# pysam-developers/pysam — health index 73/100 (Good)

> Inspection of the public repository pysam-developers/pysam by inspect.software. It holds a health index of 73 out of 100, placing it in the Good band. The index is a signal derived from publicly visible practice, not a warranty, a security audit, or an endorsement, and it is independent of payment.

- Repository: https://github.com/pysam-developers/pysam
- Report page: https://inspect.software/software/pysam-developers/pysam
- Full JSON report: https://inspect.software/api/repositories/pysam-developers/pysam/report
- Badge: https://raw.githubusercontent.com/inspect-software/badges/main/v1/p/pysam-developers/pysam.svg
- Inspected: 2026-07-21
- Methodology: metrics 1.13.0, report schema 0.23.0 (https://inspect.software/methodology.md)

## Category summary

| Category | Weight | Index | Band |
|---|---|---|---|
| Vitality | 22% | 85/100 | Excellent |
| Community & Adoption | 18% | 74/100 | Good |
| Sustainability & Governance | 24% | 63/100 | Moderate |
| Engineering Quality | 20% | 81/100 | Good |
| Security | 16% | 59/100 | Moderate |
| AI Readiness | not counted | 51/100 | Moderate |

## Repository facts

| Field | Value |
|---|---|
| Description | 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. |
| Homepage | https://pysam.readthedocs.io/en/latest/ |
| Primary language | Cython |
| License | MIT |
| Stars | 900 |
| Forks | 297 |
| Created | 2014-02-05 |
| Last push | 2026-07-19 |
| Latest release | v0.24.0 |
| Commits (last year) | 84 |
| Bus factor | 1 |
| Topics | bioinformatics, ngs, python, htslib |

## Published packages

| Registry | Package | Latest | Monthly downloads |
|---|---|---|---|
| pypi | pysam | 0.24.0 | 1,150,697 |

## Vitality — 85/100 (Excellent)

Is the project alive — is code being written and are releases shipping? Weight: 22% of the overall index.

### Development activity — 86/100 (Excellent)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Push recency | met | 36 / 36 | last push 2 days ago |
| Commit cadence | partial | 22.8 / 36 | 33/52 weeks with commits |
| Commit volume | partial | 17.3 / 18 | 84 commits in the last year |
| OpenSSF Scorecard: Maintained | met | 10 / 10 | 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |

### Release discipline — 84/100 (Good)

Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Ships releases | met | 27 / 27 | 41 releases published |
| Release recency | met | 36 / 36 | latest release 85 days ago |
| Release cadence | partial | 12.6 / 27 | a release every ~159.1 days |
| OpenSSF Scorecard: Signed-Releases | excluded | 0 / 10 | no releases found |

### Abandonment — 100/100 (Excellent)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Project is still maintained | met | 100 / 100 | last human commit 2 days ago |

## Community & Adoption — 74/100 (Good)

Does the project have users, downloads, attention, and a welcoming setup for contributors? Weight: 18% of the overall index.

### Popularity & adoption — 78/100 (Good)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Stars | partial | 47.9 / 60 | 900 stars |
| Forks | partial | 20.6 / 25 | 297 forks |
| Watchers | partial | 9 / 15 | 42 watchers |

### Community health — 50/100 (Moderate)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| README | met | 22.5 / 22.5 | — |
| License | met | 22.5 / 22.5 | recognized license (MIT) |
| CONTRIBUTING guide | not met | 0 / 18 | — |
| Code of conduct | not met | 0 / 13.5 | — |
| Issue template | not met | 0 / 7.2 | — |
| PR template | not met | 0 / 6.3 | — |

### Ecosystem adoption (downloads) — 100/100 (Excellent)

Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Monthly downloads | met | 80 / 80 | 1,150,697 downloads/month across pypi |
| Registry dependents | excluded | 0 / 20 | not reported by this ecosystem |

## Sustainability & Governance — 63/100 (Moderate)

Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep? Weight: 24% of the overall index.

### Maintainer resilience (bus factor) — 42/100 (At risk)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Bus factor | partial | 9 / 54 | 1 contributor(s) cover half of all commits |
| Commit distribution | partial | 9.2 / 22.5 | top contributor authored 59% of commits |
| Contributor breadth | met | 13.5 / 13.5 | 100 contributors |
| OpenSSF Scorecard: Contributors | met | 10 / 10 | project has 27 contributing companies or organizations |

### Issue & PR responsiveness — 67/100 (Moderate)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Issue resolution | partial | 35.2 / 46.8 | 75% of issues closed |
| PR acceptance | partial | 32 / 38.2 | 344/411 decided PRs merged |
| OpenSSF Scorecard: Code-Review | not met | 0 / 15 | Found 1/27 approved changesets -- score normalized to 0 |

### Ownership & stewardship — 54/100 (Moderate)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Ownership backing | met | 30 / 30 | organization-owned |
| Verified domain | not met | 0 / 20 | — |
| Owner reach | partial | 7.5 / 25 | 10 followers of pysam-developers |
| Track record | partial | 16.4 / 25 | 3 public repos, account ~12 yr old |

### Package maintenance — 100/100 (Excellent)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Published & resolvable | met | 25 / 25 | 1 package(s) on pypi |
| Publish recency | met | 35 / 35 | latest publish 85 days ago |
| Version history | met | 20 / 20 | 48 published versions |
| Not deprecated | met | 20 / 20 | active, not deprecated or yanked |

## Engineering Quality — 81/100 (Good)

Are baseline engineering and documentation practices in place? Weight: 20% of the overall index.

### Engineering practices — 68/100 (Moderate)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| CI workflows | met | 24 / 24 | 2 workflow(s) |
| Tests present | met | 24 / 24 | — |
| Linter config | not met | 0 / 16 | — |
| Pre-commit hooks | not met | 0 / 9.6 | — |
| .editorconfig | not met | 0 / 6.4 | — |
| OpenSSF Scorecard: CI-Tests | met | 20 / 20 | 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |

### Documentation — 100/100 (Excellent)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| README | met | 30 / 30 | — |
| Documentation directory | met | 25 / 25 | — |
| Documentation / homepage site | met | 15 / 15 | https://pysam.readthedocs.io/en/latest/ |
| Repository description | met | 10 / 10 | — |
| Topics | met | 10 / 10 | 4 topics |
| Wiki | met | 10 / 10 | — |

## Security — 59/100 (Moderate)

Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure? Weight: 16% of the overall index.

### Security posture — 49/100 (At risk)

Excluded from scoring (no data or not applicable): Dangerous-Workflow, Packaging, Pinned-Dependencies, Signed-Releases, Token-Permissions. Remaining weights renormalized.

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Binary-Artifacts | met | 7.5 / 7.5 | no binaries found in the repo |
| Branch-Protection | partial | 4.5 / 7.5 | branch protection is not maximal on development and all release branches |
| CI-Tests | met | 2.5 / 2.5 | 2 out of 2 merged PRs checked by a CI test -- score normalized to 10 |
| CII-Best-Practices | not met | 0 / 2.5 | no effort to earn an OpenSSF best practices badge detected |
| Code-Review | not met | 0 / 7.5 | Found 1/27 approved changesets -- score normalized to 0 |
| Contributors | met | 2.5 / 2.5 | project has 27 contributing companies or organizations |
| Dangerous-Workflow | excluded | 0 / 10 | no workflows found |
| Dependency-Update-Tool | not met | 0 / 7.5 | no update tool detected |
| Fuzzing | not met | 0 / 5 | project is not fuzzed |
| License | met | 2.5 / 2.5 | license file detected |
| Maintained | met | 7.5 / 7.5 | 30 commit(s) and 10 issue activity found in the last 90 days -- score normalized to 10 |
| Packaging | excluded | 0 / 5 | packaging workflow not detected |
| Pinned-Dependencies | excluded | 0 / 5 | no dependencies found |
| SAST | not met | 0 / 5 | SAST tool is not run on all commits -- score normalized to 0 |
| Security-Policy | not met | 0 / 5 | security policy file not detected |
| Signed-Releases | excluded | 0 / 7.5 | no releases found |
| Token-Permissions | excluded | 0 / 7.5 | No tokens found |
| Vulnerabilities | met | 7.5 / 7.5 | 0 existing vulnerabilities detected |

### Dependency advisories — 100/100 (Excellent)

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.

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Direct dependencies free of known advisories | met | 35 / 35 | no direct dependency carries a known advisory |
| Indirect dependencies free of known advisories | excluded | 0 / 25 | transitive set not separable from development and test dependencies in this scope |
| No advisories left outstanding | excluded | 0 / 40 | no advisory carries a publication date |

### Malicious dependencies — 100/100 (Excellent)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| No dependency reported as a malicious package | met | 100 / 100 | no dependency is reported as a malicious package |

### High-Risk Jurisdiction Exposure — 100/100 (Excellent)

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.

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Policy exposure multiplier | met | 100 / 100 | no confirmed policy-scope location match |

## AI Readiness — 51/100 (Moderate)

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.

### Agent context & guidance — 32/100 (At risk)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Agent instructions | not met | 0 / 45 | no CLAUDE.md / AGENTS.md / editor rules |
| Machine-readable docs (llms.txt) | not met | 0 / 15 | — |
| Legible commit history | partial | 31.5 / 40 | 59 of 100 human commits state their intent (structured subject or explanatory body) |

### Verify loop (build / test / typecheck) — 57/100 (Moderate)

Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.

| Criterion | Status | Points | Detail |
|---|---|---|---|
| One-command bootstrap | met | 18 / 18 | doc/Makefile, htslib/Makefile, tests/cbcf_data/Makefile, tests/pysam_data/Makefile, tests/tabix_data/Makefile |
| Automated tests | met | 22 / 22 | — |
| Lint / format config | not met | 0 / 11 | — |
| Static type checking | met | 11 / 11 | pysam/py.typed |
| Reproducible environment | not met | 0 / 10 | — |
| Demonstrated agent practice | not met | 0 / 10 | no agent-authored commits among the last 100 |
| Automated maintenance | not met | 0 / 8 | no automated dependency updates observed |
| OpenSSF Scorecard: Pinned-Dependencies | excluded | 0 / 10 | no dependencies found |

### Code legibility for models — 75/100 (Good)

| Criterion | Status | Points | Detail |
|---|---|---|---|
| Type-checkable code | partial | 27 / 45 | Cython with type-check config (pysam/py.typed) |
| Manageable file sizes | partial | 48.3 / 55 | 56/458 source files over 60KB |

## Collection warnings

- Could not fetch pypi package 'pysam.libchtslib' from its registry

## What this report is

inspect.software measures public repositories against a single published, versioned methodology and reports the result as a 1–100 health index. Findings are signals derived from what is visible in public repository data — they are not a security audit, a warranty, or an endorsement, and no result depends on payment.

- Methodology, formulas and weights: https://inspect.software/methodology.md
- What a result does and does not claim: https://inspect.software/wiki/signals-not-warranties.md
- Rating bands: https://inspect.software/wiki/scoring-bands.md
- Corrections: https://inspect.software/contact.md
- Index of all documents: https://inspect.software/llms.txt