scverse / pertpy
Single-cell perturbation analysis
scverse/pertpy holds a health index of 95 out of 100, placing it in the Exceptional band. It scores highest on Engineering Quality (100/100) and lowest on Sustainability & Governance (71/100). It was last updated today. A single contributor accounts for most of its recent work.
Software health index
Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.
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.
The weighted overall 82 is calibrated to 95 on the published index scale (record calibration 2026-08-02).
Ownership
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 | Tags |
|---|---|---|---|---|---|---|
| PyPI | pertpy | 1.3.0 | 7,588 | 30 | 0 days ago | crisprperturb-seqanndatabioinformaticscompositional-analysiscomputational-biologydifferential-abundancedifferential-expressionperturbationscrna-seqscversesingle-cell |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
Development activity
How it's scored
| 36/36 | Push recency — last push 0 days ago |
| 30.5/36 | Commit cadence — 44/52 weeks with commits |
| 18/18 | Commit volume — 158 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 30 commit(s) and 19 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 158 |
| human_commit_share | 0.75 |
| days_since_last_push | 0 |
| active_weeks_last_year | 44 |
Release discipline
How it's scored
| 27/27 | Ships releases — 28 releases published |
| 36/36 | Release recency — latest release 0 days ago |
| 27/27 | Release cadence — a release every ~44.3 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 28 |
| latest_release_tag | 1.3.0 |
| releases_from_tags | no |
| days_since_latest_release | 0 |
| mean_days_between_releases | 44.3 |
Community & Adoption
Does the project have users, downloads, attention, and a welcoming setup for contributors?
Popularity & adoption
How it's scored
| 41/60 | Stars — 337 stars |
| 15/25 | Forks — 64 forks |
| 3.3/15 | Watchers — 5 watchers |
Inputs used
| forks | 64 |
| stars | 337 |
| watchers | 5 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | no_history |
Community health
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (MIT) |
| 18/18 | CONTRIBUTING guide |
| 13.5/13.5 | Code of conduct |
| 0/7.2 | Issue template |
| 6.3/6.3 | PR template |
Inputs used
| has_readme | yes |
| has_license | yes |
| readme_badges | 8 |
| has_contributing | yes |
| has_issue_template | no |
| has_code_of_conduct | yes |
| readme_badge_services | codecov.io, github.com, shields.io |
| has_pull_request_template | yes |
How it's scored
| 51.7/80 | Monthly downloads — 7,588 downloads/month across pypi |
| 0/20 | Registry dependents — not reported by this ecosystem |
Inputs used
| packages | pertpy |
| dependents | — |
| ecosystems | pypi |
| total_downloads | — |
| monthly_downloads | 7,588 |
| unverified_packages_excluded | — |
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 6.9/22.5 | Commit distribution — top contributor authored 69% of commits |
| 13.5/13.5 | Contributor breadth — 49 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 20 contributing companies or organizations |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 49 |
| top_contributor_share | 0.693 |
Issue & PR responsiveness
How it's scored
| 41.1/42 | Issue resolution — 98% of issues closed |
| 27.1/30 | PR acceptance — 599/664 decided PRs merged |
| 13/13 | Newcomer PR acceptance — 3/3 first-time contributors' PRs merged in 30d |
| 1.5/15 | OpenSSF Scorecard: Code-Review — Found 3/24 approved changesets -- score normalized to 1 |
Inputs used
| merged_prs | 599 |
| open_issues | 9 |
| closed_issues | 398 |
| prs_merged_7d | 6 |
| prs_decided_7d | 6 |
| prs_merged_30d | 24 |
| prs_decided_30d | 24 |
| issue_closed_ratio | 0.978 |
| closed_unmerged_prs | 65 |
| first_time_authors_30d | 2 |
| first_time_prs_merged_30d | 3 |
| first_time_prs_decided_30d | 3 |
Ownership & stewardship
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 22.9/25 | Owner reach — 1,546 followers of scverse |
| 22.5/25 | Track record — 88 public repos, account ~4 yr old |
Inputs used
| followers | 1,546 |
| owner_type | Organization |
| is_verified | no |
| owner_login | scverse |
| public_repos | 88 |
| account_age_days | 1,727 |
Package maintenance
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 0 days ago |
| 20/20 | Version history — 30 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | pertpy |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 0 |
Engineering Quality
Are baseline engineering and documentation practices in place?
Engineering practices
How it's scored
| 24/24 | CI workflows — 6 workflow(s) |
| 24/24 | Tests present |
| 16/16 | Linter config — pyproject.toml ([tool.ruff]) |
| 9.6/9.6 | Pre-commit hooks |
| 6.4/6.4 | .editorconfig |
| 20/20 | OpenSSF Scorecard: CI-Tests — 29 out of 29 merged PRs checked by a CI test -- score normalized to 10 |
Inputs used
| has_ci | yes |
| has_tests | yes |
| has_editorconfig | yes |
| has_linter_config | yes |
| has_precommit_config | yes |
Documentation
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://pertpy.readthedocs.io/en/stable |
| 10/10 | Repository description |
| 10/10 | Topics — 13 topics |
| 10/10 | Wiki |
Inputs used
| topics | scverse, single-cell, perturbation, anndata, bioinformatics, computational-biology, crispr, differential-abundance, differential-expression, drug-discovery, perturb-seq, python, scrna-seq |
| has_wiki | yes |
| homepage | https://pertpy.readthedocs.io/en/stable |
| docs_site | https://pertpy.readthedocs.io/en/stable |
| 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?
Security posture
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 0/7.5 | Branch-Protection — no data |
| 2.5/2.5 | CI-Tests — 29 out of 29 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 |
| 0.8/7.5 | Code-Review — Found 3/24 approved changesets -- score normalized to 1 |
| 2.5/2.5 | Contributors — project has 20 contributing companies or organizations |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 7.5/7.5 | Dependency-Update-Tool — 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 19 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 5/5 | Pinned-Dependencies — all dependencies are pinned |
| 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 |
| 7.5/7.5 | Token-Permissions — GitHub workflow tokens follow principle of least privilege |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 16 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 2 |
| scorecard_aggregate | 7.3 |
AI Readiness
How well is the repo equipped to be developed and maintained with AI coding agents? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.
Agent context & guidance
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 15/15 | Machine-readable docs (llms.txt) — llms.txt present |
| 40/40 | Legible commit history — 71 of 75 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | yes |
| llms_txt_url | — |
| legible_history_share | 0.947 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Verify loop (build / test / typecheck)
How it's scored
| 18/18 | One-command bootstrap — docs/Makefile |
| 22/22 | Automated tests |
| 11/11 | Lint / format config — pyproject.toml ([tool.ruff]) |
| 11/11 | Static type checking — src/pertpy/py.typed |
| 0/10 | Reproducible environment |
| 10/10 | Demonstrated agent practice — 26 of the last 100 commits agent-authored or agent-credited |
| 8/8 | Automated maintenance — 6 of the last 100 commits are automated dependency updates |
| 10/10 | OpenSSF Scorecard: Pinned-Dependencies — all dependencies are pinned |
Inputs used
| has_nix | no |
| has_tests | yes |
| lockfiles | — |
| has_dockerfile | no |
| typed_language | no |
| bootstrap_files | docs/Makefile |
| has_devcontainer | no |
| has_linter_config | yes |
| typecheck_configs | src/pertpy/py.typed |
| agent_commit_share | 0.26 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0.06 |
How it's scored
| 27/45 | Type-checkable code — Python with type-check config (src/pertpy/py.typed) |
| 52.3/55 | Manageable file sizes — 5/103 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 120,143 |
| source_files_sampled | 103 |
| oversized_source_files | 5 |
Key facts
Data collection warnings
- Star history unavailable: GitHub GraphQL error: Resource not accessible by personal access token
- deps.dev does not index pypi:pertpy@1.3.0; advisories assessed against the repository dependency graph instead
- No resolved dependencies carried a version and a supported ecosystem
More detail
Star and fork history 0 ★ / 64 ⇿
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.
Each point covers 4 days.
OpenSSF Scorecard 7.3 / 10
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 |
| n/a | Branch-Protection | internal error: error during branchesHandler.setup: internal error: some github tokens can't read classic branch protection rules: https://github.com/ossf/scorecard-action/blob/main/docs/authentication/fine-grained-auth-token.md |
| 10 | CI-Tests | 29 out of 29 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 |
| 1 | Code-Review | Found 3/24 approved changesets -- score normalized to 1 |
| 10 | Contributors | project has 20 contributing companies or organizations |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 10 | Dependency-Update-Tool | update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 30 commit(s) and 19 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 10 | Pinned-Dependencies | all dependencies are pinned |
| 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 |
| 10 | Token-Permissions | GitHub workflow tokens follow principle of least privilege |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 17
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | requests | — | pyproject.toml |
| PyPI | rich | — | pyproject.toml |
| PyPI | anndata | — | pyproject.toml |
| PyPI | scanpy | — | pyproject.toml |
| PyPI | mudata | — | pyproject.toml |
| PyPI | scikit-misc | — | pyproject.toml |
| PyPI | adjusttext | — | pyproject.toml |
| PyPI | sparsecca | — | pyproject.toml |
| PyPI | openpyxl | — | pyproject.toml |
| PyPI | pubchempy | — | pyproject.toml |
| PyPI | pyarrow | — | pyproject.toml |
| PyPI | blitzgsea | — | pyproject.toml |
| PyPI | scikit-learn | >=1.4 | pyproject.toml |
| PyPI | fast-array-utils | — | pyproject.toml |
| PyPI | arviz | >=1.2.0 | pyproject.toml |
| PyPI | pooch | — | pyproject.toml |
| PyPI | scverse-misc | — | pyproject.toml |
All dependencies 8
Full resolved dependency set from the GitHub dependency graph: 2 direct and 6 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | arviz | — | direct |
| PyPI | scikit-learn | — | direct |
| PyPI | docutils | — | indirect |
| PyPI | formulaic-contrasts | — | indirect |
| PyPI | pydeseq2 | — | indirect |
| PyPI | sphinx | — | indirect |
| PyPI | sphinxcontrib-bibtex | — | indirect |
| PyPI | toytree | — | indirect |
Dependency advisories not assessed
Advisory matching could not run for this report: No resolved dependencies carried a version and a supported ecosystem
Raw JSON report machine-readable
Feedback
Spotted something off in this report, or have thoughts to share? Wrong measurements, missed tooling, ideas, questions — anything is welcome. Every message is read and gets a response.
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 v2.10.0, schema v0.34.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.