Public report — moments, published 3 Oct 2026.
Concrete security findings (which rule fired, in which file, on which line; CVE IDs, secret matches,
dependency versions) are REDACTED in this version; ask the repo owner for the full report.
Public
Codebase surveyMeasured under the Code Assurance Index · rubric rubric-2026.10.1 (frozen) · verify this surveyFiledcd_970daa91c20d4532acad42284cf62ebb
Filed 3 October 2026, 09:20 UTC
Public
Medium · 33,693 LoC · 1 projects · rebuild ~0.3 person-years · weakest lens: Readiness (50%)
Findings by grade
57 critical540 serious14 minor39 could not be resolved — could be critical — see Limitations
This survey was produced by
Watchdog
Producer
Canine Development
Analyzer
Watchdog engine 1.0.0
Measured
3 October 2026, 09:19 UTC
A measurement, not a certificate. The Code Assurance Index does not certify,
approve or guarantee this codebase; it records a reproducible number and the evidence it was computed from. The
standard is authored by Canine Development, who also build Watchdog — its only implementation today. That is said
here so the number is checked rather than believed.
Grounded in facts. Every number here is computed, not narrated — reproducible, tool-backed, and traceable to a line of code. How to trust this ▸
597findings with an exact file:lineof 611 — the remainder are repo-wide signals (a dimension-level measurement, not a single line); open any file:line and verify
37/120dimensions across the health lenses33693 LoC · 1 projects — wide & deep
This system holds an adequate standing with a health score of 57%, presenting a workable asset that carries real operational risk. While the architecture is robust, the overall reliability is compromised by gaps in production readiness and security automation. For the business, this means the system is functional but fragile under pressure, requiring immediate attention to prevent costly outages and security regressions.
The value at stake is moderate, with a rebuild effort estimated at roughly 0.3 person-years or €41,000. This is not a massive legacy monolith, but a medium-sized codebase where small changes still carry a velocity tax. The code quality signals suggest that every modification in weaker areas costs 8–18% more effort than in clean code, creating a compounding drag on delivery speed as the team grows.
The primary risk lies in production readiness, which sits at a concerning 50%. This lens covers testing, observability, and operational safety. Without these safeguards, the team faces a higher likelihood of defects reaching users and longer mean-time-to-recovery during incidents. This directly impacts customer trust and increases support costs, making it the most critical area for remediation.
A secondary concern is security exposure, currently at 75%. While not critical, the lack of automated static analysis in the CI pipeline means security regressions can land in production unnoticed. This creates a compliance risk and potential data exposure. The cost of fixing this is low compared to the cost of a breach, making it a high-leverage investment.
On the positive side, the architecture is strong at 87%, indicating that the system is well-structured and changes do not ripple uncontrollably. This stability provides a solid foundation for future improvements. The codebase is also relatively small, meaning improvements can be implemented quickly without massive refactoring efforts.
Focus first on adding automated security scanning to the CI pipeline. This single action addresses the security gap and improves overall code quality by catching issues early. It is a low-effort, high-impact change that pays for itself quickly. Once this is in place, the team can systematically improve production readiness through better testing and observability, reducing the velocity tax and ensuring long-term stability.
How the score is built — each lens's share of the headlineWidth is the lens's weight in the worst-heaviest fold (the weakest area pulls hardest); colour is that lens's own band. A lens fixes the score in proportion to its width.
0.8× (at 57% quality) — the last 20% of quality is most of the work
Size & shape
Medium · effort split not classified (source measured from disk; the effort-tier breakdown is a C#-only syntax walk)
This codebase represents roughly ~0.3 person-years of build effort (about ~€41,000 to rebuild). Its weakest lens is Readiness at 50% — the part of that asset most exposed by the findings below.
How we model this: boilerplate at a scaffolding rate + logic × domain Standard (×1.0) — standard service × a 0.8× quality factor, at €60–95/h; indicative, ±~30% · size measured directly from source · effort from total production LoC as straight-line logic (the tier split is a C#-only syntax walk), a conservative lower bound. Indicative only — most sensitive to the hourly rate and the domain tier (both tunable in config).
Top priorities
The highest-leverage moves; the full ranked list is in the Roadmap below.
1
Add a SAST step to CI running what this repository's stack ships: bandit, `semgrep --config=p/python`, or CodeQL's python pack — so a security regression fails the build instead of landing.
The release job declares an environment, but its protection rules are not visible from the repository — confirm required reviewers are attached, or publish as a draft release so a bad build can be stopped before users can download it.
Value concentrated against a weak lens · Medium · Value at risk
This is a Medium asset (~0.3 person-years to rebuild), and its weakest lens is Readiness at 50%. The operational and business risk on an asset this size concentrates there — that's where remediation buys the most protection.
→ Direct remediation budget at Readiness first — highest risk-reduction per euro on an asset this size.
Highest-leverage move · Medium · Leverage
Of everything flagged, the best return on effort is: Add a SAST step to CI running what this repository's stack ships: bandit, `semgrep --config=p/python`, or CodeQL's python pack — so a security regression fails the build instead of landing. The rest can wait behind it.
Evidence: priority ranking: top of 5 ranked by impact/effort
→ Add a SAST step to CI running what this repository's stack ships: bandit, `semgrep --config=p/python`, or CodeQL's python pack — so a security regression fails the build instead of landing.
A velocity tax on every change · Medium · Economics
The code-quality signals (complexity, duplication, cohesion) average 4.9/10, which acts as a tax on every change in the weaker areas: modifications there plausibly cost on the order of 8–18% more than in clean code, and the tax compounds as the codebase grows. (A modelled estimate, not a measured fact.)
Evidence: D1/D2/D4/D6 code quality: averaging 4.9/10 across the code-quality signals actually measured
→ Pay it down where churn is highest — the hotspots — not everywhere; that's where the tax is actually paid.
The top fix pays for itself · Medium · Economics
The top-ranked fix costs roughly 3–10 engineer-days once. Not doing it costs about 0.1–0.3 engineer-days every year, paid as drag on the ~276 lines this team changes annually — a bill that arrives whether or not anyone books it. On those figures the fix breaks even in roughly 111–2228 months and is free after that. Method, stated so this is not read as a quotation: debt from the ranked task's effort band; interest = annual changed lines (measured, annualised from the 90-day window) ÷ an ASSUMED 150–400 lines per engineer-day × the 8–18% drag implied by the code-quality signals; breaking point = debt ÷ annual interest. A modelled planning range built from measured inputs and one named assumption — not a quotation, a valuation, or a certified figure.
Evidence: D15 churn: 68 line(s) changed over a 90-day window ⇒ ~276/year · D1/D2/D4/D6 code quality: averaging 4.9/10 ⇒ a 8–18% drag on each change · top-ranked remediation: Medium effort ⇒ about 3–10 engineer-day(s)
→ Do the top-ranked fix now if this code will still be yours in 2228 months.
At a glance — Code Health · 68% · Adequate · gated by D1, D2 ·
Findings mapped to OWASP categories; the specific CVEs/secrets are in the Security dimension cards below and findings.md (redacted only on the public version of this report).
OWASP category
Findings
Severity
A03:2021 — Injection
69
High / Critical
Roadmap
First, integrate static security analysis into the CI pipeline to block regressions before they land. Second, verify deployment protection rules or use draft releases to prevent bad builds from reaching users. Third, maintain a changelog to track release contents and document key architectural decisions in a dedicated directory. Finally, update the README to include clear instructions for running the test suite.
Ranked by impact ÷ effort. "Helps" is the estimated gain on the 0–100 health score.
Do this
Helps
Effort
Dimension
Add a SAST step to CI running what this repository's stack ships: bandit, `semgrep --config=p/python`, or CodeQL's python pack — so a security regression fails the build instead of landing.
The release job declares an environment, but its protection rules are not visible from the repository — confirm required reviewers are attached, or publish as a draft release so a bad build can be stopped before users can download it.
Record significant decisions one document per decision — dated, stating the context, the decision and its consequences — and keep them together wherever your design docs already live (a conventional `docs/adr/` tree, with each file named `NNNN-title` in whatever markup those docs already use, is the most discoverable form).
Every finding carries one of four grades. Three say how serious it is. The fourth says this
survey could not settle it — and it is a grade, not a gap.
Critical — 57
A definite problem that already costs you something and drags the score down: a
missing authorisation check, a dependency with a known exploit, a build that does not reproduce. Failure here
tends to cause failures elsewhere.
Serious — 540
Likely wrong, but not failing yet. It degrades
the codebase over a longer horizon and can cause failures elsewhere — not urgent this week, not something to
carry for two years either.
Minor — 14
Recorded, with no effect on how the codebase functions.
Present so the survey is complete, not because it needs doing.
Could not be resolved — 39
Something this survey could not settle
from the outside, and which could be critical or serious. Either a control was required and no
positive evidence of it exists in the repository — a backup job that nothing shows was ever restored from proves
nothing about restores — or our own analysis could not run over that part of the tree. This is not a clean
result. These are excluded from the score rather than awarded a pass, so the number on the cover neither
rewards nor penalises them: if you act on this survey without resolving them, you carry that risk yourself. Each
one is named under Limitations.
Methodology & how to trust this report
Watchdog is a deep, periodic assessment — run each sprint, monthly, or quarterly, taking the time to go wider and deeper than a quick check and surfacing in one coherent report what you'd otherwise piece together from a dozen separate tools. It scores deterministically: the same commit yields the same score, every run. 33 of 37 evaluated dimensions are computed purely by tools and static analysis (confidence 1.0); 4 documentation/naming judgement(s) are LLM-assisted and labelled advisory. Overall confidence is 0.9 — the weighted average across measured dimensions; it falls as more of the score leans on LLM-assisted judgement and rises when it's fully tool-backed.
Every figure here is one of three kinds, and we label which: ✓ Measured — a deterministic fact (LoC, complexity, coverage); ~ Modeled — an estimate from a stated model (cost, effort, value-at-risk), always a range with its assumptions, never a precise fact; ◐ Advisory — an LLM prose judgement. We never present a modelled estimate as if it were measured. Perfect or absent scores carry their provenance too (ADR-0011): ✓ Tool-verified means the property itself was measured across the surface; ○ Nothing flagged means the probes came back clean — a claim bounded by what a repository can show; ⊘ Not evidenced means a working control (a tested restore, an automated rollback) showed no positive evidence — absence of evidence is not evidence of a control, so it's excluded from the score rather than awarded a spurious 10; ◐ Sampled · advisory marks an LLM verdict over a bounded sample — advisory, never a deterministic measurement.
What we checked — 37 dimensions across the health lenses
Each chip is a dimension scored from real signals across architecture, testing, dependencies, security & compliance, documentation, git-history and code quality — in one coherent pass. A surface report typically covers a handful.
How to trust any code-health report — three questions
Can you open the finding? Real findings cite a repo-relative file and line you can open at the cited line — never an absolute scratch path. Here, 597 of 611 do; the remainder are repo-wide signals — a dimension-level measurement, not a single line. (Every path in this report is repo-relative by construction: paths are normalized at the producer and the report is rejected if any rooted path leaks through.)
Is there a tool behind the number? Every score below names the method that produced it — Roslyn, git, a scanner, or (for a handful of documentation/naming dimensions) an LLM labelled sampled · advisory — not a narrative.
Does re-running give the same result? Run it again on the same commit and the score — and this report, byte for byte — is identical. A report whose numbers move between runs is describing the run, not the code.
This report answers yes to all three. That's the bar to hold any assessment to.
Tools & methods
The actual versions used this run (captured at analysis time) — re-run on the same commit for the identical score.
Method
Backs
Version
Evaluator
Roslyn static analysis
Complexity, cohesion, coupling, dead code, API surface, layering
What ran differently this time — a tool absent, degraded, or that fell back to an estimate. Named openly, not folded silently into the scores. A degraded run also records its exact cause in diagnostics.md.
D8 Code Coverage — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Coverage NOT MEASURED: test source is present (.py, .fs) but the built-in coverage collector has no runner for this repository's ecosystem — so this suite was never executed by it. Not scored — this is a gap in the analyzer's language coverage, not a defect in the repo. To have real coverage read, produce a coverage report in a standard format (`coverage run -m pytest` then `coverage xml`, or Cobertura — `dotnet test --collect:"XPlat Code Coverage"` with a `coverlet.collector` PackageReference) and commit it — a hosted scan measures a clone of the repository, so a report that exists only in a working tree, a CI runner's or your own, never reaches it; the artefact is commonly gitignored, so `git add -f` that one file (or un-ignore its path) and commit it alongside the code it measures. You can widen what we reach: optional: produce a coverage report in a standard format (`coverage run -m pytest` then `coverage xml`, or Cobertura — `dotnet test --collect:"XPlat Code Coverage"` with a `coverlet.collector` PackageReference) and commit it — a hosted scan measures a clone of the repository, so a report that exists only in a working tree, a CI runner's or your own, never reaches it; the artefact is commonly gitignored, so `git add -f` that one file (or un-ignore its path) and commit it alongside the code it measures — then the real number is read on the next scan.
D12 Dependency Hygiene — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. Not scored — 11 shipped Python distribution(s) were read, but the outdated signal needs pypi.org, and no declaration here carries an exact pin to ask about — a floor or a range installs the newest release it admits and cannot be behind one, so this dimension's own question is only partly answered. NOT a finding that these dependencies are current or healthy.
D22 Internal API Consistency — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. D22 identifies the intentionally-exposed surface from `IsPackable` and `.Contracts` project names, MSBuild conventions read off the loaded project set. This target exposed no such projects, so the probe never ran; this says nothing about whether the repository has a public API. This repository commits no C#/VB source at all, so there was never an MSBuild project set to read these conventions off. That is OUR side and it is a COLLECTOR gap, not an environment fault: it declares a published package (setup.py), but no published-package marker D22 reads admitted any project here, so this ecosystem's public API has no collector, and the remedy is to write one — no change to the scan image can close it.
AX1 Captive dependencies — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check reads Microsoft.Extensions.DependencyInjection registrations in C# and Spring beans in Java/Kotlin only, and no container it models, or knows cannot hold a captive, was found in this repository's source, so it had nothing of this repository's product to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
AX6 Interface segregation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is computed over the public interfaces this run's compilations declare, and none was loaded, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
C1 Data Protection — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These personal data controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks personal data controls.
C2 Access Controls — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These authorization controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks authorization controls.
C3 Audit Trail — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These audit controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks audit controls.
C4 Data Retention — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These retention controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks retention controls.
C5 Data-Subject Rights — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These data-subject rights controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks data-subject rights controls.
GD1 Unfinished & placeholder code — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
IC1 Incompleteness & stubs — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
P5 DR & Backup — not measured this run — This is a true statement about the repository that carries nothing for its owner to act on, so it is reported here rather than as a defect in their code. No backup/snapshot/replication config, RTO/RPO or restore-procedure documentation was found — and no production persistence was detected either (no data-access packages, no data-store services, no database resources), so there is nothing in this repository whose loss a DR control would recover. If this system's data lives in a platform or ops repo we can't see, that's where the DR evidence belongs.
PF1 Benchmark discipline — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check's reader does not cover the language this repository's product is written in, so it had nothing of the product to read. That is a gap in this analyzer's language reach — not a finding about this repository.
S1 Web-Security Posture — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. These web-security controls are read from declarative annotations, request middleware, entity/column names and guard methods in a C# source model, and none was loaded on this run, so there was nothing to gather. That is a gap in this analyzer's language reach — not a finding that the repository lacks web-security controls.
X1 Async correctness — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X12 Unreachable branch — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X13 Undrained process stream — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X14 Bypassable address classification — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X15 Unvalidated length from an untrusted reader — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X16 Unfloored truncation loop — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X17 Uncapped recursion over a caller-supplied document — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X18 Disposal-pattern correctness — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X19 Unrestored process-global state — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X2 Cancellation propagation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X20 Mistyped argument guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X21 Side-effecting pattern guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X22 Contradicted release guard — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X23 Unguarded diagnostic materialisation — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X24 Document value interpolated into markup unescaped — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X25 Inert configuration knob — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X26 Unsynchronised callback handoff — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X27 Collection changed while being enumerated — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X29 Per-element action decided by a fixed element — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X3 Exception handling — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X30 Support guard that admits what it rejects — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X32 Type resolved by simple name across every loaded assembly — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X4 Structured logging — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
X5 Nullable reference types — not measured this run — Watchdog could not measure this here. That is a gap on our side — a collector, parser or image we have not built yet — and it is neither a defect in this repository nor evidence that the check would have passed. This check is implemented over the C# syntax tree, and no C# was loaded on this run, so it had nothing to read. That is a gap in this analyzer's language reach — not a finding that the repository is free of what this check looks for.
Repo exclusion declarations (.gitattributes linguist-generated/vendored, .editorconfig generated_code): none declared — every source file was scored.
Limitations & what we did not check
Watchdog assesses the repository exactly as committed, and only the repository. By design it does not reach outside the source tree: the live cloud account, the running CI/CD pipeline, the host's branch-protection and approval rules, the production configuration, or a restore actually exercised against a backup are all out of scope. That boundary is a feature, not a gap — a repo-relative, deterministic scan re-runs identically on any commit and every finding opens at a real file and line, where a live audit can neither be reproduced nor traced. The visible consequence is that controls which leave no in-repo evidence are reported as "not evidenced" and excluded from the score rather than awarded a number a static scan cannot justify.
Per-dimension blind spots
For each dimension that was measured, what a static, repo-only scan structurally cannot see — the honest edge of the measurement, not a failure of it.
D1 Cyclomatic Complexity: Cyclomatic complexity counts branches statically — it cannot tell an essential decision tree from accidental tangle, nor see complexity that lives in data or configuration (large switch-case token tables, DSL lexers/parsers, data-as-code rule tables) rather than control flow: a tokenizer's many single-character cases read as high complexity though each branch is trivial.
D2 Cognitive Complexity: Cognitive-complexity heuristics approximate how hard code is to follow; genuine domain difficulty and well-named intent that eases reading are not captured.
D3 God Classes: "God class" is sized by members and responsibilities visible in the type — a deliberately broad facade over a coherent subsystem can read the same as an accidental grab-bag. For front-end JS the file-length check is cohesion-aware (a single-responsibility module — one class/IIFE — earns a 3× threshold), but cohesion is approximated from top-level declarations, not true dependency structure.
D4 Code Duplication: Duplication is token-similarity — an in-process token-stream comparison over sliding windows, with type-aware normalization — so it finds copy-paste, not semantic duplication expressed differently. Committed machine-written code (scaffolded migrations, designer/codegen output, protobuf/OpenAPI stubs, model snapshots) is EXCLUDED — its repetition is the tool's, not the team's — so the score reflects hand-written duplication only.
D6 Cohesion (LCOM4): LCOM4 cohesion is syntactic — it infers connectivity from which methods touch which fields/methods by name, not from real runtime behaviour or intent.
D9 Test Distribution: The test-pyramid shape is inferred from project/folder naming and references, with a single test host bucketed per-file by its path tier and content signals — a suite that names tiers unconventionally and gives no per-file signal can still be mis-bucketed.
D11 Test Reliability: Flakiness is inferred from history/markers — Watchdog runs the suite once (for coverage), not the repeated runs under varied conditions that reveal nondeterminism, so a flaky test never recorded as failing is invisible here.
D13 Secret Scanning: Secret detection is signature- and entropy-based on the current tree — a secret that does not match a known pattern, or one already rotated, will not be flagged (a clean scan is "nothing matched", not "no secrets exist").
D14 License Compliance: License compatibility is checked against declared package metadata and a policy — mislabelled or missing license metadata, and obligations that depend on how you distribute, are not resolved here.
D15 Churn × Complexity Hotspots: Churn hotspots come from git history — a freshly imported or squashed repository has no churn signal, and recent rewrites can mask a historically risky file.
D16 Bus Factor: Bus-factor is a time-decayed model of commit attribution (who has recently, repeatedly worked a file), not comprehension — pairing, review and reading-without-committing spread knowledge it can't see; bot commits and shared accounts still distort it.
D17 Explicit Debt: Acknowledged-debt signals (TODO/FIXME, suppressions, dead code) are textual — undocumented debt that nobody marked, and debt that lives in design rather than annotations, is invisible. Committed machine-written code (scaffolded migrations, designer/codegen output, generated stubs) is excluded — it is never the team's dead code to delete.
D19 Documentation Quality: Documentation quality is judged by an LLM over a bounded sample of docs — it reads what is written, not whether the docs match the running system, and it is advisory, not a measurement. Its critique rows are drawn from a closed category vocabulary and each row means the same thing in every run, so two scans can be compared row by row; the SET that fires is still a sample, and does not repeat exactly. Measured on one frozen input, six scans at one engine SHA: 2-5 critique rows per scan, 8 distinct rows across the six, 3 of those 8 seen in only one scan. So a D19 row is evidence about the documentation, but a COUNT of D19 rows is not a quantity — never read a change in it as an improvement or a regression.
D21 Naming Consistency: Naming quality is an LLM judgement over a bounded sample — it assesses clarity/consistency of the names it sees, not domain-correctness, and is advisory.
D26 Project Cohesion: Project focus is sized from members/namespaces per project — a project that is broad by deliberate design reads the same as one that has sprawled.
D28 Secrets (history): Secret-history scanning sweeps the git log for known patterns — a secret that predates the available history, or never matched a signature, is not found (clean means "nothing matched in the history we can see").
D29 Static Analysis (SAST): SAST findings are pattern-based (semgrep) — it finds classes of bug it has rules for; logic flaws, auth/authorization gaps and issues needing runtime context are out of reach (and clean means "no rule matched").
D30 Dependency Vulnerabilities: CVE matching depends on accurate package/version metadata and on the advisory databases — a vulnerability with no published advisory, or in code not declared as a dependency, is not seen. Coverage needs a RESOLVED graph: an unpinned requirements.txt, or a pom without a resolved build, yields partial coverage rather than a clean verdict. An ecosystem the analyzer cannot scan is reported as unmeasured, never as clean.
D34 Knowledge Freshness: Freshness is decayed commit RECENCY, not comprehension — code read often but rarely committed reads as orphaned, and stable code that genuinely needs no changes is penalised the same as forgotten code; bot/squash commits distort it like the bus factor.
D35 Change Coupling: Change coupling is co-change in COMMITS — files split across separate commits, or coupled only through a shared config/build step, read as uncoupled, and a sweeping commit (rename/format) is excluded so it doesn't couple everything. It shows that files change together, not WHY: a high coupling can be a healthy cohesive pair as readily as a hidden leak.
D43 Malicious Dependencies: Only packages some vulnerability database has already NAMED as malicious are seen — a compromise published in the last hours, or never reported at all, is invisible here, and this dimension reading 10 is not evidence that a dependency is trustworthy. There is no typosquat or dependency-confusion analysis: a package nobody has reported is simply absent from the feeds. Coverage is the dependency scan's: an ecosystem that could not be scanned is disclosed as unmeasured, never as clean.
D44 Platform End-of-Life: The support table is FROZEN, so it goes out of date by losing RECALL: a release that ended support after the table was written is missed until the table is refreshed, and this dimension reading 10 is not evidence that a platform is current. Only platforms the repository DECLARES in a place this pass reads are seen — a runtime named only in a Dockerfile (D31's subject), in a CI workflow (D29's), or in a file this pass does not parse (go.mod, a Gemfile ruby directive) is invisible here, which is why a repository declaring none of them abstains rather than scoring. Only frameworks with a PUBLISHED support policy are tracked: React, Flask and Express publish none, so their age cannot be judged and their absence from a report is not a statement that they are supported.
AX10 Code composition: Role is inferred from namespace/folder convention, not semantics — a domain concept living in a folder named "Services" reads as application, and the split is lines-of-code, not business value. The business-logic-share score is a SOFT, FLOORED signal: it contributes to the Architecture lens but is floored at the Critical gate, so an infrastructure-heavy design (a gateway, an ETL, a driver) is legitimately low without being nuked to zero.
M4 Documentation accuracy: Onboarding quality is an LLM read of the docs/setup present — it cannot run the onboarding or measure how long a real new joiner takes; the verdict is sampled and advisory.
P4 Deployment & Rollback: Approval/branch-protection rules live in repository settings the scan cannot see — only their in-repo evidence (config files, workflows) is checked, so a control enforced purely in the host's settings reads as "not evidenced".
P6 Release Hygiene: Rollback/observability controls are inferred from repo artefacts (pipelines, dashboards-as-code) — controls configured in external tooling, with no in-repo trace, cannot be credited.
The LLM boundary
LLM-set scores this run (4): D19, D21, D26, M4 (model: Local LLM). For these, a model reads a bounded sample and sets the numeric score; each names its own sample and method on its card. They are sampled and advisory by design: they vary at the margins between runs and are never a deterministic measurement. Every other score in this report is tool-computed at confidence 1.0.
What it measures: How tangled the control flow is — methods with many branches are hard to test and change.
Method: Cyclomatic complexity per method (1 + decision points), computed exhaustively across production source; test projects separated by convention. Deterministic.
+ 53 more group(s) — more in Appendix A; the complete list is findings.md.
What to do
Bring the 4 bodies over 60 down to 60 or less in Cyclomatic Complexity — start with Matrices.admix_ld (cyclomatic 216), Matrices.migration_ld (cyclomatic 103), Demes.SFS (cyclomatic 82). — This score is capped by its worst body, so a finding fixed alone moves it by almost nothing — the next one down takes its place. Refactoring these 4 together lifts Cyclomatic Complexity from 2.0 to about 3.2/10, projected with the scoring formula itself and assuming each lands exactly at 60; a cleaner split scores higher.
Enforce Cyclomatic Complexity in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.
Detailed fixes: d1_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: How hard the code is for a person to follow, beyond raw branching.
Method: Cognitive complexity per method (Sonar-style nesting-penalized score), computed exhaustively over production code, excluding test projects. Deterministic.
+ 101 more group(s) — more in Appendix A; the complete list is findings.md.
What to do
Bring the 46 bodies over 30 down to 30 or less in Cognitive Complexity — start with Matrices.migration_ld (cognitive 358), Parsing._tally_vcf (cognitive 158), Demes.SFS (cognitive 152). — This score is capped by its worst body, so a finding fixed alone moves it by almost nothing — the next one down takes its place. Refactoring these 46 together lifts Cognitive Complexity from 2.0 to about 5.6/10, projected with the scoring formula itself and assuming each lands exactly at 30; a cleaner split scores higher.
Enforce Cognitive Complexity in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.
Detailed fixes: d2_recommendation.md · top locations in Appendix A, every location in findings.md.
Do you agree with this assessment?
D3 · God Classes7.9 / 10Strong✓ Tool-verified
What it measures: Over-large classes that try to do too much ("god classes").
Method: God-class detection by line and method-count thresholds per logical type (partial classes unified), filtered for generated code and registration/contract false positives. Deterministic.
Resolve the 15 FileTooLong finding(s) in God Classes — start with Inference.py (3), Parsing.py (2), Matrices.py. — One of this dimension's main actionable groups (15 warning-level).
Resolve the 1 TooManyMethods finding(s) in God Classes — start with REDACTED. — One of this dimension's main actionable groups (1 warning-level).
Enforce God Classes in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.
Detailed fixes: d3_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Copy-pasted code that should be shared instead.
Method: Code duplication via token-stream sliding windows with type-aware normalization (locals masked, type names preserved), density-scored per KLoC of production code. Deterministic.
321 duplicated block group(s) detected. A further 17 rows report members as variants of one another; they aggregate block groups already counted above and are not themselves counted. 1 of the 338 are in trees this repository does not ship — vendored, example/demo, fixture and benchmark code — and are ranked below the shipped groups rather than excluded from them: the duplication there is real and is still counted in this dimension's score. The dimensions that publish a production-file census leave those trees out of theirs, so this count is deliberately drawn over the wider population.
+ 165 more group(s) — more in Appendix A; the complete list is findings.md.
What to do
Resolve the 19 Duplicated block (5 lines × 2) finding(s) in Code Duplication — start with stats_from_genotype_counts.py (8), Numerics.py (3), REDACTED (2). — One of this dimension's main actionable groups (19 warning-level).
Resolve the 15 Duplicated block (10 lines × 2) finding(s) in Code Duplication — start with stats_from_genotype_counts.py (4), Numerics.py (3), Demes.py. — One of this dimension's main actionable groups (15 warning-level).
Resolve the 14 Duplicated block (6 lines × 2) finding(s) in Code Duplication — start with stats_from_genotype_counts.py (3), Matrices.py (2), REDACTED (2). — One of this dimension's main actionable groups (14 warning-level).
Enforce Code Duplication in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Verified — provenance only; does not change the score.
Detailed fixes: d4_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Whether a class's methods are focused on a single responsibility.
Method: LCOM4 cohesion per production class with at least two methods: connected components of methods sharing state or calls, computed syntactically. Deterministic, not a proxy.
Coverage: Exhaustive · type-level: LCOM4 cohesion computed over every production class — the population is all types, not a name convention.
D9 · Test Distribution10.0 / 10Exemplary✓ Tool-verified
What it measures: Whether the test suite has a healthy mix of unit / integration / end-to-end tests.
Method: Test projects classified (Unit/Integration/BDD/E2E) from compiled metadata; test methods counted exhaustively across projects with placement-agnostic disk fallback. Deterministic.
298 test methods: 298 unit, 0 integration, 0 BDD, 0 e2e. The Python suite contributes 298 test function(s) across 19 file(s) declaring at least one — every `def test…` in a file pytest or unittest would collect, which is those frameworks' own definition of a case; a parametrize table counts once, so this is a floor. Its tier split is read from file names and paths only.
✓ On the Gold path — maintain.
Detailed fixes: d9_recommendation.md.
Do you agree with this assessment?
D11 · Test Reliability10.0 / 10Exemplary✓ Tool-verified
What it measures: Whether the tests pass reliably, with no flakiness.
Method: Suite re-run N times within tiered wall-clock budgets (unit to e2e); tests failing non-deterministically across runs flagged; guarded tests retried when #if guards detected.
What it measures: Whether any secrets (keys, tokens, passwords) have leaked into the code.
Method: In-process native secret scanner (entropy plus signature patterns) across all tracked files; no external tool. A clean result is a measured 10, not no-data zero. Deterministic.
What it measures: Whether the licenses of third-party packages are compatible with your policy.
Method: Third-party package licenses resolved from declared package metadata and checked against the configured policy (allow/deny/copyleft). Deterministic; clean = no incompatible license found at metadata depth.
0 of 93 shipped Python distribution(s) use a banned license. Licences were resolved from PyPI over the distributions a consumer installs — this repository's 11 declared runtime requirement(s) closed transitively over each distribution's published `requires_dist` (82 reached that way). Requirements it states ONLY under an extra, a PEP 735 dependency group, a Poetry dev group or a dev-named requirements file are excluded: pip does not install any of them for a consumer. ★ This repository commits no dependency lockfile that this pass reads, so each licence is the one PyPI publishes for the distribution's CURRENT release rather than for a pinned version. 29 of them publish no licence on PyPI this pass can read; that is missing data, not a violation, and none of them is charged. This repository publishes itself under MIT, which is its own choice and is not judged here.
What it measures: Files that change often and are also complex — the riskiest hotspots.
Method: Per production file churn times cyclomatic complexity over a rolling window, computed from git and Roslyn/JS/Razor analysis. Exhaustive, deterministic per commit date.
What it measures: Whether knowledge is concentrated in too few people (the "bus factor").
Method: Living knowledge per author via time-decayed commit attribution (6-month half-life, focus weighting) across largest source files. Deterministic, avoids blame's mechanical-refactor false positives.
4 source file(s) have their living knowledge concentrated in one author (≥90% of recent, decayed contribution). The largest is moments/Demes/Demes.py. Counted over 37 of the 55 production source files in this repository: 10 are under the ~2,400-byte size floor this dimension measures over, and the remaining 8 have no attributable history left to measure.
Off-boarding risk: anonymized user #1
What to do
Resolve the 1 Off-boarding risk finding(s) in Bus Factor. — One of this dimension's main actionable groups (1 recommendation-level).
Detailed fixes: d16_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Acknowledged debt left in the code — TODOs, dead code, suppressed warnings.
Method: Roslyn syntactic debt markers (suppressions/TODO/FIXME/HACK/empty-catch/commented-code/Obsolete) plus SymbolFinder dead-code analysis; weighted-debt-per-KLoC density deducted 2.0x per unit. Deterministic, exhaustive.
4 deducted task-comment markers across 33693 LoC (0.0/KLoC) → score 10.0. Task comments only: this repository's language is read without a compiler, so D17's suppression, dead-code and commented-out-code arms did not run and this score counts fewer marker kinds than a .NET repository's would.
XxxComment · ×2moments/Plotting.py:939
TodoComment · ×2moments/LD/Godambe.py:563
What to do
Resolve the 2 XxxComment finding(s) in Explicit Debt — start with Plotting.py, REDACTED. — One of this dimension's main actionable groups (2 warning-level).
Resolve the 2 TodoComment finding(s) in Explicit Debt — start with Godambe.py, REDACTED. — One of this dimension's main actionable groups (2 warning-level).
Enforce Explicit Debt in CI to reach Verified (currently Documented). — Hardens enforcement from Documented toward Prevented — provenance only; does not change the score.
Detailed fixes: d17_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Whether the project's documentation is clear, complete, and useful.
Method: Judged by language model at low temperature (0.0-0.1) on a deterministic doc sample (READMEs plus first 25 architecture docs), with two-pass stability filtering. Advisory, sampled.
The repository's root README (README.md) is a clear overview of moments: population-genetic analyses based on diffusion approximations to the SFS and LD statistics, with an installation section covering pip and conda install commands, plus a note about the development branch. The tests/ directory README documents that directory only; docs/index.rst serves as the project's single documentation file, outlining contents (Getting started, SFS, LD, Extensions, Modules, Data types) and linking to each topic with a max-depth of 2. Installation is detailed in docs/installation.rst, which also explains dependencies and recommends ipython for interactive analysis. The architecture/design docs are present but not shown here; the visible documentation is complete and well-structured. The repository's documentation is comprehensive: the READMEs for each module (ld/parsing, dfe/inferenc, diversity, recombination, two-locus selection, sfs/inference) are well written and cover their respective topics with code examples, while architecture/Docs markdown files provide a cohesive overview of the project. The READMEs alone do not describe what the repository is or its scope (the module-level docs say this), so the overall quality sits at 8 due to the strong content but an unverifiable missing-overview claim.
Documentation: no usage examples · ×3docs/installation.rst
What to do
Resolve the 3 Documentation finding(s) in Documentation Quality — start with installation.rst, introduction.rst, api_moments.rst. — One of this dimension's main actionable groups (3 recommendation-level).
Detailed fixes: d19_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Whether names — types, methods, variables — are clear and consistent.
Method: Judged by language model at low temperature (0.0-0.1) on a deterministic random symbol sample (fixed size, not exhaustive), with disclosed confidence band. Advisory, sampled.
1 of 1 build units (Python) flagged as possibly oversized/incoherent.
Projects may be oversized for their cohesion
What to do
Resolve the 1 Projects may be oversized for their cohesion finding(s) in Project Cohesion. — One of this dimension's main actionable groups (1 recommendation-level).
Detailed fixes: d26_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Whether any secrets were ever committed — scanned across the full git history, not just now.
Method: Secret scan via TWO gitleaks detect passes in an isolated checkout — the full git history, then a second --no-git pass over the working tree as it stands — merged and de-duplicated by (rule, file, line); each match flagged High. Both invocations are recorded in the audit trail. Exhaustive; when the tool is absent, or when its output cannot be parsed into the expected shape, the dimension is WITHHELD as an explicit measurement gap on our side — unscored and excluded from the lens, never a hedged middling score.
What it measures: Real static-analysis (SAST) findings — likely security bugs in the code, any language.
Method: Polyglot static analysis via semgrep across the repo using the pinned, image-baked p/security-audit + p/owasp-top-ten rulesets (no scan-time registry fetch); severity rules (ERROR/WARNING/INFO) map to a full-band severity-weighted score. Exhaustive, deterministic; degrades on parse failure.
Coverage: semgrep pattern rules over all files — exhaustive for the rule set, blind to classes of bug without a rule (clean = no rule matched).
69 finding(s): 0 critical, 55 high, 14 medium, 0 low. 30 unpinned-GitHub-Actions row(s) are reported here but scored by D36 (supply-chain provenance), which measures that posture as `pinned_actions` — one pinning decision is charged once, not once per lens.
REDACTED
REDACTED
REDACTED
REDACTED
REDACTED
+ 3 more group(s) — more in Appendix A; the complete list is findings.md.
What to do
Resolve the 8 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED (7), REDACTED. — One of this dimension's main actionable groups (8 issue-level).
Resolve the 8 REDACTED finding(s) in Static Analysis (SAST) — start with REDACTED (2), REDACTED (2), REDACTED (2). — One of this dimension's main actionable groups (8 issue-level).
No action in Static Analysis (SAST) — all 30 REDACTED finding(s) are reported here at file:line but scored by D36 (supply-chain provenance), so none is charged to this dimension. — One of this dimension's main actionable groups (30 issue-level, 0 of them charged here).
Detailed fixes: d29_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Whether any dependency has a known published vulnerability (CVE), direct or transitive, in ANY ecosystem the repository declares — Dart pub, Elixir and Erlang via Hex, Go modules, Java and Kotlin via Maven/Gradle, JavaScript/npm, .NET/NuGet, PHP/Composer, Python/PyPI, RubyGems, Rust/Cargo and Swift.
Method: Dependency-CVE scan across every ecosystem the repository declares, scored ONCE. Three sources are unioned and deduplicated by advisory identity (rule id + alias closure, CVE<->GHSA) scoped to package+version, keeping the worst severity: `osv-scanner --recursive` over osv.dev for Dart pub, Elixir/Hex (and Erlang, whose `rebar.lock` syft first converts to a CycloneDX SBOM the scanner reads, with rows attributed back to the lock), Go, Java and Kotlin via Maven/Gradle (and Scala, whose sbt build's pinned direct declarations are written into a CycloneDX SBOM the scanner reads, with rows attributed back to the build file), npm, PHP/Composer, Python/PyPI, RubyGems, Rust/Cargo and Swift; `trivy fs --scanners vuln` for npm lockfiles; and `dotnet list package --vulnerable --include-transitive` for NuGet (with per-advisory collapse of the project x target-framework fan-out), plus a DECLARED-dependency arm that resolves a published gem's gemspec against rubygems.org where no Gemfile.lock is committed. `SeverityScore(c,h,m,l, normalizer 8.0)`. NotApplicable only when NO ecosystem is readable; if any applicable ecosystem could not be scanned the findings are REPORTED and the score is withheld. Supersedes the npm and OSV arms, retired 2026-09-05.
What it measures: Whether anyone still has living knowledge of each file, or it has been orphaned — last understood long ago by someone now gone quiet. The sibling of the bus factor: D16 asks who owns it, D34 asks whether anyone still knows it.
Method: File orphaning as total living-knowledge decay below one focused-commit's worth within a year, computed per-file from the D16 decay model. Exhaustive, deterministic over fixed history.
6 of 45 significant source file(s) are orphaned — their living knowledge has decayed to nothing, so no one currently understands them. The largest is bench/bench.py. Counted over 45 of the 55 production source files in this repository: the rest are under the ~2,400-byte size floor this dimension measures over.
Orphaned knowledge · ×2bench/bench.py
Further orphaned files (smaller)
What to do
Resolve the 2 Orphaned knowledge finding(s) in Knowledge Freshness — start with bench.py, Parsing.py. — One of this dimension's main actionable groups (2 issue-level).
Resolve the 1 Further orphaned files (smaller) finding(s) in Knowledge Freshness. — One of this dimension's main actionable groups (1 recommendation-level).
Detailed fixes: d34_recommendation.md · top locations in Appendix A, every location in findings.md.
What it measures: Whether files that change together actually belong together — pairs that repeatedly co-change in git history despite having no explicit code dependency, surfacing the hidden/logical coupling (and boundaries in the wrong place) a static scan can't see.
Method: Pairwise co-occurrence over the per-commit file sets in git history (production source only — tests and generated dropped): Degree-of-Coupling = shared ÷ min individual revisions, reported above noise floors (each file ≥10 revisions, ≥5 shared commits, ≥50% strength); sweeping commits excluded. Deterministic over fixed history.
Coverage: Population: PRODUCTION source files only — test and generated files are dropped before pairing, so a class co-changing with its own test (trivially ~100%) can't drown the real production↔production coupling. Pairs ranked by Degree-of-Coupling. A non-source file is never a coupling PARTICIPANT either: documentation, schemas, config and data files are dropped with the rest, so a code↔docs pair — a command and the reference page that restates it — is not reported however strongly the two co-change; nor is coupling that runs THROUGH a build step or config file.
What it measures: Whether the build pipeline provides supply-chain integrity — generated provenance/attestation, signed artifacts (cosign/sigstore), an SBOM, and pinned build actions. Presence of the configuration, not a runtime guarantee.
Method: Supply-chain provenance/signing read deterministically from CI/build config (.github/workflows, .gitlab-ci.yml, azure-pipelines, Jenkinsfile, .circleci) + the release surface: four signals — generated provenance/attestation (SLSA/in-toto/actions-attest), artifact signing (cosign/sigstore/gitsign), an SBOM (syft/sbom-action/*.spdx.json/*.cdx.json), and SHA-pinned build actions — scored 10·present/denom. NotApplicable without a build pipeline. Detects configuration presence, not runtime enforcement.
What it measures: Whether any dependency the repository declares is published as MALICIOUS rather than merely vulnerable — a package that is an attacker's work, in any ecosystem osv-scanner reads. Scored apart from D30 because the answer is binary: there is no safe version to upgrade to, and the fix is to remove the package and rotate every credential it could have read.
Method: The same dependency scan D30 reads, partitioned on the scanner's own classification rather than rescanned: a row is MALICIOUS when its id is in the `MAL-` space (the ossf/malicious-packages feed) OR its `database_specific.cwe_ids` carries `CWE-506` ("Embedded Malicious Code"). Both channels are structural; the summary text is deliberately NOT read, because a malicious-package record whose summary says only "Critical severity vulnerability" is a real shape ([GHSA redacted]) and a text matcher misses it. Scored BINARY: any surviving row is 0, whatever its severity and however many CVEs sit beside it — a hostile dependency is not a quantity. Applicability and degradation are D30's: NotApplicable only when no ecosystem is readable, and an unscannable ecosystem degrades rather than reading clean. SCORED, not informational.
What it measures: Whether anyone still ships security patches for the platform this repository RUNS ON — the runtime it pins and the framework majors its own constraints hold it to. Separate from D12 because the question differs: a current Django on an end-of-life Python is perfectly up to date and completely unsupported, and the fix is a migration rather than a version bump. What the repository says it merely SUPPORTS is never charged.
Method: End-of-life PLATFORM read from the repository's own declarations and graded against a FROZEN, dated table of vendor support dates — no network, no feed, no API, so this dimension answers identically inside a closed scan fence. Two subjects: a RUNTIME the project pins (a single or all-end-of-life TargetFramework, a .nvmrc or .python-version, a requires-python CAP) and a FRAMEWORK major a dependency constraint cannot move off (a caret, tilde or exact version; `vue@^2.7.16` pins Vue 2). A FLOOR is deliberately never charged — `requires-python = ">=3.8"` states what a package SUPPORTS, not what it runs on — and a multi-target project is charged only when EVERY target is out of support. Runtime 4.0/product capped 8.0, framework 1.5 capped 4.5. The table is safe to freeze because a statement about support that ended in the past cannot become false: it loses recall as it ages, never precision, and a test asserts every entry predates the freeze date. Disjoint from D31 (a container image's OS layer) and D29 (the toolchain a CI workflow installs). Abstains when the repository declares no platform this pass reads — never scores it clean.
0 end-of-life runtime(s) and 0 end-of-life framework(s), read from 1 platform declaration(s) and 11 dependency declaration(s). This dimension reads what the repository says about ITSELF — a pinned target framework, a version file, a capped requires-python, a Rust toolchain pin, a framework major a constraint cannot move off. A FLOOR is deliberately never charged: `requires-python = ">=3.8"` states what the package SUPPORTS, not what it runs on, and a well-maintained library declares exactly that while running its own CI on a current release. The end-of-life facts are FROZEN and dated, so this dimension needs no network and answers identically inside a closed scan fence; as the table ages it loses recall and never precision, because a statement about support that ended in the past cannot become false. The OS layer of a container image is D31's question and the toolchain a CI workflow installs is D29's; this row is neither.
Other · Architecture — How the codebase splits by code ROLE — domain, application, infrastructure, test, generated. The significance map behind the knowledge/coupling weighting, and a DDD signal in its own right: a thin domain core under fat infrastructure is the anemic-domain smell, quantified. How each file's role is decided, because the split is only as good as that: a generated name or a build-output tree makes it Generated, a test project makes it Test, and otherwise the file's NAMESPACE and PATH words are matched against fixed vocabularies in a fixed ORDER — domain, then infrastructure, then application — so a file whose words hit two layers is counted under the earlier one. A production file matching none of them counts as application, so that share reads 'application or unclassified' rather than a measured application layer. Roles come from naming convention, never from what the code does. On this repository the split was taken from the source tree on disk rather than from a loaded .NET workspace, so a file's role is decided by its PATH segments alone — no declared namespace was available to add to the evidence — and generated output is excluded from the census entirely rather than counted as a generated share.
Method: Roslyn line-count by code ROLE: every source file classified Domain/Application/Infrastructure/Test/Generated by namespace + path convention (the shared CodeRoleClassifier), then significant lines summed per role. Deterministic; the advisory score is the business-logic (domain+application) share of production code.
Coverage: Population: ALL source files, each bucketed into ONE of five roles (Domain/Application/Infrastructure/Test/Generated) by namespace + path convention — a file whose layer isn't named in the convention falls to Application (the neutral default), and the split is line-count, not semantic depth or business value.
What to do
The domain core is a small share of production code, but most of the rest matched no layer vocabulary at all — so this is not yet an anemic-domain finding. The namespace/path convention could not place that code, which makes the composition above a statement about the naming, not about the design. Name the layers (or check that the repository's conventions differ from the ones this check knows) before reading a thin domain into it.
Other · Architecture — Whether the project-reference graph is acyclic (cycles block independent build/deploy and signal eroding boundaries).
Method: Project reference cycles via elementary-DFS over real .csproj references, using the engine shared with D5/D7; cyclic versus acyclic. Exhaustive, deterministic.
Other · Architecture — Whether dependencies point inward (Domain ← Application ← Infrastructure/Web) — the clean-architecture dependency rule, checked across the project graph.
Method: Layer violations by name-segment inference (Domain/Core to Application to Infrastructure/Web) over the project-reference graph. Exhaustive over all projects, deterministic.
Maturity · Maturity — Whether the repo and its projects have a README, and whether it's substantive and current.
Method: Filesystem scan: README presence, word count, and headings for depth; git history for staleness. Exhaustive across root and project dirs, deterministic.
What to do
Add a 'Testing' section to the root README — how to run the test suite.
Add an 'Architecture' / 'How it works' section to the root README — the high-level shape.
Maturity · Maturity — Whether key decisions (ADRs) and the high-level shape (C4/diagrams) are written down.
Method: Filesystem scan: ADR folder/naming conventions or content, plus Mermaid/PlantUML/C4/architecture.md discovery. Exhaustive, deterministic.
No Architecture Decision Records found — no conventional ADR directory, no numbered `NNNN-title` 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.
No C4/Structurizr/PlantUML/Mermaid/Graphviz/D2 diagram, no drawn diagram named for the architecture, no file named `architecture` or `design` in any markup this check reads, and nothing in the README, docs or contributor guides that announces the shape — no `## Architecture` heading, no "architecture overview"/"high-level design" phrasing, no "the architecture is …" 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 — not evidence that nobody wrote the shape down.
What to do
Record significant decisions one document per decision — dated, stating the context, the decision and its consequences — and keep them together wherever your design docs already live (a conventional `docs/adr/` tree, with each file named `NNNN-title` in whatever markup those docs already use, is the most discoverable form).
Add a C4 context/container diagram (Structurizr, PlantUML or Mermaid) or an architecture.md overview.
Maturity · Maturity — Whether the repo is organised deliberately — src/test separation and consistent project naming.
Method: Filesystem scan: src/test folder separation and namespace-prefix consistency (majority RootNamespace agreement). Exhaustive across projects, deterministic.
Production code isn't grouped under a src/ folder — it's spread across several top-level directories, so there's no one place that says 'this is the product'.
What to do
Group production code under src/ (or split deliberately, e.g. backend/ + frontend/) so production and tooling code aren't mixed at the root.
Maturity · Maturity — Whether the README actually describes the code that exists (LLM-judged, advisory).
Method: Judged by language model at low temperature: README accuracy versus actual projects, within a disclosed tolerance. Advisory, not a measured number.
README advertises a RAG / ML engine, but no ML/RAG code or dependency exists — searched for: `rag`, `langchain`, `llamaindex`, `pinecone`, `weaviate`, `qdrant`, `embeddings`. 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's own prose never counts, so a claim is never refuted by merely being made. Nothing outside that search was read — 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.
What to do
Reconcile the README with reality: README advertises a RAG / ML engine, but no ML/RAG code or dependency exists.
Readiness · Readiness — Whether an automated pipeline builds and tests every change.
Method: Filesystem scan: CI workflow files (.github/workflows, .gitlab-ci.yml, etc.) for build and test stages. Exhaustive, deterministic.
Do you agree with this assessment?
P10 · Library API & versioning10.0 / 10Exemplary○ Nothing flagged
Readiness · Readiness — For a library: a deliberate (small) public API surface and explicit semantic versioning so consumers can depend on it safely.
Method: Roslyn scan: public API surface area and semantic-versioning markers (SemVer attributes, changelog entries) for libraries; off .NET, a library is the ecosystem's publication act (an npm package that is not private and names an entry point, a PyPI distribution with a build system, a Rust library crate, a Maven/Gradle module that publishes, a Go module with no package main, a gemspec, a Composer library, a SwiftPM library product, a pub.dev or Hex package), its surface is the share of types the language model records as public (Rust, Swift, Java, Kotlin, Go, Dart; not measured where the model records no type visibility or, as in TypeScript, only module-level export), and its version is read from the manifest, a semver CHANGELOG, release tooling or semver git tags. Exhaustive, deterministic.
Do you agree with this assessment?
P2 · Observability7.0 / 10Strong✓ Tool-verified
Readiness · Readiness — Whether the code is diagnosable in production — structured logging, tracing/metrics, health checks.
Readiness · Readiness — Whether SAST, secret/dependency scanning and performance benchmarking are wired in (presence, not runtime).
Method: Filesystem scan: SAST configuration, dependency-update automation, secret scanning, and a benchmark harness or benchmark step — in this repository's own ecosystem. Exhaustive, deterministic.
No static application security testing detected. For this repository's stack, add bandit, `semgrep --config=p/python`, or CodeQL's 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's web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen — if that is your case the row is wrong, and saying so is more useful than adding a second scanner.
What to do
Add a SAST step to CI running what this repository's stack ships: bandit, `semgrep --config=p/python`, or CodeQL's python pack — so a security regression fails the build instead of landing.
Enable Dependabot/Renovate or a dependency-review gate.
Add gitleaks/trufflehog in CI to block PRs that introduce committed secrets.
Readiness · Readiness — Whether releases are automated and safely reversible (probes, rolling updates, approval gates) — from manifests/pipeline files, not the live environment.
Method: Filesystem scan: deployment manifests/IaC (K8s YAML, Helm, Terraform) for rolling updates, probes, approval gates, migration hooks. Exhaustive, deterministic.
What to do
The release job declares an environment, but its protection rules are not visible from the repository — confirm required reviewers are attached, or publish as a draft release so a bad build can be stopped before users can download it.
Readiness · Readiness — Whether releases are traceable — a maintained changelog and explicit version stamping.
Method: Filesystem scan: changelog file presence and version tags in csproj or git tags. Exhaustive, deterministic.
No CHANGELOG/HISTORY/RELEASES file — what shipped when isn't easy to reconstruct for support or audit. (Versioning/tagging makes releases traceable, but a changelog records the what.)
What to do
Keep a changelog (e.g. Keep-a-Changelog) recording what shipped in each release.
Do you agree with this assessment?
X28 · Index access outside its own emptiness guard10.0 / 10Exemplary○ Nothing flagged
Other · Code Health — Whether a condition that tests a value for emptiness indexes that same value only where the test holds — an `||` written one parenthesis too far to the left leaves an index access outside the guard beside it, so the empty case the guard exists to anticipate reaches the index and throws.
Method: Roslyn syntax only, no semantic model: the OUTERMOST `&&`/`||` of every boolean condition, read for a symbol the condition tests for emptiness (`string.IsNullOrEmpty`/`IsNullOrWhiteSpace`, a `Length`/`Count` comparison against a literal, `Any()`, a `Length`/`Count` pattern, or a comparison against `""`) and ALSO indexes. Each `symbol[...]` access is placed by a boolean-reachability walk from the access up to the outermost connective: an access is COVERED when some enclosing step has it in the right operand and the left operand, under the truth value that step forces, proves the symbol non-empty — a recursion over `&&`/`||` whose true- and false-directions are asymmetric. A finding needs BOTH an uncovered access and a covered one on the same symbol in the same condition, which is the agreeing twin that separates a misplaced parenthesis from an unrelated length test. Bare index accesses with no emptiness test in the condition are neither counted nor reported; a non-identifier receiver and a lambda nested inside the condition are outside the population. Deterministic, provable per finding. Advisory.
Do you agree with this assessment?
Reference — by lens
The score is the rank-weighted fold of these lenses (worst-heaviest), each including its meta-dimensions; a lens with a Critical contributor is capped at Fair (its band reads "gated by …") and is never the strongest area however high its average.
Capped at Fair by a Critical contributor — resolve it before relying on this lens.
Not evidenced — 4 control(s) we could not find positive evidence for
These checks grade a working control, and the repository shows no evidence of one. That is deliberately not scored as a zero: a repository cannot show an ops runbook, a database TTL or an infrastructure-side audit log, so absence of evidence here is not evidence the control is missing. It is also not a statement that the check is irrelevant to this codebase — the thing it grades applies; we just could not see it. Excluded from the score either way.
C3 Audit Trail — Not assessed: these audit controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks audit controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
C4 Data Retention — Not assessed: these retention controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks retention controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
C5 Data-Subject Rights — Not assessed: these data-subject rights controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks data-subject rights controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
P5 DR & Backup — not evidenced — repo shows no backup/RTO/RPO controls; absence of evidence is not evidence of a working control
Not included — 79 check(s) not relevant to this codebase
These checks had nothing to measure here (no tests, no git history, the codebase is small, or the architecture style doesn't apply), so they're omitted above rather than scored low.
AC1 Text alternatives — No web markup found — accessibility is not applicable to this repository.
AC2 Forms & labels — No web markup found — accessibility is not applicable to this repository.
AC3 Page structure — No web markup found — accessibility is not applicable to this repository.
AC4 Keyboard semantics — No web markup found — accessibility is not applicable to this repository.
AC5 ARIA correctness — No web markup found — accessibility is not applicable to this repository.
AC6 Visual & motion safety — No web markup found — accessibility is not applicable to this repository.
AC7 A11y enforcement — No web markup found — accessibility is not applicable to this repository.
AX1 Captive dependencies — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
AX2 Stateful singletons — No container singleton was found, so there is no shared instance for concurrent requests to race on. No function in this Python code is served by a threaded web framework (a Flask, Bottle or FastAPI route, a Django or Pyramid view), so no module is shared between request threads.
AX5 Architecture & structure — not assessed — architecture style/structure is computed from a project graph (projects, types, module namespaces) that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
AX6 Interface segregation — not assessed — interface segregation is computed over a type surface that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
AX7 Slice cohesion — not applicable — not a vertical-slice architecture
AX8 Test isolation — no test/production split to check
AX9 CQS / query purity — no CQRS query handlers detected — query purity is not applicable to this codebase
AXB1 Runtime evidence locked — no reproducible boot — This repository has nothing the runtime tiers could boot or serve — no markup, no UI framework or web-server dependency, no UI component source, no native UI project and no API definition — nothing here is a surface to boot — so runtime a11y/egress/header evidence has no subject here. Not applicable: this is neither a gap in the scan nor a finding about your code.
AXB2 Runtime readiness — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
C1 Data Protection — Not assessed: these personal data controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks personal data controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
C2 Access Controls — Not assessed: these authorization controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks authorization controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
D10 Test Quality — ~6192 lines of test source are present (.py, .fs) but no test cases reached the test census for this repository — no test root we could resolve declared them, or the files we read declare no cases in a test framework we recognise — so skipped/assertion-free tests couldn't be counted. Not scored — this is a gap in the analyzer, not a finding about this repository.
D12 Dependency Hygiene — Not scored — 11 shipped Python distribution(s) were read, but the outdated signal needs pypi.org, and no declaration here carries an exact pin to ask about — a floor or a range installs the newest release it admits and cannot be behind one, so this dimension's own question is only partly answered. NOT a finding that these dependencies are current or healthy.
D18 Solution Shape — D18 scores the shape of a .NET solution; this repository has no .NET solution or project files, so the dimension does not apply.
D20 ADR Quality — N/A — ADRs are expected on deployable products with a user-facing host, not consumed libraries; no ADR log is required here.
D22 Internal API Consistency — The exposed public-API surface could not be collected — no C#/VB projects loaded.
D23 Boundary Type-Coupling — No bounded-context organisation was detected either — neither a context-shaped layout nor 2+ sibling source directories each declaring an aggregate root. Declaring this codebase's bounded contexts (≥2) would let cross-boundary type coupling be assessed. Declare them in `.codehealth/config.yaml` at the repository root (create it if absent), mapping each context name to the module-path or namespace prefixes that belong to it — e.g. `architecture:` → `contexts:` → `Billing: ["src/billing", "Acme.Billing"]`, `Catalog: ["src/catalog", "Acme.Catalog"]`.
D24 Comment Value — No inline comments to assess — comment value is not applicable here.
D25 ADR Conformance — no ADRs to check
D27 Navigability — symbol resolution incomplete — navigability not assessed
D31 IaC & Container Security — No Infrastructure-as-Code or container manifests found (Dockerfile, Docker Compose, Terraform, Kubernetes/Helm, CloudFormation, ARM, Bicep, Ansible); nothing to scan.
D32 Data Compliance (PII/GDPR) — No personal data was found crossing a boundary the PII/GDPR ruleset checks — nothing written to a log or console sink, placed in a URL or query string, or persisted to browser storage. That is a clean result for the LEAK surface only: this ruleset detects personal data escaping, it does not inventory the personal data a repository holds, so it is not evidence that this repository has no personal-data surface. The personal-data map (Appendix C) and the C1-C5 compliance cards are what speak to that.
D37 Vulnerability-disclosure Policy — No vulnerability-disclosure policy file found (SECURITY.md/.markdown/.rst/.txt at root or under .github/.forgejo/.gitea/docs, .well-known/security.txt). A coordinated-disclosure policy may live off-repo, so this is not evidenced rather than failed.
D39 IL Efficiency — D39 measures the IL emitted by a .NET build; this repository has no .NET solution or project files, so the dimension does not apply.
D40 Network Egress Confinement — No Kubernetes/orchestration workloads found in the repository manifests; network egress policy is a cluster-native control that may live at the platform/firewall layer, so there is nothing to assess here.
D41 Kernel & Syscall Confinement — No Kubernetes/orchestration workloads found in the repository manifests; seccomp/AppArmor/SELinux confinement is a workload-level control, so there is nothing to assess here.
D42 Runtime Threat Enforcement — No Kubernetes/orchestration workloads found in the repository manifests; runtime threat-detection and admission-control policy are cluster-level controls, so there is nothing to assess here.
D5 Coupling — Not applicable — this Python build ships 1 production module(s), so there is no coupling BETWEEN modules to measure. (Its test and non-production modules are not part of the shipped graph.)
D7 Architectural Integrity — no checkable ADRs, and no project-reference graph for the cycle pass to read — so this dimension makes no claim about dependency cycles in either direction (where this repository's language has an import-cycle lens, cycles are reported there). Architectural integrity not assessed
D8 Code Coverage — Coverage not included — suite not readable by the collector
DM1 Domain Modelling — not scored — this repository shows none of the 3 signals this lens looks for
ED1 Event-Driven — not scored — this repository shows none of the 3 signals this lens looks for
ED5 Idempotency — no mutating command handlers or message consumers detected — idempotency check not applicable
ES1 Event Sourcing — not scored — this repository shows none of the 3 signals this lens looks for
GD1 Unfinished & placeholder code — no source files were read — this check reads C# and JavaScript/TypeScript, and neither was read for this repository's product. That is a limit of the analyzer, not a finding about your code.
IC1 Incompleteness & stubs — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
P12 CI test-gate honesty — Reported, not scored — and nothing was matched here. The coverage check applies to any stack, and the automatic-re-run check to any GitHub-Actions workflow, but the checks for excluded tests, skipped tests and sleep-based synchronisation currently recognise only some ecosystems' test-runner idioms, so on a repository built with another stack the zeros below mean 'not checked', not 'clean'.
P7 Outbound HTTP resilience — not measured — the application kind could not be determined for this repo
P8 Schema migrations — no ORM, schema-migration tool or schema auto-create was found in this repository's dependency manifests or source, so there is no database schema for this check to judge
P9 Domain vs controller coverage — no coverage report found on disk — produce a coverage report in a standard format (`coverage run -m pytest` then `coverage xml`) and commit it — a hosted scan measures a clone of the repository, so a report that exists only in a working tree, a CI runner's or your own, never reaches it; the artefact is commonly gitignored, so `git add -f` that one file (or un-ignore its path) and commit it alongside the code it measures, or wire coverage collection into CI, to enable this cross-layer check
PF1 Benchmark discipline — Benchmark discipline was not assessed: this repository is written in C, whose benchmark frameworks this check does not search yet. That is a gap in the analyzer's language reach, not a finding about your code.
PF2 Allocation hygiene — Not applicable: Python runs on a garbage-collected runtime that gives a program no allocation-control idiom to choose on a hot path — no pools, stack allocation or value types — so allocation awareness is not something this code can be rated on.
PF3 Async & latency hygiene — Not applicable: this repository declares no async functions, so there is no asynchronous code for a blocking call to stall.
S1 Web-Security Posture — Not assessed: these web-security controls are read from a source model (declarative annotations, request middleware, entity/column names, guard methods) that was not loaded for this repository — because the repository is written in a language this check does not yet model, or because its projects failed to load. Absence of an idiom this check recognises is NOT evidence that this repository lacks web-security controls: it may implement them entirely in its own ecosystem. This is a gap in the analyzer's language coverage, not a finding about this repository.
X1 Async correctness — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X10 Duplicated predicate — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
X12 Unreachable branch — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X13 Undrained process stream — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X14 Bypassable address classification — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X15 Unvalidated length from an untrusted reader — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X16 Unfloored truncation loop — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X17 Uncapped recursion over a caller-supplied document — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X18 Disposal-pattern correctness — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X19 Unrestored process-global state — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X2 Cancellation propagation — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X20 Mistyped argument guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X21 Side-effecting pattern guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X22 Contradicted release guard — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X23 Unguarded diagnostic materialisation — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X24 Document value interpolated into markup unescaped — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X25 Inert configuration knob — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X26 Unsynchronised callback handoff — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X27 Collection changed while being enumerated — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X29 Per-element action decided by a fixed element — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X3 Exception handling — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X30 Support guard that admits what it rejects — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X32 Type resolved by simple name across every loaded assembly — This check reads C# syntax; no C# was loaded for this repository, so it has nothing to report. That is a limit of the analyzer, not a finding about your code.
X4 Structured logging — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X5 Nullable reference types — not analysed — these correctness checks read a source model that was not loaded for this repository, because the repository is written in a language this check does not yet model, or because its projects failed to load. This is a gap in the analyzer, not a finding about this repository
X6 Hand-rolled structured-format parsing — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
X7 Silent fallback defaults — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
X9 Subsumed condition operand — Advisory — this card reports evidence and never carries a score, so there is nothing missing here.
Appendix A — Findings (grouped)
The findings behind the scores, grouped by severity, then by dimension and kind. The high-severity issues are enumerated in full below; items per group are capped at 25 with any overflow stated explicitly per group, never silently truncated. The complete machine-readable list of every finding (all severities) is the companion findings.md in this report's bundle.
Orphaned knowledge bench/bench.py— No living knowledge remains for this large file — 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.
Orphaned knowledge moments/Parsing.py— No living knowledge remains for this large file — 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.
Duplicated block (5 lines × 2) moments/Demes/Inference.py:405— moments/Demes/Inference.py:405-409 | moments/Demes/Inference.py:1004-1008 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (5 lines × 2) REDACTED:206— REDACTED:206-210 | REDACTED:251-255 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (5 lines × 2) moments/LD/Matrices.py:546— moments/LD/Matrices.py:546-550 | moments/LD/Matrices.py:570-574 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:667— moments/LD/stats_from_genotype_counts.py:667-671 | moments/LD/stats_from_genotype_counts.py:1357-1361 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:667` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:687— moments/LD/stats_from_genotype_counts.py:687-691 | moments/LD/stats_from_genotype_counts.py:1112-1116 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:687` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:850— moments/LD/stats_from_genotype_counts.py:850-854 | moments/LD/stats_from_genotype_counts.py:1288-1292 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:850` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:870— moments/LD/stats_from_genotype_counts.py:870-874 | moments/LD/stats_from_genotype_counts.py:1176-1180 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:870` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:1057— moments/LD/stats_from_genotype_counts.py:1057-1061 | moments/LD/stats_from_genotype_counts.py:1247-1251 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1057` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:1070— moments/LD/stats_from_genotype_counts.py:1070-1074 | moments/LD/stats_from_genotype_counts.py:1344-1348 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1070` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:1125— moments/LD/stats_from_genotype_counts.py:1125-1129 | moments/LD/stats_from_genotype_counts.py:1370-1374 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1125` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/LD/stats_from_genotype_counts.py:1247— moments/LD/stats_from_genotype_counts.py:1247-1251 | moments/LD/stats_from_genotype_counts.py:1412-1416 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1247` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/Triallele/Jackknife.py:61— moments/Triallele/Jackknife.py:61-65 | moments/Triallele/Jackknife.py:121-125 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (5 lines × 2) moments/TwoLocus/Numerics.py:94— moments/TwoLocus/Numerics.py:94-98 | moments/TwoLocus/Numerics.py:111-115 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (5 lines × 2) moments/TwoLocus/Numerics.py:1194— moments/TwoLocus/Numerics.py:1194-1198 | moments/TwoLocus/Numerics.py:1215-1219 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Numerics.py:1194` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) moments/TwoLocus/Util.py:340— moments/TwoLocus/Util.py:340-344 | moments/TwoLocus/Util.py:391-395 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Util.py:340` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 2) REDACTED:73— REDACTED:73-77 | REDACTED:115-119 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — 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.
Duplicated block (5 lines × 2) REDACTED:185— REDACTED:185-189 | REDACTED:122-126 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (5 lines × 2) REDACTED:694— REDACTED:694-698 | REDACTED:702-706 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (5 lines × 2) moments/TwoLocus/Numerics.py:408— moments/TwoLocus/Numerics.py:408-412 | moments/TwoLocus/Numerics.py:418-422 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
FileTooLong: LD/Matrices.py moments/LD/Matrices.py— FileTooLong — 3653 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 3153 over it, 7.31× 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.
FileTooLong: LD/stats_from_genotype_counts.py moments/LD/stats_from_genotype_counts.py— FileTooLong — 1279 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 779 over it, 2.56× 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.
FileTooLong: REDACTED REDACTED— FileTooLong — 1147 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 647 over it, 2.29× 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.
FileTooLong: Demes/Demes.py moments/Demes/Demes.py— FileTooLong — 1085 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 585 over it, 2.17× 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.
FileTooLong: LD/Parsing.py moments/LD/Parsing.py— FileTooLong — 1024 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 524 over it, 2.05× 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.
FileTooLong: Demes/Inference.py moments/Demes/Inference.py— FileTooLong — 928 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 428 over it, 1.86× 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.
FileTooLong: REDACTED REDACTED— FileTooLong — 896 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 396 over it, 1.79× 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.
FileTooLong: TwoLocus/Numerics.py moments/TwoLocus/Numerics.py— FileTooLong — 879 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 379 over it, 1.76× 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.
FileTooLong: moments/Plotting.py moments/Plotting.py— FileTooLong — 754 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 254 over it, 1.51× 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.
FileTooLong: REDACTED REDACTED— FileTooLong — 744 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 244 over it, 1.49× 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.
FileTooLong: moments/Inference.py moments/Inference.py— FileTooLong — 614 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 114 over it, 1.23× 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.
FileTooLong: moments/Parsing.py moments/Parsing.py— FileTooLong — 611 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 111 over it, 1.22× 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.
FileTooLong: REDACTED REDACTED— FileTooLong — 584 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 84 over it, 1.17× 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.
FileTooLong: LD/Inference.py moments/LD/Inference.py— FileTooLong — 562 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 62 over it, 1.12× 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.
FileTooLong: moments/Manips.py moments/Manips.py— FileTooLong — 506 significant lines (blank, comment-only and punctuation-only lines excluded). The bar is 500 significant lines; this is 6 over it, 1.01× 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.
Duplicated block (10 lines × 2) moments/Demes/Demes.py:951— moments/Demes/Demes.py:951-960 | moments/Demes/Demes.py:964-973 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Demes/Demes.py:951` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (10 lines × 2) moments/Demes/Inference.py:356— moments/Demes/Inference.py:356-365 | moments/Demes/Inference.py:949-958 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (10 lines × 2) moments/Godambe.py:208— moments/Godambe.py:208-217 | moments/LD/Godambe.py:252-261 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (10 lines × 2) REDACTED:1152— REDACTED:1152-1161 | REDACTED:615-624 — before extracting anything, compare `REDACTED` and `REDACTED` 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 — extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `REDACTED:1152` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (10 lines × 2) REDACTED:218— REDACTED:218-227 | REDACTED:266-275 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `REDACTED:218` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (10 lines × 2) moments/LD/Matrices.py:675— moments/LD/Matrices.py:675-684 | moments/LD/Matrices.py:756-765 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (10 lines × 2) moments/LD/stats_from_genotype_counts.py:167— moments/LD/stats_from_genotype_counts.py:167-176 | moments/LD/stats_from_genotype_counts.py:417-426 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:167` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (10 lines × 2) moments/LD/stats_from_genotype_counts.py:524— moments/LD/stats_from_genotype_counts.py:524-533 | moments/LD/stats_from_genotype_counts.py:550-559 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (10 lines × 2) moments/LD/stats_from_genotype_counts.py:586— moments/LD/stats_from_genotype_counts.py:586-595 | moments/LD/stats_from_genotype_counts.py:626-635 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (10 lines × 2) moments/LD/stats_from_genotype_counts.py:951— moments/LD/stats_from_genotype_counts.py:951-960 | moments/LD/stats_from_genotype_counts.py:1197-1206 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (10 lines × 2) moments/Misc.py:569— moments/Misc.py:569-578 | moments/Misc.py:580-589 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (10 lines × 2) moments/Triallele/Numerics.py:346— moments/Triallele/Numerics.py:346-355 | moments/Triallele/Numerics.py:448-457 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:346` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (10 lines × 2) moments/Triallele/Numerics.py:434— moments/Triallele/Numerics.py:434-443 | moments/Triallele/Numerics.py:480-489 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:434` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (10 lines × 2) moments/TwoLocus/Numerics.py:538— moments/TwoLocus/Numerics.py:538-547 | moments/TwoLocus/Numerics.py:576-585 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (10 lines × 2) REDACTED:160— REDACTED:160-169 | REDACTED:172-181 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (6 lines × 2) REDACTED:793— REDACTED:793-798 | REDACTED:804-809 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (6 lines × 2) REDACTED:625— REDACTED:625-630 | REDACTED:795-800 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (6 lines × 2) moments/LD/Godambe.py:41— moments/LD/Godambe.py:41-46 | moments/LD/Godambe.py:177-182 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (6 lines × 2) moments/LD/Matrices.py:86— moments/LD/Matrices.py:86-91 | moments/LD/Matrices.py:185-192 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:185` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (6 lines × 2) moments/LD/Matrices.py:524— moments/LD/Matrices.py:524-529 | moments/LD/Matrices.py:548-553 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:524` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 2) moments/LD/stats_from_genotype_counts.py:365— moments/LD/stats_from_genotype_counts.py:365-370 | moments/LD/stats_from_genotype_counts.py:412-417 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:365` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (6 lines × 2) moments/LD/stats_from_genotype_counts.py:661— moments/LD/stats_from_genotype_counts.py:661-666 | moments/LD/stats_from_genotype_counts.py:1351-1356 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:661` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 2) moments/LD/stats_from_genotype_counts.py:1071— moments/LD/stats_from_genotype_counts.py:1071-1076 | moments/LD/stats_from_genotype_counts.py:1413-1418 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1071` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 2) moments/Triallele/Jackknife.py:52— moments/Triallele/Jackknife.py:52-57 | moments/Triallele/Jackknife.py:112-117 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (6 lines × 2) REDACTED:275— REDACTED:275-280 | REDACTED:285-290 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (6 lines × 2) moments/TwoLocus/Numerics.py:893— moments/TwoLocus/Numerics.py:893-898 | moments/TwoLocus/Numerics.py:1176-1181 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (6 lines × 2) moments/TwoLocus/Numerics.py:1187— moments/TwoLocus/Numerics.py:1187-1192 | moments/TwoLocus/Numerics.py:1208-1213 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Numerics.py:1187` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 2) moments/LD/Parsing.py:1363— moments/LD/Parsing.py:1363-1368 | moments/LD/Parsing.py:1481-1486 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (6 lines × 2) moments/LD/stats_from_haplotype_counts.py:163— moments/LD/stats_from_haplotype_counts.py:163-168 | moments/LD/stats_from_haplotype_counts.py:315-320 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_haplotype_counts.py:163` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/LD/stats_from_haplotype_counts.py:313` calls `sum` and `moments/LD/stats_from_haplotype_counts.py:162` does not — 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.
Duplicated block (9 lines × 2) moments/Demes/Demes.py:1322— moments/Demes/Demes.py:1322-1330 | moments/Demes/Demes.py:1603-1611 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (9 lines × 2) moments/Demes/Demes.py:1392— moments/Demes/Demes.py:1392-1400 | moments/Demes/Demes.py:1648-1656 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (9 lines × 2) moments/Godambe.py:101— moments/Godambe.py:101-109 | moments/LD/Godambe.py:129-137 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (9 lines × 2) moments/LD/Matrices.py:518— moments/LD/Matrices.py:518-526 | moments/LD/Matrices.py:690-698 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:518` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 2) moments/LD/stats_from_genotype_counts.py:323— moments/LD/stats_from_genotype_counts.py:323-331 | moments/LD/stats_from_genotype_counts.py:370-378 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:323` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 2) moments/LD/stats_from_genotype_counts.py:555— moments/LD/stats_from_genotype_counts.py:555-563 | moments/LD/stats_from_genotype_counts.py:594-602 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (9 lines × 2) moments/Manips.py:318— moments/Manips.py:318-326 | moments/Manips.py:380-388 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Manips.py:318` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (9 lines × 2) moments/Misc.py:392— moments/Misc.py:392-400 | REDACTED:1687-1697 — 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 — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
Duplicated block (9 lines × 2) moments/Plotting.py:689— moments/Plotting.py:689-697 | moments/Plotting.py:1052-1060 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (9 lines × 2) moments/Triallele/Jackknife.py:187— moments/Triallele/Jackknife.py:187-195 | moments/Triallele/Jackknife.py:205-213 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (9 lines × 2) moments/Triallele/Numerics.py:370— moments/Triallele/Numerics.py:370-378 | moments/Triallele/Numerics.py:408-416 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:370` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 2) moments/TwoLocus/Numerics.py:609— moments/TwoLocus/Numerics.py:609-617 | moments/TwoLocus/Numerics.py:647-655 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Numerics.py:609` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 2) moments/TwoLocus/Numerics.py:657— moments/TwoLocus/Numerics.py:657-665 | moments/TwoLocus/Numerics.py:716-724 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Numerics.py:657` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/Demes/Demes.py:162— moments/Demes/Demes.py:162-168 | moments/Demes/Demes.py:442-448 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Demes/Demes.py:160` calls `ValueError` and `moments/Demes/Demes.py:440` does not — 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.
Duplicated block (7 lines × 2) moments/Godambe.py:28— moments/Godambe.py:28-34 | moments/LD/Godambe.py:42-48 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (7 lines × 2) REDACTED:33— REDACTED:33-39 | REDACTED:37-43 — before extracting anything, compare `REDACTED` and `REDACTED` 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 — extracting one helper per block leaves the fork in place. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (7 lines × 2) moments/LD/Matrices.py:952— moments/LD/Matrices.py:952-958 | moments/LD/Matrices.py:996-1002 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/LD/Matrices.py:1003` calls `split` and `moments/LD/Matrices.py:959` does not — 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.
Duplicated block (7 lines × 2) moments/LD/stats_from_genotype_counts.py:1118— moments/LD/stats_from_genotype_counts.py:1118-1124 | moments/LD/stats_from_genotype_counts.py:1363-1369 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1118` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/LD/stats_from_genotype_counts.py:1253— moments/LD/stats_from_genotype_counts.py:1253-1259 | moments/LD/stats_from_genotype_counts.py:1419-1425 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1253` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/Manips.py:123— moments/Manips.py:123-129 | moments/Manips.py:181-187 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Manips.py:123` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/Manips.py:308— moments/Manips.py:308-314 | moments/Manips.py:370-376 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Manips.py:308` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/Plotting.py:1068— moments/Plotting.py:1068-1074 | moments/Plotting.py:1079-1085 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Plotting.py:1068` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/Triallele/Jackknife.py:22— moments/Triallele/Jackknife.py:22-28 | moments/Triallele/Jackknife.py:82-88 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Jackknife.py:22` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/Triallele/Numerics.py:338— moments/Triallele/Numerics.py:338-344 | moments/Triallele/Numerics.py:440-446 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:338` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 2) moments/TwoLocus/Util.py:345— moments/TwoLocus/Util.py:345-351 | moments/TwoLocus/Util.py:396-402 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (7 lines × 2) moments/LD/Parsing.py:433— moments/LD/Parsing.py:433-439 | moments/LD/Parsing.py:524-530 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Parsing.py:433` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/LD/Parsing.py:523` calls `compute_D` and `moments/LD/Parsing.py:432` does not — 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.
Duplicated block (13 lines × 2) moments/Demes/Inference.py:84— moments/Demes/Inference.py:84-96 | moments/Demes/Inference.py:151-163 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (13 lines × 2) moments/Inference.py:687— moments/Inference.py:687-699 | moments/TwoLocus/Inference.py:249-262 — before extracting anything, compare `moments/Inference.py` and `moments/TwoLocus/Inference.py` 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 `moments/Inference.py:687` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (13 lines × 2) moments/LD/Godambe.py:383— moments/LD/Godambe.py:383-395 | moments/LD/Godambe.py:485-497 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/LD/Godambe.py:382` calls `deepcopy` and `moments/LD/Godambe.py:483` does not — 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.
Duplicated block (13 lines × 2) moments/LD/Plotting.py:94— moments/LD/Plotting.py:94-106 | moments/LD/Plotting.py:256-268 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (13 lines × 2) moments/LD/stats_from_genotype_counts.py:542— moments/LD/stats_from_genotype_counts.py:542-554 | moments/LD/stats_from_genotype_counts.py:573-585 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (13 lines × 2) moments/LD/stats_from_haplotype_counts.py:215— moments/LD/stats_from_haplotype_counts.py:215-227 | moments/LD/stats_from_haplotype_counts.py:232-244 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/LD/stats_from_haplotype_counts.py:246` calls `elif` and `moments/LD/stats_from_haplotype_counts.py:229` does not — 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.
Duplicated block (13 lines × 2) moments/Manips.py:398— moments/Manips.py:398-410 | moments/Manips.py:414-426 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (13 lines × 2) moments/Manips.py:430— moments/Manips.py:430-442 | moments/Manips.py:446-458 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (13 lines × 2) moments/Reversible.py:98— moments/Reversible.py:98-110 | moments/Reversible.py:168-180 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (13 lines × 2) moments/Triallele/Numerics.py:77— moments/Triallele/Numerics.py:77-89 | moments/Triallele/Numerics.py:100-112 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (13 lines × 2) moments/Triallele/Numerics.py:551— moments/Triallele/Numerics.py:551-563 | moments/Triallele/Numerics.py:579-591 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:551` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13 lines × 2) moments/TwoLocus/Numerics.py:1110— moments/TwoLocus/Numerics.py:1110-1122 | moments/TwoLocus/Numerics.py:1124-1136 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (8 lines × 2) moments/Godambe.py:36— moments/Godambe.py:36-43 | moments/LD/Godambe.py:50-57 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (8 lines × 2) moments/Godambe.py:129— moments/Godambe.py:129-136 | moments/LD/Godambe.py:168-175 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (8 lines × 2) moments/Inference.py:75— moments/Inference.py:75-82 | moments/TwoLocus/Inference.py:183-190 — before extracting anything, compare `moments/Inference.py` and `moments/TwoLocus/Inference.py` 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.
Duplicated block (8 lines × 2) moments/LD/stats_from_genotype_counts.py:344— moments/LD/stats_from_genotype_counts.py:344-351 | moments/LD/stats_from_genotype_counts.py:391-398 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:344` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 2) moments/LD/stats_from_genotype_counts.py:646— moments/LD/stats_from_genotype_counts.py:646-653 | moments/LD/stats_from_genotype_counts.py:829-836 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:646` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 2) moments/Triallele/Numerics.py:444— moments/Triallele/Numerics.py:444-451 | moments/Triallele/Numerics.py:508-515 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:444` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 2) moments/Triallele/Numerics.py:470— moments/Triallele/Numerics.py:470-477 | moments/Triallele/Numerics.py:489-496 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:470` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 2) moments/Triallele/Numerics.py:507— moments/Triallele/Numerics.py:507-514 | moments/Triallele/Numerics.py:526-533 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:507` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (12 lines × 2) moments/Demes/Demes.py:1055— moments/Demes/Demes.py:1055-1066 | moments/Demes/Demes.py:1121-1132 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (12 lines × 2) moments/Demes/Inference.py:509— moments/Demes/Inference.py:509-520 | moments/Demes/Inference.py:1097-1108 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Demes/Inference.py:509` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (12 lines × 2) REDACTED:1107— REDACTED:1107-1118 | REDACTED:583-594 — before extracting anything, compare `REDACTED` and `REDACTED` 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 — extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `REDACTED:1107` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (12 lines × 2) moments/Triallele/Numerics.py:397— moments/Triallele/Numerics.py:397-408 | moments/Triallele/Numerics.py:499-510 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:397` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Triallele/Numerics.py:396` calls `choose` and `moments/Triallele/Numerics.py:498` does not — 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.
Duplicated block (12 lines × 2) REDACTED:1029— REDACTED:1029-1040 | REDACTED:1044-1055 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `REDACTED:1029` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (12 lines × 2) moments/TwoLocus/Numerics.py:635— moments/TwoLocus/Numerics.py:635-646 | moments/TwoLocus/Numerics.py:716-727 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Numerics.py:635` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (12 lines × 2) moments/TwoLocus/Numerics.py:728— moments/TwoLocus/Numerics.py:728-739 | moments/TwoLocus/Numerics.py:749-760 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Numerics.py:728` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
D4 · Code Duplication· Members sharing a duplicated core (4 members, 50+ identical tokens) · ×5
Members sharing a duplicated core (4 members, 50+ identical tokens) moments/Demes/Inference.py:356— moments/Demes/Inference.py:356-409 | moments/Demes/Inference.py:689-889 | moments/Demes/Inference.py:949-1008 | moments/Demes/Inference.py:1276-1427 — 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 — 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' grain — 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.
Members sharing a duplicated core (4 members, 50+ identical tokens) moments/Inference.py:114— moments/Inference.py:114-216 | moments/Inference.py:723-829 | moments/Inference.py:955-1046 | moments/TwoLocus/Inference.py:222-262 — 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 — 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' grain — 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.
Members sharing a duplicated core (4 members, 50+ identical tokens) moments/TwoLocus/Demographics.py:111— moments/TwoLocus/Demographics.py:111-139 | moments/TwoLocus/Demographics.py:143-173 | moments/TwoLocus/Demographics.py:177-207 | moments/TwoLocus/Demographics.py:211-241 — 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 — 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' grain — 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.
Members sharing a duplicated core (4 members, 50+ identical tokens) moments/TwoLocus/Util.py:126— moments/TwoLocus/Util.py:126-156 | moments/TwoLocus/Util.py:160-219 | moments/TwoLocus/Util.py:223-318 | moments/TwoLocus/Util.py:322-433 — 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 — 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' grain — 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.
Members sharing a duplicated core (4 members, 50+ identical tokens) moments/TwoLocus/Util.py:504— moments/TwoLocus/Util.py:504-521 | moments/TwoLocus/Util.py:527-544 | moments/TwoLocus/Util.py:550-567 | moments/TwoLocus/Util.py:573-590 — 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 — 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' grain — 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.
Duplicated block (15 lines × 2) moments/Demes/Demes.py:1109— moments/Demes/Demes.py:1109-1123 | moments/Demes/Demes.py:1124-1138 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Demes/Demes.py:1109` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (15 lines × 2) REDACTED:1010— REDACTED:1010-1024 | REDACTED:510-524 — before extracting anything, compare `REDACTED` and `REDACTED` 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 — extracting one helper per block leaves the fork in place.
Duplicated block (15 lines × 2) moments/LD/Inference.py:322— moments/LD/Inference.py:322-336 | moments/TwoLocus/Inference.py:144-158 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — 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.
Duplicated block (15 lines × 2) moments/LD/Matrices.py:1128— moments/LD/Matrices.py:1128-1142 | moments/LD/Matrices.py:2521-2535 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:1128` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (15 lines × 2) moments/TwoLocus/Util.py:259— moments/TwoLocus/Util.py:259-273 | moments/TwoLocus/Util.py:302-316 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Util.py:259` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (14 lines × 2) moments/Demes/Inference.py:65— moments/Demes/Inference.py:65-78 | moments/Demes/Inference.py:134-147 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (14 lines × 2) moments/LD/Matrices.py:1032— moments/LD/Matrices.py:1032-1045 | moments/LD/Matrices.py:1056-1069 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:1032` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (14 lines × 2) moments/LD/stats_from_genotype_counts.py:491— moments/LD/stats_from_genotype_counts.py:491-504 | moments/LD/stats_from_genotype_counts.py:559-572 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (14 lines × 2) moments/Manips.py:224— moments/Manips.py:224-237 | moments/Manips.py:287-300 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (14 lines × 2) REDACTED:1552— REDACTED:1552-1565 | REDACTED:374-387 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `REDACTED:1550` calls `write` and `REDACTED:372` does not — 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.
Duplicated block (8 lines × 3) moments/LD/Matrices.py:646— moments/LD/Matrices.py:646-653 | moments/LD/Matrices.py:666-673 | moments/LD/Matrices.py:727-734 — 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 — 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 `moments/LD/Matrices.py:646` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 3) moments/LD/Parsing.py:863— moments/LD/Parsing.py:863-870 | moments/LD/Parsing.py:887-894 | moments/LD/Parsing.py:910-917 — 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 — 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 `moments/LD/Parsing.py:863` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (8 lines × 3) moments/Triallele/Numerics.py:369— moments/Triallele/Numerics.py:369-376 | moments/Triallele/Numerics.py:388-395 | moments/Triallele/Numerics.py:407-414 — 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 — 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 `moments/Triallele/Numerics.py:369` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/Triallele/Numerics.py:396` calls `choose` and `moments/Triallele/Numerics.py:415` does not — 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.
Duplicated block (8 lines × 3) moments/Triallele/Numerics.py:429— moments/Triallele/Numerics.py:429-436 | moments/Triallele/Numerics.py:522-529 | moments/Triallele/Numerics.py:570-577 — 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 — 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 `moments/Triallele/Numerics.py:429` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 3) moments/Triallele/Numerics.py:466— moments/Triallele/Numerics.py:466-473 | moments/Triallele/Numerics.py:551-558 | moments/Triallele/Numerics.py:579-586 — 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 — 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 `moments/Triallele/Numerics.py:466` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 3) moments/LD/Matrices.py:503— moments/LD/Matrices.py:503-507 | moments/LD/Matrices.py:525-529 | moments/LD/Matrices.py:549-553 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (5 lines × 3) moments/LD/Parsing.py:880— moments/LD/Parsing.py:880-884 | moments/LD/Parsing.py:904-908 | moments/LD/Parsing.py:935-939 — 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 — 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 `moments/LD/Parsing.py:880` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 3) moments/LD/stats_from_genotype_counts.py:662— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:662` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 3) moments/LinearSystem.py:112— moments/LinearSystem.py:112-116 | moments/LinearSystem.py:186-190 | moments/LinearSystem.py:273-277 — 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 — 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.
Duplicated block (5 lines × 3) REDACTED:87— REDACTED:87-91 | REDACTED:192-196 | REDACTED:129-133 — 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 — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made 3 times.
Duplicated block (11 lines × 2) moments/LD/stats_from_genotype_counts.py:581— moments/LD/stats_from_genotype_counts.py:581-591 | moments/LD/stats_from_genotype_counts.py:611-621 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (11 lines × 2) moments/Manips.py:800— moments/Manips.py:800-810 | moments/Manips.py:935-945 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (11 lines × 2) moments/Misc.py:831— moments/Misc.py:831-841 | REDACTED:1703-1713 — 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 — a file they already depend on, or a new one alongside them — and call it from both call sites, so a change lands once.
Duplicated block (11 lines × 2) moments/TwoLocus/Numerics.py:526— moments/TwoLocus/Numerics.py:526-536 | moments/TwoLocus/Numerics.py:564-574 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (7 lines × 3) moments/LD/Godambe.py:411— moments/LD/Godambe.py:411-417 | moments/LD/Godambe.py:508-514 | moments/LD/Godambe.py:582-588 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (7 lines × 3) moments/Triallele/Numerics.py:338— moments/Triallele/Numerics.py:338-344 | moments/Triallele/Numerics.py:372-378 | moments/Triallele/Numerics.py:512-518 — 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 — 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 `moments/Triallele/Numerics.py:338` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 3) moments/Triallele/Numerics.py:445— moments/Triallele/Numerics.py:445-451 | moments/Triallele/Numerics.py:491-497 | moments/Triallele/Numerics.py:509-515 — 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 — 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 `moments/Triallele/Numerics.py:445` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 3) moments/Triallele/Numerics.py:444— moments/Triallele/Numerics.py:444-450 | moments/Triallele/Numerics.py:508-514 | moments/Triallele/Numerics.py:527-533 — 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 — 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 `moments/Triallele/Numerics.py:444` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Triallele/Numerics.py:526` calls `choose` and `moments/Triallele/Numerics.py:443` does not — 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.
Duplicated block (6 lines × 3) moments/LD/Matrices.py:696— moments/LD/Matrices.py:696-701 | moments/LD/Matrices.py:783-788 | moments/LD/Matrices.py:810-815 — 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 — 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 `moments/LD/Matrices.py:696` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 3) moments/LD/stats_from_genotype_counts.py:154— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:154` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 3) moments/LD/stats_from_genotype_counts.py:349— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:349` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (6 lines × 3) moments/LD/stats_from_genotype_counts.py:396— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:396` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
D4 · Code Duplication· Members sharing a duplicated core (5 members, 50+ identical tokens) · ×3
Members sharing a duplicated core (5 members, 50+ identical tokens) REDACTED:599— REDACTED:599-669 | moments/Numerics.py:139-183 | REDACTED:1416-1492 | REDACTED:185-247 | REDACTED:291-339 — 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 — 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' grain — 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.
Members sharing a duplicated core (5 members, 50+ identical tokens) moments/Manips.py:85— 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 — 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 — 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' grain — 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.
Members sharing a duplicated core (5 members, 50+ identical tokens) REDACTED:210— REDACTED:210-218 | REDACTED:221-235 | REDACTED:238-252 | REDACTED:255-269 | REDACTED:272-286 — 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 — 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' grain — 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.
Duplicated block (25 lines × 2) moments/LD/Util.py:123— moments/LD/Util.py:123-147 | moments/Misc.py:125-149 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (25 lines × 2) moments/Manips.py:264— moments/Manips.py:264-292 | moments/Manips.py:330-354 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (25 lines × 2) moments/TwoLocus/Demographics.py:111— moments/TwoLocus/Demographics.py:111-135 | moments/TwoLocus/Demographics.py:177-202 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/TwoLocus/Demographics.py:205` calls `exp`, `log` and `moments/TwoLocus/Demographics.py:138` does not — 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.
Duplicated block (18 lines × 2) moments/Inference.py:1213— moments/Inference.py:1213-1230 | moments/TwoLocus/Inference.py:89-106 — before extracting anything, compare `moments/Inference.py` and `moments/TwoLocus/Inference.py` 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.
Duplicated block (18 lines × 2) moments/LD/Matrices.py:1719— moments/LD/Matrices.py:1719-1736 | moments/LD/Matrices.py:2689-2706 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:1719` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (18 lines × 2) moments/LD/stats_from_genotype_counts.py:511— moments/LD/stats_from_genotype_counts.py:511-528 | moments/LD/stats_from_genotype_counts.py:598-615 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (16 lines × 2) moments/LinearSystem.py:111— moments/LinearSystem.py:111-126 | moments/LinearSystem.py:272-287 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (16 lines × 2) moments/Misc.py:473— moments/Misc.py:473-488 | moments/Misc.py:495-510 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (16 lines × 2) moments/TwoLocus/Numerics.py:509— moments/TwoLocus/Numerics.py:509-524 | moments/TwoLocus/Numerics.py:547-562 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (12 lines × 3) moments/Godambe.py:334— moments/Godambe.py:334-345 | moments/Godambe.py:439-450 | moments/Godambe.py:504-515 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Godambe.py:438` calls `concatenate` and `moments/Godambe.py:333` does not — 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.
Duplicated block (12 lines × 3) REDACTED:1083— REDACTED:1083-1094 | REDACTED:569-580 | REDACTED:758-769 — before extracting anything, compare `REDACTED` and `REDACTED` 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 — extracting one helper per block leaves the fork in place. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `REDACTED:566` calls `any`, `ValueError` and `REDACTED:1082` does not — 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.
Duplicated block (12 lines × 3) moments/TwoLocus/Util.py:129— moments/TwoLocus/Util.py:129-140 | moments/TwoLocus/Util.py:163-174 | moments/TwoLocus/Util.py:226-237 — 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 — 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.
Duplicated block (11 lines × 3) moments/LD/stats_from_genotype_counts.py:518— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (11 lines × 3) moments/LD/stats_from_genotype_counts.py:695— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (11 lines × 3) moments/LD/stats_from_haplotype_counts.py:212— 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 — 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 — 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 `moments/LD/stats_from_haplotype_counts.py:212` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9–10 lines × 2) moments/TwoLocus/Util.py:178— moments/TwoLocus/Util.py:178-186 | moments/TwoLocus/Util.py:205-214 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Util.py:178` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (9–10 lines × 2) moments/TwoLocus/Util.py:249— moments/TwoLocus/Util.py:249-257 | moments/TwoLocus/Util.py:292-301 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Util.py:249` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (9–10 lines × 2) moments/TwoLocus/Util.py:352— moments/TwoLocus/Util.py:352-360 | moments/TwoLocus/Util.py:403-412 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Util.py:352` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (9 lines × 5) moments/LD/Matrices.py:512— 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 — 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 — 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 `moments/LD/Matrices.py:512` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 5) moments/LD/Matrices.py:744— 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 — 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 — 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 `moments/LD/Matrices.py:744` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 5) moments/LD/Matrices.py:777— 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 — 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 — 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 `moments/LD/Matrices.py:777` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (9 lines × 4) moments/LD/stats_from_genotype_counts.py:519— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (9 lines × 4) moments/LD/stats_from_haplotype_counts.py:86— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (9 lines × 4) moments/Triallele/Numerics.py:414— moments/Triallele/Numerics.py:414-422 | moments/Triallele/Numerics.py:434-442 | moments/Triallele/Numerics.py:480-488 | moments/Triallele/Numerics.py:536-544 — 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 — 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 `moments/Triallele/Numerics.py:414` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Triallele/Numerics.py:478` calls `choose` and `moments/Triallele/Numerics.py:412` does not — 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.
Duplicated block (8 lines × 4) moments/Triallele/Numerics.py:342— moments/Triallele/Numerics.py:342-349 | moments/Triallele/Numerics.py:406-413 | moments/Triallele/Numerics.py:425-432 | moments/Triallele/Numerics.py:547-554 — 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 — 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 `moments/Triallele/Numerics.py:342` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Triallele/Numerics.py:423` calls `choose` and `moments/Triallele/Numerics.py:340` does not — 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.
Duplicated block (8 lines × 4) moments/TwoLocus/Util.py:126— moments/TwoLocus/Util.py:126-133 | moments/TwoLocus/Util.py:160-167 | moments/TwoLocus/Util.py:223-230 | moments/TwoLocus/Util.py:322-329 — 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 — 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.
Duplicated block (8 lines × 4) moments/TwoLocus/Util.py:145— moments/TwoLocus/Util.py:145-152 | moments/TwoLocus/Util.py:195-202 | moments/TwoLocus/Util.py:274-281 | moments/TwoLocus/Util.py:381-388 — 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 — 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 `moments/TwoLocus/Util.py:145` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 4) moments/LD/Matrices.py:644— moments/LD/Matrices.py:644-650 | moments/LD/Matrices.py:664-670 | moments/LD/Matrices.py:725-731 | moments/LD/Matrices.py:752-758 — 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 — 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 `moments/LD/Matrices.py:644` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 4) moments/Triallele/Numerics.py:343— moments/Triallele/Numerics.py:343-349 | moments/Triallele/Numerics.py:369-375 | moments/Triallele/Numerics.py:388-394 | moments/Triallele/Numerics.py:407-413 — 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 — 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 `moments/Triallele/Numerics.py:343` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/Triallele/Numerics.py:396` calls `choose` and `moments/Triallele/Numerics.py:415` does not — 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.
Duplicated block (7 lines × 4) moments/Triallele/Numerics.py:372— moments/Triallele/Numerics.py:372-378 | moments/Triallele/Numerics.py:410-416 | moments/Triallele/Numerics.py:494-500 | moments/Triallele/Numerics.py:512-518 — 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 — 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 `moments/Triallele/Numerics.py:372` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6–7 lines × 2) moments/LD/stats_from_genotype_counts.py:680— moments/LD/stats_from_genotype_counts.py:680-686 | moments/LD/stats_from_genotype_counts.py:1377-1382 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:680` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6–7 lines × 2) moments/LD/stats_from_genotype_counts.py:863— moments/LD/stats_from_genotype_counts.py:863-869 | moments/LD/stats_from_genotype_counts.py:1170-1175 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:863` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6–7 lines × 2) moments/LD/stats_from_genotype_counts.py:1137— moments/LD/stats_from_genotype_counts.py:1137-1142 | moments/LD/stats_from_genotype_counts.py:1144-1150 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1137` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (5 lines × 5) moments/LD/stats_from_genotype_counts.py:447— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/LD/stats_from_genotype_counts.py:1400` calls `sum` and `moments/LD/stats_from_genotype_counts.py:452` does not — 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.
Duplicated block (5 lines × 5) moments/Manips.py:127— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (5 lines × 5) moments/Triallele/Jackknife.py:52— moments/Triallele/Jackknife.py:52-56 | moments/Triallele/Jackknife.py:112-116 | REDACTED:197-201 | REDACTED:217-221 | REDACTED:237-241 — there are 5 copies across 2 file(s) — 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.
Duplicated block (3–5 lines × 3) moments/LD/Parsing.py:1077— moments/LD/Parsing.py:1077-1081 | moments/LD/Parsing.py:1085-1089 | moments/LD/Parsing.py:1092-1094 — 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 — 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 `moments/LD/Parsing.py:1077` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (3–5 lines × 3) moments/LD/stats_from_genotype_counts.py:1040— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:1040` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (3–5 lines × 3) REDACTED:177— REDACTED:177-181 | REDACTED:259-261 | REDACTED:310-314 — 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 — 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 `REDACTED:177` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
XxxComment moments/Plotting.py:939— # XXX: I can't set the axis ticks to be just the endpoints. — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `# REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
XxxComment REDACTED:313— # XXX don't think this is needed — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `# REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment moments/LD/Godambe.py:563— # TODO: complete docstring — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `# REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
TodoComment REDACTED:540— ## TODO!! — source code is not a task system: move the work to your tracker and leave a reference instead (e.g. `# REF: #123`), so the task is planned where tasks live and the ticket links back to the code.
Duplicated block (40 lines × 2) moments/LD/Matrices.py:2576— moments/LD/Matrices.py:2576-2615 | moments/LD/Matrices.py:2634-2673 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:2576` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (40 lines × 2) moments/Parsing.py:868— moments/Parsing.py:868-907 | moments/Parsing.py:911-950 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (37 lines × 2) moments/Godambe.py:47— moments/Godambe.py:47-83 | moments/LD/Godambe.py:66-102 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (37 lines × 2) moments/Manips.py:85— moments/Manips.py:85-121 | moments/Manips.py:143-179 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (35 lines × 2) moments/LD/Matrices.py:4119— moments/LD/Matrices.py:4119-4153 | moments/LD/Matrices.py:4876-4910 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:4119` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (35 lines × 2) moments/LinearSystem.py:140— moments/LinearSystem.py:140-174 | moments/LinearSystem.py:223-257 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (27 lines × 2) moments/Plotting.py:711— moments/Plotting.py:711-737 | moments/Plotting.py:1083-1109 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Plotting.py:711` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (27 lines × 2) REDACTED:802— REDACTED:802-828 | REDACTED:839-865 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (22–23 lines × 4) moments/LD/Matrices.py:2757— moments/LD/Matrices.py:2757-2779 | moments/LD/Matrices.py:2847-2869 | moments/LD/Matrices.py:3065-3086 | moments/LD/Matrices.py:3173-3194 — 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 — 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 `moments/LD/Matrices.py:2757` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (22–23 lines × 4) moments/LD/Matrices.py:2787— moments/LD/Matrices.py:2787-2809 | moments/LD/Matrices.py:2877-2899 | moments/LD/Matrices.py:3101-3122 | moments/LD/Matrices.py:3209-3230 — 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 — 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 `moments/LD/Matrices.py:2787` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (21 lines × 6) moments/LD/Matrices.py:1171— 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 — 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 — 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 `moments/LD/Matrices.py:1171` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (21 lines × 6) moments/LD/Matrices.py:2763— 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 — 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 — 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 `moments/LD/Matrices.py:2763` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (19 lines × 3) REDACTED:106— REDACTED:106-124 | REDACTED:166-186 | REDACTED:195-214 — 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 — 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 `REDACTED:166` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (19 lines × 3) moments/LD/Matrices.py:1373— moments/LD/Matrices.py:1373-1391 | moments/LD/Matrices.py:1558-1576 | moments/LD/Matrices.py:1635-1653 — 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 — 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 `moments/LD/Matrices.py:1373` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (19 lines × 2) moments/LD/stats_from_genotype_counts.py:1309— moments/LD/stats_from_genotype_counts.py:1309-1327 | moments/LD/stats_from_haplotype_counts.py:246-264 — 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 — a file they already depend on, or a new one alongside them — 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 `moments/LD/stats_from_genotype_counts.py:1309` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (19 lines × 2) moments/TwoLocus/Util.py:362— moments/TwoLocus/Util.py:362-380 | moments/TwoLocus/Util.py:413-431 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/TwoLocus/Util.py:362` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (14–15 lines × 2) REDACTED:469— REDACTED:469-483 | REDACTED:691-704 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `REDACTED:469` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (14–15 lines × 2) moments/LD/Parsing.py:327— moments/LD/Parsing.py:327-341 | moments/LD/Parsing.py:345-358 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (14 lines × 3) moments/Manips.py:104— moments/Manips.py:104-117 | moments/Manips.py:162-175 | moments/Manips.py:349-362 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (14 lines × 3) moments/TwoLocus/Util.py:192— moments/TwoLocus/Util.py:192-205 | moments/TwoLocus/Util.py:271-284 | moments/TwoLocus/Util.py:378-391 — 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 — 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 `moments/TwoLocus/Util.py:192` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13 lines × 9) moments/LD/Matrices.py:1323— 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 — 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 — 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 `moments/LD/Matrices.py:1323` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13 lines × 9) moments/LD/Matrices.py:1538— 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 — 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 — 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 `moments/LD/Matrices.py:1538` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13 lines × 4) moments/LD/Matrices.py:1024— moments/LD/Matrices.py:1024-1037 | moments/LD/Matrices.py:1372-1385 | moments/LD/Matrices.py:1558-1570 | moments/LD/Matrices.py:1635-1647 — 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 — 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 `moments/LD/Matrices.py:1024` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13 lines × 4) moments/LD/Matrices.py:1343— moments/LD/Matrices.py:1343-1355 | moments/LD/Matrices.py:1357-1369 | moments/LD/Matrices.py:2582-2599 | moments/LD/Matrices.py:2640-2657 — 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 — 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 `moments/LD/Matrices.py:1343` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (12–13 lines × 2) moments/Demes/Inference.py:657— moments/Demes/Inference.py:657-669 | moments/Demes/Inference.py:1244-1255 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Demes/Inference.py:657` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (12–13 lines × 2) moments/Triallele/Numerics.py:517— moments/Triallele/Numerics.py:517-529 | moments/Triallele/Numerics.py:566-577 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Triallele/Numerics.py:517` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (11–12 lines × 2) moments/LD/Parsing.py:858— moments/LD/Parsing.py:858-869 | moments/LD/Parsing.py:906-916 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Parsing.py:858` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/LD/Parsing.py:904` calls `pi2` and `moments/LD/Parsing.py:858` does not — 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.
Duplicated block (11–12 lines × 2) moments/LD/stats_from_genotype_counts.py:877— moments/LD/stats_from_genotype_counts.py:877-888 | moments/LD/stats_from_genotype_counts.py:989-999 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (10 lines × 3) moments/LD/Matrices.py:80— moments/LD/Matrices.py:80-89 | moments/LD/Matrices.py:99-108 | moments/LD/Matrices.py:116-125 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (10 lines × 3) moments/LD/Matrices.py:459— moments/LD/Matrices.py:459-468 | moments/LD/Matrices.py:475-484 | moments/LD/Matrices.py:489-498 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (9–10 lines × 3) moments/LinearSystem.py:119— moments/LinearSystem.py:119-128 | moments/LinearSystem.py:193-201 | moments/LinearSystem.py:280-289 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (9–10 lines × 3) REDACTED:984— REDACTED:984-992 | REDACTED:1029-1038 | REDACTED:1044-1053 — 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 — 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 `REDACTED:984` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (7 lines × 5) moments/LD/stats_from_genotype_counts.py:497— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (7 lines × 5) REDACTED:210— REDACTED:210-216 | REDACTED:221-233 | REDACTED:238-250 | REDACTED:255-267 | REDACTED:272-284 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (6–7 lines × 3) moments/LD/stats_from_genotype_counts.py:659— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:659` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6–7 lines × 3) moments/LD/stats_from_haplotype_counts.py:51— 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 — 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 — 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 `moments/LD/stats_from_haplotype_counts.py:51` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Matrices.admix_ld (cyclomatic 216) moments/LD/Matrices.py:995— Matrices.admix_ld has cyclomatic complexity 216 (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. This file is where this pass's cyclomatic complexity CONCENTRATES: moments/LD/Matrices.py holds 4 of the 58 methods over the threshold — including the worst — and 315 of the 915 points over it (34%), 2.2× 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.
Matrices.migration_ld (cyclomatic 103) moments/LD/Matrices.py:415— 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. This file is where this pass's cyclomatic complexity CONCENTRATES: moments/LD/Matrices.py holds 4 of the 58 methods over the threshold — including the worst — and 315 of the 915 points over it (34%), 2.2× 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.
Demes.SFS (cyclomatic 82) moments/Demes/Demes.py:17— Demes.SFS has cyclomatic complexity 82 (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.
Parsing._tally_vcf (cyclomatic 72) moments/Parsing.py:317— 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.
Parsing._count_types_sparse (cyclomatic 43) moments/LD/Parsing.py:549— 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.
Demes._get_deme_sample_sizes (cyclomatic 40) moments/Demes/Demes.py:1023— 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.
Matrices.drift_ld (cyclomatic 40) moments/LD/Matrices.py:35— 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's cyclomatic complexity CONCENTRATES: moments/LD/Matrices.py holds 4 of the 58 methods over the threshold — including the worst — and 315 of the 915 points over it (34%), 2.2× 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.
Jackknife.closest_ijk_edges (cyclomatic 39) REDACTED:267— 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.
Integration.integrate_nD (cyclomatic 37) REDACTED:889— 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.
Misc.make_data_dict_vcf (cyclomatic 37) moments/Misc.py:409— 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.
Integration.integrate (cyclomatic 36) moments/TwoLocus/Integration.py:15— 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.
ModelPlot.plot_model (cyclomatic 34) moments/ModelPlot.py:82— 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.
Plotting.plot_ld_curves_comp (cyclomatic 32) moments/LD/Plotting.py:120— 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.
Demes.LD (cyclomatic 31) moments/Demes/Demes.py:387— 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.
Jackknife.calc_jk (cyclomatic 31) REDACTED:887— 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.
Demes.LDdecay (cyclomatic 27) moments/Demes/Demes.py:543— 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.
LDstats.integrate (cyclomatic 27) REDACTED:961— 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.
Misc.bootstrap (cyclomatic 27) moments/Misc.py:672— 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.
Jackknife.closest_ijk (cyclomatic 27) REDACTED:51— 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.
Demes._get_demographic_events (cyclomatic 26) moments/Demes/Demes.py:745— 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.
Demes._compute_sfs (cyclomatic 26) moments/Demes/Demes.py:1165— 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.
Integration_nomig.integrate_nomig (cyclomatic 26) REDACTED:402— 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.
Numerics.integrate (cyclomatic 26) moments/LD/Numerics.py:192— 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.
Spectrum.integrate (cyclomatic 26) REDACTED:672— 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.
Jackknife.closest_ijk_sides (cyclomatic 25) REDACTED:141— 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.
Inference._set_value (cyclomatic 24) moments/Demes/Inference.py:133— 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.
Numerics.steady_state (cyclomatic 24) moments/LD/Numerics.py:380— 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.
stats_from_genotype_counts.pi2 (cyclomatic 24) moments/LD/stats_from_genotype_counts.py:468— 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.
Spectrum.f4 (cyclomatic 24) REDACTED:1206— 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.
Numerics.drift (cyclomatic 24) moments/TwoLocus/Numerics.py:68— 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.
Inference._get_value (cyclomatic 23) moments/Demes/Inference.py:60— 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.
Inference._object_func (cyclomatic 23) moments/LD/Inference.py:295— 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.
stats_from_haplotype_counts.pi2 (cyclomatic 23) moments/LD/stats_from_haplotype_counts.py:105— 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.
Plotting.plot_3d_spectrum (cyclomatic 23) moments/Plotting.py:803— 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.
Plotting.plot_4d_comp_Poisson (cyclomatic 21) moments/Plotting.py:997— 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.
Integration.integrate_cn (cyclomatic 21) moments/Triallele/Integration.py:29— 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.
Inference.optimize (cyclomatic 20) moments/Demes/Inference.py:419— 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.
Integration_nomig.integrate_neutral (cyclomatic 20) REDACTED:644— 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.
Parsing.get_genotypes (cyclomatic 20) moments/LD/Parsing.py:98— 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.
Util.rescale_params (cyclomatic 20) moments/LD/Util.py:150— 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.
Parsing._parse_filters (cyclomatic 20) moments/Parsing.py:683— 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.
Plotting.plot_3d_comp_Poisson (cyclomatic 20) moments/Plotting.py:634— 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.
Spectrum.__new__ (cyclomatic 20) REDACTED:78— 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.
Parsing._call_sgc (cyclomatic 19) moments/LD/Parsing.py:790— 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.
Spectrum.f3 (cyclomatic 19) REDACTED:1134— 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.
Demes._augment_with_ancient_samples (cyclomatic 18) moments/Demes/Demes.py:683— 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.
LDstats.to_file (cyclomatic 18) REDACTED:671— 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.
Inference.optimize_LD (cyclomatic 17) moments/Demes/Inference.py:1018— 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.
Util._compute_D (cyclomatic 17) moments/TwoLocus/Util.py:125— 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 — 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.
Util._compute_D2 (cyclomatic 17) moments/TwoLocus/Util.py:159— 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 — 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.
Util._compute_Dz (cyclomatic 17) moments/TwoLocus/Util.py:222— 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 — 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.
Util._compute_pi2 (cyclomatic 17) moments/TwoLocus/Util.py:321— 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 — 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.
Matrices.mutation_ld (cyclomatic 16) moments/LD/Matrices.py:258— 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's cyclomatic complexity CONCENTRATES: moments/LD/Matrices.py holds 4 of the 58 methods over the threshold — including the worst — and 315 of the 915 points over it (34%), 2.2× 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.
Parsing.subset_data (cyclomatic 16) moments/LD/Parsing.py:1504— 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.
Plotting.plot_ld_curves (cyclomatic 16) moments/LD/Plotting.py:23— 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.
Plotting.plot_2d_comp_Poisson (cyclomatic 16) moments/Plotting.py:439— 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.
TriSpectrum.fold_ancestral (cyclomatic 16) REDACTED:346— 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.
Numerics.drift_reversible (cyclomatic 16) moments/TwoLocus/Numerics.py:960— 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.
Matrices.migration_ld (cognitive 358) moments/LD/Matrices.py:415— 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.
Parsing._tally_vcf (cognitive 158) moments/Parsing.py:317— 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.
Demes.SFS (cognitive 152) moments/Demes/Demes.py:17— 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.
Matrices.admix_ld (cognitive 134) moments/LD/Matrices.py:995— 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.
Demes._get_deme_sample_sizes (cognitive 123) moments/Demes/Demes.py:1023— 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.
Jackknife.calc_jk (cognitive 112) REDACTED:887— 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.
Parsing._count_types_sparse (cognitive 99) moments/LD/Parsing.py:549— 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.
Inference._set_value (cognitive 88) moments/Demes/Inference.py:133— 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 — 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's 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.
Numerics.drift (cognitive 84) moments/TwoLocus/Numerics.py:68— 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.
Misc.make_data_dict_vcf (cognitive 81) moments/Misc.py:409— 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.
Integration.integrate_nD (cognitive 80) REDACTED:889— 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.
Inference._get_value (cognitive 76) moments/Demes/Inference.py:60— 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 — 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's 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.
ModelPlot.plot_model (cognitive 71) moments/ModelPlot.py:82— 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.
Demes._augment_with_ancient_samples (cognitive 68) moments/Demes/Demes.py:683— 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 — 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's 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.
Numerics.integrate (cognitive 65) moments/LD/Numerics.py:192— 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 — 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's 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.
Parsing._parse_filters (cognitive 65) moments/Parsing.py:683— 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.
Misc.bootstrap (cognitive 62) moments/Misc.py:672— 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.
Integration.integrate (cognitive 62) moments/TwoLocus/Integration.py:15— 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.
Matrices.drift_ld (cognitive 61) moments/LD/Matrices.py:35— 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.
Demes._compute_sfs (cognitive 58) moments/Demes/Demes.py:1165— 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.
Integration_nomig.integrate_nomig (cognitive 56) REDACTED:402— 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.
Plotting.plot_3d_spectrum (cognitive 54) moments/Plotting.py:803— 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.
Numerics.drift_reversible (cognitive 54) moments/TwoLocus/Numerics.py:960— 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.
LinearSystem.calcM_jk3 (cognitive 52) moments/LinearSystem.py:263— 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.
Plotting.plot_ld_curves_comp (cognitive 51) moments/LD/Plotting.py:120— 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.
Integration_nomig.integrate_neutral (cognitive 48) REDACTED:644— 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.
Util._compute_D (cognitive 48) moments/TwoLocus/Util.py:125— 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 — 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.
Util._compute_D2 (cognitive 48) moments/TwoLocus/Util.py:159— 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 — 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.
Util._compute_Dz (cognitive 48) moments/TwoLocus/Util.py:222— 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 — 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.
Util._compute_pi2 (cognitive 48) moments/TwoLocus/Util.py:321— 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 — 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.
Integration.integrate_cn (cognitive 46) moments/Triallele/Integration.py:29— 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.
Demes.LD (cognitive 44) moments/Demes/Demes.py:387— 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.
Jackknife.closest_ijk_edges (cognitive 41) REDACTED:267— 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.
Matrices.mutation_ld (cognitive 40) moments/LD/Matrices.py:258— 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.
Jackknife.closest_ijk (cognitive 40) REDACTED:51— 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.
Inference._object_func (cognitive 39) moments/LD/Inference.py:295— 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.
Matrices.migration_h (cognitive 39) moments/LD/Matrices.py:367— 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.
Spectrum.integrate (cognitive 38) REDACTED:672— 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.
Jackknife.closest_ijk_sides (cognitive 38) REDACTED:141— 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.
Parsing._call_sgc (cognitive 37) moments/LD/Parsing.py:790— 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.
Parsing.subset_data (cognitive 36) moments/LD/Parsing.py:1504— 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.
Demes._get_demographic_events (cognitive 35) moments/Demes/Demes.py:745— 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.
Plotting.plot_4d_comp_Poisson (cognitive 35) moments/Plotting.py:997— 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.
Numerics.drift (cognitive 33) moments/Triallele/Numerics.py:57— 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.
Util.ld_names (cognitive 31) moments/LD/Util.py:22— 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.
Util._compute_S (cognitive 31) moments/TwoLocus/Util.py:106— 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.
DemesUtil.slice (cognitive 30) moments/Demes/DemesUtil.py:6— 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.
Numerics.steady_state (cognitive 30) moments/LD/Numerics.py:380— 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.
Plotting.plot_3d_comp_Poisson (cognitive 30) moments/Plotting.py:634— 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.
Demes.LDdecay (cognitive 28) moments/Demes/Demes.py:543— 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.
Inference.uncerts_LD (cognitive 28) moments/Demes/Inference.py:1258— 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.
LDstats.integrate (cognitive 28) REDACTED:961— 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 — checks laid out side by side rather than stacked — 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.
Matrices.mutation_h (cognitive 28) moments/LD/Matrices.py:234— 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.
Parsing.get_genotypes (cognitive 27) moments/LD/Parsing.py:98— 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.
_ModelInfo.determine_framesizes (cognitive 27) moments/ModelPlot.py:636— _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.
Spectrum.f3 (cognitive 27) REDACTED:1134— 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.
Numerics.recombination (cognitive 27) moments/TwoLocus/Numerics.py:311— 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.
Numerics.selection_two_locus (cognitive 27) moments/TwoLocus/Numerics.py:375— 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 — 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.
Numerics.selection_general (cognitive 27) moments/TwoLocus/Numerics.py:459— 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 — 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.
Matrices.recombination (cognitive 26) moments/LD/Matrices.py:322— 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.
Parsing._get_ld_stat_sums (cognitive 26) moments/LD/Parsing.py:966— 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.
Spectrum.__new__ (cognitive 26) REDACTED:78— 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.
Spectrum.f4 (cognitive 26) REDACTED:1206— 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.
Demes._apply_event (cognitive 25) moments/Demes/Demes.py:1321— 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.
Integration._apply_frozen_pops (cognitive 25) REDACTED:845— 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.
LDstats.to_file (cognitive 25) REDACTED:671— 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 — 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.
Inference._perturb_params_constrained (cognitive 24) moments/Demes/Inference.py:280— 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.
Plotting.plot_ld_curves (cognitive 24) moments/LD/Plotting.py:23— 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.
Misc.make_fux_table (cognitive 23) moments/Misc.py:152— 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.
Parsing.get_bootstrap_sets (cognitive 22) moments/LD/Parsing.py:1372— 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.
Numerics.project (cognitive 22) moments/Triallele/Numerics.py:275— 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.
TriSpectrum.fold_ancestral (cognitive 22) REDACTED:346— 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.
Numerics.mutations_reversible (cognitive 22) moments/TwoLocus/Numerics.py:886— 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 — 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.
Numerics.recombination_reversible (cognitive 22) moments/TwoLocus/Numerics.py:1088— 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 — 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.
DemesUtil.swipe (cognitive 21) moments/Demes/DemesUtil.py:97— 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.
Inference.optimize (cognitive 21) moments/Demes/Inference.py:419— 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 — checks laid out side by side rather than stacked — 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.
Plotting.plot_2d_comp_Poisson (cognitive 21) moments/Plotting.py:439— 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 — checks laid out side by side rather than stacked — 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.
Reversible._calc_FB_5pop (cognitive 21) moments/Reversible.py:161— 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.
Numerics.project (cognitive 21) moments/TwoLocus/Numerics.py:836— 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.
Inference._object_func (cognitive 20) moments/Inference.py:25— 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.
LDstats.swap_pops (cognitive 20) REDACTED:384— 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 — 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.
Plotting.plot_single_2d_sfs (cognitive 20) moments/Plotting.py:201— 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 — checks laid out side by side rather than stacked — 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.
Demes._migration_rate_in_interval (cognitive 19) moments/Demes/Demes.py:978— 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.
Demes._compute_LD (cognitive 19) moments/Demes/Demes.py:1535— 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.
Util.rescale_params (cognitive 19) moments/LD/Util.py:150— 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 — checks laid out side by side rather than stacked — 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.
Parsing._check_anc (cognitive 19) moments/Parsing.py:758— 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 — 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's 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.
Spectrum.f2 (cognitive 19) REDACTED:1080— 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.
Spectrum.from_data_dict (cognitive 19) REDACTED:1621— 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.
Inference._object_func (cognitive 19) moments/TwoLocus/Inference.py:129— 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.
Integration._make_array_sel_dom (cognitive 18) REDACTED:772— 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 — checks laid out side by side rather than stacked — 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.
Parsing._get_H_statistics (cognitive 18) moments/LD/Parsing.py:1014— 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.
Manips.admix_inplace (cognitive 18) moments/Manips.py:816— 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 — checks laid out side by side rather than stacked — 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.
Parsing._spectrum_from_tally (cognitive 18) moments/Parsing.py:991— 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.
Spectrum.marginalize (cognitive 18) REDACTED:334— 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 — checks laid out side by side rather than stacked — 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.
Numerics.cached_projection (cognitive 18) moments/TwoLocus/Numerics.py:785— 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.
Inference.optimize_log_lbfgsb (cognitive 17) moments/LD/Inference.py:810— 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 — checks laid out side by side rather than stacked — 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.
stats_from_genotype_counts.pi2 (cognitive 17) moments/LD/stats_from_genotype_counts.py:468— 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.
Plotting.plot_2d_resid (cognitive 17) moments/Plotting.py:300— 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 — checks laid out side by side rather than stacked — 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.
Reversible._calc_FB_4pop (cognitive 17) moments/Reversible.py:94— 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.
Spectrum.from_file (cognitive 17) REDACTED:1415— 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 — checks laid out side by side rather than stacked — 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.
TLSpectrum.fold (cognitive 17) REDACTED:389— 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.
Inference.uncerts (cognitive 16) moments/Demes/Inference.py:672— 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 — checks laid out side by side rather than stacked — 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.
LDstats.f3 (cognitive 16) REDACTED:188— 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 — 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.
LDstats.f4 (cognitive 16) REDACTED:234— 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 — 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.
Parsing.compute_ld_statistics (cognitive 16) moments/LD/Parsing.py:1203— 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.
Spectrum.genotype_matrix (cognitive 16) REDACTED:1346— 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.
TooManyMethods: Spectrum REDACTED:35— TooManyMethods — 49 methods. The bar is 30 methods; this is 19 over it, 1.63× the bar. To reduce it, group the members that share the same data into a smaller type of their own and delegate to it, so no single type carries every responsibility.
Change coupling: REDACTED ↔ REDACTED REDACTED— `REDACTED` and `REDACTED` 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 — 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 — 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 — the registration is the link, and it is meant not to be an import — 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 `877eabc3` Fix __array_wrap__ to be compatible with numpy 2 (#208); `cc93eb0e` Bump to 1.1.18; `b70fdcbf` extension docstrings — run `git show` on any of them.
D4 · Code Duplication· Near-duplicate member family (3 members, 38 shared lines) · ×1
Near-duplicate member family (3 members, 38 shared lines) REDACTED:905— REDACTED:905-1196 | REDACTED:417-641 | REDACTED:656-810 — 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' grain — 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.
Near-duplicate member pair (115 shared lines) moments/Plotting.py:647— moments/Plotting.py:647-800 | moments/Plotting.py:1010-1177 — 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' grain — 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.
Near-duplicate member pair (104 shared lines) REDACTED:414— REDACTED:414-541 | REDACTED:545-799 — 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' grain — 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.
Near-duplicate member pair (59 shared lines) REDACTED:143— REDACTED:143-264 | REDACTED:269-392 — 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' grain — 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.
Near-duplicate member pair (52 shared lines) moments/Godambe.py:12— moments/Godambe.py:12-83 | moments/LD/Godambe.py:21-102 — 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' grain — 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.
Near-duplicate member pair (49 shared lines) moments/LinearSystem.py:107— moments/LinearSystem.py:107-174 | moments/LinearSystem.py:181-257 — 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' grain — 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.
Near-duplicate member pair (30 shared lines) moments/Triallele/Jackknife.py:22— moments/Triallele/Jackknife.py:22-57 | moments/Triallele/Jackknife.py:82-117 — 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' grain — 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.
D4 · Code Duplication· Edited copy of a member (44 corresponding lines) · ×1
Edited copy of a member (44 corresponding lines) REDACTED:189— REDACTED:189-232 | REDACTED:235-280 — 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 — 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' grain — 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.
D4 · Code Duplication· Members sharing a duplicated core (6 members, 50+ identical tokens) · ×1
Members sharing a duplicated core (6 members, 50+ identical tokens) moments/TwoLocus/Numerics.py:69— 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 — 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 — 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' grain — 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.
Duplicated block (117–138 lines × 2) moments/LD/Inference.py:635— moments/LD/Inference.py:635-751 | moments/LD/Inference.py:837-974 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (118 lines × 2) moments/TwoLocus/Numerics.py:123— moments/TwoLocus/Numerics.py:123-240 | moments/TwoLocus/Numerics.py:968-1085 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (90–92 lines × 2) moments/Inference.py:238— moments/Inference.py:238-327 | moments/Inference.py:1068-1159 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Inference.py:1068` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/Inference.py:329` calls `log` and `moments/Inference.py:1160` does not — 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.
Duplicated block (49–79 lines × 2) moments/LinearSystem.py:321— moments/LinearSystem.py:321-369 | moments/LinearSystem.py:372-450 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (72 lines × 3) moments/Inference.py:114— moments/Inference.py:114-196 | moments/Inference.py:723-802 | moments/Inference.py:955-1026 — 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 — 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 `moments/Inference.py:955` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (67 lines × 2) moments/Inference.py:614— moments/Inference.py:614-680 | moments/Inference.py:848-915 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Inference.py:848` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (63 lines × 2) moments/Demes/Inference.py:532— moments/Demes/Inference.py:532-594 | moments/Demes/Inference.py:1123-1185 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Demes/Inference.py:532` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/Demes/Inference.py:595` calls `delayed_flush` and `moments/Demes/Inference.py:1186` does not — 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.
Duplicated block (14–60 lines × 2) moments/Demes/Inference.py:435— moments/Demes/Inference.py:435-494 | moments/Demes/Inference.py:746-759 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (58 lines × 2) moments/LD/Matrices.py:1555— moments/LD/Matrices.py:1555-1612 | moments/LD/Matrices.py:1632-1689 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:1555` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (57 lines × 3) moments/LD/Inference.py:534— moments/LD/Inference.py:534-590 | moments/LD/Inference.py:735-791 | moments/LD/Inference.py:958-1014 — 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 — 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 `moments/LD/Inference.py:534` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (48 lines × 5) moments/LD/Matrices.py:1984— 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 — 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 — 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 `moments/LD/Matrices.py:1984` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (42–43 lines × 2) moments/Plotting.py:752— moments/Plotting.py:752-793 | moments/Plotting.py:1127-1169 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (41 lines × 4) moments/LD/Matrices.py:1787— moments/LD/Matrices.py:1787-1827 | moments/LD/Matrices.py:1836-1876 | moments/LD/Matrices.py:1885-1925 | moments/LD/Matrices.py:1934-1974 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (31–41 lines × 2) moments/Manips.py:714— moments/Manips.py:714-754 | moments/Manips.py:817-847 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (27–40 lines × 2) REDACTED:250— REDACTED:250-289 | REDACTED:342-368 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (37–39 lines × 3) moments/Plotting.py:452— moments/Plotting.py:452-490 | moments/Plotting.py:647-683 | moments/Plotting.py:1010-1046 — 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 — 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 `moments/Plotting.py:452` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (26–37 lines × 4) moments/Godambe.py:223— moments/Godambe.py:223-259 | moments/Godambe.py:269-299 | moments/Godambe.py:305-335 | moments/Godambe.py:480-505 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (34–35 lines × 2) moments/Plotting.py:263— moments/Plotting.py:263-297 | moments/Plotting.py:345-378 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (26–34 lines × 8) moments/LD/Matrices.py:1454— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (26–34 lines × 7) moments/LD/Matrices.py:1510— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (29–34 lines × 3) moments/Reversible.py:62— moments/Reversible.py:62-90 | moments/Reversible.py:125-157 | moments/Reversible.py:205-238 — 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 — 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.
Duplicated block (32 lines × 2) moments/LD/Matrices.py:3999— moments/LD/Matrices.py:3999-4030 | moments/LD/Matrices.py:4756-4787 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:3999` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (30 lines × 4) moments/LD/Matrices.py:3445— moments/LD/Matrices.py:3445-3474 | moments/LD/Matrices.py:3653-3682 | moments/LD/Matrices.py:4202-4231 | moments/LD/Matrices.py:4410-4439 — 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 — 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 `moments/LD/Matrices.py:3445` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (22–29 lines × 5) REDACTED:599— REDACTED:599-623 | moments/Numerics.py:139-167 | REDACTED:1416-1444 | REDACTED:185-208 | REDACTED:291-312 — 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 — a location they all depend on today, or a new shared one if there is none — 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 `REDACTED:599` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (22–28 lines × 11) moments/LD/Matrices.py:2452— 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 — 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 — 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 `moments/LD/Matrices.py:2452` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (22–28 lines × 10) moments/LD/Matrices.py:2340— 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 — 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 — 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 `moments/LD/Matrices.py:2340` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (22–28 lines × 5) moments/LD/Matrices.py:1009— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (22–28 lines × 3) moments/LD/Matrices.py:2490— moments/LD/Matrices.py:2490-2511 | moments/LD/Matrices.py:2563-2590 | moments/LD/Matrices.py:2621-2648 — 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 — 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 `moments/LD/Matrices.py:2490` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (27–28 lines × 2) moments/LD/Matrices.py:2997— moments/LD/Matrices.py:2997-3024 | moments/LD/Matrices.py:3353-3379 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:2997` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (26–27 lines × 2) moments/LD/Godambe.py:106— moments/LD/Godambe.py:106-132 | moments/LD/Godambe.py:146-171 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (24–27 lines × 2) moments/Misc.py:800— moments/Misc.py:800-823 | REDACTED:1665-1691 — 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 — a file they already depend on, or a new one alongside them — 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.
Duplicated block (26 lines × 5) moments/LD/Matrices.py:2800— 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 — 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 — 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 `moments/LD/Matrices.py:2800` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (26 lines × 2) moments/Demes/Inference.py:369— moments/Demes/Inference.py:369-394 | moments/Demes/Inference.py:816-841 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (23–25 lines × 2) moments/Demes/Inference.py:964— moments/Demes/Inference.py:964-986 | moments/Demes/Inference.py:1330-1354 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (22–23 lines × 6) moments/LD/Matrices.py:2907— 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 — 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 — 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 `moments/LD/Matrices.py:2907` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (23 lines × 4) REDACTED:555— REDACTED:555-577 | REDACTED:618-640 | REDACTED:681-703 | REDACTED:744-766 — 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 — 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 `REDACTED:555` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (20–22 lines × 6) moments/LD/Matrices.py:1270— 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 — 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 — 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 `moments/LD/Matrices.py:1270` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (22 lines × 2) REDACTED:560— REDACTED:560-581 | REDACTED:749-770 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (21–22 lines × 2) moments/LD/Matrices.py:2817— moments/LD/Matrices.py:2817-2838 | moments/LD/Matrices.py:3137-3157 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:2817` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (21 lines × 10) moments/LD/Matrices.py:2793— 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 — 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 — 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 `moments/LD/Matrices.py:2793` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (21 lines × 8) moments/LD/Matrices.py:3401— 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 — 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 — 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 `moments/LD/Matrices.py:3401` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (21 lines × 4) moments/Inference.py:176— moments/Inference.py:176-196 | moments/Inference.py:782-802 | moments/Inference.py:1006-1026 | moments/TwoLocus/Inference.py:222-242 — before extracting anything, compare `moments/Inference.py` and `moments/TwoLocus/Inference.py` 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.
Duplicated block (18–21 lines × 2) REDACTED:106— REDACTED:106-126 | REDACTED:58-75 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — 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 `REDACTED:106` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (20–21 lines × 2) moments/TwoLocus/Numerics.py:387— moments/TwoLocus/Numerics.py:387-406 | moments/TwoLocus/Numerics.py:493-513 — both copies are in the same file, so extract the block into one function there and call it from each site — 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.
Duplicated block (18–20 lines × 10) moments/LD/Matrices.py:1990— 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 — 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 — 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 `moments/LD/Matrices.py:1990` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (20 lines × 2) moments/LD/Godambe.py:405— moments/LD/Godambe.py:405-424 | moments/LD/Godambe.py:502-521 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Godambe.py:405` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (18–20 lines × 2) moments/LD/Matrices.py:2277— moments/LD/Matrices.py:2277-2296 | moments/LD/Matrices.py:3017-3034 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:2277` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (19 lines × 8) moments/LD/Matrices.py:4041— 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 — 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 — 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 `moments/LD/Matrices.py:4041` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (14–19 lines × 3) moments/Triallele/Numerics.py:413— moments/Triallele/Numerics.py:413-427 | moments/Triallele/Numerics.py:475-488 | moments/Triallele/Numerics.py:531-549 — 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 — 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 `moments/Triallele/Numerics.py:413` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (17–19 lines × 2) moments/TwoLocus/Numerics.py:312— moments/TwoLocus/Numerics.py:312-330 | moments/TwoLocus/Numerics.py:1089-1105 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (14–18 lines × 45) moments/LD/Matrices.py:1974— 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 — 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 — 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 `moments/LD/Matrices.py:1974` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (14–18 lines × 9) moments/LD/Matrices.py:1016— 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 — 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 — 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 `moments/LD/Matrices.py:1016` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (14–18 lines × 7) moments/LD/Matrices.py:1380— 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 — 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 — 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 `moments/LD/Matrices.py:1380` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (18 lines × 6) moments/LD/Matrices.py:2679— 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 — 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 — 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 `moments/LD/Matrices.py:2679` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (18 lines × 4) REDACTED:807— REDACTED:807-824 | REDACTED:826-843 | REDACTED:845-862 | REDACTED:864-881 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — no decision has to be handed back and re-acted on.
Duplicated block (17–18 lines × 2) moments/Triallele/Integration.py:59— moments/Triallele/Integration.py:59-75 | moments/Triallele/Integration.py:101-118 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (14–17 lines × 4) moments/LD/Matrices.py:2529— moments/LD/Matrices.py:2529-2543 | moments/LD/Matrices.py:2545-2558 | moments/LD/Matrices.py:2601-2617 | moments/LD/Matrices.py:2659-2675 — 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 — 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 `moments/LD/Matrices.py:2529` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (14–17 lines × 2) moments/Demes/Demes.py:1085— moments/Demes/Demes.py:1085-1098 | moments/Demes/Demes.py:1100-1116 — both copies are in the same file, so extract the block into one function there and call it from each site — the copies drift apart the first time only one of them is edited.
Duplicated block (17 lines × 2) moments/Godambe.py:139— moments/Godambe.py:139-155 | moments/LD/Godambe.py:178-194 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice.
Duplicated block (16 lines × 8) moments/LD/Matrices.py:1778— 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 — 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 — 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 `moments/LD/Matrices.py:1778` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (15–16 lines × 5) moments/LD/Matrices.py:1095— 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 — 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 — 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 `moments/LD/Matrices.py:1095` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (16 lines × 4) moments/TwoLocus/Util.py:504— moments/TwoLocus/Util.py:504-519 | moments/TwoLocus/Util.py:527-542 | moments/TwoLocus/Util.py:550-565 | moments/TwoLocus/Util.py:573-588 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (15–16 lines × 3) REDACTED:1067— REDACTED:1067-1082 | REDACTED:551-565 | REDACTED:739-754 — before extracting anything, compare `REDACTED` and `REDACTED` 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 — extracting one helper per block leaves the fork in place. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `REDACTED:566` calls `any`, `ValueError` and `REDACTED:1083` does not — 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.
Duplicated block (15–16 lines × 2) moments/LD/Matrices.py:1063— moments/LD/Matrices.py:1063-1077 | moments/LD/Matrices.py:1087-1102 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/Matrices.py:1063` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (15 lines × 19) moments/LD/Matrices.py:2459— 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 — 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 — 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 `moments/LD/Matrices.py:2459` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (15 lines × 6) moments/LD/Matrices.py:1104— 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 — 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 — 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 `moments/LD/Matrices.py:1104` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (15 lines × 3) moments/Inference.py:1193— moments/Inference.py:1193-1207 | moments/LD/Inference.py:1051-1065 | moments/TwoLocus/Inference.py:110-124 — before extracting anything, compare `moments/Inference.py` and `moments/TwoLocus/Inference.py` 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.
Duplicated block (12–15 lines × 3) moments/Misc.py:283— moments/Misc.py:283-295 | moments/Misc.py:469-483 | moments/Misc.py:494-505 — 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 — 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 `moments/Misc.py:283` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Misc.py:466` calls `ValueError` and `moments/Misc.py:282` does not — 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.
Duplicated block (14 lines × 49) moments/LD/Matrices.py:1269— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/LD/Matrices.py:3463` calls `elif` and `moments/LD/Matrices.py:1284` does not — 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.
Duplicated block (14 lines × 12) moments/LD/Matrices.py:2321— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (14 lines × 10) moments/LD/Matrices.py:1171— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (14 lines × 8) moments/LD/Matrices.py:1009— 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 — 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 — 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 `moments/LD/Matrices.py:1009` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (14 lines × 4) moments/Demes/Inference.py:376— moments/Demes/Inference.py:376-389 | moments/Demes/Inference.py:822-835 | moments/Demes/Inference.py:967-980 | moments/Demes/Inference.py:1333-1346 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (13–14 lines × 4) moments/TwoLocus/Demographics.py:124— moments/TwoLocus/Demographics.py:124-137 | moments/TwoLocus/Demographics.py:158-170 | moments/TwoLocus/Demographics.py:191-204 | moments/TwoLocus/Demographics.py:226-238 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/TwoLocus/Demographics.py:205` calls `exp`, `log` and `moments/TwoLocus/Demographics.py:138` does not — 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.
Duplicated block (10–14 lines × 3) REDACTED:980— REDACTED:980-989 | REDACTED:486-499 | REDACTED:706-719 — before extracting anything, compare `REDACTED` and `REDACTED` 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 — extracting one helper per block leaves the fork in place. Read the line range as the matched WINDOW rather than a finished unit: at `REDACTED:486` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13–14 lines × 3) REDACTED:967— REDACTED:967-980 | REDACTED:998-1010 | REDACTED:1013-1025 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (3–14 lines × 4) moments/Triallele/Jackknife.py:33— moments/Triallele/Jackknife.py:33-46 | moments/Triallele/Jackknife.py:47-49 | moments/Triallele/Jackknife.py:93-106 | moments/Triallele/Jackknife.py:107-109 — 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 — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just after the matched lines, `moments/Triallele/Jackknife.py:47` calls `array`, `sum` and `moments/Triallele/Jackknife.py:49` does not — 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.
Duplicated block (13 lines × 13) moments/LD/Matrices.py:1510— 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 — 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 — 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 `moments/LD/Matrices.py:1510` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13 lines × 6) moments/LD/Matrices.py:1009— 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 — 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 — 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 `moments/LD/Matrices.py:1009` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (13 lines × 3) moments/LD/Parsing.py:869— moments/LD/Parsing.py:869-881 | moments/LD/Parsing.py:893-905 | moments/LD/Parsing.py:920-932 — 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 — 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 `moments/LD/Parsing.py:869` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (12–13 lines × 3) moments/Manips.py:231— moments/Manips.py:231-242 | moments/Manips.py:294-306 | moments/Manips.py:356-368 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (12 lines × 20) moments/LD/Matrices.py:2261— 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 — 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 — 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 `moments/LD/Matrices.py:2261` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (9–12 lines × 14) REDACTED:464— REDACTED:464-475 | REDACTED:478-489 | REDACTED:492-503 | REDACTED:506-517 | REDACTED:520-531 | REDACTED:532-540 | REDACTED:579-590 | REDACTED:591-602 | REDACTED:642-653 | REDACTED:654-665 | REDACTED:705-716 | REDACTED:717-728 | REDACTED:768-779 | REDACTED:780-791 — 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 — 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 `REDACTED:464` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (12 lines × 8) REDACTED:184— REDACTED:184-195 | REDACTED:204-215 | REDACTED:224-235 | REDACTED:244-255 | REDACTED:317-328 | REDACTED:334-345 | REDACTED:351-362 | REDACTED:368-379 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (12 lines × 4) moments/Manips.py:50— moments/Manips.py:50-61 | moments/Manips.py:104-115 | moments/Manips.py:162-173 | moments/Manips.py:349-360 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (11–12 lines × 3) REDACTED:911— REDACTED:911-922 | REDACTED:926-936 | REDACTED:940-950 — 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 — 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 `REDACTED:911` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (10–12 lines × 2) moments/Demes/Inference.py:757— moments/Demes/Inference.py:757-766 | moments/Demes/Inference.py:1304-1315 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/Demes/Inference.py:1304` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (4–12 lines × 5) REDACTED:549— REDACTED:549-552 | REDACTED:603-614 | REDACTED:666-677 | REDACTED:732-736 | REDACTED:738-741 — 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 — 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 `REDACTED:603` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (10–11 lines × 4) moments/LD/Parsing.py:849— moments/LD/Parsing.py:849-859 | moments/LD/Parsing.py:871-880 | moments/LD/Parsing.py:895-904 | moments/LD/Parsing.py:922-931 — 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 — 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 `moments/LD/Parsing.py:849` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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.
Duplicated block (11 lines × 4) moments/LD/stats_from_genotype_counts.py:443— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:443` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7–10 lines × 16) REDACTED:422— REDACTED:422-428 | REDACTED:433-442 | REDACTED:444-453 | REDACTED:454-461 | REDACTED:572-581 | REDACTED:584-593 | REDACTED:596-605 | REDACTED:635-644 | REDACTED:647-656 | REDACTED:659-668 | REDACTED:698-707 | REDACTED:710-719 | REDACTED:722-731 | REDACTED:761-770 | REDACTED:773-782 | REDACTED:785-794 — 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 — 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 `REDACTED:422` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (5–10 lines × 4) moments/Triallele/Numerics.py:415— moments/Triallele/Numerics.py:415-424 | moments/Triallele/Numerics.py:537-546 | moments/Triallele/Numerics.py:557-561 | moments/Triallele/Numerics.py:585-589 — 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 — 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 `moments/Triallele/Numerics.py:415` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/Triallele/Numerics.py:534` calls `choose` and `moments/Triallele/Numerics.py:412` does not — 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.
Duplicated block (6–10 lines × 4) moments/LD/Matrices.py:122— moments/LD/Matrices.py:122-131 | moments/LD/Matrices.py:133-142 | moments/LD/Matrices.py:143-148 | moments/LD/Matrices.py:163-172 — 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 — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately. ★ These copies have DRIFTED, and that is worth reading before extracting anything: just before the matched lines, `moments/LD/Matrices.py:133` calls `zip` and `moments/LD/Matrices.py:143` does not — 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.
Duplicated block (8–10 lines × 2) moments/Inference.py:76— moments/Inference.py:76-83 | moments/LD/Inference.py:392-401 — the copies span different directories, so extracting a shared function means choosing where it lives: put it somewhere both call sites can already reach — a location they all depend on today, or a new shared one if there is none — and call it from each site; until then, every change has to be made twice. The `return` at the foot of the matched lines is the enclosing body's own terminal exit, not an early one: it moves with them unchanged, and each site calls the extracted unit from the position that `return` occupied — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (9 lines × 9) REDACTED:909— REDACTED:909-918 | REDACTED:924-932 | REDACTED:938-946 | REDACTED:966-976 | REDACTED:982-991 | REDACTED:997-1006 | REDACTED:1012-1021 | REDACTED:1027-1036 | REDACTED:1042-1051 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (7–9 lines × 6) moments/TwoLocus/Numerics.py:72— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (9 lines × 3) moments/LD/Matrices.py:653— moments/LD/Matrices.py:653-661 | moments/LD/Matrices.py:714-722 | moments/LD/Matrices.py:734-742 — 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 — 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 `moments/LD/Matrices.py:653` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8–9 lines × 2) moments/LD/stats_from_genotype_counts.py:1062— moments/LD/stats_from_genotype_counts.py:1062-1069 | moments/LD/stats_from_genotype_counts.py:1335-1343 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:1062` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (8 lines × 11) REDACTED:908— REDACTED:908-915 | REDACTED:923-930 | REDACTED:937-944 | REDACTED:951-958 | REDACTED:965-972 | REDACTED:981-988 | REDACTED:996-1003 | REDACTED:1011-1018 | REDACTED:1026-1033 | REDACTED:1041-1048 | REDACTED:1056-1063 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (7–8 lines × 2) moments/LD/stats_from_genotype_counts.py:842— moments/LD/stats_from_genotype_counts.py:842-849 | moments/LD/stats_from_genotype_counts.py:1281-1287 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `moments/LD/stats_from_genotype_counts.py:842` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (7 lines × 20) moments/LD/Matrices.py:651— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (7 lines × 6) moments/LD/Matrices.py:765— 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 — 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 — 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 `moments/LD/Matrices.py:765` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6–7 lines × 6) moments/LD/stats_from_genotype_counts.py:323— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:323` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 16) moments/LD/Matrices.py:707— 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 — 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 — 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 `moments/LD/Matrices.py:707` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (6 lines × 6) moments/LD/Matrices.py:539— 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 — 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 — 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 `moments/LD/Matrices.py:539` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (3–6 lines × 3) REDACTED:67— REDACTED:67-69 | REDACTED:171-176 | REDACTED:304-309 — 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 — 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 `REDACTED:171` it does not close everything it opens, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (5 lines × 14) moments/LD/Matrices.py:518— 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 — 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 — 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 `moments/LD/Matrices.py:518` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 11) moments/LD/stats_from_genotype_counts.py:155— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:453` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 9) moments/LD/Matrices.py:627— 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 — 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 — resolving only two of them leaves the rest to drift apart the first time one is edited.
Duplicated block (5 lines × 8) moments/LD/stats_from_genotype_counts.py:167— 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 — 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 — 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 `moments/LD/stats_from_genotype_counts.py:167` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Duplicated block (5 lines × 4) moments/Triallele/Numerics.py:351— moments/Triallele/Numerics.py:351-355 | moments/Triallele/Numerics.py:377-385 | moments/Triallele/Numerics.py:453-457 | moments/Triallele/Numerics.py:462-469 — 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 — 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 `moments/Triallele/Numerics.py:351` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (4–5 lines × 3) moments/Demes/Demes.py:1410— moments/Demes/Demes.py:1410-1413 | moments/Demes/Demes.py:1420-1424 | moments/Demes/Demes.py:1438-1444 — 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 — 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 `moments/Demes/Demes.py:1420` it begins part-way through the construct above it, so those exact lines cannot be lifted as they stand — 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 — the matched region ends inside that line. Extract the lines above it, and read the last line of each site separately.
Duplicated block (14–26 lines × 2) bench/report.py:39— bench/report.py:39-52 | bench/report.py:55-80 — both copies are in the same file, so extract the block into one function there and call it from each site — 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 `bench/report.py:39` it does not close everything it opens, so those exact lines cannot be lifted as they stand — widen the region to the smallest complete statement or declaration that contains it, and extract that.
Documentation: no usage examples docs/installation.rst— The installation guide is complete but there are no usage examples showing how to run the code. Add a short 'How to run it' section or a one-line command block demonstrating an example call.
Documentation: contradicts the code docs/introduction.rst— 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.
Documentation: hard to navigate docs/api/api_moments.rst— 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's purpose.
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.
D26 · Project Cohesion· Projects may be oversized for their cohesion · ×1
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 `(repository root)` (33676 LoC, 58 module-visible types across 12 directories). Review these for cohesion — 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.
D34 · Knowledge Freshness· Further orphaned files (smaller) · ×1
Further orphaned files (smaller) — 4 smaller file(s) also have no living knowledge — folded into the freshness score and metrics rather than raised one row each — 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.
No ADRs — No Architecture Decision Records found — no conventional ADR directory, no numbered `NNNN-title` 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.
M2 · Architecture documentation· No architecture diagram/doc · ×1
No architecture diagram/doc — No C4/Structurizr/PlantUML/Mermaid/Graphviz/D2 diagram, no drawn diagram named for the architecture, no file named `architecture` or `design` in any markup this check reads, and nothing in the README, docs or contributor guides that announces the shape — no `## Architecture` heading, no "architecture overview"/"high-level design" phrasing, no "the architecture is …" 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 — not evidence that nobody wrote the shape down.
No src/ separation — Production code isn't grouped under a src/ folder — it's spread across several top-level directories, so there's no one place that says 'this is the product'.
README/code drift — README advertises a RAG / ML engine, but no ML/RAG code or dependency exists — searched for: `rag`, `langchain`, `llamaindex`, `pinecone`, `weaviate`, `qdrant`, `embeddings`. 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's own prose never counts, so a claim is never refuted by merely being made. Nothing outside that search was read — 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.
No SAST — No static application security testing detected. For this repository's stack, add bandit, `semgrep --config=p/python`, or CodeQL's 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's web UI rather than in a committed file, or a tool whose name is none of those this check carries, is not seen — if that is your case the row is wrong, and saying so is more useful than adding a second scanner.
No changelog — No CHANGELOG/HISTORY/RELEASES file — what shipped when isn't easy to reconstruct for support or audit. (Versioning/tagging makes releases traceable, but a changelog records the what.)
Appendix B — Reproduction & audit trail
Every external tool invocation behind a deep-scan dimension — the tool, its captured version, the exact command, how many findings it yielded, and a link to the retained raw output. To reproduce any finding: check out the same commit and run the command shown (repo-relative — never an absolute scratch path). The complete raw scanner output is retained verbatim under artifacts/raw/ (indexed in artifacts/raw/index.json); per-invocation exit codes and wall-clock durations are in sidecar.json — kept out of this table so the rendered report stays byte-identical across runs of the same commit.
trivy: not applicable — No Infrastructure-as-Code or container manifests found (Dockerfile, Docker Compose, Terraform, Kubernetes/Helm, CloudFormation, ARM, Bicep, Ansible); nothing to scan.
semgrep: not applicable — No personal data was found crossing a boundary the PII/GDPR ruleset checks — nothing written to a log or console sink, placed in a URL or query string, or persisted to browser storage. That is a clean result for the LEAK surface only: this ruleset detects personal data escaping, it does not inventory the personal data a repository holds, so it is not evidence that this repository has no personal-data surface. The personal-data map (Appendix C) and the C1-C5 compliance cards are what speak to that.
disclosure: not applicable — No vulnerability-disclosure policy file found (SECURITY.md/.markdown/.rst/.txt at root or under .github/.forgejo/.gitea/docs, .well-known/security.txt). A coordinated-disclosure policy may live off-repo, so this is not evidenced rather than failed.
runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; network egress policy is a cluster-native control that may live at the platform/firewall layer, so there is nothing to assess here.
runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; seccomp/AppArmor/SELinux confinement is a workload-level control, so there is nothing to assess here.
runtime-hardening: not applicable — No Kubernetes/orchestration workloads found in the repository manifests; runtime threat-detection and admission-control policy are cluster-level controls, so there is nothing to assess here.
Run 01a1010f-61aa-7c22-97d4-dadbddaf325e · every finding is also locatable in findings.md, and the complete scoring record (with exit codes + durations) in sidecar.json.
Issues: 57 · Warnings: 540 · Recommendations: 14 — Appendix A · all findings · full markdown report.
Generated by Watchdog — deterministic code-health analysis. 03-10-2026 @ 09:19 UTC.
Downloadable artifacts
Machine-readable and reproducible from this commit + frozen rubric — drop them straight into a contract appendix, a CRA dossier, or a downstream SCA / VEX tool.