166bdc8db316f913e25e0a3a147f16623d6"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference.uncerts_LD (cognitive 28): Inference.uncerts_LD has cognitive complexity 28 (threshold 15). Drivers by points: if/else 12 (21 pts), loops 2 (7 pts) (nesting depth added 14). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":1258}}}],"partialFingerprints":{"codehealthFindingId/v1":"31404b7da428029a2af0185ca0b01b0d08be51f8744d5e6cef8f969d2767a3ad"}},{"ruleId":"D2","level":"warning","message":{"text":"LDstats.integrate (cognitive 28): LDstats.integrate has cognitive complexity 28 (threshold 15). Drivers by points: if/else 16 (21 pts), boolean chains 7 (nesting depth added 5). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":961}}}],"partialFingerprints":{"codehealthFindingId/v1":"55cd655035827217ae3ce3e0e7c6480cdfebaa137ae8b3a6c79bbbd9a206d5cb"}},{"ruleId":"D2","level":"warning","message":{"text":"Matrices.mutation_h (cognitive 28): Matrices.mutation_h has cognitive complexity 28 (threshold 15). Drivers by points: if/else 8 (19 pts), loops 3 (8 pts), boolean chains 1 (nesting depth added 16). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":234}}}],"partialFingerprints":{"codehealthFindingId/v1":"2242cf083bf829eb125bdce65c2e8485e9cf0d7c23e048103d59beee75a5e5f2"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing.get_genotypes (cognitive 27): Parsing.get_genotypes has cognitive complexity 27 (threshold 15). Drivers by points: if/else 13 (19 pts), ternaries 2 (3 pts), error handling 2, loops 1 (2 pts), boolean chains 1 (nesting depth added 8). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":98}}}],"partialFingerprints":{"codehealthFindingId/v1":"03545524a24d62ad45e07c37c0a6e32166196edd96d9692e5d9f0cf48e8c3c62"}},{"ruleId":"D2","level":"warning","message":{"text":"_ModelInfo.determine_framesizes (cognitive 27): _ModelInfo.determine_framesizes has cognitive complexity 27 (threshold 15). Drivers by points: if/else 6 (17 pts), loops 4 (10 pts) (nesting depth added 17). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/ModelPlot.py"},"region":{"startLine":636}}}],"partialFingerprints":{"codehealthFindingId/v1":"155ae4446b9750049828dd2de3d86be9bfcdab17732e2a732c2f9528c35398cb"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.f3 (cognitive 27): Spectrum.f3 has cognitive complexity 27 (threshold 15). Drivers by points: if/else 11 (18 pts), boolean chains 5, loops 2 (4 pts) (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1134}}}],"partialFingerprints":{"codehealthFindingId/v1":"94bae60a740165dfffee8524951c26015eeddaf81d4900fccefb521e3ddb4bd3"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.recombination (cognitive 27): Numerics.recombination has cognitive complexity 27 (threshold 15). Drivers by points: if/else 5 (20 pts), loops 3 (6 pts), boolean chains 1 (nesting depth added 18). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":311}}}],"partialFingerprints":{"codehealthFindingId/v1":"ac95d2a9dc77883aaf0df095cac5b91c9b5522cc073f71e6d55bb3d777126286"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.selection_two_locus (cognitive 27): Numerics.selection_two_locus has cognitive complexity 27 (threshold 15). Drivers by points: if/else 5 (20 pts), loops 3 (6 pts), boolean chains 1 (nesting depth added 18). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: one other method here (Numerics.selection_general) has the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":375}}}],"partialFingerprints":{"codehealthFindingId/v1":"cd7d1f14bc1d0297ac042d0a7c92c9295559a3d2a2fdb844b9e3233c30bad472"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.selection_general (cognitive 27): Numerics.selection_general has cognitive complexity 27 (threshold 15). Drivers by points: if/else 5 (20 pts), loops 3 (6 pts), boolean chains 1 (nesting depth added 18). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: one other method here (Numerics.selection_two_locus) has the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":459}}}],"partialFingerprints":{"codehealthFindingId/v1":"bec0a771ccdc97c2dc6ed236d53caec57734e49c118f5ed00544ecc43502dba7"}},{"ruleId":"D2","level":"warning","message":{"text":"Matrices.recombination (cognitive 26): Matrices.recombination has cognitive complexity 26 (threshold 15). Drivers by points: if/else 9 (17 pts), loops 3 (8 pts), boolean chains 1 (nesting depth added 13). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":322}}}],"partialFingerprints":{"codehealthFindingId/v1":"0798dae536392266def4fa8f11c2b57e68afdb40eca2890c7e3530aaf6567e17"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._get_ld_stat_sums (cognitive 26): Parsing._get_ld_stat_sums has cognitive complexity 26 (threshold 15). Drivers by points: loops 7 (17 pts), if/else 4 (9 pts) (nesting depth added 15). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":966}}}],"partialFingerprints":{"codehealthFindingId/v1":"f85b9a10ab07c51bd65684946a9afe2a1c27b0c4deb7fa928a84b360f596adb3"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.__new__ (cognitive 26): Spectrum.__new__ has cognitive complexity 26 (threshold 15). Drivers by points: if/else 14 (21 pts), boolean chains 5 (nesting depth added 7). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":78}}}],"partialFingerprints":{"codehealthFindingId/v1":"5b5077b7900b452a86efbb88bcee8ec8a8e56d410f6456db7f7f038350c75182"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.f4 (cognitive 26): Spectrum.f4 has cognitive complexity 26 (threshold 15). Drivers by points: if/else 9 (15 pts), boolean chains 6, loops 3 (5 pts) (nesting depth added 8). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1206}}}],"partialFingerprints":{"codehealthFindingId/v1":"91167b39484dd60004422187007ba4946f73bea87312470d211cbb55dd709553"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes._apply_event (cognitive 25): Demes._apply_event has cognitive complexity 25 (threshold 15). Drivers by points: if/else 8 (18 pts), loops 3 (7 pts) (nesting depth added 14). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1321}}}],"partialFingerprints":{"codehealthFindingId/v1":"d6d6182380765c3d82db632fc063ef46f06cc1658e154e4a815b224c8cf6076d"}},{"ruleId":"D2","level":"warning","message":{"text":"Integration._apply_frozen_pops (cognitive 25): Integration._apply_frozen_pops has cognitive complexity 25 (threshold 15). Drivers by points: if/else 10 (18 pts), loops 2 (7 pts) (nesting depth added 13). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":845}}}],"partialFingerprints":{"codehealthFindingId/v1":"bce91e04e704e9b3ae464e45851b61388a4fa0b800f33adec2bf1d2c1f804a7d"}},{"ruleId":"D2","level":"warning","message":{"text":"LDstats.to_file (cognitive 25): LDstats.to_file has cognitive complexity 25 (threshold 15). Drivers by points: if/else 12 (13 pts), loops 8 (12 pts) (nesting depth added 5). To reduce it, split the body: this score is breadth rather than depth \u2014 many checks laid out side by side rather than nested inside one another, so inverting conditions into early returns has nothing left to flatten. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":671}}}],"partialFingerprints":{"codehealthFindingId/v1":"f6bccda0b001d2d2a9821b85bba87c583f4f7d69b19a8aac6764ab0f032dd294"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference._perturb_params_constrained (cognitive 24): Inference._perturb_params_constrained has cognitive complexity 24 (threshold 15). Drivers by points: if/else 5 (14 pts), loops 3 (8 pts), boolean chains 2 (nesting depth added 14). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":280}}}],"partialFingerprints":{"codehealthFindingId/v1":"f7da9370ef4ba87db88820608ca806542885e1f66b605ede440539ad3a9c777e"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_ld_curves (cognitive 24): Plotting.plot_ld_curves has cognitive complexity 24 (threshold 15). Drivers by points: if/else 11 (17 pts), loops 3 (5 pts), boolean chains 2 (nesting depth added 8). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Plotting.py"},"region":{"startLine":23}}}],"partialFingerprints":{"codehealthFindingId/v1":"ae80976d3778b23d0326ce21cc672b11069f8e712ad92a57fc64bc11d952e0b0"}},{"ruleId":"D2","level":"warning","message":{"text":"Misc.make_fux_table (cognitive 23): Misc.make_fux_table has cognitive complexity 23 (threshold 15). Drivers by points: loops 6 (16 pts), if/else 3 (7 pts) (nesting depth added 14). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":152}}}],"partialFingerprints":{"codehealthFindingId/v1":"b5100e18ac05adaeeb373f2d997b1892a41f43e0d6952daeec9249b8d6e93334"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing.get_bootstrap_sets (cognitive 22): Parsing.get_bootstrap_sets has cognitive complexity 22 (threshold 15). Drivers by points: if/else 6 (13 pts), loops 4 (9 pts) (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":1372}}}],"partialFingerprints":{"codehealthFindingId/v1":"b1b55c1b721a7c6c02f6403cfff8aab5498ea5f6e5b263f7fce4734ab667c7d7"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.project (cognitive 22): Numerics.project has cognitive complexity 22 (threshold 15). Drivers by points: if/else 4 (10 pts), loops 4 (10 pts), boolean chains 2 (nesting depth added 12). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":275}}}],"partialFingerprints":{"codehealthFindingId/v1":"dfa08693b7924b24b6832678473b3d9c830ee8b960db5d59a993bb261689a9a7"}},{"ruleId":"D2","level":"warning","message":{"text":"TriSpectrum.fold_ancestral (cognitive 22): TriSpectrum.fold_ancestral has cognitive complexity 22 (threshold 15). Drivers by points: if/else 6 (13 pts), loops 4 (6 pts), boolean chains 3 (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/TriSpectrum_mod.py"},"region":{"startLine":346}}}],"partialFingerprints":{"codehealthFindingId/v1":"5383b800f35b2def02585330f60ffbdf3c23a82deb0646982431cd61d254da26"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.mutations_reversible (cognitive 22): Numerics.mutations_reversible has cognitive complexity 22 (threshold 15). Drivers by points: if/else 4 (16 pts), loops 3 (6 pts) (nesting depth added 15). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: one other method here (Numerics.recombination_reversible) has the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":886}}}],"partialFingerprints":{"codehealthFindingId/v1":"7bcf99afef840ee52e957028bfeb3ebe6e908c64a4c8dd8efc3d3a5a8a5e2a51"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.recombination_reversible (cognitive 22): Numerics.recombination_reversible has cognitive complexity 22 (threshold 15). Drivers by points: if/else 4 (16 pts), loops 3 (6 pts) (nesting depth added 15). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: one other method here (Numerics.mutations_reversible) has the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":1088}}}],"partialFingerprints":{"codehealthFindingId/v1":"bf9547e4de1029c5573e7718e52b8ddcfecb47609250b16d2e9a44d889bd7292"}},{"ruleId":"D2","level":"warning","message":{"text":"DemesUtil.swipe (cognitive 21): DemesUtil.swipe has cognitive complexity 21 (threshold 15). Drivers by points: if/else 11 (16 pts), loops 3 (5 pts) (nesting depth added 7). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/DemesUtil.py"},"region":{"startLine":97}}}],"partialFingerprints":{"codehealthFindingId/v1":"69900de07e8448d068455c6bdec486d601d06926966ce05bdb066668a83da3af"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference.optimize (cognitive 21): Inference.optimize has cognitive complexity 21 (threshold 15). Drivers by points: if/else 16 (19 pts), boolean chains 2 (nesting depth added 3). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":419}}}],"partialFingerprints":{"codehealthFindingId/v1":"c3f3599b371ad48487bec1be3614093d023378fe529604d8422be2018a055f2a"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_2d_comp_Poisson (cognitive 21): Plotting.plot_2d_comp_Poisson has cognitive complexity 21 (threshold 15). Drivers by points: if/else 17 (20 pts), boolean chains 1 (nesting depth added 3). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":439}}}],"partialFingerprints":{"codehealthFindingId/v1":"6308502032393103af32e6f88a5eb5d0238276384b7e5025e5ecc50558610565"}},{"ruleId":"D2","level":"warning","message":{"text":"Reversible._calc_FB_5pop (cognitive 21): Reversible._calc_FB_5pop has cognitive complexity 21 (threshold 15). Drivers by points: if/else 10 (20 pts), loops 1 (nesting depth added 10). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Reversible.py"},"region":{"startLine":161}}}],"partialFingerprints":{"codehealthFindingId/v1":"a68b27f071db983491af53694f37148ed9a2847faf49a037c88fccf7cd34d736"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.project (cognitive 21): Numerics.project has cognitive complexity 21 (threshold 15). Drivers by points: loops 5 (13 pts), if/else 4 (8 pts) (nesting depth added 12). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":836}}}],"partialFingerprints":{"codehealthFindingId/v1":"e57dda0bf9ce4fceb506bb23b5fbf1ab6d5cf9f82c96f0686a363f52af70d55e"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference._object_func (cognitive 20): Inference._object_func has cognitive complexity 20 (threshold 15). Drivers by points: if/else 9 (13 pts), loops 2 (4 pts), boolean chains 3 (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":25}}}],"partialFingerprints":{"codehealthFindingId/v1":"7baaa448c237c4267ed62bcd549c8710f6de05a008fb256716eb5003c7feaecc"}},{"ruleId":"D2","level":"warning","message":{"text":"LDstats.swap_pops (cognitive 20): LDstats.swap_pops has cognitive complexity 20 (threshold 15). Drivers by points: if/else 10 (12 pts), loops 3 (7 pts), boolean chains 1 (nesting depth added 6). To reduce it, split the body: this score is breadth rather than depth \u2014 many checks laid out side by side rather than nested inside one another, so inverting conditions into early returns has nothing left to flatten. Group the statements between the checks into named steps and move each step into its own function, so the body reads as a short sequence of named stages."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":384}}}],"partialFingerprints":{"codehealthFindingId/v1":"f7f2dc41f8a525737ca90ecf603376dfc73ff2d49fe34c8bc0d7b28c6c568801"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_single_2d_sfs (cognitive 20): Plotting.plot_single_2d_sfs has cognitive complexity 20 (threshold 15). Drivers by points: if/else 14 (17 pts), error handling 1 (2 pts), loops 1 (nesting depth added 4). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":201}}}],"partialFingerprints":{"codehealthFindingId/v1":"b7c79e02785dc5673a1a11ed9e46fe45f459affd54a4efb52843806836fae075"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes._migration_rate_in_interval (cognitive 19): Demes._migration_rate_in_interval has cognitive complexity 19 (threshold 15). Drivers by points: if/else 4 (12 pts), boolean chains 4, error handling 1 (2 pts), loops 1 (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":978}}}],"partialFingerprints":{"codehealthFindingId/v1":"c07704663c9547ba5cb374e9d50284907a7e50e4ad9a39488f404be83534e056"}},{"ruleId":"D2","level":"warning","message":{"text":"Demes._compute_LD (cognitive 19): Demes._compute_LD has cognitive complexity 19 (threshold 15). Drivers by points: if/else 5 (10 pts), loops 3 (6 pts), ternaries 1 (3 pts) (nesting depth added 10). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1535}}}],"partialFingerprints":{"codehealthFindingId/v1":"63c48b3425c9c1904470e87798c58b82c52239b13b4ed6639dac9d99fa727669"}},{"ruleId":"D2","level":"warning","message":{"text":"Util.rescale_params (cognitive 19): Util.rescale_params has cognitive complexity 19 (threshold 15). Drivers by points: if/else 11 (14 pts), loops 2 (3 pts), boolean chains 2 (nesting depth added 4). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Util.py"},"region":{"startLine":150}}}],"partialFingerprints":{"codehealthFindingId/v1":"ec0b4efc67c40ba60c28e77c8d9c54c8b50c5a649b6f8877ec90d062d01c339b"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._check_anc (cognitive 19): Parsing._check_anc has cognitive complexity 19 (threshold 15). Drivers by points: if/else 9 (19 pts) (nesting depth added 10). To reduce it, flatten the nesting: this score is depth rather than breadth \u2014 most of its points come from checks stacked inside one another, so the work sits several levels in. Invert each enclosing check into an early exit (a return, or the language\u0027s equivalent) so the happy path stays at one level, and where a level cannot be exited early, lift the block it encloses into its own named function."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":758}}}],"partialFingerprints":{"codehealthFindingId/v1":"af68aa99d3682a146c225261d342fdff0541674d712f0f1478966501b90206c9"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.f2 (cognitive 19): Spectrum.f2 has cognitive complexity 19 (threshold 15). Drivers by points: if/else 7 (12 pts), loops 2 (4 pts), boolean chains 3 (nesting depth added 7). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1080}}}],"partialFingerprints":{"codehealthFindingId/v1":"d0cfd7a47ed4113dc9d25351b5e4dcd7166a71dcf62b64f501c691563c0cb3c7"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.from_data_dict (cognitive 19): Spectrum.from_data_dict has cognitive complexity 19 (threshold 15). Drivers by points: if/else 8 (13 pts), loops 3 (5 pts), boolean chains 1 (nesting depth added 7). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1621}}}],"partialFingerprints":{"codehealthFindingId/v1":"5e06eb03ff7a34768cfee3da7b6a330147a10bb0be21d3965c2fac63124aeeb8"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference._object_func (cognitive 19): Inference._object_func has cognitive complexity 19 (threshold 15). Drivers by points: if/else 8 (12 pts), loops 2 (4 pts), boolean chains 3 (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Inference.py"},"region":{"startLine":129}}}],"partialFingerprints":{"codehealthFindingId/v1":"b955f1962ef0268732e6ab14a377080d69beb59f584c45dad9e8807aa1d16c4b"}},{"ruleId":"D2","level":"warning","message":{"text":"Integration._make_array_sel_dom (cognitive 18): Integration._make_array_sel_dom has cognitive complexity 18 (threshold 15). Drivers by points: if/else 15 (18 pts) (nesting depth added 3). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":772}}}],"partialFingerprints":{"codehealthFindingId/v1":"8529d23665403e52e267b02474f933e34b3635c301d5d6506bd200dc4a809317"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._get_H_statistics (cognitive 18): Parsing._get_H_statistics has cognitive complexity 18 (threshold 15). Drivers by points: if/else 8 (11 pts), loops 4 (6 pts), boolean chains 1 (nesting depth added 5). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":1014}}}],"partialFingerprints":{"codehealthFindingId/v1":"62754bf3f2f03d1036f5814253cb599d1e6b9d86eab2f28c57d31ae9ea2916ec"}},{"ruleId":"D2","level":"warning","message":{"text":"Manips.admix_inplace (cognitive 18): Manips.admix_inplace has cognitive complexity 18 (threshold 15). Drivers by points: if/else 14 (16 pts), loops 2 (nesting depth added 2). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":816}}}],"partialFingerprints":{"codehealthFindingId/v1":"eb009eaf8d375990620c75ffb2eee2605c46f4effb42cff29b8ee8f8e1851c29"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing._spectrum_from_tally (cognitive 18): Parsing._spectrum_from_tally has cognitive complexity 18 (threshold 15). Drivers by points: if/else 8 (14 pts), loops 2 (4 pts) (nesting depth added 8). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":991}}}],"partialFingerprints":{"codehealthFindingId/v1":"8b2cddc67836ffd553eb54f606a5eb2b2a389360f665311adf2ef0012e702a56"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.marginalize (cognitive 18): Spectrum.marginalize has cognitive complexity 18 (threshold 15). Drivers by points: if/else 12 (14 pts), loops 2 (3 pts), boolean chains 1 (nesting depth added 3). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":334}}}],"partialFingerprints":{"codehealthFindingId/v1":"4c4ae35c4ccc135dece880328e5d80ea76076924623dffa13f6b26b27bb26d35"}},{"ruleId":"D2","level":"warning","message":{"text":"Numerics.cached_projection (cognitive 18): Numerics.cached_projection has cognitive complexity 18 (threshold 15). Drivers by points: loops 3 (9 pts), if/else 2 (7 pts), boolean chains 1, error handling 1 (nesting depth added 11). To reduce it, break up the iteration: give each loop body a named function, and split a multi-phase loop into one function per phase so no single body carries the whole pipeline."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":785}}}],"partialFingerprints":{"codehealthFindingId/v1":"97e85d0e12a36d90c2e24560ab4b55425e5e01df579f4a37917cc45e026edfcc"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference.optimize_log_lbfgsb (cognitive 17): Inference.optimize_log_lbfgsb has cognitive complexity 17 (threshold 15). Drivers by points: if/else 13 (15 pts), error handling 1 (2 pts) (nesting depth added 3). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Inference.py"},"region":{"startLine":810}}}],"partialFingerprints":{"codehealthFindingId/v1":"34af8d7031d7406606c57fb68b4b37b3217da023d605f4c6adba4824ef053eb9"}},{"ruleId":"D2","level":"warning","message":{"text":"stats_from_genotype_counts.pi2 (cognitive 17): stats_from_genotype_counts.pi2 has cognitive complexity 17 (threshold 15). Drivers by points: if/else 7 (10 pts), boolean chains 7 (nesting depth added 3). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":468}}}],"partialFingerprints":{"codehealthFindingId/v1":"f7bc76e96d6a079dc520c8e9d82774200f086a36ae20cd7f1238f15cfa2e493d"}},{"ruleId":"D2","level":"warning","message":{"text":"Plotting.plot_2d_resid (cognitive 17): Plotting.plot_2d_resid has cognitive complexity 17 (threshold 15). Drivers by points: if/else 11 (14 pts), error handling 1 (2 pts), loops 1 (nesting depth added 4). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":300}}}],"partialFingerprints":{"codehealthFindingId/v1":"32ce50aeb4415ceb7cf545b435c379e2518f4867fc1220444e2d35ef32ca80f3"}},{"ruleId":"D2","level":"warning","message":{"text":"Reversible._calc_FB_4pop (cognitive 17): Reversible._calc_FB_4pop has cognitive complexity 17 (threshold 15). Drivers by points: if/else 8 (16 pts), loops 1 (nesting depth added 8). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Reversible.py"},"region":{"startLine":94}}}],"partialFingerprints":{"codehealthFindingId/v1":"2fd8a1241402d7c1c0cb765d3f01f20b14d7e55f99459356e4dd240bfd7ebca3"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.from_file (cognitive 17): Spectrum.from_file has cognitive complexity 17 (threshold 15). Drivers by points: if/else 11 (13 pts), loops 2 (3 pts), boolean chains 1 (nesting depth added 3). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1415}}}],"partialFingerprints":{"codehealthFindingId/v1":"b9366339436048a9e62bcbeb717e1fbcd769777b2ad0f5360986419cce4a69a9"}},{"ruleId":"D2","level":"warning","message":{"text":"TLSpectrum.fold (cognitive 17): TLSpectrum.fold has cognitive complexity 17 (threshold 15). Drivers by points: if/else 4 (10 pts), loops 3 (6 pts), boolean chains 1 (nesting depth added 9). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/TLSpectrum_mod.py"},"region":{"startLine":389}}}],"partialFingerprints":{"codehealthFindingId/v1":"ffd7d27dec9f87624cf89510f5158212f083090d0aee8901065baa6f0629537c"}},{"ruleId":"D2","level":"warning","message":{"text":"Inference.uncerts (cognitive 16): Inference.uncerts has cognitive complexity 16 (threshold 15). Drivers by points: if/else 13 (16 pts) (nesting depth added 3). To reduce it, split the body: most of this score is breadth rather than depth \u2014 checks laid out side by side rather than stacked \u2014 so group the statements between the checks into named steps and move each step into its own function. Some of it IS depth: where a check sits inside another whose only job is to reach it, merge the two into one condition, and where an else follows a branch that already returns, drop the trailing else and let the rest of the body continue at one level."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":672}}}],"partialFingerprints":{"codehealthFindingId/v1":"7be2c7fa3f06b99cb8d340beb71291f225427afde1372ee5bf7310bea59caf37"}},{"ruleId":"D2","level":"warning","message":{"text":"LDstats.f3 (cognitive 16): LDstats.f3 has cognitive complexity 16 (threshold 15). Drivers by points: if/else 6 (11 pts), boolean chains 3, loops 1 (2 pts) (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: one other method here (LDstats.f4) has the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":188}}}],"partialFingerprints":{"codehealthFindingId/v1":"79d0c7c2af42ea4c55fdda5757ef63638f537b2b32f6c203feffb4ced234f084"}},{"ruleId":"D2","level":"warning","message":{"text":"LDstats.f4 (cognitive 16): LDstats.f4 has cognitive complexity 16 (threshold 15). Drivers by points: if/else 6 (11 pts), boolean chains 3, loops 1 (2 pts) (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body. This shape REPEATS in the file: one other method here (LDstats.f3) has the same decision points, in the same order, at the same nesting depths \u2014 so this is one pattern written twice rather than two separate problems. Splitting this body alone leaves the other exactly as it is. Where these are variations on one operation, the change that clears both is the shared one: lift the common shape into a single routine the variants call, parameterised by whatever genuinely differs between them, and keep in each method only the part that is not shared."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":234}}}],"partialFingerprints":{"codehealthFindingId/v1":"532ef93ff7a278ab5a220b4f01e1ee5db85b85c7b2359c1a60430f8821b0b41a"}},{"ruleId":"D2","level":"warning","message":{"text":"Parsing.compute_ld_statistics (cognitive 16): Parsing.compute_ld_statistics has cognitive complexity 16 (threshold 15). Drivers by points: if/else 10 (14 pts), boolean chains 2 (nesting depth added 4). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":1203}}}],"partialFingerprints":{"codehealthFindingId/v1":"69a14c40b55df13d10e9cb959c09537c50555d0d764fd32d97ddcd36bf886f8b"}},{"ruleId":"D2","level":"warning","message":{"text":"Spectrum.genotype_matrix (cognitive 16): Spectrum.genotype_matrix has cognitive complexity 16 (threshold 15). Drivers by points: if/else 6 (8 pts), loops 4 (8 pts) (nesting depth added 6). To reduce it, split the body into named stages: move each independent step or branch into its own named function so the body reads as a short sequence of named calls rather than one long body."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1346}}}],"partialFingerprints":{"codehealthFindingId/v1":"474c628240e0009d81998be2dc678e6a858b488335e782ac3f6730227fda5b0e"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: LD/Matrices.py: FileTooLong \u2014 3653 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 3153 over it, 7.31\u00D7 the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"0eecd4d3e1c2e2e85247ba4bd69df56fe5a6cc3840c5ad72bbe74ed5e0144279"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: LD/stats_from_genotype_counts.py: FileTooLong \u2014 1279 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 779 over it, 2.56\u00D7 the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"8e28420499c7fa19d1ab5c35b56c707c22c16ef70f0b523944a5d99a4ee33b48"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: moments/Spectrum_mod.py: FileTooLong \u2014 1147 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 647 over it, 2.29\u00D7 the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"38106297731935496345070f2a2e361c1928783621a0cbb9ccc14f9e9887ca52"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: Demes/Demes.py: FileTooLong \u2014 1085 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 585 over it, 2.17\u00D7 the bar. 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To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"f2b0fdd2b9085a3be78e7b59bc971b311b450997c238e09cb073b12d24647ccf"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: LD/LDstats_mod.py: FileTooLong \u2014 584 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 84 over it, 1.17\u00D7 the bar. 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To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Inference.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"035de18bdc893aee1492a46081c41e1d011d609bfdc001b95f6438423949ca1a"}},{"ruleId":"D3","level":"warning","message":{"text":"FileTooLong: moments/Manips.py: FileTooLong \u2014 506 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 6 over it, 1.01\u00D7 the bar. To reduce it, split the file along the responsibilities already in it: move each cohesive group of declarations into its own sibling file in the same module or package, so no one file has to be read whole to change one of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"fad487fc010d15128c30b7d9889f41ebc9da63c9df72c5c431c8901c9e7aa907"}},{"ruleId":"D4","level":"warning","message":{"text":"Near-duplicate member family (3 members, 38 shared lines): moments/Integration.py:905-1196 | moments/Integration_nomig.py:417-641 | moments/Integration_nomig.py:656-810 \u2014 These 3 members are variants of one another: a block of 38 lines reported below appears in every one of them, and the pairwise near-duplicate rows they would otherwise produce are collapsed into this row. Read them as one construct written 3 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 3 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":905}}}],"partialFingerprints":{"codehealthFindingId/v1":"08e71c63afa1e9e70d62c3a1af5ffabee0353d328c6eaba5be912e322a30c896"}},{"ruleId":"D4","level":"warning","message":{"text":"Near-duplicate member pair (115 shared lines): moments/Plotting.py:647-800 | moments/Plotting.py:1010-1177 \u2014 These two members are variants of one another: 115 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members\u0027 grain \u2014 factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":647}}}],"partialFingerprints":{"codehealthFindingId/v1":"0a5d607c6b0368382782f91e8d63eefd7c4daab5ac9d2bce1dfef20ebeb0a5d9"}},{"ruleId":"D4","level":"warning","message":{"text":"Near-duplicate member pair (104 shared lines): moments/TwoLocus/Jackknife.py:414-541 | moments/TwoLocus/Jackknife.py:545-799 \u2014 These two members are variants of one another: 104 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members\u0027 grain \u2014 factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":414}}}],"partialFingerprints":{"codehealthFindingId/v1":"b2a64a01500d95a7ef0244a0ebcc28ba4dc8549dc9861c1db52a5061eb7eb27f"}},{"ruleId":"D4","level":"warning","message":{"text":"Near-duplicate member pair (59 shared lines): moments/TwoLocus/Jackknife.py:143-264 | moments/TwoLocus/Jackknife.py:269-392 \u2014 These two members are variants of one another: 59 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members\u0027 grain \u2014 factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":143}}}],"partialFingerprints":{"codehealthFindingId/v1":"49197224abc2a915fd6a2be5a91c177e2a87b06bae0d2da612b9d15628f115af"}},{"ruleId":"D4","level":"warning","message":{"text":"Near-duplicate member pair (52 shared lines): moments/Godambe.py:12-83 | moments/LD/Godambe.py:21-102 \u2014 These two members are variants of one another: 52 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members\u0027 grain \u2014 factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":12}}}],"partialFingerprints":{"codehealthFindingId/v1":"fd79c691a6782c65b1df7d38401518b1d504929b6b2f4161198b59a01e46480c"}},{"ruleId":"D4","level":"warning","message":{"text":"Near-duplicate member pair (49 shared lines): moments/LinearSystem.py:107-174 | moments/LinearSystem.py:181-257 \u2014 These two members are variants of one another: 49 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members\u0027 grain \u2014 factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LinearSystem.py"},"region":{"startLine":107}}}],"partialFingerprints":{"codehealthFindingId/v1":"bc218c986a9bc262919ed941d7f7c3817412e95c586c28ba3152e8800908065a"}},{"ruleId":"D4","level":"warning","message":{"text":"Near-duplicate member pair (30 shared lines): moments/Triallele/Jackknife.py:22-57 | moments/Triallele/Jackknife.py:82-117 \u2014 These two members are variants of one another: 30 of their lines are already reported as duplicated blocks below, spread through both bodies rather than gathered into one. Read them as a single construct written twice. The repair is at the members\u0027 grain \u2014 factor the shared pipeline into one implementation the two call with their differences as parameters or as an injected step, or, where the difference is systematic (sync against async, one transport against another), generate one from the other. Extracting the individual blocks below is not the same fix: it leaves the two bodies in place and the next edit still has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Jackknife.py"},"region":{"startLine":22}}}],"partialFingerprints":{"codehealthFindingId/v1":"41379a9ebbf99bce55f1a15d63cafd1186565dc54e03de9c733a6d40c90917cc"}},{"ruleId":"D4","level":"warning","message":{"text":"Edited copy of a member (44 corresponding lines): moments/LD/LDstats_mod.py:189-232 | moments/LD/LDstats_mod.py:235-280 \u2014 These two members are one piece of code written twice and then edited apart: 44 consecutive lines correspond almost exactly, broken only by small local edits. Most of that correspondence is NOT reported as duplicated blocks below \u2014 the edits cut it into fragments and only the largest of them clear the block floor, so the rows below understate it. The repair is at the members\u0027 grain \u2014 factor the shared implementation into one the two call with their differences as parameters or as an injected step, or, where the difference is systematic (an extra return value, one transport against another), generate one from the other. Left alone, the next edit has to be made twice and the two will drift further apart."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":189}}}],"partialFingerprints":{"codehealthFindingId/v1":"ec586b2a6a361d1c9d8fcf9d79353904f868e3d45590c322336bf5eb411f04d3"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (6 members, 50\u002B identical tokens): moments/TwoLocus/Numerics.py:69-240 | moments/TwoLocus/Numerics.py:312-372 | moments/TwoLocus/Numerics.py:376-456 | moments/TwoLocus/Numerics.py:460-774 | moments/TwoLocus/Numerics.py:961-1085 | moments/TwoLocus/Numerics.py:1089-1166 \u2014 These 6 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 6 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 6 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":69}}}],"partialFingerprints":{"codehealthFindingId/v1":"09faa82f40ae2364c27b3513fb453295ddd7eda0da74c7dfa9092b78da486211"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (5 members, 50\u002B identical tokens): moments/LD/LDstats_mod.py:599-669 | moments/Numerics.py:139-183 | moments/Spectrum_mod.py:1416-1492 | moments/Triallele/TriSpectrum_mod.py:185-247 | moments/TwoLocus/TLSpectrum_mod.py:291-339 \u2014 These 5 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 5 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 5 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":599}}}],"partialFingerprints":{"codehealthFindingId/v1":"1e58fb598628cf71ea9caf5ff7599266cacd5903b11dd88deae451db21d27479"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (5 members, 50\u002B identical tokens): moments/Manips.py:85-139 | moments/Manips.py:143-197 | moments/Manips.py:201-260 | moments/Manips.py:264-326 | moments/Manips.py:330-388 \u2014 These 5 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 5 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 5 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":85}}}],"partialFingerprints":{"codehealthFindingId/v1":"1a5d0fd73e2c7415f21a303ef415bcf7c77a2af7257ea16fb763ddf42c0ebb0c"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (5 members, 50\u002B identical tokens): moments/TwoLocus/TLSpectrum_mod.py:210-218 | moments/TwoLocus/TLSpectrum_mod.py:221-235 | moments/TwoLocus/TLSpectrum_mod.py:238-252 | moments/TwoLocus/TLSpectrum_mod.py:255-269 | moments/TwoLocus/TLSpectrum_mod.py:272-286 \u2014 These 5 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 5 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 5 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/TLSpectrum_mod.py"},"region":{"startLine":210}}}],"partialFingerprints":{"codehealthFindingId/v1":"737e00f6fbac0ee341e01c4f609e561a4d85488eaa5e71ab66b5d65e09211da2"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (4 members, 50\u002B identical tokens): moments/Demes/Inference.py:356-409 | moments/Demes/Inference.py:689-889 | moments/Demes/Inference.py:949-1008 | moments/Demes/Inference.py:1276-1427 \u2014 These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":356}}}],"partialFingerprints":{"codehealthFindingId/v1":"aab12504c0cfcd2e0d56359f26a21772fe1c5bcb8da4153d2b11a37aa877974d"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (4 members, 50\u002B identical tokens): moments/Inference.py:114-216 | moments/Inference.py:723-829 | moments/Inference.py:955-1046 | moments/TwoLocus/Inference.py:222-262 \u2014 These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":114}}}],"partialFingerprints":{"codehealthFindingId/v1":"875f8e272adfd2281b0eedcbce7145155214bb8f2811ce0eeaed4fb42c8857eb"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (4 members, 50\u002B identical tokens): moments/TwoLocus/Demographics.py:111-139 | moments/TwoLocus/Demographics.py:143-173 | moments/TwoLocus/Demographics.py:177-207 | moments/TwoLocus/Demographics.py:211-241 \u2014 These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Demographics.py"},"region":{"startLine":111}}}],"partialFingerprints":{"codehealthFindingId/v1":"d4b692abc99b574b4371686650b801c495fc3d304e922bd0abd6cefbe35f7086"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (4 members, 50\u002B identical tokens): moments/TwoLocus/Util.py:126-156 | moments/TwoLocus/Util.py:160-219 | moments/TwoLocus/Util.py:223-318 | moments/TwoLocus/Util.py:322-433 \u2014 These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":126}}}],"partialFingerprints":{"codehealthFindingId/v1":"c6836938a7c5d70323f696fa741a511c95327e325e99313bf9e3719e85934b0c"}},{"ruleId":"D4","level":"warning","message":{"text":"Members sharing a duplicated core (4 members, 50\u002B identical tokens): moments/TwoLocus/Util.py:504-521 | moments/TwoLocus/Util.py:527-544 | moments/TwoLocus/Util.py:550-567 | moments/TwoLocus/Util.py:573-590 \u2014 These 4 members share a duplicated core: a run of at least 50 identical tokens appears in every one of them. That run is NOT broken out as duplicated-block rows below \u2014 it is what admitted this row, and the blocks below cover only the part of it that clears the block floor, so they understate the correspondence. Read the members as one construct written 4 times. The repair is at the members\u0027 grain \u2014 factor the shared implementation out once and have all of them call it with their differences as parameters or as an injected step, or, where the difference is systematic, generate them from one template. Extracting the individual blocks below is not the same fix: it leaves every body in place and the next edit still has to be made 4 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":504}}}],"partialFingerprints":{"codehealthFindingId/v1":"edaef0da33f9a65d72026dec830f97c4b73b41f66f8cb1647d061122af38e257"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (117\u2013138 lines \u00D7 2): moments/LD/Inference.py:635-751 | moments/LD/Inference.py:837-974 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Inference.py"},"region":{"startLine":635}}}],"partialFingerprints":{"codehealthFindingId/v1":"672f38b72e4a2c65b0c7c560a908920d956d3c78bcd3dde22323851be2b87334"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (118 lines \u00D7 2): moments/TwoLocus/Numerics.py:123-240 | moments/TwoLocus/Numerics.py:968-1085 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":123}}}],"partialFingerprints":{"codehealthFindingId/v1":"b8d8da3de74eaeabe9274517288b2274375a323b3142dd43dc622edaa06e0e36"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (90\u201392 lines \u00D7 2): moments/Inference.py:238-327 | moments/Inference.py:1068-1159 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Inference.py:1068\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/Inference.py:329\u0060 calls \u0060log\u0060 and \u0060moments/Inference.py:1160\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":238}}}],"partialFingerprints":{"codehealthFindingId/v1":"aaf57c82e66e74e23a2d161317c05a349ca21a5aaa2a6acfc1f6e0fc2d9b7714"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (49\u201379 lines \u00D7 2): moments/LinearSystem.py:321-369 | moments/LinearSystem.py:372-450 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LinearSystem.py"},"region":{"startLine":321}}}],"partialFingerprints":{"codehealthFindingId/v1":"843484f586336f0ece18eba46278aef72f1e0de5b8fa8dc833ecf57504accf14"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (72 lines \u00D7 3): moments/Inference.py:114-196 | moments/Inference.py:723-802 | moments/Inference.py:955-1026 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Inference.py:955\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":114}}}],"partialFingerprints":{"codehealthFindingId/v1":"10d8a46ec5f66e0771c3bda6a8edc6ed9155155e715895bfa28a7c1514187b96"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (67 lines \u00D7 2): moments/Inference.py:614-680 | moments/Inference.py:848-915 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Inference.py:848\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":614}}}],"partialFingerprints":{"codehealthFindingId/v1":"081044f9cdc0404f8cfbf72b1468f606713c9fc518db49b7684abfc2e54432ee"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (63 lines \u00D7 2): moments/Demes/Inference.py:532-594 | moments/Demes/Inference.py:1123-1185 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Demes/Inference.py:532\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/Demes/Inference.py:595\u0060 calls \u0060delayed_flush\u0060 and \u0060moments/Demes/Inference.py:1186\u0060 does not \u2014 after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":532}}}],"partialFingerprints":{"codehealthFindingId/v1":"d03c2dd8ef4c70e941106a1cc7ff62df451c8adc87fa2dd6a0d0d837336db845"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201360 lines \u00D7 2): moments/Demes/Inference.py:435-494 | moments/Demes/Inference.py:746-759 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":435}}}],"partialFingerprints":{"codehealthFindingId/v1":"d8fd72fdc0ff45fe74b70d6fb0acf2b222c69f73e5698792e107efbf006eb27c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (58 lines \u00D7 2): moments/LD/Matrices.py:1555-1612 | moments/LD/Matrices.py:1632-1689 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1555\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1555}}}],"partialFingerprints":{"codehealthFindingId/v1":"66d939abaa91c63128e3234480f8b1789c3952e775b29bc9a5302a6b89731efe"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (57 lines \u00D7 3): moments/LD/Inference.py:534-590 | moments/LD/Inference.py:735-791 | moments/LD/Inference.py:958-1014 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Inference.py:534\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Inference.py"},"region":{"startLine":534}}}],"partialFingerprints":{"codehealthFindingId/v1":"3fd3b112c295d36ef28f6707db9232659e8a3bb18b6917f568839aaeac0ee3da"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (48 lines \u00D7 5): moments/LD/Matrices.py:1984-2031 | moments/LD/Matrices.py:2041-2088 | moments/LD/Matrices.py:2098-2145 | moments/LD/Matrices.py:2155-2202 | moments/LD/Matrices.py:2214-2261 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1984\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1984}}}],"partialFingerprints":{"codehealthFindingId/v1":"90e300f92b675239a1a4628b3b5067bfabc4fca9b159232caf3bfadaf60d5d10"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (42\u201343 lines \u00D7 2): moments/Plotting.py:752-793 | moments/Plotting.py:1127-1169 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":752}}}],"partialFingerprints":{"codehealthFindingId/v1":"7b944cd2dcce877b656f8765f14a267a3a93233bb63714630697bb563dd77a21"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (41 lines \u00D7 4): moments/LD/Matrices.py:1787-1827 | moments/LD/Matrices.py:1836-1876 | moments/LD/Matrices.py:1885-1925 | moments/LD/Matrices.py:1934-1974 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1787}}}],"partialFingerprints":{"codehealthFindingId/v1":"6e55c5fec175c60b5a2e4019788bbde809e8145a12e36ef1e146058837784440"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (31\u201341 lines \u00D7 2): moments/Manips.py:714-754 | moments/Manips.py:817-847 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":714}}}],"partialFingerprints":{"codehealthFindingId/v1":"81d81654a2f3f794f6f068f5f9c381776ea003af7b18cdfca6a1110a49f7b793"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (40 lines \u00D7 2): moments/LD/Matrices.py:2576-2615 | moments/LD/Matrices.py:2634-2673 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2576\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2576}}}],"partialFingerprints":{"codehealthFindingId/v1":"caad31801834e5501aeaefecb250f02f249f9b6c25259f3c871fe7b758951941"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (40 lines \u00D7 2): moments/Parsing.py:868-907 | moments/Parsing.py:911-950 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":868}}}],"partialFingerprints":{"codehealthFindingId/v1":"fae60aa7b61ead64686cfc4247ea7acf32ce1b7a11a67b5ad8aa5725ce792e7a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (27\u201340 lines \u00D7 2): moments/Triallele/TriSpectrum_mod.py:250-289 | moments/TwoLocus/TLSpectrum_mod.py:342-368 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/TriSpectrum_mod.py"},"region":{"startLine":250}}}],"partialFingerprints":{"codehealthFindingId/v1":"001461f625bf4aae8e9cbc738161b7463a7e758a86839475986e1a26faec5826"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (37\u201339 lines \u00D7 3): moments/Plotting.py:452-490 | moments/Plotting.py:647-683 | moments/Plotting.py:1010-1046 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Plotting.py:452\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":452}}}],"partialFingerprints":{"codehealthFindingId/v1":"259af7f2b6a48d439c9807bf9846ceb30a09b4161c31d38cced0329365afe3bf"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (26\u201337 lines \u00D7 4): moments/Godambe.py:223-259 | moments/Godambe.py:269-299 | moments/Godambe.py:305-335 | moments/Godambe.py:480-505 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":223}}}],"partialFingerprints":{"codehealthFindingId/v1":"a6ef6af161f450b927412213d47829cd22e12f583a4f10ff98cefe3887ecf6a7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (37 lines \u00D7 2): moments/Godambe.py:47-83 | moments/LD/Godambe.py:66-102 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":47}}}],"partialFingerprints":{"codehealthFindingId/v1":"f02ed34414adaeff95d406b0091d47fccd7e16e014c27f0cd616b92ed2e72b94"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (37 lines \u00D7 2): moments/Manips.py:85-121 | moments/Manips.py:143-179 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":85}}}],"partialFingerprints":{"codehealthFindingId/v1":"9cd4fed761f4df949c1631062176e115c0caf9e28a0ec22427f8dc35800fe222"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (35 lines \u00D7 2): moments/LD/Matrices.py:4119-4153 | moments/LD/Matrices.py:4876-4910 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:4119\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":4119}}}],"partialFingerprints":{"codehealthFindingId/v1":"055fcfa8f2138808e3b4519a79b94c86020c5775b788ef3339a2c2e5c18ed272"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (35 lines \u00D7 2): moments/LinearSystem.py:140-174 | moments/LinearSystem.py:223-257 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LinearSystem.py"},"region":{"startLine":140}}}],"partialFingerprints":{"codehealthFindingId/v1":"0635828a8ed23c31a96534e4f81eb7ef6522e1c832962f549e68409c984b9fd9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (34\u201335 lines \u00D7 2): moments/Plotting.py:263-297 | moments/Plotting.py:345-378 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":263}}}],"partialFingerprints":{"codehealthFindingId/v1":"49b7e683d2041b7eee645268e764f5ccb7ea4738aa4ff1dbc1164636b8cc9eaa"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (26\u201334 lines \u00D7 8): moments/LD/Matrices.py:1454-1479 | moments/LD/Matrices.py:1482-1507 | moments/LD/Matrices.py:1538-1563 | moments/LD/Matrices.py:1615-1640 | moments/LD/Matrices.py:3039-3072 | moments/LD/Matrices.py:3075-3108 | moments/LD/Matrices.py:3147-3180 | moments/LD/Matrices.py:3183-3216 \u2014 all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1454}}}],"partialFingerprints":{"codehealthFindingId/v1":"306e64971f8d5d165e8465f5c0df2abb2a7d62db5c1ac73816a159f722dc1a45"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (26\u201334 lines \u00D7 7): moments/LD/Matrices.py:1510-1535 | moments/LD/Matrices.py:1692-1717 | moments/LD/Matrices.py:3111-3144 | moments/LD/Matrices.py:3219-3252 | moments/LD/Matrices.py:3255-3288 | moments/LD/Matrices.py:3291-3324 | moments/LD/Matrices.py:3327-3360 \u2014 all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1510}}}],"partialFingerprints":{"codehealthFindingId/v1":"663745e392f267a1c4f6431169f59b7c94fb0949f7e2a4c71917fcdedbecce90"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (29\u201334 lines \u00D7 3): moments/Reversible.py:62-90 | moments/Reversible.py:125-157 | moments/Reversible.py:205-238 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Reversible.py"},"region":{"startLine":62}}}],"partialFingerprints":{"codehealthFindingId/v1":"7e39e9a2fc64eae529b4aab1d1de70e560927544ebc2333b23f838f318663151"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (32 lines \u00D7 2): moments/LD/Matrices.py:3999-4030 | moments/LD/Matrices.py:4756-4787 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:3999\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":3999}}}],"partialFingerprints":{"codehealthFindingId/v1":"cfb6cb7caadb58032ff73dd7d7caccb8e24ddcd501dbbee14942b92b058104e5"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (30 lines \u00D7 4): moments/LD/Matrices.py:3445-3474 | moments/LD/Matrices.py:3653-3682 | moments/LD/Matrices.py:4202-4231 | moments/LD/Matrices.py:4410-4439 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:3445\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":3445}}}],"partialFingerprints":{"codehealthFindingId/v1":"557b6ca11b086c5475cf474e1827bc7a716e15cdde450468a58b1adbf1a56692"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201329 lines \u00D7 5): moments/LD/LDstats_mod.py:599-623 | moments/Numerics.py:139-167 | moments/Spectrum_mod.py:1416-1444 | moments/Triallele/TriSpectrum_mod.py:185-208 | moments/TwoLocus/TLSpectrum_mod.py:291-312 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere all 5 call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made 5 times. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/LDstats_mod.py:599\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":599}}}],"partialFingerprints":{"codehealthFindingId/v1":"142e0a4254e379c0966a64de3c85920e70f6a91049d04b8ed14f51d1975bfea7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201328 lines \u00D7 11): moments/LD/Matrices.py:2452-2473 | moments/LD/Matrices.py:3571-3598 | moments/LD/Matrices.py:3779-3806 | moments/LD/Matrices.py:3859-3886 | moments/LD/Matrices.py:3939-3966 | moments/LD/Matrices.py:4019-4046 | moments/LD/Matrices.py:4328-4355 | moments/LD/Matrices.py:4536-4563 | moments/LD/Matrices.py:4616-4643 | moments/LD/Matrices.py:4696-4723 | moments/LD/Matrices.py:4776-4803 \u2014 all 11 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2452\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2452}}}],"partialFingerprints":{"codehealthFindingId/v1":"40cd34e85e3206ca586468955bede221d36997f052650beaa40af8450d266e38"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201328 lines \u00D7 10): moments/LD/Matrices.py:2340-2361 | moments/LD/Matrices.py:2388-2409 | moments/LD/Matrices.py:3427-3454 | moments/LD/Matrices.py:3491-3518 | moments/LD/Matrices.py:3635-3662 | moments/LD/Matrices.py:3699-3726 | moments/LD/Matrices.py:4184-4211 | moments/LD/Matrices.py:4248-4275 | moments/LD/Matrices.py:4392-4419 | moments/LD/Matrices.py:4456-4483 \u2014 all 10 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2340\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2340}}}],"partialFingerprints":{"codehealthFindingId/v1":"78580294467e64eb96448042ebfc6900b37de670c59442b7fee246ec1e79ff93"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201328 lines \u00D7 5): moments/LD/Matrices.py:1009-1030 | moments/LD/Matrices.py:2738-2765 | moments/LD/Matrices.py:2768-2795 | moments/LD/Matrices.py:2828-2855 | moments/LD/Matrices.py:2858-2885 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1009}}}],"partialFingerprints":{"codehealthFindingId/v1":"51428ed34d96813ad46c83909faf5395bd7bb7018e55b2ce49dff12056eba9e2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201328 lines \u00D7 3): moments/LD/Matrices.py:2490-2511 | moments/LD/Matrices.py:2563-2590 | moments/LD/Matrices.py:2621-2648 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2490\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2490}}}],"partialFingerprints":{"codehealthFindingId/v1":"28136480b9277b4cf035c8f3a5589b78688ff70265369232ab1fa756595d7299"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (27\u201328 lines \u00D7 2): moments/LD/Matrices.py:2997-3024 | moments/LD/Matrices.py:3353-3379 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2997\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2997}}}],"partialFingerprints":{"codehealthFindingId/v1":"4706b28f92f0e7b22dac9fa6e3d4e96409d41a41672e3bd9b8261166c03a3b46"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (26\u201327 lines \u00D7 2): moments/LD/Godambe.py:106-132 | moments/LD/Godambe.py:146-171 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Godambe.py"},"region":{"startLine":106}}}],"partialFingerprints":{"codehealthFindingId/v1":"8e9968107ef41edd19c2be8375fffc86a7f9875c5f47d995abf37b8fa7139700"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (24\u201327 lines \u00D7 2): moments/Misc.py:800-823 | moments/Spectrum_mod.py:1665-1691 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":800}}}],"partialFingerprints":{"codehealthFindingId/v1":"91d804dace91861b57909086e0194bdc55261caa7bff882c0cc707f433eeadae"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (27 lines \u00D7 2): moments/Plotting.py:711-737 | moments/Plotting.py:1083-1109 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Plotting.py:711\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":711}}}],"partialFingerprints":{"codehealthFindingId/v1":"ea4c081382bb579c3606381f865777a43df3f51e3d08bc5bce5e89a57b08dd59"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (27 lines \u00D7 2): moments/Spectrum_mod.py:802-828 | moments/Spectrum_mod.py:839-865 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":802}}}],"partialFingerprints":{"codehealthFindingId/v1":"978b16e737c90204e4c445088839f99327aeb9de80ecfe89220cc8643433989d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (26 lines \u00D7 5): moments/LD/Matrices.py:2800-2825 | moments/LD/Matrices.py:2890-2915 | moments/LD/Matrices.py:2920-2945 | moments/LD/Matrices.py:2950-2975 | moments/LD/Matrices.py:2980-3005 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2800\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2800}}}],"partialFingerprints":{"codehealthFindingId/v1":"ea85f33c15bdb1a272da542768d8d2a496be86afbdb2e66b6cf9f7d6b984ccdc"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (26 lines \u00D7 2): moments/Demes/Inference.py:369-394 | moments/Demes/Inference.py:816-841 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":369}}}],"partialFingerprints":{"codehealthFindingId/v1":"72e0c286527addb28c204e5a317de7927e2fa9b68717a2247155f636b2a2f6d6"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (23\u201325 lines \u00D7 2): moments/Demes/Inference.py:964-986 | moments/Demes/Inference.py:1330-1354 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":964}}}],"partialFingerprints":{"codehealthFindingId/v1":"45b595baaba635f61d9faf73d17b8c39bcb6e7cd6b79f290600cdd4afaa00e72"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (25 lines \u00D7 2): moments/LD/Util.py:123-147 | moments/Misc.py:125-149 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Util.py"},"region":{"startLine":123}}}],"partialFingerprints":{"codehealthFindingId/v1":"5d4ec5dfac0f4f1e1527c42d85408f3a521389d8b2f8e293c93c64b21a4c3d86"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (25 lines \u00D7 2): moments/Manips.py:264-292 | moments/Manips.py:330-354 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":264}}}],"partialFingerprints":{"codehealthFindingId/v1":"b0ed2d9dbe9218209858f97fb379ae08d2f3247c8aaaba9aed6c3cd44e6bf486"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (25 lines \u00D7 2): moments/TwoLocus/Demographics.py:111-135 | moments/TwoLocus/Demographics.py:177-202 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/TwoLocus/Demographics.py:205\u0060 calls \u0060exp\u0060, \u0060log\u0060 and \u0060moments/TwoLocus/Demographics.py:138\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Demographics.py"},"region":{"startLine":111}}}],"partialFingerprints":{"codehealthFindingId/v1":"0c6603cb29fff7e4531b6644a1c89fa7de2daa0532a8fa096a61fb862c93eeb4"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201323 lines \u00D7 6): moments/LD/Matrices.py:2907-2929 | moments/LD/Matrices.py:2937-2959 | moments/LD/Matrices.py:2967-2989 | moments/LD/Matrices.py:3245-3266 | moments/LD/Matrices.py:3281-3302 | moments/LD/Matrices.py:3317-3338 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2907\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2907}}}],"partialFingerprints":{"codehealthFindingId/v1":"1d486c5b6acb11a8513dc14e4d25c009e53387001efb7f93298fdbc3d086c329"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201323 lines \u00D7 4): moments/LD/Matrices.py:2757-2779 | moments/LD/Matrices.py:2847-2869 | moments/LD/Matrices.py:3065-3086 | moments/LD/Matrices.py:3173-3194 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2757\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2757}}}],"partialFingerprints":{"codehealthFindingId/v1":"124f7038339898a7130dc00542bf91d7e6d92501cfd4e76c0c6be56e0d35a6ec"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22\u201323 lines \u00D7 4): moments/LD/Matrices.py:2787-2809 | moments/LD/Matrices.py:2877-2899 | moments/LD/Matrices.py:3101-3122 | moments/LD/Matrices.py:3209-3230 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2787\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2787}}}],"partialFingerprints":{"codehealthFindingId/v1":"cb8226addd731444d7f777023d7ed6f72ae1839dd1beeba4f8db9fc0a0b87064"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (23 lines \u00D7 4): moments/TwoLocus/Jackknife.py:555-577 | moments/TwoLocus/Jackknife.py:618-640 | moments/TwoLocus/Jackknife.py:681-703 | moments/TwoLocus/Jackknife.py:744-766 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:555\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":555}}}],"partialFingerprints":{"codehealthFindingId/v1":"b699b615fc625380477a1292d890f726cfac3721a0325641a9a646e580fe50af"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (20\u201322 lines \u00D7 6): moments/LD/Matrices.py:1270-1289 | moments/LD/Matrices.py:1978-1999 | moments/LD/Matrices.py:2035-2056 | moments/LD/Matrices.py:2092-2113 | moments/LD/Matrices.py:2149-2170 | moments/LD/Matrices.py:2208-2229 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1270\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1270}}}],"partialFingerprints":{"codehealthFindingId/v1":"99f0bc295de57347a2da4cf400b331171d2afc60f2a608f6181c52e5fe24d9fd"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (22 lines \u00D7 2): moments/Integration_nomig.py:560-581 | moments/Integration_nomig.py:749-770 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration_nomig.py"},"region":{"startLine":560}}}],"partialFingerprints":{"codehealthFindingId/v1":"c0e564f916b7a87ec502b30210cf0a6637758485f7d7ec34172761ed36082485"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (21\u201322 lines \u00D7 2): moments/LD/Matrices.py:2817-2838 | moments/LD/Matrices.py:3137-3157 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2817\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2817}}}],"partialFingerprints":{"codehealthFindingId/v1":"8b302aae5d79f5e530b659cdc27c4faff8b30f7217fc23c15382d9834dc094a1"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (21 lines \u00D7 10): moments/LD/Matrices.py:2793-2813 | moments/LD/Matrices.py:2883-2903 | moments/LD/Matrices.py:2913-2933 | moments/LD/Matrices.py:2943-2963 | moments/LD/Matrices.py:2973-2993 | moments/LD/Matrices.py:3106-3126 | moments/LD/Matrices.py:3214-3234 | moments/LD/Matrices.py:3250-3270 | moments/LD/Matrices.py:3286-3306 | moments/LD/Matrices.py:3322-3342 \u2014 all 10 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2793\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2793}}}],"partialFingerprints":{"codehealthFindingId/v1":"2ce1384b799625395e558df97ae603d1c63379a7d7dc819643758073cf53eb33"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (21 lines \u00D7 8): moments/LD/Matrices.py:3401-3421 | moments/LD/Matrices.py:3465-3485 | moments/LD/Matrices.py:3609-3629 | moments/LD/Matrices.py:3673-3693 | moments/LD/Matrices.py:4158-4178 | moments/LD/Matrices.py:4222-4242 | moments/LD/Matrices.py:4366-4386 | moments/LD/Matrices.py:4430-4450 \u2014 all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:3401\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":3401}}}],"partialFingerprints":{"codehealthFindingId/v1":"a6a7251a1466f3449e0a6c96af0ab31e18a0b897ece1b52ae512783c4e923e88"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (21 lines \u00D7 6): moments/LD/Matrices.py:1171-1191 | moments/LD/Matrices.py:1220-1240 | moments/LD/Matrices.py:1781-1801 | moments/LD/Matrices.py:1830-1850 | moments/LD/Matrices.py:1879-1899 | moments/LD/Matrices.py:1928-1948 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1171\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1171}}}],"partialFingerprints":{"codehealthFindingId/v1":"989f759a3fb87e7c2b0e34a8c661ad2e0c6e409f037bf56ef80b4611506cb2a9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (21 lines \u00D7 6): moments/LD/Matrices.py:2763-2783 | moments/LD/Matrices.py:2823-2843 | moments/LD/Matrices.py:2853-2873 | moments/LD/Matrices.py:3070-3090 | moments/LD/Matrices.py:3142-3162 | moments/LD/Matrices.py:3178-3198 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2763\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2763}}}],"partialFingerprints":{"codehealthFindingId/v1":"0a1e9a43be7903c9600c73717c81bb8eb00fb5f21c19fcb5fbeac1c2716c4acf"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (21 lines \u00D7 4): moments/Inference.py:176-196 | moments/Inference.py:782-802 | moments/Inference.py:1006-1026 | moments/TwoLocus/Inference.py:222-242 \u2014 before extracting anything, compare \u0060moments/Inference.py\u0060 and \u0060moments/TwoLocus/Inference.py\u0060 as WHOLE FILES: this scan already matched 5 separate duplicated blocks between them, totalling at least 76 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":176}}}],"partialFingerprints":{"codehealthFindingId/v1":"c768cc0353f086dde38aa30c808d6ba154900a320deaba1d5e160165344ec7b1"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18\u201321 lines \u00D7 2): moments/Spectrum_mod.py:106-126 | moments/TwoLocus/TLSpectrum_mod.py:58-75 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Spectrum_mod.py:106\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":106}}}],"partialFingerprints":{"codehealthFindingId/v1":"3533d1d242b6d453db70ffbd65c4c1bb9390ce514c580c754086d8d2f0881320"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (20\u201321 lines \u00D7 2): moments/TwoLocus/Numerics.py:387-406 | moments/TwoLocus/Numerics.py:493-513 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":387}}}],"partialFingerprints":{"codehealthFindingId/v1":"df14ab7f0f5c7025992fbb83b3b770365e300c934b05ef4c35d8771cd69f4f66"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18\u201320 lines \u00D7 10): moments/LD/Matrices.py:1990-2009 | moments/LD/Matrices.py:2047-2066 | moments/LD/Matrices.py:2104-2123 | moments/LD/Matrices.py:2161-2180 | moments/LD/Matrices.py:2220-2239 | moments/LD/Matrices.py:2807-2824 | moments/LD/Matrices.py:2897-2914 | moments/LD/Matrices.py:2927-2944 | moments/LD/Matrices.py:2957-2974 | moments/LD/Matrices.py:2987-3004 \u2014 all 10 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1990\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1990}}}],"partialFingerprints":{"codehealthFindingId/v1":"b8dd94d60365cc6a04ad34ae4227b160f355b2cfa41d3ef4968cf241bbbd9a0c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (20 lines \u00D7 2): moments/LD/Godambe.py:405-424 | moments/LD/Godambe.py:502-521 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Godambe.py:405\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Godambe.py"},"region":{"startLine":405}}}],"partialFingerprints":{"codehealthFindingId/v1":"402a0911f9f364c6217a96897c53e3bf6c2147e4c6872fe675675acf8abfd4b5"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18\u201320 lines \u00D7 2): moments/LD/Matrices.py:2277-2296 | moments/LD/Matrices.py:3017-3034 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2277\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2277}}}],"partialFingerprints":{"codehealthFindingId/v1":"8d852fed6656eb8a7ec431124e5974fc56ef480389e09c1ebfc007d60341ad5f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (19 lines \u00D7 8): moments/LD/Matrices.py:4041-4059 | moments/LD/Matrices.py:4061-4079 | moments/LD/Matrices.py:4081-4099 | moments/LD/Matrices.py:4101-4119 | moments/LD/Matrices.py:4798-4816 | moments/LD/Matrices.py:4818-4836 | moments/LD/Matrices.py:4838-4856 | moments/LD/Matrices.py:4858-4876 \u2014 all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:4041\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":4041}}}],"partialFingerprints":{"codehealthFindingId/v1":"53fe53438008be04bf05dae2d304e35b5b14b3490fffdb626fc81f0a89728d92"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (19 lines \u00D7 3): moments/Integration.py:106-124 | moments/Integration.py:166-186 | moments/Integration.py:195-214 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Integration.py:166\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":106}}}],"partialFingerprints":{"codehealthFindingId/v1":"eaaec27253c9659981d0dad5d2455b2641492d038a1b727309388f636c0cfc4d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (19 lines \u00D7 3): moments/LD/Matrices.py:1373-1391 | moments/LD/Matrices.py:1558-1576 | moments/LD/Matrices.py:1635-1653 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1373\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1373}}}],"partialFingerprints":{"codehealthFindingId/v1":"403d033d3105b7d0d87bf599d6b21aa8ae8a6edd7c16e8695940c4b128ce8f80"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201319 lines \u00D7 3): moments/Triallele/Numerics.py:413-427 | moments/Triallele/Numerics.py:475-488 | moments/Triallele/Numerics.py:531-549 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:413\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":413}}}],"partialFingerprints":{"codehealthFindingId/v1":"524da680126bf19c556e522f3d30c4bd23f249676ba6a15ee0f786d6a52014b7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (19 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1309-1327 | moments/LD/stats_from_haplotype_counts.py:246-264 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1309\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1309}}}],"partialFingerprints":{"codehealthFindingId/v1":"66dd2e168385b4a86ddad00a4ed7f73fba0c67cea09996f243185c36e16b17c3"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (17\u201319 lines \u00D7 2): moments/TwoLocus/Numerics.py:312-330 | moments/TwoLocus/Numerics.py:1089-1105 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":312}}}],"partialFingerprints":{"codehealthFindingId/v1":"059a5b585d24bd8cb771f8fd7f708f8747a24de6031a4ce7f36f02113d2a91d7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (19 lines \u00D7 2): moments/TwoLocus/Util.py:362-380 | moments/TwoLocus/Util.py:413-431 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:362\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":362}}}],"partialFingerprints":{"codehealthFindingId/v1":"df4ac4833b52416e5c9985fc8dfe9d935923f1bb31bd8b618dce6a110159d3a3"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201318 lines \u00D7 45): moments/LD/Matrices.py:1974-1987 | moments/LD/Matrices.py:2031-2044 | moments/LD/Matrices.py:2088-2101 | moments/LD/Matrices.py:2145-2158 | moments/LD/Matrices.py:2350-2363 | moments/LD/Matrices.py:2398-2411 | moments/LD/Matrices.py:2414-2427 | moments/LD/Matrices.py:2430-2443 | moments/LD/Matrices.py:2446-2459 | moments/LD/Matrices.py:3441-3458 | moments/LD/Matrices.py:3505-3522 | moments/LD/Matrices.py:3525-3542 | moments/LD/Matrices.py:3545-3562 | moments/LD/Matrices.py:3565-3582 | moments/LD/Matrices.py:3649-3666 | moments/LD/Matrices.py:3713-3730 | moments/LD/Matrices.py:3733-3750 | moments/LD/Matrices.py:3753-3770 | moments/LD/Matrices.py:3773-3790 | moments/LD/Matrices.py:3813-3830 | moments/LD/Matrices.py:3833-3850 | moments/LD/Matrices.py:3853-3870 | moments/LD/Matrices.py:3893-3910 | moments/LD/Matrices.py:3913-3930 | moments/LD/Matrices.py:3933-3950 | moments/LD/Matrices.py:3973-3990 | moments/LD/Matrices.py:3993-4010 | moments/LD/Matrices.py:4198-4215 | moments/LD/Matrices.py:4262-4279 | moments/LD/Matrices.py:4282-4299 | moments/LD/Matrices.py:4302-4319 | moments/LD/Matrices.py:4322-4339 | moments/LD/Matrices.py:4406-4423 | moments/LD/Matrices.py:4470-4487 | moments/LD/Matrices.py:4490-4507 | moments/LD/Matrices.py:4510-4527 | moments/LD/Matrices.py:4530-4547 | moments/LD/Matrices.py:4570-4587 | moments/LD/Matrices.py:4590-4607 | moments/LD/Matrices.py:4610-4627 | moments/LD/Matrices.py:4650-4667 | moments/LD/Matrices.py:4670-4687 | moments/LD/Matrices.py:4690-4707 | moments/LD/Matrices.py:4730-4747 | moments/LD/Matrices.py:4750-4767 \u2014 all 45 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1974\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1974}}}],"partialFingerprints":{"codehealthFindingId/v1":"c024fd616d5aeca108b5864162cef701ee490b756c0b06341f5681399b945beb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201318 lines \u00D7 9): moments/LD/Matrices.py:1016-1029 | moments/LD/Matrices.py:1794-1809 | moments/LD/Matrices.py:1843-1858 | moments/LD/Matrices.py:1892-1907 | moments/LD/Matrices.py:1941-1956 | moments/LD/Matrices.py:2747-2764 | moments/LD/Matrices.py:2777-2794 | moments/LD/Matrices.py:2837-2854 | moments/LD/Matrices.py:2867-2884 \u2014 all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1016\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1016}}}],"partialFingerprints":{"codehealthFindingId/v1":"2ab68c8cea74e634329a7eb08d1d2123960b3d70e781c8587930eeb40c0a4430"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201318 lines \u00D7 7): moments/LD/Matrices.py:1380-1393 | moments/LD/Matrices.py:1565-1578 | moments/LD/Matrices.py:1642-1655 | moments/LD/Matrices.py:2498-2511 | moments/LD/Matrices.py:2514-2527 | moments/LD/Matrices.py:2573-2590 | moments/LD/Matrices.py:2631-2648 \u2014 all 7 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1380\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1380}}}],"partialFingerprints":{"codehealthFindingId/v1":"a15765fa2990c9aff27890fbfd0b1a52be400975386cfb5cb5bca858047064dc"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18 lines \u00D7 6): moments/LD/Matrices.py:2679-2696 | moments/LD/Matrices.py:2798-2815 | moments/LD/Matrices.py:2888-2905 | moments/LD/Matrices.py:2918-2935 | moments/LD/Matrices.py:2948-2965 | moments/LD/Matrices.py:2978-2995 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2679\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2679}}}],"partialFingerprints":{"codehealthFindingId/v1":"3dde42d2706637cf41c962ec47cf8f7e9e23a2160dbe3f6f16930590a40f7111"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18 lines \u00D7 4): moments/TwoLocus/Jackknife.py:807-824 | moments/TwoLocus/Jackknife.py:826-843 | moments/TwoLocus/Jackknife.py:845-862 | moments/TwoLocus/Jackknife.py:864-881 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":807}}}],"partialFingerprints":{"codehealthFindingId/v1":"a1f5d0d6cc0eed07c6e85121ff24dba470cae7036670489f109ad3bf45c19feb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18 lines \u00D7 2): moments/Inference.py:1213-1230 | moments/TwoLocus/Inference.py:89-106 \u2014 before extracting anything, compare \u0060moments/Inference.py\u0060 and \u0060moments/TwoLocus/Inference.py\u0060 as WHOLE FILES: this scan already matched 5 separate duplicated blocks between them, totalling at least 76 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":1213}}}],"partialFingerprints":{"codehealthFindingId/v1":"1f02b582d7a6e4f00ea151fc0d9bdb3421cfd7409f5214464ef3f30b0361e004"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18 lines \u00D7 2): moments/LD/Matrices.py:1719-1736 | moments/LD/Matrices.py:2689-2706 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1719\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1719}}}],"partialFingerprints":{"codehealthFindingId/v1":"3b2a7476f72035e9ea36666b3eb776de88d80818a0463d09de17a97771c7dc8a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (18 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:511-528 | moments/LD/stats_from_genotype_counts.py:598-615 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":511}}}],"partialFingerprints":{"codehealthFindingId/v1":"bba4f062d831e7eaa12bd0a51a2ba83427ab9196328bcb9df63749bdc97fbf0f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (17\u201318 lines \u00D7 2): moments/Triallele/Integration.py:59-75 | moments/Triallele/Integration.py:101-118 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Integration.py"},"region":{"startLine":59}}}],"partialFingerprints":{"codehealthFindingId/v1":"7b6c2a0b672551324e95b3151efaea19abdc91b8f95db46595bdda6f3d95bd82"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201317 lines \u00D7 4): moments/LD/Matrices.py:2529-2543 | moments/LD/Matrices.py:2545-2558 | moments/LD/Matrices.py:2601-2617 | moments/LD/Matrices.py:2659-2675 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2529\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2529}}}],"partialFingerprints":{"codehealthFindingId/v1":"fd33c63382ecb40b17034795f98e38ddf0979d89f00a30b3b309e181bd349c62"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201317 lines \u00D7 2): moments/Demes/Demes.py:1085-1098 | moments/Demes/Demes.py:1100-1116 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1085}}}],"partialFingerprints":{"codehealthFindingId/v1":"a174b912ead1398cebac35e2d225e590b40e0d11058d978e995e6c6ecf585ed9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (17 lines \u00D7 2): moments/Godambe.py:139-155 | moments/LD/Godambe.py:178-194 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":139}}}],"partialFingerprints":{"codehealthFindingId/v1":"eaecbe33e28941a7ccb415d0c1ce9eebbfbcac3f2acca00ab3fbe377ac93d738"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (16 lines \u00D7 8): moments/LD/Matrices.py:1778-1793 | moments/LD/Matrices.py:1827-1842 | moments/LD/Matrices.py:1876-1891 | moments/LD/Matrices.py:1925-1940 | moments/LD/Matrices.py:2318-2333 | moments/LD/Matrices.py:2334-2349 | moments/LD/Matrices.py:2366-2381 | moments/LD/Matrices.py:2382-2397 \u2014 all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1778\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1778}}}],"partialFingerprints":{"codehealthFindingId/v1":"163857d0c702cb00b7d7e239a7b63f81b18cff59eba4838fc98ed8a0b1a551b5"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15\u201316 lines \u00D7 5): moments/LD/Matrices.py:1095-1110 | moments/LD/Matrices.py:1112-1126 | moments/LD/Matrices.py:1144-1158 | moments/LD/Matrices.py:2505-2519 | moments/LD/Matrices.py:2537-2551 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1095\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1095}}}],"partialFingerprints":{"codehealthFindingId/v1":"9334889230c55495854d9860687795a7298b26c7d24efb754a9a64188d97093a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (16 lines \u00D7 4): moments/TwoLocus/Util.py:504-519 | moments/TwoLocus/Util.py:527-542 | moments/TwoLocus/Util.py:550-565 | moments/TwoLocus/Util.py:573-588 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":504}}}],"partialFingerprints":{"codehealthFindingId/v1":"c71f0fd28f7b1afe5e98b8d974ffd989ee2cf4d227be51e8327cd92bb30e3d83"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15\u201316 lines \u00D7 3): moments/Integration.py:1067-1082 | moments/Integration_nomig.py:551-565 | moments/Integration_nomig.py:739-754 \u2014 before extracting anything, compare \u0060moments/Integration.py\u0060 and \u0060moments/Integration_nomig.py\u0060 as WHOLE FILES: this scan already matched 7 separate duplicated blocks between them, totalling at least 86 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together \u2014 extracting one helper per block leaves the fork in place. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/Integration_nomig.py:566\u0060 calls \u0060any\u0060, \u0060ValueError\u0060 and \u0060moments/Integration.py:1083\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":1067}}}],"partialFingerprints":{"codehealthFindingId/v1":"729be27d706382cbcd4a63a0cfa53fca04d01afa596088fa9ecddd476ff86fcb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15\u201316 lines \u00D7 2): moments/LD/Matrices.py:1063-1077 | moments/LD/Matrices.py:1087-1102 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1063\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1063}}}],"partialFingerprints":{"codehealthFindingId/v1":"fe080638c84c5bef0a7d6a4781e85e851719b1769c63365bc34375f78f9be364"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (16 lines \u00D7 2): moments/LinearSystem.py:111-126 | moments/LinearSystem.py:272-287 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LinearSystem.py"},"region":{"startLine":111}}}],"partialFingerprints":{"codehealthFindingId/v1":"b1641e71100a1716c179a4a03f47795f6b7bb8a5b3e6e054cf0d627948ee3d3c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (16 lines \u00D7 2): moments/Misc.py:473-488 | moments/Misc.py:495-510 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":473}}}],"partialFingerprints":{"codehealthFindingId/v1":"025f9defabf5a33b3f2733283514aa8990a1aeaf1bf03a05e8fc1c53fd1c4b2c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (16 lines \u00D7 2): moments/TwoLocus/Numerics.py:509-524 | moments/TwoLocus/Numerics.py:547-562 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":509}}}],"partialFingerprints":{"codehealthFindingId/v1":"80e00bbc7463f119cb043d0e1d8152c695e2aeb938f90a9ab9d8d80c7ac06672"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 19): moments/LD/Matrices.py:2459-2473 | moments/LD/Matrices.py:3581-3599 | moments/LD/Matrices.py:3789-3807 | moments/LD/Matrices.py:3869-3887 | moments/LD/Matrices.py:3949-3967 | moments/LD/Matrices.py:4029-4047 | moments/LD/Matrices.py:4049-4067 | moments/LD/Matrices.py:4069-4087 | moments/LD/Matrices.py:4089-4107 | moments/LD/Matrices.py:4109-4127 | moments/LD/Matrices.py:4338-4356 | moments/LD/Matrices.py:4546-4564 | moments/LD/Matrices.py:4626-4644 | moments/LD/Matrices.py:4706-4724 | moments/LD/Matrices.py:4786-4804 | moments/LD/Matrices.py:4806-4824 | moments/LD/Matrices.py:4826-4844 | moments/LD/Matrices.py:4846-4864 | moments/LD/Matrices.py:4866-4884 \u2014 all 19 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2459\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2459}}}],"partialFingerprints":{"codehealthFindingId/v1":"8a5470456b4fab261241619755c3225828dc7c8da466d323e90115a84604f38c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 6): moments/LD/Matrices.py:1104-1118 | moments/LD/Matrices.py:1120-1134 | moments/LD/Matrices.py:1136-1150 | moments/LD/Matrices.py:1152-1166 | moments/LD/Matrices.py:1395-1409 | moments/LD/Matrices.py:1427-1441 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1104\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1104}}}],"partialFingerprints":{"codehealthFindingId/v1":"c9f54243e06e0b06563e0d83bce0389ac7959f634583f454a7256691c1e897c8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 3): moments/Inference.py:1193-1207 | moments/LD/Inference.py:1051-1065 | moments/TwoLocus/Inference.py:110-124 \u2014 before extracting anything, compare \u0060moments/Inference.py\u0060 and \u0060moments/TwoLocus/Inference.py\u0060 as WHOLE FILES: this scan already matched 5 separate duplicated blocks between them, totalling at least 76 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":1193}}}],"partialFingerprints":{"codehealthFindingId/v1":"f70ac838d48a88403c7c91b1002274ed7475fbff3f4c0c3f0648839d30fe5b10"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12\u201315 lines \u00D7 3): moments/Misc.py:283-295 | moments/Misc.py:469-483 | moments/Misc.py:494-505 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Misc.py:283\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Misc.py:466\u0060 calls \u0060ValueError\u0060 and \u0060moments/Misc.py:282\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":283}}}],"partialFingerprints":{"codehealthFindingId/v1":"24ece41050a39cc90e1423be75b436f0aa9369b47dd199743bdf7030c4ccaff3"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 2): moments/Demes/Demes.py:1109-1123 | moments/Demes/Demes.py:1124-1138 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Demes/Demes.py:1109\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1109}}}],"partialFingerprints":{"codehealthFindingId/v1":"45aa824c36e784d300fb4c0170fbda15bbd90b1612e82449428d2be4613ddc38"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 2): moments/Integration.py:1010-1024 | moments/Integration_nomig.py:510-524 \u2014 before extracting anything, compare \u0060moments/Integration.py\u0060 and \u0060moments/Integration_nomig.py\u0060 as WHOLE FILES: this scan already matched 7 separate duplicated blocks between them, totalling at least 86 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together \u2014 extracting one helper per block leaves the fork in place."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":1010}}}],"partialFingerprints":{"codehealthFindingId/v1":"b6a8c4aae9bf8909fbdc472055f29b26ec81b2ffb1b7f8085f438a722c5b4111"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201315 lines \u00D7 2): moments/Integration_nomig.py:469-483 | moments/Integration_nomig.py:691-704 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Integration_nomig.py:469\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration_nomig.py"},"region":{"startLine":469}}}],"partialFingerprints":{"codehealthFindingId/v1":"269b4ee4c840e0be84c3c05c1e634536669e7db7e7cddfb30d17abc378b60db2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 2): moments/LD/Inference.py:322-336 | moments/TwoLocus/Inference.py:144-158 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Inference.py"},"region":{"startLine":322}}}],"partialFingerprints":{"codehealthFindingId/v1":"71153fd47edbec0e506dd57f102e53ec27f825aeb6b2406e197b34ded382e4bb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 2): moments/LD/Matrices.py:1128-1142 | moments/LD/Matrices.py:2521-2535 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1128\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1128}}}],"partialFingerprints":{"codehealthFindingId/v1":"332309d29f2831b8f86a1dc8176e55425eaf62c33fe8f2be81a218a73ded8b67"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201315 lines \u00D7 2): moments/LD/Parsing.py:327-341 | moments/LD/Parsing.py:345-358 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":327}}}],"partialFingerprints":{"codehealthFindingId/v1":"de37996e762abf6e9beea4bf7da4dd555949ad3ac4429eb729b40ed5ab58b945"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (15 lines \u00D7 2): moments/TwoLocus/Util.py:259-273 | moments/TwoLocus/Util.py:302-316 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:259\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":259}}}],"partialFingerprints":{"codehealthFindingId/v1":"fd12ea4b4fd607e1b6d27ba463175c845313741be849730a35dc166b48e0b401"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 49): moments/LD/Matrices.py:1269-1282 | moments/LD/Matrices.py:1977-1990 | moments/LD/Matrices.py:2034-2047 | moments/LD/Matrices.py:2091-2104 | moments/LD/Matrices.py:2148-2161 | moments/LD/Matrices.py:2207-2220 | moments/LD/Matrices.py:2353-2366 | moments/LD/Matrices.py:2401-2414 | moments/LD/Matrices.py:2417-2430 | moments/LD/Matrices.py:2433-2446 | moments/LD/Matrices.py:2449-2462 | moments/LD/Matrices.py:3444-3461 | moments/LD/Matrices.py:3508-3525 | moments/LD/Matrices.py:3528-3545 | moments/LD/Matrices.py:3548-3565 | moments/LD/Matrices.py:3568-3585 | moments/LD/Matrices.py:3652-3669 | moments/LD/Matrices.py:3716-3733 | moments/LD/Matrices.py:3736-3753 | moments/LD/Matrices.py:3756-3773 | moments/LD/Matrices.py:3776-3793 | moments/LD/Matrices.py:3816-3833 | moments/LD/Matrices.py:3836-3853 | moments/LD/Matrices.py:3856-3873 | moments/LD/Matrices.py:3896-3913 | moments/LD/Matrices.py:3916-3933 | moments/LD/Matrices.py:3936-3953 | moments/LD/Matrices.py:3976-3993 | moments/LD/Matrices.py:3996-4013 | moments/LD/Matrices.py:4016-4033 | moments/LD/Matrices.py:4201-4218 | moments/LD/Matrices.py:4265-4282 | moments/LD/Matrices.py:4285-4302 | moments/LD/Matrices.py:4305-4322 | moments/LD/Matrices.py:4325-4342 | moments/LD/Matrices.py:4409-4426 | moments/LD/Matrices.py:4473-4490 | moments/LD/Matrices.py:4493-4510 | moments/LD/Matrices.py:4513-4530 | moments/LD/Matrices.py:4533-4550 | moments/LD/Matrices.py:4573-4590 | moments/LD/Matrices.py:4593-4610 | moments/LD/Matrices.py:4613-4630 | moments/LD/Matrices.py:4653-4670 | moments/LD/Matrices.py:4673-4690 | moments/LD/Matrices.py:4693-4710 | moments/LD/Matrices.py:4733-4750 | moments/LD/Matrices.py:4753-4770 | moments/LD/Matrices.py:4773-4790 \u2014 all 49 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/LD/Matrices.py:3463\u0060 calls \u0060elif\u0060 and \u0060moments/LD/Matrices.py:1284\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1269}}}],"partialFingerprints":{"codehealthFindingId/v1":"330591977b3563a68cbd466bebc9809a567e37bace0b107df305e6dcf9034f0e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 12): moments/LD/Matrices.py:2321-2334 | moments/LD/Matrices.py:2337-2350 | moments/LD/Matrices.py:2369-2382 | moments/LD/Matrices.py:2385-2398 | moments/LD/Matrices.py:3424-3441 | moments/LD/Matrices.py:3488-3505 | moments/LD/Matrices.py:3632-3649 | moments/LD/Matrices.py:3696-3713 | moments/LD/Matrices.py:4181-4198 | moments/LD/Matrices.py:4245-4262 | moments/LD/Matrices.py:4389-4406 | moments/LD/Matrices.py:4453-4470 \u2014 all 12 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2321}}}],"partialFingerprints":{"codehealthFindingId/v1":"b9e4096975c1cb8162369e0294fe4bbeef02954a688642cb43269bd95a595583"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 10): moments/LD/Matrices.py:1171-1184 | moments/LD/Matrices.py:1220-1233 | moments/LD/Matrices.py:1781-1794 | moments/LD/Matrices.py:1830-1843 | moments/LD/Matrices.py:1879-1892 | moments/LD/Matrices.py:1928-1941 | moments/LD/Matrices.py:2321-2334 | moments/LD/Matrices.py:2337-2350 | moments/LD/Matrices.py:2369-2382 | moments/LD/Matrices.py:2385-2398 \u2014 all 10 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1171}}}],"partialFingerprints":{"codehealthFindingId/v1":"e2e6937773a5ea7eb47e553ac211a332871afb50874a5c2d35d520c2f2c5cc33"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 8): moments/LD/Matrices.py:1009-1022 | moments/LD/Matrices.py:2490-2503 | moments/LD/Matrices.py:2563-2580 | moments/LD/Matrices.py:2621-2638 | moments/LD/Matrices.py:2738-2755 | moments/LD/Matrices.py:2768-2785 | moments/LD/Matrices.py:2828-2845 | moments/LD/Matrices.py:2858-2875 \u2014 all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1009\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1009}}}],"partialFingerprints":{"codehealthFindingId/v1":"60bc4617972436c16533bc3b247e85227e52cf2550767fa3382d647c4be8295d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 4): moments/Demes/Inference.py:376-389 | moments/Demes/Inference.py:822-835 | moments/Demes/Inference.py:967-980 | moments/Demes/Inference.py:1333-1346 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":376}}}],"partialFingerprints":{"codehealthFindingId/v1":"a10c25eb38f28b79b69086a941bc923337764e94cfe552f8a79d5e6b71fadf1f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13\u201314 lines \u00D7 4): moments/TwoLocus/Demographics.py:124-137 | moments/TwoLocus/Demographics.py:158-170 | moments/TwoLocus/Demographics.py:191-204 | moments/TwoLocus/Demographics.py:226-238 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/TwoLocus/Demographics.py:205\u0060 calls \u0060exp\u0060, \u0060log\u0060 and \u0060moments/TwoLocus/Demographics.py:138\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Demographics.py"},"region":{"startLine":124}}}],"partialFingerprints":{"codehealthFindingId/v1":"e984342ab6ad5271d4b3ac08b3e55017a60e7e4505a34118f3453c9543dd1cb1"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10\u201314 lines \u00D7 3): moments/Integration.py:980-989 | moments/Integration_nomig.py:486-499 | moments/Integration_nomig.py:706-719 \u2014 before extracting anything, compare \u0060moments/Integration.py\u0060 and \u0060moments/Integration_nomig.py\u0060 as WHOLE FILES: this scan already matched 7 separate duplicated blocks between them, totalling at least 86 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together \u2014 extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Integration_nomig.py:486\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":980}}}],"partialFingerprints":{"codehealthFindingId/v1":"dbc52c64cba08511486700c5316116214e60a9ab04dadce2d27b0a1f659aeac2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 3): moments/Manips.py:104-117 | moments/Manips.py:162-175 | moments/Manips.py:349-362 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":104}}}],"partialFingerprints":{"codehealthFindingId/v1":"ec62d0ff55f1202f4ad6792d99e73f21aaaa41102b5078b411aeebf4107dce50"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13\u201314 lines \u00D7 3): moments/TwoLocus/Jackknife.py:967-980 | moments/TwoLocus/Jackknife.py:998-1010 | moments/TwoLocus/Jackknife.py:1013-1025 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":967}}}],"partialFingerprints":{"codehealthFindingId/v1":"7131ad9f9ac044ab8168f2a90b15b83a9484159ab3649361d9fdd13d9702917c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 3): moments/TwoLocus/Util.py:192-205 | moments/TwoLocus/Util.py:271-284 | moments/TwoLocus/Util.py:378-391 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:192\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":192}}}],"partialFingerprints":{"codehealthFindingId/v1":"9046b2894781404744d764b54f2d6cca6f8008613823f0ce9160fca9461d5bb2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 2): moments/Demes/Inference.py:65-78 | moments/Demes/Inference.py:134-147 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":65}}}],"partialFingerprints":{"codehealthFindingId/v1":"a0332d07aab87a0d1800ca3fa846e6541ceae591be3b3997ab46481852be9913"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 2): moments/LD/Matrices.py:1032-1045 | moments/LD/Matrices.py:1056-1069 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1032\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1032}}}],"partialFingerprints":{"codehealthFindingId/v1":"d47ef34f0f9ff07f252cdb7b4256f872b347a03f8e77ed2e4c5ea81232d14153"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:491-504 | moments/LD/stats_from_genotype_counts.py:559-572 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":491}}}],"partialFingerprints":{"codehealthFindingId/v1":"796adb76efc7215452d93434698d0b10a5912ca809a1ef7d47773de27cb48614"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 2): moments/Manips.py:224-237 | moments/Manips.py:287-300 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":224}}}],"partialFingerprints":{"codehealthFindingId/v1":"bc4a36901a477d37b4db73af37e27e3feab3a6b3f8025ae0e743d75bbf1b8cf9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14 lines \u00D7 2): moments/Spectrum_mod.py:1552-1565 | moments/TwoLocus/TLSpectrum_mod.py:374-387 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Spectrum_mod.py:1550\u0060 calls \u0060write\u0060 and \u0060moments/TwoLocus/TLSpectrum_mod.py:372\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":1552}}}],"partialFingerprints":{"codehealthFindingId/v1":"c08f3cd0673f265a8a38c30058a9ac1a44482d10b495813d6e428122f26f7d41"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (3\u201314 lines \u00D7 4): moments/Triallele/Jackknife.py:33-46 | moments/Triallele/Jackknife.py:47-49 | moments/Triallele/Jackknife.py:93-106 | moments/Triallele/Jackknife.py:107-109 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/Triallele/Jackknife.py:47\u0060 calls \u0060array\u0060, \u0060sum\u0060 and \u0060moments/Triallele/Jackknife.py:49\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Jackknife.py"},"region":{"startLine":33}}}],"partialFingerprints":{"codehealthFindingId/v1":"6aba92ba48647a9a5bd9ecb887a82a017b9ba4fa6a5f6ae17c71b5b84328f70e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 13): moments/LD/Matrices.py:1510-1522 | moments/LD/Matrices.py:1692-1704 | moments/LD/Matrices.py:2679-2695 | moments/LD/Matrices.py:2798-2814 | moments/LD/Matrices.py:2888-2904 | moments/LD/Matrices.py:2918-2934 | moments/LD/Matrices.py:2948-2964 | moments/LD/Matrices.py:2978-2994 | moments/LD/Matrices.py:3111-3127 | moments/LD/Matrices.py:3219-3235 | moments/LD/Matrices.py:3255-3271 | moments/LD/Matrices.py:3291-3307 | moments/LD/Matrices.py:3327-3343 \u2014 all 13 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1510\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1510}}}],"partialFingerprints":{"codehealthFindingId/v1":"72b3c5ea564461a3315be96fbf492aa505c12cb6ad089fc6935df9549fee6845"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 9): moments/LD/Matrices.py:1323-1335 | moments/LD/Matrices.py:1454-1466 | moments/LD/Matrices.py:1482-1494 | moments/LD/Matrices.py:1538-1550 | moments/LD/Matrices.py:1615-1627 | moments/LD/Matrices.py:3039-3055 | moments/LD/Matrices.py:3075-3091 | moments/LD/Matrices.py:3147-3163 | moments/LD/Matrices.py:3183-3199 \u2014 all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1323\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1323}}}],"partialFingerprints":{"codehealthFindingId/v1":"83a64b0ddead6344030f5ef71aa352d1b3b01ceada951fe540f704500a03381c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 9): moments/LD/Matrices.py:1538-1550 | moments/LD/Matrices.py:1615-1627 | moments/LD/Matrices.py:2768-2784 | moments/LD/Matrices.py:2828-2844 | moments/LD/Matrices.py:2858-2874 | moments/LD/Matrices.py:3039-3055 | moments/LD/Matrices.py:3075-3091 | moments/LD/Matrices.py:3147-3163 | moments/LD/Matrices.py:3183-3199 \u2014 all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1538\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1538}}}],"partialFingerprints":{"codehealthFindingId/v1":"0ede0b0a982f679b69f283bf2724ac5b4a02f6eaddc952d0b3d62151b2ca10ac"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 6): moments/LD/Matrices.py:1009-1021 | moments/LD/Matrices.py:1323-1335 | moments/LD/Matrices.py:1454-1466 | moments/LD/Matrices.py:1482-1494 | moments/LD/Matrices.py:2490-2502 | moments/LD/Matrices.py:2738-2754 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1009\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1009}}}],"partialFingerprints":{"codehealthFindingId/v1":"ac8de4faf4a64a6f4b055fd9926d57b2113ee1509ac5ed10a024b4ca7f61efd8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 4): moments/LD/Matrices.py:1024-1037 | moments/LD/Matrices.py:1372-1385 | moments/LD/Matrices.py:1558-1570 | moments/LD/Matrices.py:1635-1647 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1024\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1024}}}],"partialFingerprints":{"codehealthFindingId/v1":"506b1977d353cf418623d465a341567696a4af0a62e479ff85012bc02467091c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 4): moments/LD/Matrices.py:1343-1355 | moments/LD/Matrices.py:1357-1369 | moments/LD/Matrices.py:2582-2599 | moments/LD/Matrices.py:2640-2657 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:1343\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":1343}}}],"partialFingerprints":{"codehealthFindingId/v1":"fdbb89a8f5a3abea01840cf974483ce23e99a6ffac5b4700dd92a188f56417a4"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 3): moments/LD/Parsing.py:869-881 | moments/LD/Parsing.py:893-905 | moments/LD/Parsing.py:920-932 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Parsing.py:869\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":869}}}],"partialFingerprints":{"codehealthFindingId/v1":"ac8089bae4141dc4a7cd6d11088e83c9a601a649a1d6ce513b6c3c9f47fed6e8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12\u201313 lines \u00D7 3): moments/Manips.py:231-242 | moments/Manips.py:294-306 | moments/Manips.py:356-368 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":231}}}],"partialFingerprints":{"codehealthFindingId/v1":"75c9e95951d002cb09eca710072aa717560b418134a0a8cd4ee45f93642a653a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/Demes/Inference.py:84-96 | moments/Demes/Inference.py:151-163 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":84}}}],"partialFingerprints":{"codehealthFindingId/v1":"5efd2e2a38ffcde778122798c8d9db899b4ed08453c4e51c3ba021a591b6b831"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12\u201313 lines \u00D7 2): moments/Demes/Inference.py:657-669 | moments/Demes/Inference.py:1244-1255 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Demes/Inference.py:657\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":657}}}],"partialFingerprints":{"codehealthFindingId/v1":"da2f36d77335602e7da943fb350658058d5af915da1b4a9f762698966dc9085b"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/Inference.py:687-699 | moments/TwoLocus/Inference.py:249-262 \u2014 before extracting anything, compare \u0060moments/Inference.py\u0060 and \u0060moments/TwoLocus/Inference.py\u0060 as WHOLE FILES: this scan already matched 5 separate duplicated blocks between them, totalling at least 76 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Inference.py:687\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":687}}}],"partialFingerprints":{"codehealthFindingId/v1":"f03e15f04ed4d04911ed86e39d438b3327898b3dbce5ff477e5a1520cf8ba4c2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/LD/Godambe.py:383-395 | moments/LD/Godambe.py:485-497 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/LD/Godambe.py:382\u0060 calls \u0060deepcopy\u0060 and \u0060moments/LD/Godambe.py:483\u0060 does not \u2014 after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Godambe.py"},"region":{"startLine":383}}}],"partialFingerprints":{"codehealthFindingId/v1":"54dd38bbd34d36e0682c71b84bddeeb22494f0fcf1094c215b1c812a89c45816"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/LD/Plotting.py:94-106 | moments/LD/Plotting.py:256-268 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Plotting.py"},"region":{"startLine":94}}}],"partialFingerprints":{"codehealthFindingId/v1":"fc36aa65b58f2c32f309b4f4821184b5a6b160513a9614381aa08fb80ebdd3c8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:542-554 | moments/LD/stats_from_genotype_counts.py:573-585 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":542}}}],"partialFingerprints":{"codehealthFindingId/v1":"4d4a952c7a390933f33278b047e76aab814a1fd2201c9f5b57ae31a26f969c18"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/LD/stats_from_haplotype_counts.py:215-227 | moments/LD/stats_from_haplotype_counts.py:232-244 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/LD/stats_from_haplotype_counts.py:246\u0060 calls \u0060elif\u0060 and \u0060moments/LD/stats_from_haplotype_counts.py:229\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_haplotype_counts.py"},"region":{"startLine":215}}}],"partialFingerprints":{"codehealthFindingId/v1":"2252be0a29a5d07b38af832103d5c062c0ced2d6ac163e4ceb5fa28e774752ac"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/Manips.py:398-410 | moments/Manips.py:414-426 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":398}}}],"partialFingerprints":{"codehealthFindingId/v1":"6762d3811c014714c224c775b10a0cfb36ddd0e82209b1403e558cd47daf8f92"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/Manips.py:430-442 | moments/Manips.py:446-458 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":430}}}],"partialFingerprints":{"codehealthFindingId/v1":"02f97a4b2adf4dc888f00414c2885e2e433cc75e3bf6c93c53f756afb2109c6e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/Reversible.py:98-110 | moments/Reversible.py:168-180 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Reversible.py"},"region":{"startLine":98}}}],"partialFingerprints":{"codehealthFindingId/v1":"938cad1a61aa79b193e622135bd5d76f816de4a9f15bb1b1ab0dc2d66ca5d5d8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/Triallele/Numerics.py:77-89 | moments/Triallele/Numerics.py:100-112 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":77}}}],"partialFingerprints":{"codehealthFindingId/v1":"ee5ffb5c9a610c2aca7a5e465bf4c5348d93c1918dddc2e25f93464810d7d281"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12\u201313 lines \u00D7 2): moments/Triallele/Numerics.py:517-529 | moments/Triallele/Numerics.py:566-577 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:517\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":517}}}],"partialFingerprints":{"codehealthFindingId/v1":"c6b65d82eb7f3a08e4ef099e1ab731f316e3d2c5a88f3e7920d450f624d97721"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/Triallele/Numerics.py:551-563 | moments/Triallele/Numerics.py:579-591 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:551\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":551}}}],"partialFingerprints":{"codehealthFindingId/v1":"963df219d232faf6b8a7868ff842f2abcea2ac438cee808e3d65defd65185b7b"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (13 lines \u00D7 2): moments/TwoLocus/Numerics.py:1110-1122 | moments/TwoLocus/Numerics.py:1124-1136 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":1110}}}],"partialFingerprints":{"codehealthFindingId/v1":"ec3c8f48ce8f15ba68af59907815e515dd2a801b56e473d09e5c0b3f30a0db4f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 20): moments/LD/Matrices.py:2261-2272 | moments/LD/Matrices.py:2462-2473 | moments/LD/Matrices.py:3585-3600 | moments/LD/Matrices.py:3793-3808 | moments/LD/Matrices.py:3873-3888 | moments/LD/Matrices.py:3953-3968 | moments/LD/Matrices.py:4033-4048 | moments/LD/Matrices.py:4053-4068 | moments/LD/Matrices.py:4073-4088 | moments/LD/Matrices.py:4093-4108 | moments/LD/Matrices.py:4113-4128 | moments/LD/Matrices.py:4342-4357 | moments/LD/Matrices.py:4550-4565 | moments/LD/Matrices.py:4630-4645 | moments/LD/Matrices.py:4710-4725 | moments/LD/Matrices.py:4790-4805 | moments/LD/Matrices.py:4810-4825 | moments/LD/Matrices.py:4830-4845 | moments/LD/Matrices.py:4850-4865 | moments/LD/Matrices.py:4870-4885 \u2014 all 20 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:2261\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":2261}}}],"partialFingerprints":{"codehealthFindingId/v1":"65a0143309e0c21dfa849b30b66958f8248ae4f888941ec3f65ed69a2945738c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9\u201312 lines \u00D7 14): moments/TwoLocus/Jackknife.py:464-475 | moments/TwoLocus/Jackknife.py:478-489 | moments/TwoLocus/Jackknife.py:492-503 | moments/TwoLocus/Jackknife.py:506-517 | moments/TwoLocus/Jackknife.py:520-531 | moments/TwoLocus/Jackknife.py:532-540 | moments/TwoLocus/Jackknife.py:579-590 | moments/TwoLocus/Jackknife.py:591-602 | moments/TwoLocus/Jackknife.py:642-653 | moments/TwoLocus/Jackknife.py:654-665 | moments/TwoLocus/Jackknife.py:705-716 | moments/TwoLocus/Jackknife.py:717-728 | moments/TwoLocus/Jackknife.py:768-779 | moments/TwoLocus/Jackknife.py:780-791 \u2014 all 14 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:464\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":464}}}],"partialFingerprints":{"codehealthFindingId/v1":"f3f056de3b52c03270a29bd2f0dd429eb4b44ab78802d263dc68147f8091fa35"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 8): moments/TwoLocus/Jackknife.py:184-195 | moments/TwoLocus/Jackknife.py:204-215 | moments/TwoLocus/Jackknife.py:224-235 | moments/TwoLocus/Jackknife.py:244-255 | moments/TwoLocus/Jackknife.py:317-328 | moments/TwoLocus/Jackknife.py:334-345 | moments/TwoLocus/Jackknife.py:351-362 | moments/TwoLocus/Jackknife.py:368-379 \u2014 all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":184}}}],"partialFingerprints":{"codehealthFindingId/v1":"41a956e90a7add366b8bb4d03d94d458aba826b05c9dbc6a571bee23b1ceaee9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 4): moments/Manips.py:50-61 | moments/Manips.py:104-115 | moments/Manips.py:162-173 | moments/Manips.py:349-360 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":50}}}],"partialFingerprints":{"codehealthFindingId/v1":"3c73a982c5ce00a7afea86d64923b5c2a99797e2b69a12d20f8efaa087e8a979"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 3): moments/Godambe.py:334-345 | moments/Godambe.py:439-450 | moments/Godambe.py:504-515 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Godambe.py:438\u0060 calls \u0060concatenate\u0060 and \u0060moments/Godambe.py:333\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":334}}}],"partialFingerprints":{"codehealthFindingId/v1":"a58753f8a2d04fcd96f77ec84a3d6d94f5994f3df4787a4c8ac11e64a42946b8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 3): moments/Integration.py:1083-1094 | moments/Integration_nomig.py:569-580 | moments/Integration_nomig.py:758-769 \u2014 before extracting anything, compare \u0060moments/Integration.py\u0060 and \u0060moments/Integration_nomig.py\u0060 as WHOLE FILES: this scan already matched 7 separate duplicated blocks between them, totalling at least 86 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together \u2014 extracting one helper per block leaves the fork in place. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Integration_nomig.py:566\u0060 calls \u0060any\u0060, \u0060ValueError\u0060 and \u0060moments/Integration.py:1082\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":1083}}}],"partialFingerprints":{"codehealthFindingId/v1":"9dd4f515f096b86f51464f7ac944b51178572fa58bd58c640515cbb7b188a663"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11\u201312 lines \u00D7 3): moments/TwoLocus/Jackknife.py:911-922 | moments/TwoLocus/Jackknife.py:926-936 | moments/TwoLocus/Jackknife.py:940-950 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:911\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":911}}}],"partialFingerprints":{"codehealthFindingId/v1":"c49054018e76bacd1b8eecd4f6d18d48c7ebb15f5bc7cc2414766ce96e66aefb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 3): moments/TwoLocus/Util.py:129-140 | moments/TwoLocus/Util.py:163-174 | moments/TwoLocus/Util.py:226-237 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":129}}}],"partialFingerprints":{"codehealthFindingId/v1":"a61620089c1c08d7727a9059491680baa67a566a5e7391352a892d1e7b6133e8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 2): moments/Demes/Demes.py:1055-1066 | moments/Demes/Demes.py:1121-1132 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1055}}}],"partialFingerprints":{"codehealthFindingId/v1":"cb3098a23e1703769d990cf8146e9ba024032d57a950e6f38b64b208d704600e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 2): moments/Demes/Inference.py:509-520 | moments/Demes/Inference.py:1097-1108 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Demes/Inference.py:509\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":509}}}],"partialFingerprints":{"codehealthFindingId/v1":"7f0613eda74aec33584c3a5a27a7d19ec61a44683413ea3bf31294ba10f87652"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10\u201312 lines \u00D7 2): moments/Demes/Inference.py:757-766 | moments/Demes/Inference.py:1304-1315 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Demes/Inference.py:1304\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":757}}}],"partialFingerprints":{"codehealthFindingId/v1":"88a6b3f61e2c1b02742801248dbb81550ed8f89f21bb55d7f74d02583ce58aaa"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 2): moments/Integration.py:1107-1118 | moments/Integration_nomig.py:583-594 \u2014 before extracting anything, compare \u0060moments/Integration.py\u0060 and \u0060moments/Integration_nomig.py\u0060 as WHOLE FILES: this scan already matched 7 separate duplicated blocks between them, totalling at least 86 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together \u2014 extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Integration.py:1107\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":1107}}}],"partialFingerprints":{"codehealthFindingId/v1":"8ebfc18c91cdefca27ff70b456a7620c64d91299fd4cdc07d7ee05cc56419496"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11\u201312 lines \u00D7 2): moments/LD/Parsing.py:858-869 | moments/LD/Parsing.py:906-916 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Parsing.py:858\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/LD/Parsing.py:904\u0060 calls \u0060pi2\u0060 and \u0060moments/LD/Parsing.py:858\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":858}}}],"partialFingerprints":{"codehealthFindingId/v1":"1e91195beafb900a2378a5dfe1c46fc9ac6740830355ef5b286e578e61d3c189"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11\u201312 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:877-888 | moments/LD/stats_from_genotype_counts.py:989-999 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":877}}}],"partialFingerprints":{"codehealthFindingId/v1":"a107a97a08aa79af3014061fc3c608845a41d38e65c8723597e6072135d703eb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 2): moments/Triallele/Numerics.py:397-408 | moments/Triallele/Numerics.py:499-510 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:397\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Triallele/Numerics.py:396\u0060 calls \u0060choose\u0060 and \u0060moments/Triallele/Numerics.py:498\u0060 does not \u2014 after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":397}}}],"partialFingerprints":{"codehealthFindingId/v1":"afa8911851f273b6bf98b7d061c3a5fba3725816b9ad8d9be096aa9332c30563"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (4\u201312 lines \u00D7 5): moments/TwoLocus/Jackknife.py:549-552 | moments/TwoLocus/Jackknife.py:603-614 | moments/TwoLocus/Jackknife.py:666-677 | moments/TwoLocus/Jackknife.py:732-736 | moments/TwoLocus/Jackknife.py:738-741 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:603\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":549}}}],"partialFingerprints":{"codehealthFindingId/v1":"5c7f48f3cd4ab772747c3226e836bad31c38da8a00c77365fd4b70d1e5f06762"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 2): moments/TwoLocus/Jackknife.py:1029-1040 | moments/TwoLocus/Jackknife.py:1044-1055 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:1029\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":1029}}}],"partialFingerprints":{"codehealthFindingId/v1":"1702683c24bf70feecaae52020d9334f757faac1a2db69fb2e7fd92772798a80"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 2): moments/TwoLocus/Numerics.py:635-646 | moments/TwoLocus/Numerics.py:716-727 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Numerics.py:635\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":635}}}],"partialFingerprints":{"codehealthFindingId/v1":"6ebf093859179fe1b09f8799dd35668bec12856ee680afed41dda1cab9d60e18"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (12 lines \u00D7 2): moments/TwoLocus/Numerics.py:728-739 | moments/TwoLocus/Numerics.py:749-760 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Numerics.py:728\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":728}}}],"partialFingerprints":{"codehealthFindingId/v1":"8ff55301d3fc24df77420a92f6cf89563ff52b768cfefe1fd2e1154f9946cdbd"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10\u201311 lines \u00D7 4): moments/LD/Parsing.py:849-859 | moments/LD/Parsing.py:871-880 | moments/LD/Parsing.py:895-904 | moments/LD/Parsing.py:922-931 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Parsing.py:849\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":849}}}],"partialFingerprints":{"codehealthFindingId/v1":"68bf107da26715d2e740770f81e1b39a24689aae1bd38a0f0b7ecb0277fa0f41"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 4): moments/LD/stats_from_genotype_counts.py:443-453 | moments/LD/stats_from_genotype_counts.py:1228-1238 | moments/LD/stats_from_genotype_counts.py:1269-1279 | moments/LD/stats_from_genotype_counts.py:1325-1335 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:443\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":443}}}],"partialFingerprints":{"codehealthFindingId/v1":"078b28e0ebfed3f9a49419375517945e87c4d52ba77288f99759d33b90799f5a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:518-528 | moments/LD/stats_from_genotype_counts.py:568-578 | moments/LD/stats_from_genotype_counts.py:605-615 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":518}}}],"partialFingerprints":{"codehealthFindingId/v1":"b94f356265d1d528b0a5307cacb3f43a1113b661d8c2de0476a3ff8eaab291c3"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:695-705 | moments/LD/stats_from_genotype_counts.py:715-725 | moments/LD/stats_from_genotype_counts.py:735-745 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":695}}}],"partialFingerprints":{"codehealthFindingId/v1":"5a9cd85a268417408c35f8c3f5338c0ae6feb7302e29a5a23e13bb275518fd44"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 3): moments/LD/stats_from_haplotype_counts.py:212-222 | moments/LD/stats_from_haplotype_counts.py:229-239 | moments/LD/stats_from_haplotype_counts.py:261-271 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_haplotype_counts.py:212\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_haplotype_counts.py"},"region":{"startLine":212}}}],"partialFingerprints":{"codehealthFindingId/v1":"08da9de1b09aafbca768c87ade5797f986170ccb4cdbdbbffddeea62c084afe6"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:581-591 | moments/LD/stats_from_genotype_counts.py:611-621 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":581}}}],"partialFingerprints":{"codehealthFindingId/v1":"ea3eecbf7f96d4aeae32693dc0a205896a901a2dbcbf812a76c8ace8beffa70c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 2): moments/Manips.py:800-810 | moments/Manips.py:935-945 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":800}}}],"partialFingerprints":{"codehealthFindingId/v1":"06336727ae8f225cb722684f9ded5a454b9133a43322ea6e8fb8482617bd4fe9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 2): moments/Misc.py:831-841 | moments/Spectrum_mod.py:1703-1713 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":831}}}],"partialFingerprints":{"codehealthFindingId/v1":"75744ef5fe9a372f0201a2a6f94acbcbe0fcbee03f735650c90b639f15ae8b2f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (11 lines \u00D7 2): moments/TwoLocus/Numerics.py:526-536 | moments/TwoLocus/Numerics.py:564-574 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":526}}}],"partialFingerprints":{"codehealthFindingId/v1":"a7a8d2ee2434b3949425fd53cdd4ad0c621d9a73a3138e23978faca8821179df"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7\u201310 lines \u00D7 16): moments/TwoLocus/Jackknife.py:422-428 | moments/TwoLocus/Jackknife.py:433-442 | moments/TwoLocus/Jackknife.py:444-453 | moments/TwoLocus/Jackknife.py:454-461 | moments/TwoLocus/Jackknife.py:572-581 | moments/TwoLocus/Jackknife.py:584-593 | moments/TwoLocus/Jackknife.py:596-605 | moments/TwoLocus/Jackknife.py:635-644 | moments/TwoLocus/Jackknife.py:647-656 | moments/TwoLocus/Jackknife.py:659-668 | moments/TwoLocus/Jackknife.py:698-707 | moments/TwoLocus/Jackknife.py:710-719 | moments/TwoLocus/Jackknife.py:722-731 | moments/TwoLocus/Jackknife.py:761-770 | moments/TwoLocus/Jackknife.py:773-782 | moments/TwoLocus/Jackknife.py:785-794 \u2014 all 16 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:422\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":422}}}],"partialFingerprints":{"codehealthFindingId/v1":"ab25278da7ab25cd6751ce97ca88ad1844651bf153c75529b8608ea8e5516c58"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5\u201310 lines \u00D7 4): moments/Triallele/Numerics.py:415-424 | moments/Triallele/Numerics.py:537-546 | moments/Triallele/Numerics.py:557-561 | moments/Triallele/Numerics.py:585-589 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:415\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Triallele/Numerics.py:534\u0060 calls \u0060choose\u0060 and \u0060moments/Triallele/Numerics.py:412\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":415}}}],"partialFingerprints":{"codehealthFindingId/v1":"be893750517741aadbceef18124785b85186b33aa40805e0d60792ac20b89f38"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 3): moments/LD/Matrices.py:80-89 | moments/LD/Matrices.py:99-108 | moments/LD/Matrices.py:116-125 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":80}}}],"partialFingerprints":{"codehealthFindingId/v1":"be9ec24df0c01c8b4c701ced4e1a452537882c561cee040792d2f247c7abbe3e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6\u201310 lines \u00D7 4): moments/LD/Matrices.py:122-131 | moments/LD/Matrices.py:133-142 | moments/LD/Matrices.py:143-148 | moments/LD/Matrices.py:163-172 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/LD/Matrices.py:133\u0060 calls \u0060zip\u0060 and \u0060moments/LD/Matrices.py:143\u0060 does not \u2014 after which the two agree again for 5 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":122}}}],"partialFingerprints":{"codehealthFindingId/v1":"6e3a3ecc7950e1fe4c9fe92aef95108b9e3319186234d37d73f85b812f033b43"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 3): moments/LD/Matrices.py:459-468 | moments/LD/Matrices.py:475-484 | moments/LD/Matrices.py:489-498 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":459}}}],"partialFingerprints":{"codehealthFindingId/v1":"c180b36f6d13aab11b9be9dfaf2c509dd260798b8374cbdeb5e52358d5ec6af3"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9\u201310 lines \u00D7 3): moments/LinearSystem.py:119-128 | moments/LinearSystem.py:193-201 | moments/LinearSystem.py:280-289 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LinearSystem.py"},"region":{"startLine":119}}}],"partialFingerprints":{"codehealthFindingId/v1":"da432be7c4a770806a71c6b1c50c3e81ad559598e3877e6fbd28fe0beab792aa"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9\u201310 lines \u00D7 3): moments/TwoLocus/Jackknife.py:984-992 | moments/TwoLocus/Jackknife.py:1029-1038 | moments/TwoLocus/Jackknife.py:1044-1053 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:984\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":984}}}],"partialFingerprints":{"codehealthFindingId/v1":"22ddb8eb21c29c228f28e77cd4c78a7a57db27a26d143c1b403a9e4a8144ef33"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/Demes/Demes.py:951-960 | moments/Demes/Demes.py:964-973 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Demes/Demes.py:951\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":951}}}],"partialFingerprints":{"codehealthFindingId/v1":"49d652ec93c28a880c86afe2fc29826c65810fcf53c7f3345d31c0b104217e0c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/Demes/Inference.py:356-365 | moments/Demes/Inference.py:949-958 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":356}}}],"partialFingerprints":{"codehealthFindingId/v1":"a9085c392617bd75515e4f64ac8d8b5a013a1c2c9c3e408cb17af770088520e0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/Godambe.py:208-217 | moments/LD/Godambe.py:252-261 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":208}}}],"partialFingerprints":{"codehealthFindingId/v1":"7e4b9dbdf44749a267ac053903e5b83a566a2a32b0ba195b91dbe51411070227"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8\u201310 lines \u00D7 2): moments/Inference.py:76-83 | moments/LD/Inference.py:392-401 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":76}}}],"partialFingerprints":{"codehealthFindingId/v1":"4517467a1f4b96ce6c8b96f850d2a8a455bcd3cb6b1666e15815e3c7a50163cf"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/Integration.py:1152-1161 | moments/Integration_nomig.py:615-624 \u2014 before extracting anything, compare \u0060moments/Integration.py\u0060 and \u0060moments/Integration_nomig.py\u0060 as WHOLE FILES: this scan already matched 7 separate duplicated blocks between them, totalling at least 86 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together \u2014 extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Integration.py:1152\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":1152}}}],"partialFingerprints":{"codehealthFindingId/v1":"97d35a6d43287d11816609d6c074db1b96206e5d228b71b86663f92727b6fa2f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/LD/LDstats_mod.py:218-227 | moments/LD/LDstats_mod.py:266-275 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/LDstats_mod.py:218\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":218}}}],"partialFingerprints":{"codehealthFindingId/v1":"d2c924fb977867542a793c2514c7c461cdc31bfe52e6b7c7ff0f93e416dcfcb1"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/LD/Matrices.py:675-684 | moments/LD/Matrices.py:756-765 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":675}}}],"partialFingerprints":{"codehealthFindingId/v1":"2019220890fc50c5c8e8ae38f9b1e04c6e3e9527c7d3952fc7dfb5b9ce65708f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:167-176 | moments/LD/stats_from_genotype_counts.py:417-426 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:167\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":167}}}],"partialFingerprints":{"codehealthFindingId/v1":"ed003d504d79dc47cd418c33c6128e7aa7f35f25cd7fa6520c6e08e0c5364c54"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:524-533 | moments/LD/stats_from_genotype_counts.py:550-559 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":524}}}],"partialFingerprints":{"codehealthFindingId/v1":"39abc3f31eae01827766632e7cf69a501983622914288b5ea611d4d66bc18aa0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:586-595 | moments/LD/stats_from_genotype_counts.py:626-635 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":586}}}],"partialFingerprints":{"codehealthFindingId/v1":"0065cf7a8b38e583224979944db3900992d964e8121901f1e7f4a5dca6fe9a02"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:951-960 | moments/LD/stats_from_genotype_counts.py:1197-1206 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":951}}}],"partialFingerprints":{"codehealthFindingId/v1":"28df134cccce83dd1b4250bfb8d081a64233152cfd8078f911219942250cd5ec"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/Misc.py:569-578 | moments/Misc.py:580-589 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":569}}}],"partialFingerprints":{"codehealthFindingId/v1":"5edab0f18b934b6ca852a77ccb4b7e2622b86af67b834b42dfd3508ce68e880e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/Triallele/Numerics.py:346-355 | moments/Triallele/Numerics.py:448-457 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:346\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":346}}}],"partialFingerprints":{"codehealthFindingId/v1":"8f38ad822feca04fe6e65ab9f20c348277b6a8904d6d9a543b8cef1eb10954ea"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/Triallele/Numerics.py:434-443 | moments/Triallele/Numerics.py:480-489 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:434\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":434}}}],"partialFingerprints":{"codehealthFindingId/v1":"f990eba337bba0fc49d9b18ede3c18b92073a35fc0d6184d0e98eb7c3eebf650"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/TwoLocus/Numerics.py:538-547 | moments/TwoLocus/Numerics.py:576-585 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":538}}}],"partialFingerprints":{"codehealthFindingId/v1":"1a4934b4d9d5568e32e0b708c2aea66a3677ad74126cefe777fa065798d95bab"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (10 lines \u00D7 2): moments/TwoLocus/TLSpectrum_mod.py:160-169 | moments/TwoLocus/TLSpectrum_mod.py:172-181 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/TLSpectrum_mod.py"},"region":{"startLine":160}}}],"partialFingerprints":{"codehealthFindingId/v1":"675d61e1464fc5efd16f2f4f2a8504b3a31e746a5fda9e91d9e3ae08596e2786"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9\u201310 lines \u00D7 2): moments/TwoLocus/Util.py:178-186 | moments/TwoLocus/Util.py:205-214 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:178\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":178}}}],"partialFingerprints":{"codehealthFindingId/v1":"6f6f4af7d42c855a49d7cf5272b7708b6d9d7a2d9d8d4308bad7949160860336"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9\u201310 lines \u00D7 2): moments/TwoLocus/Util.py:249-257 | moments/TwoLocus/Util.py:292-301 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:249\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":249}}}],"partialFingerprints":{"codehealthFindingId/v1":"264a965d54aaed47918fd109d92f73479002ff54d6c7f0fc675dc6fc3f593d38"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9\u201310 lines \u00D7 2): moments/TwoLocus/Util.py:352-360 | moments/TwoLocus/Util.py:403-412 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:352\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":352}}}],"partialFingerprints":{"codehealthFindingId/v1":"bb5e37dbca568c08685504a8b8ad445799b45a274083ec76b77b19ba1b5705a0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 9): moments/TwoLocus/Jackknife.py:909-918 | moments/TwoLocus/Jackknife.py:924-932 | moments/TwoLocus/Jackknife.py:938-946 | moments/TwoLocus/Jackknife.py:966-976 | moments/TwoLocus/Jackknife.py:982-991 | moments/TwoLocus/Jackknife.py:997-1006 | moments/TwoLocus/Jackknife.py:1012-1021 | moments/TwoLocus/Jackknife.py:1027-1036 | moments/TwoLocus/Jackknife.py:1042-1051 \u2014 all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":909}}}],"partialFingerprints":{"codehealthFindingId/v1":"d9382f12d9401988a1facab946a71fb2cd9bfe09cf55d0ade8558ed05dabb5f2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7\u20139 lines \u00D7 6): moments/TwoLocus/Numerics.py:72-78 | moments/TwoLocus/Numerics.py:319-326 | moments/TwoLocus/Numerics.py:388-395 | moments/TwoLocus/Numerics.py:494-502 | moments/TwoLocus/Numerics.py:961-967 | moments/TwoLocus/Numerics.py:1094-1101 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":72}}}],"partialFingerprints":{"codehealthFindingId/v1":"d80b7b6b3c3c81ce8f8186e72d071d09b3e99848164e27666c0deaaeb2fc5cdd"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 5): moments/LD/Matrices.py:512-520 | moments/LD/Matrices.py:533-541 | moments/LD/Matrices.py:557-565 | moments/LD/Matrices.py:578-586 | moments/LD/Matrices.py:602-610 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:512\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":512}}}],"partialFingerprints":{"codehealthFindingId/v1":"25aaeabb26b854bed0ce81d836c79647a877e9697db187c56d46b06f6e613fd6"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 5): moments/LD/Matrices.py:744-752 | moments/LD/Matrices.py:767-775 | moments/LD/Matrices.py:841-849 | moments/LD/Matrices.py:868-876 | moments/LD/Matrices.py:902-910 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:744\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":744}}}],"partialFingerprints":{"codehealthFindingId/v1":"11006a2e4ad5da4a95dd8ccbfcf02956eeb6e6acae4b7d481e0aeb4331766eaa"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 5): moments/LD/Matrices.py:777-785 | moments/LD/Matrices.py:804-812 | moments/LD/Matrices.py:831-839 | moments/LD/Matrices.py:858-866 | moments/LD/Matrices.py:885-893 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:777\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":777}}}],"partialFingerprints":{"codehealthFindingId/v1":"1882767540efa3ea32dfe91f663874f685b6c76ca820311e8a244cc140a2ef31"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 4): moments/LD/stats_from_genotype_counts.py:519-527 | moments/LD/stats_from_genotype_counts.py:544-552 | moments/LD/stats_from_genotype_counts.py:569-577 | moments/LD/stats_from_genotype_counts.py:606-614 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":519}}}],"partialFingerprints":{"codehealthFindingId/v1":"419db883498bf48a9b691f2a0f7992578e23b682d2a93adc4be80304427002ee"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 4): moments/LD/stats_from_haplotype_counts.py:86-94 | moments/LD/stats_from_haplotype_counts.py:213-221 | moments/LD/stats_from_haplotype_counts.py:230-238 | moments/LD/stats_from_haplotype_counts.py:262-270 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_haplotype_counts.py"},"region":{"startLine":86}}}],"partialFingerprints":{"codehealthFindingId/v1":"15ab3a2721840d73d37dc8d421290460d73699aad3793260fc8a247f8600f26f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 4): moments/Triallele/Numerics.py:414-422 | moments/Triallele/Numerics.py:434-442 | moments/Triallele/Numerics.py:480-488 | moments/Triallele/Numerics.py:536-544 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:414\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Triallele/Numerics.py:478\u0060 calls \u0060choose\u0060 and \u0060moments/Triallele/Numerics.py:412\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":414}}}],"partialFingerprints":{"codehealthFindingId/v1":"568d201d223df5642c81d959815db6162a2f27c80fa32707c60e3dabf32ce602"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 3): moments/LD/Matrices.py:653-661 | moments/LD/Matrices.py:714-722 | moments/LD/Matrices.py:734-742 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:653\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":653}}}],"partialFingerprints":{"codehealthFindingId/v1":"df355c41cea9578dc7d83579c23cc90c26817aab975676860cbc37ca7b5781ad"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Demes/Demes.py:1322-1330 | moments/Demes/Demes.py:1603-1611 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1322}}}],"partialFingerprints":{"codehealthFindingId/v1":"48d2c2636f80fef45c2f43c31ef49526e6bcc5273128dd9f99c5a57ab05bf78c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Demes/Demes.py:1392-1400 | moments/Demes/Demes.py:1648-1656 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1392}}}],"partialFingerprints":{"codehealthFindingId/v1":"95d94915e478872fe25071f62585df52466740b115ef54f003ea9a4fcb2ffde8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Godambe.py:101-109 | moments/LD/Godambe.py:129-137 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":101}}}],"partialFingerprints":{"codehealthFindingId/v1":"23b78e673acdd61cf0a2ae3e5c7d3c4f22490e36ccc5db35b67c8ab71afa04ec"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/LD/Matrices.py:518-526 | moments/LD/Matrices.py:690-698 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:518\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":518}}}],"partialFingerprints":{"codehealthFindingId/v1":"074483b16d0c9f2d183a981bab78904fed035ed3e8d8c3d339ebb529b2663937"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:323-331 | moments/LD/stats_from_genotype_counts.py:370-378 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:323\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":323}}}],"partialFingerprints":{"codehealthFindingId/v1":"f11c0d0812e961849b0ba5ce7a77de2cdb3d451ccceeac12d9769982e075552f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:555-563 | moments/LD/stats_from_genotype_counts.py:594-602 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":555}}}],"partialFingerprints":{"codehealthFindingId/v1":"9cbbf3fa77426cc7a365d72611f696cfa550cf8aa615bf634ab290bcf5124e3f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8\u20139 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1062-1069 | moments/LD/stats_from_genotype_counts.py:1335-1343 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1062\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1062}}}],"partialFingerprints":{"codehealthFindingId/v1":"eba852bbba01cd07b1da21f97b7d71ffb151f5a549a554ddeaccdcadfdd61c45"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Manips.py:318-326 | moments/Manips.py:380-388 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Manips.py:318\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":318}}}],"partialFingerprints":{"codehealthFindingId/v1":"c8f44389ee6f505deae7a89b9e8ba9b6600b82b608a0af3e876e98160dc05082"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Misc.py:392-400 | moments/Spectrum_mod.py:1687-1697 \u2014 the copies sit in sibling files of one directory, so a shared home is within easy reach: extract the block into a single shared function the call sites can all reach \u2014 a file they already depend on, or a new one alongside them \u2014 and call it from both call sites, so a change lands once."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Misc.py"},"region":{"startLine":392}}}],"partialFingerprints":{"codehealthFindingId/v1":"0155dfce3fb3e5d3f73127e10aaf912c87bb6a799b174748e51ae8d80bd36140"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Plotting.py:689-697 | moments/Plotting.py:1052-1060 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":689}}}],"partialFingerprints":{"codehealthFindingId/v1":"b1f04dc435bef2bf170be090e6f8b7571dfb970bf1963670d88cea1a3d3b928c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Triallele/Jackknife.py:187-195 | moments/Triallele/Jackknife.py:205-213 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Jackknife.py"},"region":{"startLine":187}}}],"partialFingerprints":{"codehealthFindingId/v1":"7226b832468158d8afb69b10d05829c08dec91a259fffa3fb03392547855003a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/Triallele/Numerics.py:370-378 | moments/Triallele/Numerics.py:408-416 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:370\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":370}}}],"partialFingerprints":{"codehealthFindingId/v1":"11b16cddb21280976d696ab0c0555d6512ffd6c7cd73dc9faf5791174ce54fe9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/TwoLocus/Numerics.py:609-617 | moments/TwoLocus/Numerics.py:647-655 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Numerics.py:609\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":609}}}],"partialFingerprints":{"codehealthFindingId/v1":"ec4d9631eb8ce7de5f0073977fbe0d7a1efd8d7082ae091b8f479de257f1defc"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (9 lines \u00D7 2): moments/TwoLocus/Numerics.py:657-665 | moments/TwoLocus/Numerics.py:716-724 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Numerics.py:657\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":657}}}],"partialFingerprints":{"codehealthFindingId/v1":"58220727a8b5636831fb1a9ec8cea04c134c2303a8f6e1df32057247658bfbd5"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 11): moments/TwoLocus/Jackknife.py:908-915 | moments/TwoLocus/Jackknife.py:923-930 | moments/TwoLocus/Jackknife.py:937-944 | moments/TwoLocus/Jackknife.py:951-958 | moments/TwoLocus/Jackknife.py:965-972 | moments/TwoLocus/Jackknife.py:981-988 | moments/TwoLocus/Jackknife.py:996-1003 | moments/TwoLocus/Jackknife.py:1011-1018 | moments/TwoLocus/Jackknife.py:1026-1033 | moments/TwoLocus/Jackknife.py:1041-1048 | moments/TwoLocus/Jackknife.py:1056-1063 \u2014 all 11 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":908}}}],"partialFingerprints":{"codehealthFindingId/v1":"87a8b29276d003853431db49c7351cac87802313cc2cedf2a762f51d202f4f59"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 4): moments/Triallele/Numerics.py:342-349 | moments/Triallele/Numerics.py:406-413 | moments/Triallele/Numerics.py:425-432 | moments/Triallele/Numerics.py:547-554 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:342\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Triallele/Numerics.py:423\u0060 calls \u0060choose\u0060 and \u0060moments/Triallele/Numerics.py:340\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":342}}}],"partialFingerprints":{"codehealthFindingId/v1":"f0735aceefc76e2cbac0314c16b710d6ee5e81f9924d4141e0c87d3c60047df2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 4): moments/TwoLocus/Util.py:126-133 | moments/TwoLocus/Util.py:160-167 | moments/TwoLocus/Util.py:223-230 | moments/TwoLocus/Util.py:322-329 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":126}}}],"partialFingerprints":{"codehealthFindingId/v1":"d2787e2a0c32f7592244efc376fb079c590f81c62b378bf6fd3c54edd2a4a16a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 4): moments/TwoLocus/Util.py:145-152 | moments/TwoLocus/Util.py:195-202 | moments/TwoLocus/Util.py:274-281 | moments/TwoLocus/Util.py:381-388 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:145\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":145}}}],"partialFingerprints":{"codehealthFindingId/v1":"e277588608e3f0778992c5915ba4f1c084bb9864ede6dc1db504908245358ea7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 3): moments/LD/Matrices.py:646-653 | moments/LD/Matrices.py:666-673 | moments/LD/Matrices.py:727-734 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:646\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":646}}}],"partialFingerprints":{"codehealthFindingId/v1":"aa85cc6825295924356ff268725bb83e89359fde85c019dcd48c62cc65e40c73"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 3): moments/LD/Parsing.py:863-870 | moments/LD/Parsing.py:887-894 | moments/LD/Parsing.py:910-917 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Parsing.py:863\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":863}}}],"partialFingerprints":{"codehealthFindingId/v1":"c191df0864ac278609f4cfa4f0670c505e77a04360aab8cc328ab2f75df92981"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 3): moments/Triallele/Numerics.py:369-376 | moments/Triallele/Numerics.py:388-395 | moments/Triallele/Numerics.py:407-414 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:369\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/Triallele/Numerics.py:396\u0060 calls \u0060choose\u0060 and \u0060moments/Triallele/Numerics.py:415\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":369}}}],"partialFingerprints":{"codehealthFindingId/v1":"019dbb70df1b57fc3fa49a222cba434069e509428010e5b850dc678d31492db6"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 3): moments/Triallele/Numerics.py:429-436 | moments/Triallele/Numerics.py:522-529 | moments/Triallele/Numerics.py:570-577 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:429\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":429}}}],"partialFingerprints":{"codehealthFindingId/v1":"0169a73d637304a352bbad9a547ff383ba174042296b4254c9e17bcd9553ac7f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 3): moments/Triallele/Numerics.py:466-473 | moments/Triallele/Numerics.py:551-558 | moments/Triallele/Numerics.py:579-586 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:466\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":466}}}],"partialFingerprints":{"codehealthFindingId/v1":"ae6056da317b10d0aba894196109cb65fa83014551ea8235200e93c6f0b26795"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/Godambe.py:36-43 | moments/LD/Godambe.py:50-57 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":36}}}],"partialFingerprints":{"codehealthFindingId/v1":"34607e073e5e288d6e8ba3a1d2be0f1a8bf80312398a3f4657c4418a9c1e7444"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/Godambe.py:129-136 | moments/LD/Godambe.py:168-175 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":129}}}],"partialFingerprints":{"codehealthFindingId/v1":"b953f01fe8f1714f88c59e4a7caa17a09a68c9576310bd057a1f340c85e0ca3a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/Inference.py:75-82 | moments/TwoLocus/Inference.py:183-190 \u2014 before extracting anything, compare \u0060moments/Inference.py\u0060 and \u0060moments/TwoLocus/Inference.py\u0060 as WHOLE FILES: this scan already matched 5 separate duplicated blocks between them, totalling at least 76 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. The two sit in different directories, so one cannot simply be deleted in favour of the other while both are reached separately: hoist the shared part into a location both already depend on and have each file call it, and retire whichever file turns out to have no caller of its own left. Extracting one helper per block leaves the fork in place."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Inference.py"},"region":{"startLine":75}}}],"partialFingerprints":{"codehealthFindingId/v1":"d8a102104a9ff2fcd55f26377f67bb7165d21177c2685e590f833735d2ba845d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:344-351 | moments/LD/stats_from_genotype_counts.py:391-398 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:344\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":344}}}],"partialFingerprints":{"codehealthFindingId/v1":"ac2b5f1b1a2c2400a7187f4af541c094f380d3210358247f9653fa8d9a42a55b"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:646-653 | moments/LD/stats_from_genotype_counts.py:829-836 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:646\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":646}}}],"partialFingerprints":{"codehealthFindingId/v1":"a5bc5c11bd993ff2051ee729b8f65821ea140bc5b08c927cd7ac64db49d4ee68"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7\u20138 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:842-849 | moments/LD/stats_from_genotype_counts.py:1281-1287 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:842\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":842}}}],"partialFingerprints":{"codehealthFindingId/v1":"63bff2e8352ea7d627a97c13c64c56f63c4a2181e55aabd68d85586a294c82b4"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/Triallele/Numerics.py:444-451 | moments/Triallele/Numerics.py:508-515 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:444\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":444}}}],"partialFingerprints":{"codehealthFindingId/v1":"736f07e78f0f3fb0fafa55aafe8cda4c04fd56187262c5284a2dc8e2f127ec8d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/Triallele/Numerics.py:470-477 | moments/Triallele/Numerics.py:489-496 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:470\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":470}}}],"partialFingerprints":{"codehealthFindingId/v1":"0455f095540d539b7c0a91a41b3d71cfdd4b8bf75dbbee2be65d624becd9ccb0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (8 lines \u00D7 2): moments/Triallele/Numerics.py:507-514 | moments/Triallele/Numerics.py:526-533 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:507\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":507}}}],"partialFingerprints":{"codehealthFindingId/v1":"0453d1e4d087b559f4c2571eca0680d2b76c775e4fd93109c087bd7571cf287a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 20): moments/LD/Matrices.py:651-657 | moments/LD/Matrices.py:671-677 | moments/LD/Matrices.py:705-711 | moments/LD/Matrices.py:712-718 | moments/LD/Matrices.py:732-738 | moments/LD/Matrices.py:742-748 | moments/LD/Matrices.py:795-801 | moments/LD/Matrices.py:802-808 | moments/LD/Matrices.py:822-828 | moments/LD/Matrices.py:829-835 | moments/LD/Matrices.py:839-845 | moments/LD/Matrices.py:856-862 | moments/LD/Matrices.py:866-872 | moments/LD/Matrices.py:883-889 | moments/LD/Matrices.py:893-899 | moments/LD/Matrices.py:900-906 | moments/LD/Matrices.py:919-925 | moments/LD/Matrices.py:926-932 | moments/LD/Matrices.py:933-939 | moments/LD/Matrices.py:940-946 \u2014 all 20 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":651}}}],"partialFingerprints":{"codehealthFindingId/v1":"1370d784a3ca69c7f3bf87a3679297920ba82483c0c527d263d77a16f92abcf4"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 6): moments/LD/Matrices.py:765-771 | moments/LD/Matrices.py:775-781 | moments/LD/Matrices.py:788-794 | moments/LD/Matrices.py:815-821 | moments/LD/Matrices.py:849-855 | moments/LD/Matrices.py:876-882 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:765\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":765}}}],"partialFingerprints":{"codehealthFindingId/v1":"69bd86d3039b16fe2390a7213d0b90647749ddd63eef29bf0a1c7f33517ddd3a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6\u20137 lines \u00D7 6): moments/LD/stats_from_genotype_counts.py:323-329 | moments/LD/stats_from_genotype_counts.py:370-376 | moments/LD/stats_from_genotype_counts.py:646-652 | moments/LD/stats_from_genotype_counts.py:829-835 | moments/LD/stats_from_genotype_counts.py:1009-1014 | moments/LD/stats_from_genotype_counts.py:1050-1055 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:323\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":323}}}],"partialFingerprints":{"codehealthFindingId/v1":"fea558802d19239c194bb0379059a6c4d748f7ea38bda6ccc7d215bb092d73c1"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 5): moments/LD/stats_from_genotype_counts.py:497-503 | moments/LD/stats_from_genotype_counts.py:520-526 | moments/LD/stats_from_genotype_counts.py:545-551 | moments/LD/stats_from_genotype_counts.py:565-571 | moments/LD/stats_from_genotype_counts.py:607-613 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":497}}}],"partialFingerprints":{"codehealthFindingId/v1":"21e35dc111f5b6f691d29d4ae3b16ed32de1148be7b9c8b411f6d71cbc4ff564"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 5): moments/TwoLocus/TLSpectrum_mod.py:210-216 | moments/TwoLocus/TLSpectrum_mod.py:221-233 | moments/TwoLocus/TLSpectrum_mod.py:238-250 | moments/TwoLocus/TLSpectrum_mod.py:255-267 | moments/TwoLocus/TLSpectrum_mod.py:272-284 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/TLSpectrum_mod.py"},"region":{"startLine":210}}}],"partialFingerprints":{"codehealthFindingId/v1":"e4d478193930662b56c537afeb5c1011f2d2c7a9dd78f6f64e4dcff0835eeba9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 4): moments/LD/Matrices.py:644-650 | moments/LD/Matrices.py:664-670 | moments/LD/Matrices.py:725-731 | moments/LD/Matrices.py:752-758 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:644\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":644}}}],"partialFingerprints":{"codehealthFindingId/v1":"c7a2752de973e9fa93b530e7ae942d7d813f273362d18205ccb66c800d105006"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 4): moments/Triallele/Numerics.py:343-349 | moments/Triallele/Numerics.py:369-375 | moments/Triallele/Numerics.py:388-394 | moments/Triallele/Numerics.py:407-413 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:343\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/Triallele/Numerics.py:396\u0060 calls \u0060choose\u0060 and \u0060moments/Triallele/Numerics.py:415\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":343}}}],"partialFingerprints":{"codehealthFindingId/v1":"fcd9e332b094678211b1f17774a18e8119fa6fd28ba3439d4336990fa1cce0bb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 4): moments/Triallele/Numerics.py:372-378 | moments/Triallele/Numerics.py:410-416 | moments/Triallele/Numerics.py:494-500 | moments/Triallele/Numerics.py:512-518 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:372\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":372}}}],"partialFingerprints":{"codehealthFindingId/v1":"94460e37e20ed5861a29b71a125cafeabb61f2aa821d0172abdddf200d09e867"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 3): moments/LD/Godambe.py:411-417 | moments/LD/Godambe.py:508-514 | moments/LD/Godambe.py:582-588 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Godambe.py"},"region":{"startLine":411}}}],"partialFingerprints":{"codehealthFindingId/v1":"06deeeed3fc1f7a6aae7f1aee80252a21295c28144273dabbf12035edfb252e5"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6\u20137 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:659-665 | moments/LD/stats_from_genotype_counts.py:1240-1245 | moments/LD/stats_from_genotype_counts.py:1405-1410 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:659\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":659}}}],"partialFingerprints":{"codehealthFindingId/v1":"7df1b5243e9d91ce82478667e927048841b821e2e0f464afcc1c348d81dce670"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6\u20137 lines \u00D7 3): moments/LD/stats_from_haplotype_counts.py:51-57 | moments/LD/stats_from_haplotype_counts.py:63-69 | moments/LD/stats_from_haplotype_counts.py:75-80 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_haplotype_counts.py:51\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_haplotype_counts.py"},"region":{"startLine":51}}}],"partialFingerprints":{"codehealthFindingId/v1":"a40e29680f298e977ee51601688621a2e700b0b2354f136e56513f5e834e74d7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 3): moments/Triallele/Numerics.py:338-344 | moments/Triallele/Numerics.py:372-378 | moments/Triallele/Numerics.py:512-518 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:338\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":338}}}],"partialFingerprints":{"codehealthFindingId/v1":"33364154fec430a80a540b473af070a5f36225c4597fc3fbe6ec403b5ffc55de"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 3): moments/Triallele/Numerics.py:445-451 | moments/Triallele/Numerics.py:491-497 | moments/Triallele/Numerics.py:509-515 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:445\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":445}}}],"partialFingerprints":{"codehealthFindingId/v1":"b57a0a64ff2b1a985e3a79df6141bd3f43ef98360dff0dbaf7c1e86b3cf8139b"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 3): moments/Triallele/Numerics.py:444-450 | moments/Triallele/Numerics.py:508-514 | moments/Triallele/Numerics.py:527-533 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:444\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Triallele/Numerics.py:526\u0060 calls \u0060choose\u0060 and \u0060moments/Triallele/Numerics.py:443\u0060 does not \u2014 after which the two agree again for 4 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":444}}}],"partialFingerprints":{"codehealthFindingId/v1":"89e22c052719a52503e7008f010eb6a8631671ed411314bbff6abb0f1994bd4c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Demes/Demes.py:162-168 | moments/Demes/Demes.py:442-448 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/Demes/Demes.py:160\u0060 calls \u0060ValueError\u0060 and \u0060moments/Demes/Demes.py:440\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":162}}}],"partialFingerprints":{"codehealthFindingId/v1":"67e333c81df65ec9bec93b39e606d252ecb66d09b3b41ad5abe6b3bad83821dd"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Godambe.py:28-34 | moments/LD/Godambe.py:42-48 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Godambe.py"},"region":{"startLine":28}}}],"partialFingerprints":{"codehealthFindingId/v1":"481cfa8335eb5008f491fd850747056e1db3680eae3b7319dc4680169fd511ef"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Integration.py:33-39 | moments/Integration_nomig.py:37-43 \u2014 before extracting anything, compare \u0060moments/Integration.py\u0060 and \u0060moments/Integration_nomig.py\u0060 as WHOLE FILES: this scan already matched 7 separate duplicated blocks between them, totalling at least 86 lines, which is the signature of one file having been copied from the other rather than of a helper waiting to be extracted. If that is what happened, the fix is to keep one copy and have the other call it (or delete it), which resolves this row and its siblings together \u2014 extracting one helper per block leaves the fork in place. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":33}}}],"partialFingerprints":{"codehealthFindingId/v1":"0f30a161952afa2f3fcb1c4b77eb7f95441da4721f7e7eeed235cd4cba1d5b1c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/LD/Matrices.py:952-958 | moments/LD/Matrices.py:996-1002 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/LD/Matrices.py:1003\u0060 calls \u0060split\u0060 and \u0060moments/LD/Matrices.py:959\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":952}}}],"partialFingerprints":{"codehealthFindingId/v1":"9a41c77e06e034d552d796542d1d02a9efb89042b3158ba4098356c38781534c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6\u20137 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:680-686 | moments/LD/stats_from_genotype_counts.py:1377-1382 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:680\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":680}}}],"partialFingerprints":{"codehealthFindingId/v1":"48e9305d2d55fe07f1b2309fd68dff89f34dfb6c78cea178757fef5d910921ed"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6\u20137 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:863-869 | moments/LD/stats_from_genotype_counts.py:1170-1175 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:863\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":863}}}],"partialFingerprints":{"codehealthFindingId/v1":"240c7db624330706db2df384a0968a983a90333128856b19f369cb3f9f49e03f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1118-1124 | moments/LD/stats_from_genotype_counts.py:1363-1369 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1118\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1118}}}],"partialFingerprints":{"codehealthFindingId/v1":"38868789fe00013a5138e4c98cf59e942b29e33e0c2b63f295262b18f392cc68"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6\u20137 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1137-1142 | moments/LD/stats_from_genotype_counts.py:1144-1150 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1137\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1137}}}],"partialFingerprints":{"codehealthFindingId/v1":"5299e13f2df698d1b8b5716b8c50555c0711ea535c14bd28c3bfc237d3870bae"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1253-1259 | moments/LD/stats_from_genotype_counts.py:1419-1425 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1253\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1253}}}],"partialFingerprints":{"codehealthFindingId/v1":"1970448d9f3090d25bff00ace5b997a83b3c3d33d9a7415b068b4de842085ba0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Manips.py:123-129 | moments/Manips.py:181-187 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Manips.py:123\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":123}}}],"partialFingerprints":{"codehealthFindingId/v1":"ddc97b2034dd9ab6670bf240d3c0ff813259c171f7d48879d6494226b0ade343"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Manips.py:308-314 | moments/Manips.py:370-376 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Manips.py:308\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":308}}}],"partialFingerprints":{"codehealthFindingId/v1":"c6a8f365e7233b884c93805710bef0524ded0e1de665dc48c6d08bf6ef802fc8"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Plotting.py:1068-1074 | moments/Plotting.py:1079-1085 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Plotting.py:1068\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":1068}}}],"partialFingerprints":{"codehealthFindingId/v1":"28045337cf2ef0b4311bb39ececb484d3316275a52278c2c9fc9c38757438073"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Triallele/Jackknife.py:22-28 | moments/Triallele/Jackknife.py:82-88 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Jackknife.py:22\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Jackknife.py"},"region":{"startLine":22}}}],"partialFingerprints":{"codehealthFindingId/v1":"ee9c772f0cd7722cd91ab20b031a7443d6d1170b059be9225150235d179828ab"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/Triallele/Numerics.py:338-344 | moments/Triallele/Numerics.py:440-446 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:338\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":338}}}],"partialFingerprints":{"codehealthFindingId/v1":"587de65420bdf6a804b277b920bdd097da5bfdb326df7fde8072e7b664e7478e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/TwoLocus/Util.py:345-351 | moments/TwoLocus/Util.py:396-402 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":345}}}],"partialFingerprints":{"codehealthFindingId/v1":"4de6b4d7953936be76bfefc94df88daa0a862d1869ed8f7a72241b7bb54b9ae7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 16): moments/LD/Matrices.py:707-712 | moments/LD/Matrices.py:744-749 | moments/LD/Matrices.py:767-772 | moments/LD/Matrices.py:790-795 | moments/LD/Matrices.py:797-802 | moments/LD/Matrices.py:817-822 | moments/LD/Matrices.py:824-829 | moments/LD/Matrices.py:841-846 | moments/LD/Matrices.py:851-856 | moments/LD/Matrices.py:868-873 | moments/LD/Matrices.py:878-883 | moments/LD/Matrices.py:895-900 | moments/LD/Matrices.py:902-907 | moments/LD/Matrices.py:921-926 | moments/LD/Matrices.py:928-933 | moments/LD/Matrices.py:935-940 \u2014 all 16 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:707\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":707}}}],"partialFingerprints":{"codehealthFindingId/v1":"f05bccc36029f14d2aee323db0074d534ca35938c9c68f62528686a6a618b04a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 6): moments/LD/Matrices.py:539-544 | moments/LD/Matrices.py:563-568 | moments/LD/Matrices.py:584-589 | moments/LD/Matrices.py:608-613 | moments/LD/Matrices.py:683-688 | moments/LD/Matrices.py:700-705 \u2014 all 6 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:539\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":539}}}],"partialFingerprints":{"codehealthFindingId/v1":"60b35186321672cc8c2d1d0ba2263888ea5b7515f524ca4ec379da574bfc805c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 3): moments/LD/Matrices.py:696-701 | moments/LD/Matrices.py:783-788 | moments/LD/Matrices.py:810-815 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:696\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":696}}}],"partialFingerprints":{"codehealthFindingId/v1":"add52d976256ef9860f8820caba25669b59b8606e2cc908b7cabd550a40bcd3d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:154-159 | moments/LD/stats_from_genotype_counts.py:344-351 | moments/LD/stats_from_genotype_counts.py:391-398 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:154\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":154}}}],"partialFingerprints":{"codehealthFindingId/v1":"0ff76c4181f09b39eed7af1f9065ef6c3dafdb2791aea0774dd7d22976229a8e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:349-354 | moments/LD/stats_from_genotype_counts.py:359-364 | moments/LD/stats_from_genotype_counts.py:431-436 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:349\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":349}}}],"partialFingerprints":{"codehealthFindingId/v1":"406d1a45b8254adddfba3cb9b3c4f7d156b120c06ec549fa737508cb568cc15e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:396-401 | moments/LD/stats_from_genotype_counts.py:406-411 | moments/LD/stats_from_genotype_counts.py:456-461 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:396\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":396}}}],"partialFingerprints":{"codehealthFindingId/v1":"f169f02b67ac49d1fe89b0b1d29e4421ac8ff961a656cd7ecd876d28febc35c4"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/Integration.py:793-798 | moments/Integration.py:804-809 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":793}}}],"partialFingerprints":{"codehealthFindingId/v1":"5a5e699495442313a500cd00e0163d61b4eeb4d112b41c22527bc2615d8a91f1"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/Integration_nomig.py:625-630 | moments/Integration_nomig.py:795-800 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration_nomig.py"},"region":{"startLine":625}}}],"partialFingerprints":{"codehealthFindingId/v1":"4b306de9a923ed164dd91b03d40a09a7944e05ba70d8623132a0797d2c29eb39"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/Godambe.py:41-46 | moments/LD/Godambe.py:177-182 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Godambe.py"},"region":{"startLine":41}}}],"partialFingerprints":{"codehealthFindingId/v1":"392cb8b1ce1a0d8cdb27ab7e40536b62ba01d2fb31dbb17934242052523c5fd4"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/Matrices.py:86-91 | moments/LD/Matrices.py:185-192 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:185\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":86}}}],"partialFingerprints":{"codehealthFindingId/v1":"ac189d10343d1d6f667d841f8d81f3d158b8276208676d5b20454f38d4f5c3fb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/Matrices.py:524-529 | moments/LD/Matrices.py:548-553 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:524\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":524}}}],"partialFingerprints":{"codehealthFindingId/v1":"cb5b9502243fab331fe1f0884c678f621372916d1cab051d1546f40bb68a77ec"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:365-370 | moments/LD/stats_from_genotype_counts.py:412-417 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:365\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":365}}}],"partialFingerprints":{"codehealthFindingId/v1":"514c2317668dd9dc7a3bd7f3c9089310a66d59117b8eed498e6c2c4d8c5a2eee"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:661-666 | moments/LD/stats_from_genotype_counts.py:1351-1356 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:661\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":661}}}],"partialFingerprints":{"codehealthFindingId/v1":"bbdcecdd382e7b7abd84710a081c5be5ebb00da3f2d2914c9db32fb3dfd7bf5a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1071-1076 | moments/LD/stats_from_genotype_counts.py:1413-1418 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1071\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1071}}}],"partialFingerprints":{"codehealthFindingId/v1":"f8aef9b28f631a451f8daf2827acd2a9382a4814400af7c0c39742c11c3449fb"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/Triallele/Jackknife.py:52-57 | moments/Triallele/Jackknife.py:112-117 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Jackknife.py"},"region":{"startLine":52}}}],"partialFingerprints":{"codehealthFindingId/v1":"95f4c2a7264446c3006004de8cbeee75ddf08ef4c32bdf18ead3c8bade6883cd"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (3\u20136 lines \u00D7 3): moments/TwoLocus/Jackknife.py:67-69 | moments/TwoLocus/Jackknife.py:171-176 | moments/TwoLocus/Jackknife.py:304-309 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:171\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":67}}}],"partialFingerprints":{"codehealthFindingId/v1":"ab4f9ec49b05365c86392e0c4cb5cfacd3d01a353f2ff321a3fc9f2e9f87e20e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/TwoLocus/Jackknife.py:275-280 | moments/TwoLocus/Jackknife.py:285-290 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":275}}}],"partialFingerprints":{"codehealthFindingId/v1":"b9610fff3baeb17cdb67a3ff6e12aa452a024dea5f870f7a21738fe6ede2fe2c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/TwoLocus/Numerics.py:893-898 | moments/TwoLocus/Numerics.py:1176-1181 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":893}}}],"partialFingerprints":{"codehealthFindingId/v1":"51d5422d25deb39d9103652ef2328f5035cd9d748459cadeabe95f2b717b085e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/TwoLocus/Numerics.py:1187-1192 | moments/TwoLocus/Numerics.py:1208-1213 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Numerics.py:1187\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":1187}}}],"partialFingerprints":{"codehealthFindingId/v1":"7daf4bd4b3ed5a7b24abe14e3d3ea6b3526a50a6364a70aa7e3cdcec39f37c7f"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 14): moments/LD/Matrices.py:518-522 | moments/LD/Matrices.py:539-543 | moments/LD/Matrices.py:563-567 | moments/LD/Matrices.py:584-588 | moments/LD/Matrices.py:608-612 | moments/LD/Matrices.py:630-634 | moments/LD/Matrices.py:643-647 | moments/LD/Matrices.py:663-667 | moments/LD/Matrices.py:683-687 | moments/LD/Matrices.py:690-694 | moments/LD/Matrices.py:700-704 | moments/LD/Matrices.py:724-728 | moments/LD/Matrices.py:751-755 | moments/LD/Matrices.py:909-913 \u2014 all 14 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Matrices.py:518\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":518}}}],"partialFingerprints":{"codehealthFindingId/v1":"be8065726bb54738378b9dcafb040d8ead2d39878ca2c72caf5e5fda26ce42f9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 11): moments/LD/stats_from_genotype_counts.py:155-159 | moments/LD/stats_from_genotype_counts.py:172-176 | moments/LD/stats_from_genotype_counts.py:179-183 | moments/LD/stats_from_genotype_counts.py:312-316 | moments/LD/stats_from_genotype_counts.py:347-351 | moments/LD/stats_from_genotype_counts.py:357-361 | moments/LD/stats_from_genotype_counts.py:394-398 | moments/LD/stats_from_genotype_counts.py:404-408 | moments/LD/stats_from_genotype_counts.py:422-426 | moments/LD/stats_from_genotype_counts.py:429-433 | moments/LD/stats_from_genotype_counts.py:453-458 \u2014 all 11 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:453\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":155}}}],"partialFingerprints":{"codehealthFindingId/v1":"5f12fb50d9727c4c969003322069d7c4a9b9c1a78a2013a2b230c0f28a8c4d6a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 9): moments/LD/Matrices.py:627-631 | moments/LD/Matrices.py:640-644 | moments/LD/Matrices.py:660-664 | moments/LD/Matrices.py:680-684 | moments/LD/Matrices.py:697-701 | moments/LD/Matrices.py:721-725 | moments/LD/Matrices.py:761-765 | moments/LD/Matrices.py:784-788 | moments/LD/Matrices.py:811-815 \u2014 all 9 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":627}}}],"partialFingerprints":{"codehealthFindingId/v1":"19a36b7941300e6c325beb004d14a33b0e5e88823d2eb05a65e78cc365dfe7c7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 8): moments/LD/stats_from_genotype_counts.py:167-171 | moments/LD/stats_from_genotype_counts.py:323-327 | moments/LD/stats_from_genotype_counts.py:370-374 | moments/LD/stats_from_genotype_counts.py:417-421 | moments/LD/stats_from_genotype_counts.py:646-650 | moments/LD/stats_from_genotype_counts.py:829-833 | moments/LD/stats_from_genotype_counts.py:1009-1013 | moments/LD/stats_from_genotype_counts.py:1050-1054 \u2014 all 8 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:167\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":167}}}],"partialFingerprints":{"codehealthFindingId/v1":"9e56716dc671e3094b88c343629a7f3147e7f6e7609a3a9cf5269677ee193301"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 5): moments/LD/stats_from_genotype_counts.py:447-451 | moments/LD/stats_from_genotype_counts.py:1232-1236 | moments/LD/stats_from_genotype_counts.py:1273-1277 | moments/LD/stats_from_genotype_counts.py:1329-1333 | moments/LD/stats_from_genotype_counts.py:1395-1399 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, \u0060moments/LD/stats_from_genotype_counts.py:1400\u0060 calls \u0060sum\u0060 and \u0060moments/LD/stats_from_genotype_counts.py:452\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":447}}}],"partialFingerprints":{"codehealthFindingId/v1":"f9339ef38e8d0de89db7e08ffc6f25228db366f506e56b94480f616f40aa100c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 5): moments/Manips.py:127-131 | moments/Manips.py:185-189 | moments/Manips.py:248-252 | moments/Manips.py:312-316 | moments/Manips.py:374-378 \u2014 all 5 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Manips.py"},"region":{"startLine":127}}}],"partialFingerprints":{"codehealthFindingId/v1":"107774873f0e97f8827f83d4c3e18060d5006239b12ac0e2ef887bb65a68a20b"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 5): moments/Triallele/Jackknife.py:52-56 | moments/Triallele/Jackknife.py:112-116 | moments/TwoLocus/Jackknife.py:197-201 | moments/TwoLocus/Jackknife.py:217-221 | moments/TwoLocus/Jackknife.py:237-241 \u2014 there are 5 copies across 2 file(s) \u2014 more copies than files, so at least one file holds the block twice. Extract it once into a single shared function every call site can reach and call it from all 5 sites; resolving a subset leaves the remainder to drift apart."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Jackknife.py"},"region":{"startLine":52}}}],"partialFingerprints":{"codehealthFindingId/v1":"25b89ef54e386d6adce74ef1f81cccb4db576ac448230c05d242ec8ac114066c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 4): moments/Triallele/Numerics.py:351-355 | moments/Triallele/Numerics.py:377-385 | moments/Triallele/Numerics.py:453-457 | moments/Triallele/Numerics.py:462-469 \u2014 all 4 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Triallele/Numerics.py:351\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Numerics.py"},"region":{"startLine":351}}}],"partialFingerprints":{"codehealthFindingId/v1":"22e337afea6299783138a80f0a4af35ec7ba480fe1ee11bb71ee09930e114e9d"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 3): moments/LD/Matrices.py:503-507 | moments/LD/Matrices.py:525-529 | moments/LD/Matrices.py:549-553 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":503}}}],"partialFingerprints":{"codehealthFindingId/v1":"f463529115ee29c5e00c77ac7eb6daaea0f5e231325a6c01fe35c764f6ad4222"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 3): moments/LD/Parsing.py:880-884 | moments/LD/Parsing.py:904-908 | moments/LD/Parsing.py:935-939 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Parsing.py:880\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":880}}}],"partialFingerprints":{"codehealthFindingId/v1":"41f7b6378dadfb431d49245cc28ebcb0006f78d10ebd560079704747b2d8ea71"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:662-666 | moments/LD/stats_from_genotype_counts.py:1090-1094 | moments/LD/stats_from_genotype_counts.py:1352-1356 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:662\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":662}}}],"partialFingerprints":{"codehealthFindingId/v1":"ecff3fc3d4885e60fd8fb1f805b5b616862536dda5c1a58b1a22a1a3902123b0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 3): moments/LinearSystem.py:112-116 | moments/LinearSystem.py:186-190 | moments/LinearSystem.py:273-277 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LinearSystem.py"},"region":{"startLine":112}}}],"partialFingerprints":{"codehealthFindingId/v1":"2d9e7b1eb2c4a24e122be98b64d80f0e7c25dd76f8a71501efd0059f3609ac6e"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (4\u20135 lines \u00D7 3): moments/Demes/Demes.py:1410-1413 | moments/Demes/Demes.py:1420-1424 | moments/Demes/Demes.py:1438-1444 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/Demes/Demes.py:1420\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Demes.py"},"region":{"startLine":1410}}}],"partialFingerprints":{"codehealthFindingId/v1":"af3ebe53dd9f9d4a65e78fa7bbe082bb4d854fe31d43b92e58299da79e6bc645"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/Demes/Inference.py:405-409 | moments/Demes/Inference.py:1004-1008 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Demes/Inference.py"},"region":{"startLine":405}}}],"partialFingerprints":{"codehealthFindingId/v1":"40eab4367e16713b010b5dfcd41b1e9f57073fb5d6654b1a8e19229f3cc7077c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/LDstats_mod.py:206-210 | moments/LD/LDstats_mod.py:251-255 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":206}}}],"partialFingerprints":{"codehealthFindingId/v1":"cb21a4a7bb416b1b937b3f2e75cefb785903db40952410ea8693ec720851e2da"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/Matrices.py:546-550 | moments/LD/Matrices.py:570-574 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Matrices.py"},"region":{"startLine":546}}}],"partialFingerprints":{"codehealthFindingId/v1":"3d61a7bf30a1f489bf3ae9ad0605a721c418949112d11718c71f6b86ef9de66c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (3\u20135 lines \u00D7 3): moments/LD/Parsing.py:1077-1081 | moments/LD/Parsing.py:1085-1089 | moments/LD/Parsing.py:1092-1094 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Parsing.py:1077\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":1077}}}],"partialFingerprints":{"codehealthFindingId/v1":"c180585e51d4f83709331cc6a004f644f49d6729dc16e30ca23b4ba43be873ad"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:667-671 | moments/LD/stats_from_genotype_counts.py:1357-1361 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:667\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":667}}}],"partialFingerprints":{"codehealthFindingId/v1":"b2fec2547c0478f62880fbfbabc0ebd1493107a240bbf8f9682a843c519d1712"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:687-691 | moments/LD/stats_from_genotype_counts.py:1112-1116 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:687\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":687}}}],"partialFingerprints":{"codehealthFindingId/v1":"6965df8857ed8f70fe4e48457862edac85f7d28c68146b8e9af594cce292a7a9"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:850-854 | moments/LD/stats_from_genotype_counts.py:1288-1292 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:850\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":850}}}],"partialFingerprints":{"codehealthFindingId/v1":"95a9f60127371fb5e2f929f05045571d655782e2351287c0ea2f2de5c6eab5dc"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:870-874 | moments/LD/stats_from_genotype_counts.py:1176-1180 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:870\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":870}}}],"partialFingerprints":{"codehealthFindingId/v1":"9f99ab8d6bdb3974c91a60c61dbaa76da32f35d5b8bf8918b562864efc2ceef2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1057-1061 | moments/LD/stats_from_genotype_counts.py:1247-1251 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1057\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1057}}}],"partialFingerprints":{"codehealthFindingId/v1":"ea31886bd13dc11d8cefc654eeeb7d3be5ae91b114e1571743259c3b24c8a98c"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1070-1074 | moments/LD/stats_from_genotype_counts.py:1344-1348 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1070\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1070}}}],"partialFingerprints":{"codehealthFindingId/v1":"e24454285b95ebbfa48f85d166f0e4c39b0a7253090743048e57052776c4da2a"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1125-1129 | moments/LD/stats_from_genotype_counts.py:1370-1374 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1125\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1125}}}],"partialFingerprints":{"codehealthFindingId/v1":"038f8a21ea04c0f5c46e4043decedb96a0ea4c89f3ed929569345f5ffab2f6bf"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/stats_from_genotype_counts.py:1247-1251 | moments/LD/stats_from_genotype_counts.py:1412-1416 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1247\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1247}}}],"partialFingerprints":{"codehealthFindingId/v1":"75aded458ed7f3ca52cbe3237048c328c61cad31fde6afe4e95cdfa7e2bdc60b"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (3\u20135 lines \u00D7 3): moments/LD/stats_from_genotype_counts.py:1040-1042 | moments/LD/stats_from_genotype_counts.py:1260-1264 | moments/LD/stats_from_genotype_counts.py:1426-1430 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_genotype_counts.py:1040\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_genotype_counts.py"},"region":{"startLine":1040}}}],"partialFingerprints":{"codehealthFindingId/v1":"92912a5a62dcc87d2327cdcb588d4d489894ff6270e2846c51b2f2418aca79f0"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/Triallele/Jackknife.py:61-65 | moments/Triallele/Jackknife.py:121-125 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/Jackknife.py"},"region":{"startLine":61}}}],"partialFingerprints":{"codehealthFindingId/v1":"d95d38bc9f9c9813381dfd3c286fbb1dd547f0c1e51b0a11a638ad0bf67b9df3"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (3\u20135 lines \u00D7 3): moments/TwoLocus/Jackknife.py:177-181 | moments/TwoLocus/Jackknife.py:259-261 | moments/TwoLocus/Jackknife.py:310-314 \u2014 all 3 copies are in the same file, so extract the block into one function there and call it from every one of those sites \u2014 resolving only two of them leaves the rest to drift apart the first time one is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Jackknife.py:177\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. Note that the copies do not run to the end of the range shown: their LAST lines are different code, not the same code under different names \u2014 the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":177}}}],"partialFingerprints":{"codehealthFindingId/v1":"c581cc0bbe0af7566648a6fb906a9d94ec65526184a842ee4779671be7e68dd3"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/TwoLocus/Numerics.py:94-98 | moments/TwoLocus/Numerics.py:111-115 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":94}}}],"partialFingerprints":{"codehealthFindingId/v1":"f125fa598ffc3a5905da6b5c40b181a7ee8e5f37cf337d54ad050e6d5d760ff7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/TwoLocus/Numerics.py:1194-1198 | moments/TwoLocus/Numerics.py:1215-1219 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Numerics.py:1194\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":1194}}}],"partialFingerprints":{"codehealthFindingId/v1":"b6e06daa1064e193f36a586660d6e30597005223b5d1400ce7fba277ff0b23ee"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/TwoLocus/Util.py:340-344 | moments/TwoLocus/Util.py:391-395 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/TwoLocus/Util.py:340\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Util.py"},"region":{"startLine":340}}}],"partialFingerprints":{"codehealthFindingId/v1":"83498d5041bbb1df2fce11ed6ec20f45ff6eea2d6f7be3b91a89b4db0aaaaf63"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/LD/LDstats_mod.py:73-77 | moments/Triallele/TriSpectrum_mod.py:115-119 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":73}}}],"partialFingerprints":{"codehealthFindingId/v1":"d8d5054398b28898cdc539ec4b5ce746a45e21d50fbb14d6c8d8bea12aaa75d2"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 3): moments/LD/LDstats_mod.py:87-91 | moments/Spectrum_mod.py:192-196 | moments/Triallele/TriSpectrum_mod.py:129-133 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere all 3 call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made 3 times."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/LDstats_mod.py"},"region":{"startLine":87}}}],"partialFingerprints":{"codehealthFindingId/v1":"2143d46eca3c201901e39adb64ebfd4eb97b55d84842d275ca0f1b4c82ef9e10"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/Spectrum_mod.py:185-189 | moments/Triallele/TriSpectrum_mod.py:122-126 \u2014 the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach \u2014 a location they all depend on today, or a new shared one if there is none \u2014 and call it from each site; until then, every change has to be made twice. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Spectrum_mod.py"},"region":{"startLine":185}}}],"partialFingerprints":{"codehealthFindingId/v1":"bb5d635e05594b0943a46e21bfe6eee915bc8edeb3793c33cda77f630de08c89"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/Integration.py:694-698 | moments/Integration.py:702-706 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Integration.py"},"region":{"startLine":694}}}],"partialFingerprints":{"codehealthFindingId/v1":"1f2b614bc2160f018af06223c498d9f2cab80478aa0a263354932bbddaab2da7"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (7 lines \u00D7 2): moments/LD/Parsing.py:433-439 | moments/LD/Parsing.py:524-530 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/Parsing.py:433\u0060 it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. The \u0060return\u0060 at the foot of the matched lines is the enclosing body\u0027s own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that \u0060return\u0060 occupied \u2014 no decision has to be handed back and re-acted on. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/LD/Parsing.py:523\u0060 calls \u0060compute_D\u0060 and \u0060moments/LD/Parsing.py:432\u0060 does not \u2014 after which the two agree again for 3 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":433}}}],"partialFingerprints":{"codehealthFindingId/v1":"efe075b1dd660d0ee8a7c0e56b967ed3923470f4acbd1f360c1a296be8546325"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/Parsing.py:1363-1368 | moments/LD/Parsing.py:1481-1486 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Parsing.py"},"region":{"startLine":1363}}}],"partialFingerprints":{"codehealthFindingId/v1":"d2691c9ba7fefc3ae629d58a19eebf466eda3787687c92c47cdf26958280da08"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (6 lines \u00D7 2): moments/LD/stats_from_haplotype_counts.py:163-168 | moments/LD/stats_from_haplotype_counts.py:315-320 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060moments/LD/stats_from_haplotype_counts.py:163\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that. \u2605 These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, \u0060moments/LD/stats_from_haplotype_counts.py:313\u0060 calls \u0060sum\u0060 and \u0060moments/LD/stats_from_haplotype_counts.py:162\u0060 does not \u2014 after which the two agree again for 2 more lines. One of those two behaviours is the intended one and the other is what a copy-paste left behind, so decide which BEFORE unifying them: extracting the shared part will silently settle it, and if the copy that skips the call is the wrong one, that bug is already live."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/stats_from_haplotype_counts.py"},"region":{"startLine":163}}}],"partialFingerprints":{"codehealthFindingId/v1":"96ed3bfc41277216df68ff9e26025346afa0e39234478427608cb4a758ea9869"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (5 lines \u00D7 2): moments/TwoLocus/Numerics.py:408-412 | moments/TwoLocus/Numerics.py:418-422 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. The matched lines also transfer control out of the body holding them, which cannot survive a move into a called unit unchanged: have the extracted unit return that decision and let each site act on it."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Numerics.py"},"region":{"startLine":408}}}],"partialFingerprints":{"codehealthFindingId/v1":"742fd4916c2454113e1c7e8209241f754ca928427409014239caf5a4134656bf"}},{"ruleId":"D4","level":"warning","message":{"text":"Duplicated block (14\u201326 lines \u00D7 2): bench/report.py:39-52 | bench/report.py:55-80 \u2014 both copies are in the same file, so extract the block into one function there and call it from each site \u2014 the copies drift apart the first time only one of them is edited. Read the line range as the matched WINDOW rather than a finished unit: at \u0060bench/report.py:39\u0060 it does not close everything it opens, so those exact lines cannot be lifted as they stand \u2014 widen the region to the smallest complete statement or declaration that contains it, and extract that."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"bench/report.py"},"region":{"startLine":39}}}],"partialFingerprints":{"codehealthFindingId/v1":"0353dcb8eee32e59cae9c83d9b1fd2a055189f4dfabdf17706a28c5fd0917f24"}},{"ruleId":"D16","level":"note","message":{"text":"Off-boarding risk: anonymized user #1: If anonymized user #1 becomes unavailable, 4 significant file(s) lose their only recent owner: moments/Demes/Demes.py, moments/Demes/Inference.py, moments/LD/Inference.py, moments/Misc.py. Pair on, review, or document these before any departure."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"9714108971388e8bb3482c24434b6137aa64986bcf714baeef88e9e4a7bccb71"}},{"ruleId":"D17","level":"warning","message":{"text":"XxxComment: # XXX: I can\u0027t set the axis ticks to be just the endpoints. \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060# REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Plotting.py"},"region":{"startLine":939}}}],"partialFingerprints":{"codehealthFindingId/v1":"5d9ec0ac226c06a4e2eeba1bdabe46a118baf8ba4687ca9a822bf0f0f42207b4"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: # TODO: complete docstring \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060# REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/LD/Godambe.py"},"region":{"startLine":563}}}],"partialFingerprints":{"codehealthFindingId/v1":"31f0c5312cac88925f8aabb7d0cb01e31a7aba021061822150985fe4ec9bcbe2"}},{"ruleId":"D17","level":"warning","message":{"text":"TodoComment: ## TODO!! \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060# REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/TLSpectrum_mod.py"},"region":{"startLine":540}}}],"partialFingerprints":{"codehealthFindingId/v1":"e0e95ce53e3673b5f0ef8f8b9d967ec769fddf8fc0dfcf69f66c8f139c8e12b0"}},{"ruleId":"D17","level":"warning","message":{"text":"XxxComment: # XXX don\u0027t think this is needed \u2014 source code is not a task system: move the work to your tracker and leave a reference instead (e.g. \u0060# REF: #123\u0060), so the task is planned where tasks live and the ticket links back to the code."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/TwoLocus/Jackknife.py"},"region":{"startLine":313}}}],"partialFingerprints":{"codehealthFindingId/v1":"fae0c05ea55bfc41afc99b83c5a6f500cc794b90245d9f846fb1554338a3ad6b"}},{"ruleId":"D19","level":"note","message":{"text":"Documentation: no usage examples: The installation guide is complete but there are no usage examples showing how to run the code. Add a short \u0027How to run it\u0027 section or a one-line command block demonstrating an example call."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"docs/installation.rst"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"ec9c46b9a9eed78fab637a610077c840417dca3636d9c5f6d267da0fba0af90d"}},{"ruleId":"D19","level":"note","message":{"text":"Documentation: contradicts the code: The document states that many modules have not yet been completed and some extensions are not documented, but the SFS and LD sections describe new methods introduced in version 1.1. Update any outdated module or extension references to reflect current status."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"docs/introduction.rst"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"6efcf0bb4cc0dec2006c3451d606e1839cd5ca2660ad7ff2882a5012e973515d"}},{"ruleId":"D19","level":"note","message":{"text":"Documentation: hard to navigate: The API reference is a collection of automodule entries with no headings, making it hard to navigate. Add a brief table of contents or an outline linking each module\u0027s purpose."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"docs/api/api_moments.rst"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"39d1e25c3d6402cc494530f06b3a91ade32911740c2a05efe99963e640252e48"}},{"ruleId":"D26","level":"note","message":{"text":"Projects may be oversized for their cohesion: 1 of 1 project(s) overshoot their size bounds, lowering Project Cohesion to 0.0/10. The most over is \u0060(repository root)\u0060 (33676 LoC, 58 module-visible types across 12 directories). Review these for cohesion \u2014 draw the boundary inside the module first (group each responsibility into its own package or directory and keep the cross-boundary members non-public), since splitting a published package moves types between packages and breaks consumers."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"d5a94650dc74886a0f1f08eb9fb6775f1fc395279ef7e901c970c9d26f767a72"}},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. 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Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"ef496612c2e601f63b5cef7497cd7e1e2c07ee1993a36abf4943b3147792b1e6"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"dbfe94a695a95129e1b089d59225de7353acf7161f1892c5a1f3fe6564ee9cbf"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"bad4edd09d01f252504c21f63627917ea91a738d4bcb8ab44f545ae4e00fa065"},"taxa":[{"id":"CWE-522","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-829","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"529b37cdbd1a54445624522ce901b2cf83dd184fde8df430ff4d9d2a9ac40c55"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"2bd14c41fe72ce5f62709a7cceb4b29a2f22e4b37474bb46cc16f2a5b247c8a7"},"taxa":[{"id":"CWE-1357","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-353","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"f5d523aacbc6fe129fe55e964047c787b5516a1f1db3950d7f34837b0e0b2890"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"68ce63ecbabc9139840c60a1acaae428c1509bdb8aa4da95ca43f7047fdeb0ed"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"4d3cde3aab32ab24e4cba775083814533869a4273e20ac6fcd8bfe099a214c2a"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"09f7a7eea6486ebead232a35897c96072031fa2614d5f0146a868733ba3d7430"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"c9b8f20141158ab50f3ced536fb4374752423fb80af0608e33d397dd927c1953"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"1845183e8c6863e1aca26a79339bde03ee13a1bd9f64896b65db6175164c510a"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"2b706786c79ddb924511b4ae682c3c8d2ae2cc227bf53e4b0f73268409f671c7"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"4514f7d38eb962296c3774a88ce6eb7765ebe4f86750828e0b8f0fa72d0a8af2"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"e5b232a6bc8935e674e195b3afa22a02b7c8961dc60e8e29cdf0129ee6344071"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"2e795cf5cd0ed5e0988be1a76c8be02d01db5a0dc5da6ec34e7bb13ef87088ac"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"87d8f598889b6f9da19917244d27fef549f2fd3cc449ce3f563a727e102671df"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"13ec03865d76fe0e180e63bf663c181cdd48df407a71000eafdb709b05a00711"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"error","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"d8e9505b433d38e92f9b8b2594bd81571d027a200a8173efe3b4044114585346"},"taxa":[{"id":"CWE-95","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"7dee8993a716034921b4aeceebdab2f6709666e2c909065314227a298a8e9533"},"taxa":[{"id":"CWE-522","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-552","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"e148e86d0b09ae72c8ffeb42b79d7ccc290285e97913835c0551d67ffc4843ae"},"taxa":[{"id":"CWE-1104","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-1329","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"41a1125bbb7c80939921818a2353ec42f7d9790ae7c6ed639dd472df1e444427"},"taxa":[{"id":"CWE-1104","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-1329","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"6fadae380fa6201e86dc2a3da9be9a4a21fc9c46cf302d2da06e4743f81689f4"},"taxa":[{"id":"CWE-1104","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-1329","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"b80147f3c15a2f74d58cb01ce065de278e008c0a0e2494f4041d71849ff9ddc2"},"taxa":[{"id":"CWE-1104","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}},{"id":"CWE-1329","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"31e3a7517e33757c291a50d263a139f6f8da8512973572da3675c700bdbc214f"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"2fa76448873175be752777df4cbf8ae414773119cdb63372a9d06e4c3efe4102"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"f1d3ac440a1a4100d887151ed3475ffea3fd1715e792f75c408d869a5948aa3e"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"956bb93aa1e5c581cb168871f7018e228958b200c28ee313c72e1ce171548921"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"24ed3f9c2e2c71e938b3fecef9554b5611b3246b2f8821e54c09a0d04910b862"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"22da3f8413a9266b9d9491699e1f0b73e1ea63a7da057b4c7cfe5c8078ab2c1b"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"e80ca2003562591fd8794011c37004a4e6f4b41e944b0340f490ffcfc349dcc6"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"2895051d665de5dd8c086347241fde67c8bec8021b1cf76dc8f95c2f6434ef42"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D29","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"06e86270a883e28ff39f93060b435de831407d06a31f4426682315dec5d62357"},"taxa":[{"id":"CWE-502","toolComponent":{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d"}}]},{"ruleId":"D34","level":"error","message":{"text":"Orphaned knowledge: No living knowledge remains for this large file \u2014 its last meaningful change has decayed away; if it breaks, no one currently understands it. Schedule a read-through / add characterisation tests before it bites."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"bench/bench.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"6777172e7f18a5dae1c914294fd708a11f97b44cd018a91fdbcd5cea3cca99ea"}},{"ruleId":"D34","level":"error","message":{"text":"Orphaned knowledge: No living knowledge remains for this large file \u2014 its last meaningful change has decayed away; if it breaks, no one currently understands it. Schedule a read-through / add characterisation tests before it bites."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Parsing.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"b6ee3cbf8a55ed9115da7f86d7fbf4ac4aeb90beb0abc827ec96059eee0b5259"}},{"ruleId":"D34","level":"note","message":{"text":"Further orphaned files (smaller): 4 smaller file(s) also have no living knowledge \u2014 folded into the freshness score and metrics rather than raised one row each \u2014 most significant first: moments/LinearSystem.py, bench/gen_lim_fs_extrap.py, moments/Numerics.py, bench/demographic_models_dadi.py (6 orphaned of 45 analysed files in total, counted over production source files of roughly 2,400 bytes or more, excluding vendored, generated and example/demo trees and test files identified by path convention, largest first; 45 of the 55 production source files in this repository met that bar). Attach the read to the next change that touches one of them: have a second person review that change, and leave behind a short comment or test recording what the file is for, so the knowledge comes back at the cost of a change you were making anyway."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"ce861fd78f6935114d3a342cb90ad25870f984e1042954fcbbe27c0e23be3658"}},{"ruleId":"D35","level":"warning","message":{"text":"Change coupling: TriSpectrum_mod.py \u2194 TLSpectrum_mod.py: \u0060moments/Triallele/TriSpectrum_mod.py\u0060 and \u0060moments/TwoLocus/TLSpectrum_mod.py\u0060 change together 64% of the time (7 of the 11 commits that touched whichever of the two files changed less often, counting a file under its earlier names as well \u2014 a repo-wide or module-wide sweep is evidence about the sweep rather than about any pair inside it and is left out of BOTH sides of this ratio, while a dependency bump, a formatter/rename sweep, or a commit whose edit to one of the two files was a tool directive such as //go:generate or whitespace only is left out of the shared count ONLY, so the two sides are not taken over identical commit sets) with no explicit dependency \u2014 the edge is real but nothing declares it. Read the pair before acting: if one registers itself into the other through a hook or an initialiser, the missing dependency is DELIBERATE \u2014 the registration is the link, and it is meant not to be an import \u2014 and the thing to add is a comment on each side naming the other, not a merge; if they simply belong together, co-locate them; if neither holds, the coupling is hidden and worth breaking. You can check this without leaving the row: of the 7 shared commits counted here, the most recent 3 are \u0060877eabc3\u0060 Fix __array_wrap__ to be compatible with numpy 2 (#208); \u0060cc93eb0e\u0060 Bump to 1.1.18; \u0060b70fdcbf\u0060 extension docstrings \u2014 run \u0060git show\u0060 on any of them."},"locations":[{"physicalLocation":{"artifactLocation":{"uri":"moments/Triallele/TriSpectrum_mod.py"},"region":{"startLine":1}}}],"partialFingerprints":{"codehealthFindingId/v1":"faf311c9ee493ff09f1ab4b0bc7cf00352aeaf5e0bd8d4cea48b9ed3077a43b0"}},{"ruleId":"D36","level":"note","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"eb00976a698a5d68999b7ee6d27206fd374e916853e7ff1ead5eed42386f043f"}},{"ruleId":"D36","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"90f83b4fa27db32740afe9540c905f3c0499caed87f61049a8a903ecc95b41c3"}},{"ruleId":"D36","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"0752d0df7434000fcabf1048e2de30a7a1a8b982b3db9a19898c4dec199856b4"}},{"ruleId":"D36","level":"warning","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"35f64a0396611dfd8e0191313b0d7cdc759890497b52affaaa727cf6ce876cfd"}},{"ruleId":"D36","level":"note","message":{"text":"A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."},"partialFingerprints":{"codehealthFindingId/v1":"ace515990e7ee0f17b5c17e44dd168a5bdecf90804a3a3dd845cf05540978013"}},{"ruleId":"M2","level":"note","message":{"text":"No ADRs: No Architecture Decision Records found \u2014 no conventional ADR directory, no numbered \u0060NNNN-title\u0060 documents in any markup this check reads, and nothing ADR-shaped by content. Design rationale recorded elsewhere (a design-notes tree, a mailing list, pull-request discussion) is not visible to this check and is not re-findable per decision, so a future maintainer cannot ask why one choice was made and get an answer."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"670b3d6e36a756d63097d0dfbf90afd5fc761308800b9354894a07c3f4e4aa14"}},{"ruleId":"M2","level":"note","message":{"text":"No architecture diagram/doc: No C4/Structurizr/PlantUML/Mermaid/Graphviz/D2 diagram, no drawn diagram named for the architecture, no file named \u0060architecture\u0060 or \u0060design\u0060 in any markup this check reads, and nothing in the README, docs or contributor guides that announces the shape \u2014 no \u0060## Architecture\u0060 heading, no \u0022architecture overview\u0022/\u0022high-level design\u0022 phrasing, no \u0022the architecture is \u2026\u0022 introduction, no guided code tour. A shape laid out in prose that never names itself as the architecture is not visible to this check, and neither is one kept outside the repository, so this row reports the absence of a re-findable shape document \u2014 not evidence that nobody wrote the shape down."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"0c190e7c159d1850ee706c3ac4486e151e8a4fe169de4bf61436b9f399654f06"}},{"ruleId":"M3","level":"note","message":{"text":"No src/ separation: Production code isn\u0027t grouped under a src/ folder \u2014 it\u0027s spread across several top-level directories, so there\u0027s no one place that says \u0027this is the product\u0027."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"fdf7f5b24e313364d10170a5c2542959902fe0d26ed70edef3eaa10ec5bcdb1d"}},{"ruleId":"M4","level":"note","message":{"text":"README/code drift: README advertises a RAG / ML engine, but no ML/RAG code or dependency exists \u2014 searched for: \u0060rag\u0060, \u0060langchain\u0060, \u0060llamaindex\u0060, \u0060pinecone\u0060, \u0060weaviate\u0060, \u0060qdrant\u0060, \u0060embeddings\u0060. Each was matched case- and separator-insensitively against file and directory NAMES anywhere in the tree, and against the CONTENTS of manifest files (package.json, *.csproj, *.props, *.slnx, *.yml, Dockerfile); the README\u0027s own prose never counts, so a claim is never refuted by merely being made. Nothing outside that search was read \u2014 a footprint living only in a submodule, in a file type not listed here, or under a name none of those terms matches is not seen, and this row is then wrong."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"343bbbd51ceb8de7a9ff88d79f7c797abf9b5921f8727b67b4d0f4f8a22c5e49"}},{"ruleId":"P3","level":"note","message":{"text":"No SAST: No static application security testing detected. For this repository\u0027s stack, add bandit, \u0060semgrep --config=p/python\u0060, or CodeQL\u0027s python pack as a CI step. What was searched, so you can tell an absence from a miss: the 8854 CI workflow file(s) in this repository, and the scanner and linter configuration checked in beside them. A scan that runs outside CI, one configured in your forge\u0027s web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen \u2014 if that is your case the row is wrong, and saying so is more useful than adding a second scanner."},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"6e54424179c892f03ef2fd003130ac4bd43f39bbf3b1ca0a0143e25acb80ec87"}},{"ruleId":"P6","level":"note","message":{"text":"No changelog: No CHANGELOG/HISTORY/RELEASES file \u2014 what shipped when isn\u0027t easy to reconstruct for support or audit. (Versioning/tagging makes releases traceable, but a changelog records the what.)"},"locations":[],"partialFingerprints":{"codehealthFindingId/v1":"dda5aa5aed8cbb292c3ef2b733bc138f614293ae6426c85e98bf31ef330d9415"}}],"taxonomies":[{"name":"CWE","guid":"c3a2b1d0-7f3e-4b2a-9c1d-5e6f7a8b9c0d","organization":"MITRE","informationUri":"https://cwe.mitre.org/","isComprehensive":false,"shortDescription":{"text":"The MITRE Common Weakness Enumeration (CWE)."},"taxa":[{"id":"CWE-1104","guid":"4c918cb5-b2a6-6c55-9963-a44ee464305e","name":"CWE-1104","shortDescription":{"text":"CWE-1104"},"helpUri":"https://cwe.mitre.org/data/definitions/1104.html"},{"id":"CWE-1329","guid":"f70f1c3f-4ccf-cb5e-bdd3-03ba4868d36d","name":"CWE-1329","shortDescription":{"text":"CWE-1329"},"helpUri":"https://cwe.mitre.org/data/definitions/1329.html"},{"id":"CWE-1357","guid":"e4d2e772-757e-0a5c-bd7d-77052949d866","name":"Reliance on Insufficiently Trustworthy Component","shortDescription":{"text":"Reliance on Insufficiently Trustworthy Component"},"helpUri":"https://cwe.mitre.org/data/definitions/1357.html"},{"id":"CWE-1395","guid":"800e09e7-c11a-8654-9fa6-86f398995fed","name":"Dependency on Vulnerable Third-Party Component","shortDescription":{"text":"Dependency on Vulnerable Third-Party Component"},"helpUri":"https://cwe.mitre.org/data/definitions/1395.html"},{"id":"CWE-259","guid":"ae9ad959-fbb6-9d5e-892d-3dca66da0b69","name":"Use of Hard-coded Password","shortDescription":{"text":"Use of Hard-coded Password"},"helpUri":"https://cwe.mitre.org/data/definitions/259.html"},{"id":"CWE-353","guid":"09d7e902-d4ee-f05d-ae6c-0a1554d0c18f","name":"CWE-353","shortDescription":{"text":"CWE-353"},"helpUri":"https://cwe.mitre.org/data/definitions/353.html"},{"id":"CWE-494","guid":"b8a65e0d-e459-4a55-a931-fc1136482375","name":"Download of Code Without Integrity Check","shortDescription":{"text":"Download of Code Without Integrity Check"},"helpUri":"https://cwe.mitre.org/data/definitions/494.html"},{"id":"CWE-502","guid":"f7d3b296-aac0-5c5a-b706-e07faba26c36","name":"CWE-502","shortDescription":{"text":"CWE-502"},"helpUri":"https://cwe.mitre.org/data/definitions/502.html"},{"id":"CWE-506","guid":"401d6455-56e3-0552-9a39-f77461673e3f","name":"CWE-506","shortDescription":{"text":"CWE-506"},"helpUri":"https://cwe.mitre.org/data/definitions/506.html"},{"id":"CWE-522","guid":"71fb233e-ce6a-ae57-9419-ef8373540b09","name":"CWE-522","shortDescription":{"text":"CWE-522"},"helpUri":"https://cwe.mitre.org/data/definitions/522.html"},{"id":"CWE-552","guid":"3492436b-eca2-9c54-9ba3-5dade427c903","name":"CWE-552","shortDescription":{"text":"CWE-552"},"helpUri":"https://cwe.mitre.org/data/definitions/552.html"},{"id":"CWE-77","guid":"332c8ade-6612-9f56-a06b-d8d90b1a8750","name":"Command Injection","shortDescription":{"text":"Command Injection"},"helpUri":"https://cwe.mitre.org/data/definitions/77.html"},{"id":"CWE-78","guid":"2e31ceaf-c7ae-2e5e-9661-cfb1362789cf","name":"OS Command Injection","shortDescription":{"text":"OS Command Injection"},"helpUri":"https://cwe.mitre.org/data/definitions/78.html"},{"id":"CWE-79","guid":"fd45580b-e8c4-fc5e-8c2f-aa8fab0b4dbf","name":"Cross-site Scripting (XSS)","shortDescription":{"text":"Cross-site Scripting (XSS)"},"helpUri":"https://cwe.mitre.org/data/definitions/79.html"},{"id":"CWE-798","guid":"5e8f057d-fee3-995a-a0cb-9fc5b0d174d1","name":"Use of Hard-coded Credentials","shortDescription":{"text":"Use of Hard-coded Credentials"},"helpUri":"https://cwe.mitre.org/data/definitions/798.html"},{"id":"CWE-829","guid":"13c33925-97fb-5a5e-b40c-56d328b8a4d7","name":"CWE-829","shortDescription":{"text":"CWE-829"},"helpUri":"https://cwe.mitre.org/data/definitions/829.html"},{"id":"CWE-89","guid":"6d08fdad-37eb-c150-bbf0-d7d946863407","name":"SQL Injection","shortDescription":{"text":"SQL Injection"},"helpUri":"https://cwe.mitre.org/data/definitions/89.html"},{"id":"CWE-937","guid":"16f316ae-415c-b354-a59b-1f7905f756e9","name":"Using Components with Known Vulnerabilities","shortDescription":{"text":"Using Components with Known Vulnerabilities"},"helpUri":"https://cwe.mitre.org/data/definitions/937.html"},{"id":"CWE-94","guid":"75e7f50c-6c2f-dd52-bf40-bf6c52b861fd","name":"Code Injection","shortDescription":{"text":"Code Injection"},"helpUri":"https://cwe.mitre.org/data/definitions/94.html"},{"id":"CWE-95","guid":"400bba4e-483c-5c50-a695-114fa9168003","name":"CWE-95","shortDescription":{"text":"CWE-95"},"helpUri":"https://cwe.mitre.org/data/definitions/95.html"}]}],"properties":{"codehealthPublication":{"public":true,"notice":"This is the PUBLIC form of this artifact. Findings are listed in full, but the details of SECURITY findings \u2014 which rule fired, in which file, on which line, and how to fix it \u2014 are deliberately withheld, and any secret-scanner results are excluded entirely. Where detail is absent here it was REMOVED FOR PUBLICATION; it is not missing from the analysis. The complete artifact is available from the repository owner.","securityFindingsRedacted":74,"secretScannerRunsExcluded":0}},"redactionTokens":["A security finding was recorded here. Its details are withheld on the public artifact \u2014 ask the repository owner for the full report."]}]}