Public recordGood
Software health reportschema 0.23.0 · metrics 1.13.0 · 2026-07-21 20:30 UTC
pysam-developers / pysam
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
pysam-developers/pysam holds a health index of 73 out of 100, placing it in the Good band. It scores highest on Vitality (85/100) and lowest on AI Readiness (51/100). It was last updated 2 days ago. A single contributor accounts for most of its recent work.
73
overall / 100Software health index
Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At risk ceiling of 49. AI Readiness sits outside the overall score.
73
Excellent85-100Exemplary; meets essentially all checked criteria
Good70-84Healthy; minor gaps
Moderate50-69Acceptable with notable gaps; review recommended
At risk30-49Significant weaknesses; adoption warrants caution
Critical1-29Severe problems (abandoned, single-maintainer, no hygiene)
Score profile
Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.
Ownership
pysam-developersOrganization
10 followers3 public repossince Feb 2014
This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.
Package ecosystems
| Registry | Package | Version | Downloads / mo | Versions | Last publish |
|---|---|---|---|---|---|
| PyPI | pysam | 0.24.0 | 1,150,697 | 48 | 85 days ago |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
85
Development activity
86Excellent
How it's scored
| 36/36 | Push recency — last push 2 days ago |
| 22.8/36 | Commit cadence — 33/52 weeks with commits |
| 17.3/18 | Commit volume — 84 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 84 |
| human_commit_share | 1 |
| days_since_last_push | 2 |
| active_weeks_last_year | 33 |
Release discipline
84Good
How it's scored
| 27/27 | Ships releases — 41 releases published |
| 36/36 | Release recency — latest release 85 days ago |
| 12.6/27 | Release cadence — a release every ~159.1 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 41 |
| latest_release_tag | v0.24.0 |
| releases_from_tags | no |
| days_since_latest_release | 85 |
| mean_days_between_releases | 159.1 |
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.
Community & Adoption
Does the project have users, downloads, attention, and a welcoming setup for contributors?
74
Popularity & adoption
78Good
How it's scored
| 47.9/60 | Stars — 900 stars |
| 20.6/25 | Forks — 297 forks |
| 9/15 | Watchers — 42 watchers |
Inputs used
| forks | 297 |
| stars | 900 |
| watchers | 42 |
| growth_state | organic |
| growth_factor_pct | 100 |
Community health
50Moderate
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (MIT) |
| 0/18 | CONTRIBUTING guide |
| 0/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 0/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| has_contributing | no |
| has_issue_template | no |
| has_code_of_conduct | no |
| has_pull_request_template | no |
Ecosystem adoption (downloads)
100Excellent
How it's scored
| 80/80 | Monthly downloads — 1,150,697 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | pysam |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 1,150,697 |
Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
63
Maintainer resilience (bus factor)
42At risk
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 9.2/22.5 | Commit distribution — top contributor authored 59% of commits |
| 13.5/13.5 | Contributor breadth — 100 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 27 contributing companies or organizations |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 100 |
| top_contributor_share | 0.589 |
Issue & PR responsiveness
67Moderate
How it's scored
| 35.2/46.8 | Issue resolution — 75% of issues closed |
| 32/38.3 | PR acceptance — 344/411 decided PRs merged |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 1/27 approved changesets -- score normalized to 0 |
Inputs used
| merged_prs | 344 |
| open_issues | 242 |
| closed_issues | 734 |
| issue_closed_ratio | 0.752 |
| closed_unmerged_prs | 67 |
Ownership & stewardship
54Moderate
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 7.5/25 | Owner reach — 10 followers of pysam-developers |
| 16.4/25 | Track record — 3 public repos, account ~12 yr old |
Inputs used
| followers | 10 |
| owner_type | Organization |
| is_verified | — |
| owner_login | pysam-developers |
| public_repos | 3 |
| account_age_days | 4,548 |
Package maintenance
100Excellent
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 85 days ago |
| 20/20 | Version history — 48 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | pysam |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 85 |
Engineering Quality
Are baseline engineering and documentation practices in place?
81
Engineering practices
68Moderate
How it's scored
| 24/24 | CI workflows — 2 workflow(s) |
| 24/24 | Tests present |
| 0/16 | Linter config |
| 0/9.6 | Pre-commit hooks |
| 0/6.4 | .editorconfig |
| 20/20 | OpenSSF Scorecard: CI-Tests — 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | no |
| has_linter_config | no |
| has_precommit_config | no |
Documentation
100Excellent
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://pysam.readthedocs.io/en/latest/ |
| 10/10 | Repository description |
| 10/10 | Topics — 4 topics |
| 10/10 | Wiki |
Inputs used
| topics | bioinformatics, ngs, python, htslib |
| has_wiki | yes |
| homepage | https://pysam.readthedocs.io/en/latest/ |
| has_readme | yes |
| has_docs_dir | yes |
| has_description | yes |
Security
Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?
59
Security posture
49At risk
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 4.5/7.5 | Branch-Protection — branch protection is not maximal on development and all release branches |
| 2.5/2.5 | CI-Tests — 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |
| 0/2.5 | CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected |
| 0/7.5 | Code-Review — Found 1/27 approved changesets -- score normalized to 0 |
| 2.5/2.5 | Contributors — project has 27 contributing companies or organizations |
| 0/10 | Dangerous-Workflow — no data |
| 0/7.5 | Dependency-Update-Tool — no update tool detected |
| 0/5 | Fuzzing — project is not fuzzed |
| 2.5/2.5 | License — license file detected |
| 7.5/7.5 | Maintained — 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |
| 0/5 | Packaging — no data |
| 0/5 | Pinned-Dependencies — no data |
| 0/5 | SAST — SAST tool is not run on all commits -- score normalized to 0 |
| 0/5 | Security-Policy — security policy file not detected |
| 0/7.5 | Signed-Releases — no data |
| 0/7.5 | Token-Permissions — no data |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 13 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 5 |
| scorecard_aggregate | 4.9 |
Excluded from scoring (no data or not applicable): dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions. Remaining weights renormalized.
Dependency advisories
100Excellent
How it's scored
| 35/35 | Direct dependencies free of known advisories — no direct dependency carries a known advisory |
| 0/25 | Indirect dependencies free of known advisories — transitive set not separable from development and test dependencies in this scope |
| 0/40 | No advisories left outstanding — no advisory carries a publication date |
Inputs used
| source | osv |
| advisories | 0 |
| affected_packages | 0 |
| assessed_packages | 2 |
| unassessed_packages | 2 |
| affected_by_severity | none |
| direct_affected_packages | 0 |
Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 2 resolved dependencies against OSV. 2 could not be assessed — no resolved version, an unsupported ecosystem, or beyond the reported package list. This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.
AI Readiness
How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score.
51
Agent context & guidance
32At risk
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 31.5/40 | Legible commit history — 59 of 100 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | no |
| legible_history_share | 0.59 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Verify loop (build / test / typecheck)
57Moderate
How it's scored
| 18/18 | One-command bootstrap — doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile |
| 22/22 | Automated tests |
| 0/11 | Lint / format config |
| 11/11 | Static type checking — pysam/py.typed |
| 0/10 | Reproducible environment |
| 0/10 | Demonstrated agent practice — no agent-authored commits among the last 100 |
| 0/8 | Automated maintenance — no automated dependency updates observed |
| 0/10 | OpenSSF Scorecard: Pinned-Dependencies — no data |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | — |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile |
| has_devcontainer | no |
| has_linter_config | no |
| typecheck_configs | pysam/py.typed |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.
How it's scored
| 27/45 | Type-checkable code — Cython with type-check config (pysam/py.typed) |
| 48.3/55 | Manageable file sizes — 56/458 source files over 60KB |
Inputs used
| primary_language | Cython |
| largest_source_bytes | 230,215 |
| source_files_sampled | 458 |
| oversized_source_files | 56 |
Key facts
900GitHub stars
100contributors
84commits, last 12 months
2days since last push
41releases
1bus factor
242open issues
PyPIpackage ecosystems
Data collection warnings
- Could not fetch pypi package 'pysam.libchtslib' from its registry
More detail
Star and fork history 900 ★ / 297 ⇿
900Stars
297Forks
41Releases
When each star and fork was added, collected from GitHub and bucketed by day. Cumulative growth sits directly above the daily additions it is made of, so the two read against each other: steady organic accretion looks nothing like an abrupt, short-lived burst. Where that difference is measurable, it is reported as growth authenticity.
Major 0Minor 15Patch 17
Each point covers 12 days.
OpenSSF Scorecard 4.9 / 10
4.9aggregate
Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).
| 10 | Binary-Artifacts | no binaries found in the repo |
| 6 | Branch-Protection | branch protection is not maximal on development and all release branches |
| 10 | CI-Tests | 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |
| 0 | CII-Best-Practices | no effort to earn an OpenSSF best practices badge detected |
| 0 | Code-Review | Found 1/27 approved changesets -- score normalized to 0 |
| 10 | Contributors | project has 27 contributing companies or organizations |
| n/a | Dangerous-Workflow | no workflows found |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |
| n/a | Packaging | packaging workflow not detected |
| n/a | Pinned-Dependencies | no dependencies found |
| 0 | SAST | SAST tool is not run on all commits -- score normalized to 0 |
| 0 | Security-Policy | security policy file not detected |
| n/a | Signed-Releases | no releases found |
| n/a | Token-Permissions | No tokens found |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
All dependencies 4
Full resolved dependency set from the GitHub dependency graph: 0 direct and 4 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | cython | — | indirect |
| PyPI | setuptools | — | indirect |
| PyPI | sphinx | 8.2.3 | indirect |
| PyPI | sphinx-rtd-theme | 3.0.2 | indirect |
Dependency advisories 0
This repository publishes no package the index resolves, so its own dependency graph was assessed — 2 packages, which also include development and test pins that never ship: 0 carry known advisories, of which 0 are direct. 2 could not be assessed — no resolved version, an unsupported ecosystem, or beyond the reported package list.
No known advisories affect the assessed dependencies.
An advisory means the version recorded in the dependency graph falls inside an advisory’s affected range. Reachability is not analysed, and the graph includes development and test pins — a finding may concern tooling rather than shipped software.
Raw JSON report machine-readable
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"headline": "Adjust some linter trivia (mostly whitespace and formatting)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-13T11:06:17Z",
"body_truncated": false,
"is_coding_agent": false
},
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"oid": "ea541d7ce72591bb44e7e8c921111712f2445511",
"body": "Use plain `assert`. Don't subclass unitest.TestCase (hence use\nsetup_method/teardown_method instead of setUp/tearDown) and ensure\ntest class names match /^Test/. Remove __main__.\n\nConvert linking_test.py et al, but note that these tests haven't worked for\nquite some time, due at least in part to increasing setuptools strictness.",
"is_bot": false,
"headline": "Convert tests to be natively pytest-based",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-13T11:05:56Z",
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"oid": "bd1c78fec84a97b6e29d1c9852dc023545f756c8",
"body": "This appears to be another instance of #1151, crashing on NetBSD when run\nvia pytest (but passing when run under unittest!). And it turns out that\ntestIteratorOutOfScope() crashes only on exactly Python 3.11 (so far) and\nalso on NetBSD.\n\nNonetheless both tests are flaky tests of flaky behaviour, which is what\nshould really be fixed.",
"is_bot": false,
"headline": "Suppress testAccessOnClosedIterator() on NetBSD, where it crashes",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-13T10:18:33Z",
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"body": null,
"is_bot": false,
"headline": "Adjust for FreeBSD image moving to Python 3.12",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-13T07:23:15Z",
"body_truncated": false,
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"body": null,
"is_bot": false,
"headline": "Adjust some linter trivia (mostly whitespace and formatting)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-12T05:35:52Z",
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"body": null,
"is_bot": false,
"headline": "Re-enable these tests on macOS as segfaults are now in the distant past",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-08T07:04:32Z",
"body_truncated": false,
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"body": null,
"is_bot": false,
"headline": "Introduce slurp_file() and use it to refactor check_lines_equal()",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-01T06:57:04Z",
"body_truncated": false,
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},
{
"oid": "8c28afbb020f10392a2ce92b1e9105807e38e97a",
"body": null,
"is_bot": false,
"headline": "Refactor checkFieldEqual() to compare fields directly in inline asserts",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-01T06:57:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e0a2c4b936d7230afc9eeeaaee6e1ba9fdf81535",
"body": "… years",
"is_bot": false,
"headline": "Remove TestRemoteFileFTP test cases, which have been disabled for 10+…",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-07-01T06:57:04Z",
"body_truncated": false,
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},
{
"oid": "1f32fb4deca38a601d8e3f9b73f8a0d64966b0d2",
"body": "Specify needed permissions and persist repo credentials only if necessary.\nUpdate setup-miniconda to a node24-based version. `${{ matrix.arch }}` is\nnot particularly attackable, but move it to an environment variable anyway.",
"is_bot": false,
"headline": "Apply basic GitHub Actions workflow hardening",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-06-28T08:34:12Z",
"body_truncated": false,
"is_coding_agent": false
},
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"oid": "ebabcd8a376b850fa807852cef22deee92033e9a",
"body": "There's no real need to test with invalid headers. In fact this would\nneed to be escaped for both CRAM and SAM: test_SAM() only worked because\nit was run after test_CRAM(), which inadvertently altered self.header too.\nRunning with `pytest -k test_SAM tests/AlignmentFileHeader_test.py`\npreviously failed.",
"is_bot": false,
"headline": "Remove invalid SAM header TAB character from test case",
"author_name": "John Marshall",
"author_login": "jmarshall",
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},
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"oid": "30542fae25dad67e8d80e4057b6957984c3f258d",
"body": "Add `= ...` to `Literal[False]` and `bool` throughout, so that omitted\narguments select the same return type as an explicit False argument.\nWe must also add `= ...` to any following `Literal[True]` arguments\nfor syntactic reasons, but happily these will never match an omitted\nargument as such overlo\n[…]\nalse] = ...` which will also match and be chosen by\ntype checkers.\n\nAdd `ignore[overload-overlap]` as needed now that the overloads are\nno long disjoint.\n\nHat tip @gshiba. Supersedes and closes #1371.",
"is_bot": false,
"headline": "Further improve AlignedSegment.get_aligned_pairs() type hints",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-06-23T07:52:09Z",
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"body": "…411)",
"is_bot": false,
"headline": "Merge PyUnicode-API-based str-returning method implementations (PR #1…",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-06-22T20:36:46Z",
"body_truncated": false,
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},
{
"oid": "1b17d8ae898d7f1a826dc7309245303fe4fd7eb1",
"body": "Simplify update_bin() as bam_endpos() handles unmapped reads etc itself.\n\nRecode infer_query_length() to just use bam_cigar2qlen().\n\nSet up CIGAR_OP_CONSUMES_QUERY_OR_HARDCLIP that works like bam_cigar_type()\nbut also includes BAM_CHARD_CLIP as a query-consuming CIGAR operator, and\nrecode infer_read\n[…]\nength() to use it. Remove previous helper routines.\n\nRemove unused variables.\n\nHat tip @nh13 for identifying the refactoring opportunities. Supersedes and\ncloses #1382, closes #1383, and closes #1388.",
"is_bot": false,
"headline": "Refactor update_bin(), infer_query_length(), and infer_read_length()",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-06-03T09:45:06Z",
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"body": null,
"is_bot": false,
"headline": "Add Python 3.15 beta to CI testing",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-06-03T09:30:17Z",
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},
{
"oid": "11c1560cbfdb0b9886524e0a4b5e4b1bcce31ebc",
"body": "Allow anything that can be coerced to a writable bytes memory view,\nthough possibly that is just bytearray anyway.",
"is_bot": false,
"headline": "Relax reverse_complement_inplace() argument type",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-29T07:55:15Z",
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"oid": "07801ea5bb82fd84b33678705d5bcff4f13a3d84",
"body": "Also optimise it to unpack high and low nibbles explicitly.",
"is_bot": false,
"headline": "Recode getSequenceInRange() to return str directly",
"author_name": "John Marshall",
"author_login": "jmarshall",
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},
{
"oid": "662641554f6d3bb4bd90c266e792b38b1baebe5f",
"body": "This code wants the SEQ bases as bytes rather than str. Recode it to\nunpack each base individually instead, as get_query_sequences() does.\n\nThere is only one caller of build_alignment_sequence() and that raises\nValueError if it returns None. Instead raise ValueError here directly\nso we can provide a\n[…]\nand check SEQ length.\nRemove src==NULL check as by construction this is never NULL (and\nother methods don't check src). Check all _delegate/src initialisations\nso that this statement is actually true.",
"is_bot": false,
"headline": "Recode the one getSequenceInRange() call that actually wants bytes",
"author_name": "John Marshall",
"author_login": "jmarshall",
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},
{
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"body": "Historically we set REF_PATH=: when running pytest to speed up the tests\nby preventing remote reference lookups. Now that we use HTSlib >=1.22,\nthis may be less necessary. This moves sanitising REF_PATH inside pytest\nand will still be useful if users *do* have it set themselves.\n\n(Probably having side-effects inside pytest_report_header() is a bit of\na hack, but the warning is useful and adding an autouse fixture alongside\njust to set REF_PATH would be tedious.)",
"is_bot": false,
"headline": "Set REF_PATH=: automatically during pytest initialisation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-22T11:25:12Z",
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{
"oid": "042f59e3d8176999eb065d68d01e28d9d46e7d0a",
"body": null,
"is_bot": false,
"headline": "Update to cross-platform-actions/action v1.1-style usage",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-20T10:39:41Z",
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"body": null,
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"headline": "Build the documentation on a subset of CI configurations",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-14T10:07:33Z",
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},
{
"oid": "d7315358ab2a1cee2c5c3db6eca757197aeb3060",
"body": null,
"is_bot": false,
"headline": "Add pysam.reverse_complement_inplace() utility function",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-14T08:55:57Z",
"body_truncated": false,
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},
{
"oid": "e8b08a71d0e0f8ec6072c92e194c0c1debeccee1",
"body": "Implement it via low-level code for str, bytes, and int.\nA small script was used to generate pysam_seq_comp_table:\n\n import pysam\n iupac = \"=ACMGRSVTWYHKDBN\"\n for c in range(256):\n\tif c % 16 == 0: print(\"\\n \", end='')\n\tbase = chr(c).upper()\n\tif base == 'U': base = 'T'\n\tif (b := iupac.find\n[…]\nomplement(b)]\n\t if chr(c).islower(): comp = comp.lower()\n\t print(f\" '{comp}', \", end='')\n\telse:\n\t print(f\" 0x{c:02x},\", end='')\n\nUse the new function in AlignedSegment.get_forward_sequence().",
"is_bot": false,
"headline": "Add pysam.reverse_complement() utility function",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-13T11:52:50Z",
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"oid": "aadf7dc2354546ba82c0f19b9a5cb945ce7dc7f6",
"body": null,
"is_bot": false,
"headline": "Rename tests with duplicate names",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-12T09:21:15Z",
"body_truncated": false,
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},
{
"oid": "c3d8be192dd70e40bc8936b5435951750684e268",
"body": "I originally wrote these tests as pytest but recoded them to fit in with\nthe rest of AlignedSegment_test.py. But the new intention is to move the\ntestsuite as a whole towards being pytest-native and using fixtures more.",
"is_bot": false,
"headline": "Parametrise tests by recoding against the pytest API",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-12T09:04:37Z",
"body_truncated": false,
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},
{
"oid": "2baef1602eb2606615386766b2f73812892ef330",
"body": null,
"is_bot": false,
"headline": "Belated happy new year",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-10T08:32:12Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "11dea5e656ca2806e0f83436a5c56d0bcfb25634",
"body": "…ties\n\nPyUnicode_MAX_CHAR_VALUE() is not declared by Cython's cpython/unicode.pxd\nso these wrappers around PyUnicode_New() encapsulate its use.",
"is_bot": false,
"headline": "Add PysamUnicode_NewClone() and PysamUnicode_NewCloneWithSize() utili…",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-10T04:09:31Z",
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},
{
"oid": "3fcfcf28f5125a9c2830bdf0d09f7decfb7e04fe",
"body": null,
"is_bot": false,
"headline": "Remove unused cpython imports, and cimport from approriate sub-modules",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-10T03:23:15Z",
"body_truncated": false,
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},
{
"oid": "4c612926d36d6f5209e9f1114f0e6346ce10156d",
"body": "AlignmentFile has bespoke code for file descriptors et al, but in fact\nVariantFile also supports them due to HTSFile._open_htsfile()'s special\nhandling. Fixes #1406.\n\nAdd test cases exercising all possibilities for AlignmentFile and\nVariantFile filenames. Only check .closed if the property exists.",
"is_bot": false,
"headline": "Fix VariantFile type hints to allow file descriptors",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-08T08:26:13Z",
"body_truncated": false,
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},
{
"oid": "d1c86903e38431dfcf15cde1c52dcc457004ed79",
"body": "These should have been removed when `sys.version_info` was removed\nwhen we dropped Python 3.8.",
"is_bot": false,
"headline": "Remove now-unused imports etc from stub files",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-08T05:52:38Z",
"body_truncated": false,
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},
{
"oid": "2bf94ad19fe771f73df3345231bb0953b96caec2",
"body": "Sadly Cirrus CI will soon shut down. Instead test BSD on GitHub Actions\nunder emulation via cross-platform-actions/action. This has x86-64 running\non x86-64, so performs about as well as the native jobs.\n\nOn FreeBSD, we need to add /usr/local/include to the search path for\nlibcurl headers to be found. NetBSD Python's sysconfig.CFLAGS uses -I\nfor its system header directories, but we don't want those to override\npysam's own -I options so we downgrade them to -isystem.",
"is_bot": false,
"headline": "Migrate FreeBSD CI to GH actions, and add NetBSD",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-05-07T05:47:36Z",
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},
{
"oid": "38b94a847cb7adca3eea49f910662e8b7b212334",
"body": null,
"is_bot": false,
"headline": "Bump version number to 0.24.0 and add release notes",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T11:51:56Z",
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},
{
"oid": "7067acf8097224fc3266e368b387edd210261007",
"body": null,
"is_bot": false,
"headline": "The Profiling section should not be a subsection of PyPI installation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T11:49:36Z",
"body_truncated": false,
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},
{
"oid": "0d39f2ffd077f3fe4a650a5102873035cb518547",
"body": null,
"is_bot": false,
"headline": "The htslib.org website has not been updated for this point release",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T10:02:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "09c3dc6b68b3111632f09eec3ce2744d346f8f90",
"body": null,
"is_bot": false,
"headline": "Move the VCF/BCF documentation up alongside SAM/BAM/CRAM",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T08:59:29Z",
"body_truncated": false,
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},
{
"oid": "3f2aaf8e9eb20249745d012e77fb08d41328c235",
"body": null,
"is_bot": false,
"headline": "Rearrange Variant* class documentation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T08:33:43Z",
"body_truncated": false,
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},
{
"oid": "8a96ea0b91bb7327748cef5b7860631ed1de398f",
"body": null,
"is_bot": false,
"headline": "Further clarify VariantRecord properties documentation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-27T02:46:54Z",
"body_truncated": false,
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},
{
"oid": "8a9f7f8dd0aefdafb96262c4bdb4bd68d32ec2c7",
"body": "The filenames should also take pathlib.Path; VariantFile does not currently\nsupport file descriptors. HTSlib modes can include comma-separated format\noptions, so Literal is too limited and we should (TODO) remove pysam's\nruntime restrictions on this argument. Fixes #1405.",
"is_bot": false,
"headline": "Correct the AlignmentFile/VariantFile filename/mode type hints",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-26T07:05:38Z",
"body_truncated": false,
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},
{
"oid": "9aa4d1a1cd6eee0483c8f1fc45479f83705a3cdb",
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"is_bot": false,
"headline": "Add documentation for all VariantHeader-related classes (PR #1394)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-04-25T22:36:58Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "48688fc3f4e2b7f58c1cdf250a2097833d142e87",
"body": "The data is contiguous so we can use [::1] to omit stride calculations.\nUsing explicit memoryviews rather than the previous array indexing code \nleads to a 100x speedup within this function.",
"is_bot": false,
"headline": "Use memoryviews to optimize array_to_qualitystring (PR #1363)",
"author_name": "Josh Chorlton",
"author_login": "jchorl",
"committed_at": "2026-04-17T10:08:11Z",
"body_truncated": false,
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},
{
"oid": "d12398616afaa3ca4f2ad86592dcabba74a4b1b0",
"body": null,
"is_bot": false,
"headline": "Add VariantContig and VariantMetadata documentation (PR #1361)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-04-12T12:49:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6aa975c485a2678d99c685698b6c53981c15eeb6",
"body": "Fixes #882; fixes #1368.",
"is_bot": false,
"headline": "Add documentation for all VariantRecord-related classes (PR #1359)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-04-12T01:27:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "427650a8bf5ff38eb6d035f8085d0e488df9ec67",
"body": null,
"is_bot": false,
"headline": "Adjust for FreeBSD py311-cython package name change",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-07T12:27:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7f508219393604218fab9b5e54715d9401bd339c",
"body": "Also remove setup-miniconda's unnecessary auto-activate-base override.",
"is_bot": false,
"headline": "Update to node24-based GitHub Actions",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-07T11:48:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a91efe36089dcdc1b2eebee2916643d68499cab6",
"body": "Mypy 1.20.0 was released today and reports types such as int\nas \"int\" rather than \"builtins.int\" as in previous versions.",
"is_bot": false,
"headline": "Handle mypy 1.20.0's changed output in typechecking testcases",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-01T10:54:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ec689af1918406185773b5a2cdf3645f6317ff6f",
"body": null,
"is_bot": false,
"headline": "Reformat get_tag() documentation to our usual NumPy style and tidy up",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-04-01T08:23:38Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "32752e938adc67c86d9f29c8d7b5c22ed6f3b151",
"body": "Apply similar changes as made previously to VariantRecordSample.update().",
"is_bot": false,
"headline": "Fix other update() methods with iterables and keyword args only",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-31T10:47:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ce2242855f83fdc8d57ee6033c46153e65fa46a4",
"body": "Add documentation for the class and its methods.\nFixes #407; fixes #720.",
"is_bot": false,
"headline": "Add VariantRecordSample documentation (PR #1358)",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2026-03-31T09:15:16Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0f5a36a157f412d7ad943c7fdc148d14c2dc342a",
"body": "This is documented as accepting an iterable or solely keyword arguments,\nso check before using `items.items()`. Changing the default argument value\ncauses changes only within pysam/libcbcf.c, so has no ABI implications.",
"is_bot": false,
"headline": "Fix VariantRecordSample.update() with iterables and keyword args only",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-31T07:29:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2a3911171f3c6b3b4d907566cf0380edc77e7b62",
"body": "Link from the AlignmentFile(format_options) and HTSFile.add_hts_options()\nentries. Bring the AlignmentFile constructor signature docstring uptodate.",
"is_bot": false,
"headline": "Add link to samtools --input/output-fmt-option keyword documentation",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-25T12:45:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a417ba16ef7c4bcb4bc08db86c6653a859388e65",
"body": "Add force_bytes() to convert the input str to bytes as hts_opt_add()\nis expecting.\n\nSimplify the function's signature by making format_options non-optional:\nthere is no point calling this function without specifying format_options,\nand [] is a more suitable no-op.\n\nSimplify the function's implementation by using `finally` for cleanup.\n(Both hts_opt_free() and hts_opt_apply() accept NULL as a no-op.)\nRaise ValueError rather than the more generic RuntimeError.",
"is_bot": false,
"headline": "Fix HTSFile.add_hts_options() str vs bytes handling",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-24T11:38:09Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4c50e83be0e787fe0c3dd179cc6dd4c32de50e75",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.23.1\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.23.1\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.23.1\n\nTake care to preserve these additional manual changes:\n\n* remov\n[…]\nom htslib/Makefile\n* the wheel-building PKI workaround in htslib/hfile_libcurl.c\n* the #define additions to bcftools/regidx.h\n\nand don't bother adding {sam,bcf}tools/htslib-1.23.1/{LICENSE,**/README}.",
"is_bot": false,
"headline": "Import upstream htslib/samtools/bcftools 1.23.1",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-19T07:00:23Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "54f3d41f380f095e8bfb16fd430b00fe02fb5063",
"body": "Regularise pysam/*.pyx directives to include `language_level=3` and exclude\n`profile=True`. Reactivate profiling if a PYSAM_PROFILE environment variable\nis set to a true value for both sdist and build_ext commands. Fixes #1350.\n\n(We could set `force` if PYSAM_PROFILE is set differently from the previous\nbuild, but it seems better to leave that to Cython's build_ext and require\nclean_ext when changing settings.)",
"is_bot": false,
"headline": "Update cython directives, turning profiling off by default",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-15T08:52:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e03c4e31dc8b6d2d3f1c81e3b666b4bf4f2a4dc7",
"body": "… HACK]\n\nLinux wheels are (currently) built on AlmaLinux, so the libcurl.so\nbundled into the wheel follows Alma/Red Hat/Fedora conventions for the\nlocation of its certificate bundle. This fails when the wheel is used on\na Debian/Ubuntu platform with a different convention for this location.\nWhen not\n[…]\nbian bundle location if the Red Hat one isn't present.\n\nReinstates b18dde87, which was inadvertently removed when importing 1.22.\nTake more care to preserve this patch when importing HTSlib in future!",
"is_bot": false,
"headline": "Fix wheels' bundled libcurl.so incompatibility with Debian [REINSTATE…",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-03-09T07:36:03Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "79293854c45889bedef09491ee7d20de3dbc76a6",
"body": null,
"is_bot": false,
"headline": "Update cibuildwheel and use the new GH Actions case() function",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-01-31T06:04:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b7bf2cf7cb5e5263863d444223c63c150ec75eb2",
"body": null,
"is_bot": false,
"headline": "Update imports to htslib/samtools/bcftools 1.23 (PR #1372)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-01-12T07:31:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0a1997ea122541e6f00cc32f1dfa16a8fe42a820",
"body": "Remove pkg_resources, which is deprecated and slated for removal soon:\n_get_egg_name() has been unused since 2017 anyway.\n\nTake Extension from setuptools instead of distutils.\n\nUse sysconfig.get_config_var[s]() instead of distutils's wrappers.\nOverride LDSHARED properly in cy_build_ext.run() instead\n[…]\nig's own config_vars.\n\nThis linker_tests/link_pre_489/* test is unused anyway, and is present\nin the codebase for reference only. All of linker_tests/* deserves an\noverhaul; see also PR #489 and #503.",
"is_bot": false,
"headline": "Apply setup.py's modernisation to (unused) linker_tests/link_pre_489",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2026-01-11T09:34:39Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "0e05d9456fbd22432fa929b844eab7e442a0b992",
"body": "This symbol check is intended for detecting duplicate *pysam* symbols.\nIgnore any __pyx_* etc symbols, not just the particular function that\nCython 3.1.2 inadvertently left non-static, in case similar mistakes\noccur again in future.\n\nRemove the `License :: OSI Approved` classifier; License classifiers\nare apparently deprecated and cause warnings with recent setuptools.",
"is_bot": false,
"headline": "Generalise workaround for non-static Cython internal symbols",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-24T10:37:53Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "da8e5fee23ef9b30a3808fd331deb81d2281073c",
"body": "No longer need to be miserly with macOS actions runners, but continue to\nsuppress 3.8 to avoid a spurious error annotation. Update Python versions\nused for sdist and conda CI tests, and use newish setup-miniconda facility\nto suppress the defaults channel and avoid another annotation.\n\nBuild the release sdist on the latest Python release.",
"is_bot": false,
"headline": "Add Python 3.14 to CI and test most Python versions on macOS",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T18:22:49Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ac06a2152046806ed12c1d7e73ad728ac85b80eb",
"body": null,
"is_bot": false,
"headline": "Update pysam/libchtslib.pxd to HTSlib 1.23 htslib/*.h declarations",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T10:23:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "24c2b31cdbebd190f0bf36026e05015d2cf0a720",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.23\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.23\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.23\n\nTake care to preserve the #define additions to bcftools/regidx.h.\n(Don't bother adding {sam,bcf}tools/htslib-1.23/{LICENSE,**/README}.)\n\nAlso take care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
"is_bot": false,
"headline": "Import upstream htslib/samtools/bcftools 1.23",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T10:18:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "30475d23723df8ff19df6a20df1996d57df496bd",
"body": null,
"is_bot": false,
"headline": "Update Cirrus FreeBSD image (freebsd-14-2 is no longer available on GCP)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-12-18T09:33:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "caf56b2617472243e9a64a81de1a7f6846247703",
"body": null,
"is_bot": false,
"headline": "Update imports to htslib/samtools 1.22.1 and bcftools 1.22 (PR #1343)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-25T09:36:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3db05f9e7e8be9718cd8008af012010fba65f4c8",
"body": "Add Python 3.14 to release workflows and update cibuildwheel to a release\nthat uses 3.14-final. Use the new macos-15-intel image instead of macos-13,\nwhich is obsolete.\n\nReorganise the build matrix to separate the manylinux and musllinux jobs\nso they run in parallel.\n\nMove all wheel building to GitH\n[…]\ne's\ndefault Python can no longer run current cibuildwheel (which requires 3.11),\nso it is time to move the ARM wheels to be built on GitHub Actions, now that\nthat supports both Linux and macOS on ARM.",
"is_bot": false,
"headline": "Update release workflows for Python 3.14, Intel macOS runner, etc",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-22T06:04:37Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "d6fbe29d51049cee8adc23059f82885c01cb3ac5",
"body": "Store the output of `force_bytes(stdout_f)` in a live object to ensure\nit is not garbage-collected before it is used within samtools_dispatch().\nThis fixes a test failure on i386 (SamtoolsTest/PysamTest for calmd).",
"is_bot": false,
"headline": "Ensure stdout filename object is not garbage-collected while in use in C",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-17T05:41:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "23d81183ad9c00467bdafbb359abffada5797f15",
"body": null,
"is_bot": false,
"headline": "Update pysam/libchtslib.pxd to HTSlib 1.22.1 htslib/*.h declarations",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-15T07:23:17Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1de219ab4a66ee35e485e47e78ed659a6069bad7",
"body": "These tests fail on e.g. i386 because scalar types and layout differ\non this platform. Restrict the tests to run only on the common 64-bit\nplatforms -- we care mostly about incompatibilities on these platforms,\nand failures here will be generally indicative anyway. Fixes #1367.",
"is_bot": false,
"headline": "Run class size tests only on aarch64 and x86_64",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-14T22:50:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c4c0f8d5d50f8b8ed2ab39353029f480d0b7de17",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.22.1\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.22.1\n\nTake care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
"is_bot": false,
"headline": "Import upstream htslib/samtools 1.22.1",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:54:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1190ab7e0c22a5fa63bcacd2f995a165b63c90ec",
"body": null,
"is_bot": false,
"headline": "Add new `samtools checksum` command",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:32:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a4a502880718b28a23ef999310933410cb360959",
"body": "For each package:\n\nrm -rf htslib; python3 devtools/import.py htslib .../htslib-1.22\nrm -rf samtools; python3 devtools/import.py samtools .../samtools-1.22\nrm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.22\n\nTake care to preserve the #define additions to bcftools/regidx.h.\n(Don't bother adding {sam,bcf}tools/htslib-1.22/{LICENSE,**/README}.)\n\nAlso take care to preserve removing the regeneration of htscodecs.mk\nfrom htslib/Makefile.",
"is_bot": false,
"headline": "Import upstream htslib/samtools/bcftools 1.22",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:32:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "345625eb43bc3974c671f78a0097294a523053d3",
"body": "Omit the htslib/ref_cache/ source code, and hard-code a configure\n--disable-ref-cache argument accordingly.\n\nBCFtools's mpileup2/* is currently used only by plugins/vrfs.c which\nwe don't wrap, so we can (for now) omit this mpileup2/* code too.",
"is_bot": false,
"headline": "Don't import ref_cache/ external tool source code or mpileup2/*.[ch]",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-08T04:32:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "bbad7c553341b63cace60bce0302e30094a2d7a7",
"body": null,
"is_bot": false,
"headline": "Update common GitHub Actions to their Node24-based versions",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-11-07T10:08:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6a78ccad576ae5b973998a9b25a0b8f84623b0eb",
"body": "These operate by adjusting for clipping, so when there is no CIGAR there\nis no adjustment from 0 and query_length. Documentation fixes #1319.",
"is_bot": false,
"headline": "Clarify query_alignment_start/_end/_length values for unmapped reads",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-16T07:09:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b59a459cfac40f74451ca4f5b29665057f159646",
"body": "Use bam_mods_recorded() to query how many mods may be returned\nby bam_next_basemod() and allocate accordingly. Fixes #1348.",
"is_bot": false,
"headline": "Remove AlignedSegment.modified_bases's limit on number of mods",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-12T02:38:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "529ec4289c628294c5cfbfc870d824d8861b16e5",
"body": "Cython 3.0 was released two years ago and is now available in the system\npackage repositories of all major distributions as well as via pip etc.\n\nThe `globals().update(getattr(CIGAR_OPS, \"__members__\"))` work-around for\nCython 3.1.0's non-global enumerator behaviour change in fact does not work\nwith Cython 0.x so 3.x is already required for pysam.",
"is_bot": false,
"headline": "Require Cython 3.x",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-12T02:21:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ea43c089e572ecbe914aa29fafb27c5fac2877bf",
"body": null,
"is_bot": false,
"headline": "Merge pysam/libchtslib.pxd declaration updates (PR #1362)",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-12T02:03:24Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4f45505aed209254ccd8b0e5279de1416501f2f9",
"body": "Use the full form of source_suffix, which has long been supported,\nas the simple form produces a warning with recent Sphinx versions.",
"is_bot": false,
"headline": "Update to current Sphinx and ReadTheDocs theme",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-10-08T10:03:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4c563185e8708a6691b413d7fc937ee75a157e03",
"body": "We intend to make these structs opaque in future: their fields are\npresent in the C declarations for implementation reasons but should\nnot be used by user code, so there is no reason why the corresponding\nCython declarations should not be as incomplete structs.\n\nCython needs named types for some fields that can be anonymous structs\nin C. Rename some of these pysam-local structs so that they follow\nhts_opt_val_union's pattern and avoid polluting the namespace.",
"is_bot": false,
"headline": "Deprecate future opaque structs and rename member structs/unions",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-09-27T09:29:23Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c7d83cba39e86ade79994ce44e42ee2eefd99000",
"body": "Some BGZF, htsFile, hts_itr_t, and sam_hdr_t struct fields are omitted\nfrom these Cython declarations. This commit updates the types of existing\nfields but generally does not add new or previously omitted fields, as we\naim in future to make these structs (and some others) properly opaque.\n\nMark depr\n[…]\nmay be removed\nat a later date.\n\nFix bam_cigar_gen() arguments (`l` is the length) and use `int` for\nCIGAR opcodes in these functions.\n\nExpose only the HTSlib 1.12+ cram_block_method enumerator items.",
"is_bot": false,
"headline": "Update pysam/libchtslib.pxd to HTSlib 1.21 htslib/*.h declarations",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-09-26T09:48:45Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "2f9d50dde8eea7ddcdb643dcde0a088380f4549a",
"body": null,
"is_bot": false,
"headline": "Minor documentation wordsmithing and alphabetising [trivial]",
"author_name": "Tim Dunn",
"author_login": "TimD1",
"committed_at": "2025-09-18T20:16:23Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5ac440fa55179133d55c3f3251e9fa82ac378873",
"body": "We need to search /usr/local/include to find curl/curl.h etc.\nHowever it needs to be searched AFTER ./htslib et al so that pysam\nis compiled against headers from ./htslib/htslib/*.h rather than\nany system-installed HTSlib headers in /usr/local/include.",
"is_bot": false,
"headline": "Ensure -I./htslib takes priority over /usr/local/include",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-09-15T11:52:48Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "94b24cb3d9abf278d7e54e59c89a392807f14926",
"body": "Add `const`; apply bam_hdr_t to sam_hdr_t renaming; rewrite most SAM_hdr\ntypedef usage; use samFile typedef; use array parameter forms.",
"is_bot": false,
"headline": "Apply trivial differences w.r.t. htslib/*.h declarations",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-09-04T09:45:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "bfa5a41a2e1f226c91ecb2baa63b9f1f0881582a",
"body": "Prevents \"Casting a GIL-requiring function into a nogil function\" warnings.",
"is_bot": false,
"headline": "Mark callback functions used from C as nogil and (mostly) noexcept",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-08-26T07:31:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "89380af7c06118a91ad48065d6fbfd2c3627679b",
"body": "…ormat",
"is_bot": false,
"headline": "Use hts_get_format() accessor instead of directly accessing htsFile.f…",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-08-23T11:25:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8354e1213325132e9bf39363aa1ec2ee5a634eaf",
"body": "…b/*.h",
"is_bot": false,
"headline": "Reorder existing declarations similarly to upcoming import from htsli…",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-07-27T11:09:29Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c479b720e7ed1bb6e9a59d61555d14385d3a4101",
"body": "Keep hfile.h, bgzf.h, hts.h, sam.h first as other headers require types\ndeclared therein, but alphabetise the remaining header sections.",
"is_bot": false,
"headline": "Reorder cram.h alphabetically within pysam/libchtslib.pxd sections",
"author_name": "John Marshall",
"author_login": "jmarshall",
"committed_at": "2025-07-03T06:57:12Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "34e36247c2f5c1cc0ceef0f866009b70541809ea",
"body": "Tidy up whitepace, canonicalise pointer declarations as `int *p`,\nreformat onto a single line where appropriate. Fix `bed` typos\nfor `beg`, spell out parameter names as per htslib/*.h declarations.\n\nPrefix struct/union/enum with cdef or ctypedef as appropriate.\nThis PyFile_AsFile declaration from Python.h is long-since unused.",
"is_bot": false,
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}
],
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{
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"detail": "33/52 weeks with commits",
"points": 22.8,
"status": "partial",
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}
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{
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"points": 10,
"status": "met",
"details": [],
"max_points": 10
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]
},
{
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"notes": [
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"code": "excluded_no_data",
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},
{
"code": "weights_renormalized",
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}
],
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"inputs": {
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"latest_release_tag": "v0.24.0",
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"days_since_latest_release": 85,
"mean_days_between_releases": 159.1
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"components": [
{
"key": "ships_releases",
"name": "Ships releases",
"detail": "41 releases published",
"points": 27,
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"code": "releases_published",
"params": {
"count": 41
}
}
],
"max_points": 27
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{
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"detail": "latest release 85 days ago",
"points": 36,
"status": "met",
"details": [
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],
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{
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"points": 12.6,
"status": "partial",
"details": [
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"code": "release_cadence",
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]
},
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"note": null,
"notes": [],
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"inputs": {
"cap": null,
"state": "maintained",
"guards": [],
"signals": [],
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"multiplier_pct": 100,
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"days_since_last_human_commit_is_floor": false
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"code": "abandonment_maintained",
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}
],
"max_points": 100
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]
}
],
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},
{
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"name": "Community & Adoption",
"value": 74,
"weight": 0.18,
"metrics": [
{
"key": "popularity",
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"name": "Popularity & adoption",
"note": null,
"notes": [],
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"inputs": {
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"stars": 900,
"watchers": 42,
"growth_state": "organic",
"growth_factor_pct": 100
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"components": [
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"name": "Stars",
"detail": "900 stars",
"points": 47.9,
"status": "partial",
"details": [
{
"code": "stars",
"params": {
"count": 900
}
}
],
"max_points": 60
},
{
"key": "forks",
"name": "Forks",
"detail": "297 forks",
"points": 20.6,
"status": "partial",
"details": [
{
"code": "forks",
"params": {
"count": 297
}
}
],
"max_points": 25
},
{
"key": "watchers",
"name": "Watchers",
"detail": "42 watchers",
"points": 9,
"status": "partial",
"details": [
{
"code": "watchers",
"params": {
"count": 42
}
}
],
"max_points": 15
}
]
},
{
"key": "community_health",
"band": "moderate",
"name": "Community health",
"note": null,
"notes": [],
"value": 50,
"inputs": {
"has_readme": true,
"has_license": true,
"has_contributing": false,
"has_issue_template": false,
"has_code_of_conduct": false,
"has_pull_request_template": false
},
"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 22.5,
"status": "met",
"details": [],
"max_points": 22.5
},
{
"key": "license",
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"detail": "recognized license (MIT)",
"points": 22.5,
"status": "met",
"details": [
{
"code": "license_standard",
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},
{
"code": "license_spdx",
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}
],
"max_points": 22.5
},
{
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"points": 0,
"status": "missed",
"details": [],
"max_points": 18
},
{
"key": "code_of_conduct",
"name": "Code of conduct",
"detail": null,
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"status": "missed",
"details": [],
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},
{
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"points": 0,
"status": "missed",
"details": [],
"max_points": 7.2
},
{
"key": "pr_template",
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"points": 0,
"status": "missed",
"details": [],
"max_points": 6.3
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]
},
{
"key": "ecosystem_adoption",
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"name": "Ecosystem adoption (downloads)",
"note": "Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.",
"notes": [
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"code": "excluded_no_data",
"params": {
"components": [
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}
},
{
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}
],
"value": 100,
"inputs": {
"packages": [
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"dependents": null,
"ecosystems": "pypi",
"total_downloads": null,
"monthly_downloads": 1150697
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"components": [
{
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"points": 80,
"status": "met",
"details": [
{
"code": "downloads_monthly",
"params": {
"count": 1150697,
"ecosystems": "pypi"
}
}
],
"max_points": 80
},
{
"key": "registry_dependents",
"name": "Registry dependents",
"detail": "not reported by this ecosystem",
"points": 0,
"status": "excluded",
"details": [
{
"code": "not_reported_by_this_ecosystem",
"params": {}
}
],
"max_points": 20
}
]
}
],
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},
{
"key": "governance",
"band": "moderate",
"name": "Sustainability & Governance",
"value": 63,
"weight": 0.24,
"metrics": [
{
"key": "maintainer_resilience",
"band": "at_risk",
"name": "Maintainer resilience (bus factor)",
"note": null,
"notes": [],
"value": 42,
"inputs": {
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"contributors_sampled": 100,
"top_contributor_share": 0.589
},
"components": [
{
"key": "bus_factor",
"name": "Bus factor",
"detail": "1 contributor(s) cover half of all commits",
"points": 9,
"status": "partial",
"details": [
{
"code": "bus_factor",
"params": {
"count": 1
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}
],
"max_points": 54
},
{
"key": "commit_distribution",
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"detail": "top contributor authored 59% of commits",
"points": 9.2,
"status": "partial",
"details": [
{
"code": "top_contributor_share",
"params": {
"share": 59
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}
],
"max_points": 22.5
},
{
"key": "contributor_breadth",
"name": "Contributor breadth",
"detail": "100 contributors",
"points": 13.5,
"status": "met",
"details": [
{
"code": "contributors_sampled",
"params": {
"count": 100
}
}
],
"max_points": 13.5
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{
"key": "openssf_scorecard_contributors",
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"detail": "project has 27 contributing companies or organizations",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
},
{
"key": "responsiveness",
"band": "moderate",
"name": "Issue & PR responsiveness",
"note": null,
"notes": [],
"value": 67,
"inputs": {
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"open_issues": 242,
"closed_issues": 734,
"issue_closed_ratio": 0.752,
"closed_unmerged_prs": 67
},
"components": [
{
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"points": 35.2,
"status": "partial",
"details": [
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"code": "issues_closed_share",
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}
],
"max_points": 46.75
},
{
"key": "pr_acceptance",
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"detail": "344/411 decided PRs merged",
"points": 32,
"status": "partial",
"details": [
{
"code": "decided_prs_merged",
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}
],
"max_points": 38.25
},
{
"key": "openssf_scorecard_code_review",
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"detail": "Found 1/27 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
}
]
},
{
"key": "stewardship",
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"name": "Ownership & stewardship",
"note": null,
"notes": [],
"value": 54,
"inputs": {
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"owner_type": "Organization",
"is_verified": null,
"owner_login": "pysam-developers",
"public_repos": 3,
"account_age_days": 4548
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"components": [
{
"key": "ownership_backing",
"name": "Ownership backing",
"detail": "organization-owned",
"points": 30,
"status": "met",
"details": [
{
"code": "owner_organization",
"params": {}
}
],
"max_points": 30
},
{
"key": "verified_domain",
"name": "Verified domain",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "owner_reach",
"name": "Owner reach",
"detail": "10 followers of pysam-developers",
"points": 7.5,
"status": "partial",
"details": [
{
"code": "owner_followers",
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"count": 10,
"login": "pysam-developers"
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}
],
"max_points": 25
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{
"key": "track_record",
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"detail": "3 public repos, account ~12 yr old",
"points": 16.4,
"status": "partial",
"details": [
{
"code": "public_repos",
"params": {
"count": 3
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},
{
"code": "account_age_years",
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}
],
"max_points": 25
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]
},
{
"key": "package_maintenance",
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"name": "Package maintenance",
"note": null,
"notes": [],
"value": 100,
"inputs": {
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"ecosystems": "pypi",
"any_deprecated": false,
"min_days_since_publish": 85
},
"components": [
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"key": "published_resolvable",
"name": "Published & resolvable",
"detail": "1 package(s) on pypi",
"points": 25,
"status": "met",
"details": [
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"code": "packages_published",
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"ecosystems": "pypi"
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}
],
"max_points": 25
},
{
"key": "publish_recency",
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"detail": "latest publish 85 days ago",
"points": 35,
"status": "met",
"details": [
{
"code": "publish_recency",
"params": {
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}
],
"max_points": 35
},
{
"key": "version_history",
"name": "Version history",
"detail": "48 published versions",
"points": 20,
"status": "met",
"details": [
{
"code": "published_versions",
"params": {
"count": 48
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}
],
"max_points": 20
},
{
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"details": [
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"code": "package_not_deprecated",
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}
],
"max_points": 20
}
]
}
],
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},
{
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"name": "Engineering Quality",
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"weight": 0.2,
"metrics": [
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"key": "engineering_practices",
"band": "moderate",
"name": "Engineering practices",
"note": null,
"notes": [],
"value": 68,
"inputs": {
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"has_linter_config": false,
"has_precommit_config": false
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"components": [
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"name": "CI workflows",
"detail": "2 workflow(s)",
"points": 24,
"status": "met",
"details": [
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"code": "ci_workflows",
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}
],
"max_points": 24
},
{
"key": "tests_present",
"name": "Tests present",
"detail": null,
"points": 24,
"status": "met",
"details": [],
"max_points": 24
},
{
"key": "linter_config",
"name": "Linter config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 16
},
{
"key": "pre_commit_hooks",
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"points": 0,
"status": "missed",
"details": [],
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},
{
"key": "editorconfig",
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"detail": null,
"points": 0,
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{
"key": "openssf_scorecard_ci_tests",
"name": "OpenSSF Scorecard: CI-Tests",
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"details": [],
"max_points": 20
}
]
},
{
"key": "documentation",
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"note": null,
"notes": [],
"value": 100,
"inputs": {
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"htslib"
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"components": [
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},
{
"key": "documentation_directory",
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{
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{
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}
],
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},
{
"key": "wiki",
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"details": [],
"max_points": 10
}
]
}
],
"description": "Are baseline engineering and documentation practices in place?"
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{
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"name": "Security",
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"weight": 0.16,
"metrics": [
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"key": "security_posture",
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"notes": [
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"code": "excluded_no_data",
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}
},
{
"code": "weights_renormalized",
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}
],
"value": 49,
"inputs": {
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"scorecard_version": "v5.5.0",
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"components": [
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},
{
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"status": "partial",
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},
{
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{
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"status": "missed",
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},
{
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},
{
"key": "contributors",
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"detail": "project has 27 contributing companies or organizations",
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"details": [],
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},
{
"key": "dangerous_workflow",
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"status": "excluded",
"details": [
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"code": "no_data",
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}
],
"max_points": 10
},
{
"key": "dependency_update_tool",
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"points": 0,
"status": "missed",
"details": [],
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},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
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"status": "missed",
"details": [],
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},
{
"key": "license",
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"detail": "license file detected",
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"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
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"detail": "packaging workflow not detected",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 5
},
{
"key": "sast",
"name": "SAST",
"detail": "SAST tool is not run on all commits -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "security_policy",
"name": "Security-Policy",
"detail": "security policy file not detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "signed_releases",
"name": "Signed-Releases",
"detail": "no releases found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "token_permissions",
"name": "Token-Permissions",
"detail": "No tokens found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "0 existing vulnerabilities detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
}
]
},
{
"key": "dependency_advisories",
"band": "excellent",
"name": "Dependency advisories",
"note": "Excluded from scoring (no data or not applicable): Indirect dependencies free of known advisories, No advisories left outstanding. Remaining weights renormalized. Matched 2 resolved dependencies against OSV; 2 could not be assessed (no resolved version, an unsupported ecosystem, or beyond the reported package list). This repository publishes no package the index resolves, so the repository dependency graph was assessed instead. That graph mixes development and test pins with shipped dependencies, so only the declared runtime dependencies are scored; transitive findings are reported as context and excluded from the score. Reachability is not analyzed.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"indirect_dependencies_free_of_known_advisories",
"no_advisories_left_outstanding"
]
}
},
{
"code": "weights_renormalized",
"params": {}
},
{
"code": "advisories_scope_repository",
"params": {
"assessed": 2
}
},
{
"code": "advisories_unassessed",
"params": {
"count": 2
}
},
{
"code": "advisories_repo_graph_caveat",
"params": {}
},
{
"code": "advisories_reachability",
"params": {}
}
],
"value": 100,
"inputs": {
"source": "osv",
"advisories": 0,
"affected_packages": 0,
"assessed_packages": 2,
"unassessed_packages": 2,
"affected_by_severity": "none",
"direct_affected_packages": 0
},
"components": [
{
"key": "direct_dependencies_free_of_known_advisories",
"name": "Direct dependencies free of known advisories",
"detail": "no direct dependency carries a known advisory",
"points": 35,
"status": "met",
"details": [
{
"code": "no_direct_advisories",
"params": {}
}
],
"max_points": 35
},
{
"key": "indirect_dependencies_free_of_known_advisories",
"name": "Indirect dependencies free of known advisories",
"detail": "transitive set not separable from development and test dependencies in this scope",
"points": 0,
"status": "excluded",
"details": [
{
"code": "advisories_scope_not_separable",
"params": {}
}
],
"max_points": 25
},
{
"key": "no_advisories_left_outstanding",
"name": "No advisories left outstanding",
"detail": "no advisory carries a publication date",
"points": 0,
"status": "excluded",
"details": [
{
"code": "advisories_no_publication_date",
"params": {}
}
],
"max_points": 40
}
]
},
{
"key": "malicious_dependencies",
"band": "excellent",
"name": "Malicious dependencies",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"source": "osv",
"meaning": "reported as a malicious package by the OpenSSF corpus; the remedy is removal or moving off the compromised name, never an upgrade of the same artifact. Versions the registry has since pulled are listed but not scored",
"packages": [],
"red_flag": false,
"assessed_packages": 2,
"malicious_packages": 0,
"direct_malicious_packages": 0,
"withdrawn_malicious_packages": 0,
"installable_malicious_packages": 0
},
"components": [
{
"key": "no_dependency_reported_as_a_malicious_package",
"name": "No dependency reported as a malicious package",
"detail": "no dependency is reported as a malicious package",
"points": 100,
"status": "met",
"details": [
{
"code": "no_malicious_dependencies",
"params": {}
}
],
"max_points": 100
}
]
},
{
"key": "high_risk_jurisdiction_exposure",
"band": "excellent",
"name": "High-Risk Jurisdiction Exposure",
"note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
"notes": [
{
"code": "jurisdiction_evidence_limits",
"params": {}
}
],
"value": 100,
"inputs": {
"meaning": "self-published location evidence; not nationality or citizenship",
"red_flag": false,
"exposures": [],
"policy_countries": [
"Russia",
"Iran",
"North Korea"
],
"review_only_matches": 0,
"assessed_self_published_locations": 12
},
"components": [
{
"key": "policy_exposure_multiplier",
"name": "Policy exposure multiplier",
"detail": "no confirmed policy-scope location match",
"points": 100,
"status": "met",
"details": [
{
"code": "jurisdiction_no_match",
"params": {}
}
],
"max_points": 100
}
]
}
],
"description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
},
{
"key": "ai_readiness",
"band": "moderate",
"name": "AI Readiness",
"value": 51,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "at_risk",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 32,
"inputs": {
"has_llms_txt": false,
"legible_history_share": 0.59,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"components": [
{
"key": "agent_instructions",
"name": "Agent instructions",
"detail": "no CLAUDE.md / AGENTS.md / editor rules",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_instructions",
"params": {}
}
],
"max_points": 45
},
{
"key": "machine_readable_docs_llms_txt",
"name": "Machine-readable docs (llms.txt)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
},
{
"key": "legible_commit_history",
"name": "Legible commit history",
"detail": "59 of 100 human commits state their intent (structured subject or explanatory body)",
"points": 31.5,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 59,
"sampled": 100
}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "moderate",
"name": "Verify loop (build / test / typecheck)",
"note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"openssf_scorecard_pinned_dependencies"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 57,
"inputs": {
"has_nix": false,
"has_tests": true,
"lockfiles": [],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [
"doc/Makefile",
"htslib/Makefile",
"tests/cbcf_data/Makefile",
"tests/pysam_data/Makefile",
"tests/tabix_data/Makefile"
],
"has_devcontainer": false,
"has_linter_config": false,
"typecheck_configs": [
"pysam/py.typed"
],
"agent_commit_share": 0,
"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": "doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile",
"points": 18,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile"
}
}
],
"max_points": 18
},
{
"key": "automated_tests",
"name": "Automated tests",
"detail": null,
"points": 22,
"status": "met",
"details": [],
"max_points": 22
},
{
"key": "lint_format_config",
"name": "Lint / format config",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": "pysam/py.typed",
"points": 11,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "pysam/py.typed"
}
}
],
"max_points": 11
},
{
"key": "reproducible_environment",
"name": "Reproducible environment",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "demonstrated_agent_practice",
"name": "Demonstrated agent practice",
"detail": "no agent-authored commits among the last 100",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_agent_authored_commits",
"params": {
"sampled": 100
}
}
],
"max_points": 10
},
{
"key": "automated_maintenance",
"name": "Automated maintenance",
"detail": "no automated dependency updates observed",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_dependency_automation",
"params": {}
}
],
"max_points": 8
},
{
"key": "openssf_scorecard_pinned_dependencies",
"name": "OpenSSF Scorecard: Pinned-Dependencies",
"detail": "no dependencies found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "good",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 75,
"inputs": {
"primary_language": "Cython",
"largest_source_bytes": 230215,
"source_files_sampled": 458,
"oversized_source_files": 56
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Cython with type-check config (pysam/py.typed)",
"points": 27,
"status": "partial",
"details": [
{
"code": "typecheck_config_language",
"params": {
"files": "pysam/py.typed",
"language": "Cython"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "56/458 source files over 60KB",
"points": 48.3,
"status": "partial",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 458,
"oversized": 56
}
}
],
"max_points": 55
}
]
}
],
"description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
}
],
"metrics_version": "1.13.0"
},
"warnings": [
"Could not fetch pypi package 'pysam.libchtslib' from its registry"
],
"report_type": "repository",
"generated_at": "2026-07-21T20:30:14.249715Z",
"schema_version": "0.23.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/p/pysam-developers/pysam.svg",
"full_name": "pysam-developers/pysam",
"license_state": "standard",
"license_spdx": "MIT"
}Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.
Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v1.13.0, schema v0.23.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.