Public recordGood
Software health reportschema 0.26.0 · metrics 1.13.0 · 2026-07-22 04:32 UTC
YosefLab / scib-metrics
Accelerated, Python-only, single-cell integration benchmarking metrics
YosefLab/scib-metrics holds a health index of 73 out of 100, placing it in the Good band. It scores highest on Engineering Quality (92/100) and lowest on AI Readiness (47/100). It was last updated today. 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
Yosef LabOrganization
138 followers73 public repossince Aug 2015
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 | scib-metrics | 0.5.10 | - | 28 | 8 days ago |
Metrics by category
Vitality
Is the project alive — is code being written and are releases shipping?
90
Development activity
88Excellent
How it's scored
| 36/36 | Push recency — last push 0 days ago |
| 26.3/36 | Commit cadence — 38/52 weeks with commits |
| 15.6/18 | Commit volume — 54 commits in the last year |
| 10/10 | OpenSSF Scorecard: Maintained — 15 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 |
Inputs used
| commits_last_year | 54 |
| human_commit_share | 0.31 |
| days_since_last_push | 0 |
| active_weeks_last_year | 38 |
Release discipline
92Excellent
How it's scored
| 27/27 | Ships releases — 29 releases published |
| 36/36 | Release recency — latest release 8 days ago |
| 19.8/27 | Release cadence — a release every ~96.7 days |
| 0/10 | OpenSSF Scorecard: Signed-Releases — no data |
Inputs used
| releases_count | 29 |
| latest_release_tag | v0.5.10 |
| releases_from_tags | no |
| days_since_latest_release | 8 |
| mean_days_between_releases | 96.7 |
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?
58
Popularity & adoption
47At risk
How it's scored
| 32.1/60 | Stars — 96 stars |
| 11/25 | Forks — 22 forks |
| 3.9/15 | Watchers — 6 watchers |
Inputs used
| forks | 22 |
| stars | 96 |
| watchers | 6 |
| growth_state | unverified |
| growth_factor_pct | 100 |
| growth_unverified_reason | below_threshold |
Community health
70Good
How it's scored
| 22.5/22.5 | README |
| 22.5/22.5 | License — recognized license (BSD-3-Clause) |
| 18/18 | 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 | yes |
| has_issue_template | no |
| has_code_of_conduct | no |
| has_pull_request_template | no |
Sustainability & Governance
Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?
68
Maintainer resilience (bus factor)
38At risk
How it's scored
| 9/54 | Bus factor — 1 contributor(s) cover half of all commits |
| 7.2/22.5 | Commit distribution — top contributor authored 68% of commits |
| 12.2/13.5 | Contributor breadth — 9 contributors |
| 10/10 | OpenSSF Scorecard: Contributors — project has 5 contributing companies or organizations |
Inputs used
| bus_factor | 1 |
| contributors_sampled | 9 |
| top_contributor_share | 0.679 |
How it's scored
| 40.8/46.8 | Issue resolution — 87% of issues closed |
| 35.5/38.3 | PR acceptance — 203/219 decided PRs merged |
| 0/15 | OpenSSF Scorecard: Code-Review — Found 0/9 approved changesets -- score normalized to 0 |
Inputs used
| merged_prs | 203 |
| open_issues | 7 |
| closed_issues | 48 |
| issue_closed_ratio | 0.873 |
| closed_unmerged_prs | 16 |
Ownership & stewardship
70Good
How it's scored
| 30/30 | Ownership backing — organization-owned |
| 0/20 | Verified domain |
| 15.4/25 | Owner reach — 138 followers of YosefLab |
| 25/25 | Track record — 73 public repos, account ~10 yr old |
Inputs used
| followers | 138 |
| owner_type | Organization |
| is_verified | — |
| owner_login | YosefLab |
| public_repos | 73 |
| account_age_days | 3,991 |
Package maintenance
100Excellent
How it's scored
| 25/25 | Published & resolvable — 1 package(s) on pypi |
| 35/35 | Publish recency — latest publish 8 days ago |
| 20/20 | Version history — 28 published versions |
| 20/20 | Not deprecated — active, not deprecated or yanked |
Inputs used
| packages | scib-metrics |
| ecosystems | pypi |
| any_deprecated | no |
| min_days_since_publish | 8 |
Engineering Quality
Are baseline engineering and documentation practices in place?
92
Engineering practices
100Excellent
How it's scored
| 24/24 | CI workflows — 8 workflow(s) |
| 24/24 | Tests present |
| 16/16 | Linter config |
| 9.6/9.6 | Pre-commit hooks |
| 6.4/6.4 | .editorconfig |
| 20/20 | OpenSSF Scorecard: CI-Tests — 24 out of 24 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
80Good
How it's scored
| 30/30 | README |
| 25/25 | Documentation directory |
| 15/15 | Documentation / homepage site — https://scib-metrics.readthedocs.io/ |
| 10/10 | Repository description |
| 0/10 | Topics |
| 0/10 | Wiki |
Inputs used
| topics | — |
| has_wiki | no |
| homepage | https://scib-metrics.readthedocs.io/ |
| 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?
50
Security posture
50Moderate
How it's scored
| 7.5/7.5 | Binary-Artifacts — no binaries found in the repo |
| 3.8/7.5 | Branch-Protection — branch protection is not maximal on development and all release branches |
| 2.5/2.5 | CI-Tests — 24 out of 24 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 0/9 approved changesets -- score normalized to 0 |
| 2.5/2.5 | Contributors — project has 5 contributing companies or organizations |
| 10/10 | Dangerous-Workflow — no dangerous workflow patterns detected |
| 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 — 15 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 |
| 5/5 | Packaging — packaging workflow detected |
| 0/5 | Pinned-Dependencies — dependency not pinned by hash detected -- score normalized to 0 |
| 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 — detected GitHub workflow tokens with excessive permissions |
| 7.5/7.5 | Vulnerabilities — 0 existing vulnerabilities detected |
Inputs used
| source | openssf_scorecard |
| checks_evaluated | 17 |
| scorecard_version | v5.5.0 |
| checks_inconclusive | 1 |
| scorecard_aggregate | 5 |
Excluded from scoring (no data or not applicable): signed_releases. Remaining weights renormalized.
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.
47
Agent context & guidance
40At risk
How it's scored
| 0/45 | Agent instructions — no CLAUDE.md / AGENTS.md / editor rules |
| 0/15 | Machine-readable docs (llms.txt) |
| 39.6/40 | Legible commit history — 23 of 31 human commits state their intent (structured subject or explanatory body) |
Inputs used
| has_llms_txt | no |
| legible_history_share | 0.742 |
| agent_instruction_files | — |
| agent_instruction_max_bytes | — |
Verify loop (build / test / typecheck)
51Moderate
How it's scored
| 18/18 | One-command bootstrap — docs/Makefile |
| 22/22 | Automated tests |
| 11/11 | Lint / format config |
| 0/11 | Static type checking |
| 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 — dependency not pinned by hash detected -- score normalized to 0 |
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 | — |
| agent_commit_share | 0 |
| toolchain_manifests | — |
| dependency_bot_commit_share | 0 |
Code legibility for models
55Moderate
How it's scored
| 0/45 | Type-checkable code — Python without a type-check config |
| 55/55 | Manageable file sizes — 0/40 source files over 60KB |
Inputs used
| primary_language | Python |
| largest_source_bytes | 16,779 |
| source_files_sampled | 40 |
| oversized_source_files | 0 |
Machine-readable interfaces
40At risk
How it's scored
| 0/40 | API schema (OpenAPI/GraphQL/proto) |
| 0/20 | MCP server |
| 40/40 | Runnable examples — notebooks |
Inputs used
| example_dirs | notebooks |
| has_mcp_signal | no |
| api_schema_files | — |
Key facts
96GitHub stars
9contributors
54commits, last 12 months
0days since last push
29releases
1bus factor
7open issues
PyPIpackage ecosystems
Data collection warnings
- deps.dev does not index pypi:scib-metrics@0.5.10; advisories assessed against the repository dependency graph instead
- No resolved dependencies carried a version and a supported ecosystem
More detail
Star and fork history 96 ★ / 22 ⇿
96Stars
22Forks
25Releases
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 5Patch 20
Each point covers 4 days.
OpenSSF Scorecard 5.0 / 10
5.0aggregate
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 |
| 5 | Branch-Protection | branch protection is not maximal on development and all release branches |
| 10 | CI-Tests | 24 out of 24 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 0/9 approved changesets -- score normalized to 0 |
| 10 | Contributors | project has 5 contributing companies or organizations |
| 10 | Dangerous-Workflow | no dangerous workflow patterns detected |
| 0 | Dependency-Update-Tool | no update tool detected |
| 0 | Fuzzing | project is not fuzzed |
| 10 | License | license file detected |
| 10 | Maintained | 15 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10 |
| 10 | Packaging | packaging workflow detected |
| 0 | Pinned-Dependencies | dependency not pinned by hash detected -- score normalized to 0 |
| 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 |
| 0 | Token-Permissions | detected GitHub workflow tokens with excessive permissions |
| 10 | Vulnerabilities | 0 existing vulnerabilities detected |
Direct dependencies 16
| Registry | Package | Version constraint | Manifest |
|---|---|---|---|
| PyPI | anndata | — | pyproject.toml |
| PyPI | chex | — | pyproject.toml |
| PyPI | jax | — | pyproject.toml |
| PyPI | jaxlib | — | pyproject.toml |
| PyPI | numpy | — | pyproject.toml |
| PyPI | pandas | — | pyproject.toml |
| PyPI | scipy | — | pyproject.toml |
| PyPI | scikit-learn | — | pyproject.toml |
| PyPI | scanpy | >=1.9 | pyproject.toml |
| PyPI | rich | — | pyproject.toml |
| PyPI | pynndescent | — | pyproject.toml |
| PyPI | igraph | >0.9.0 | pyproject.toml |
| PyPI | matplotlib | — | pyproject.toml |
| PyPI | plottable | — | pyproject.toml |
| PyPI | tqdm | — | pyproject.toml |
| PyPI | umap-learn | >=0.5.0 | pyproject.toml |
All dependencies 11
Full resolved dependency set from the GitHub dependency graph: 3 direct and 8 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.
| Registry | Package | Version | Relation |
|---|---|---|---|
| PyPI | igraph | — | direct |
| PyPI | scanpy | — | direct |
| PyPI | umap-learn | — | direct |
| PyPI | numba | — | indirect |
| PyPI | pybtex-docutils | — | indirect |
| PyPI | scanpydoc | — | indirect |
| PyPI | scib | — | indirect |
| PyPI | sphinx | — | indirect |
| PyPI | sphinx-book-theme | — | indirect |
| PyPI | sphinxcontrib-bibtex | — | indirect |
| PyPI | twine | — | 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
{
"data": {
"repo": {
"topics": [],
"is_fork": false,
"size_kb": 1437,
"has_wiki": false,
"homepage": "https://scib-metrics.readthedocs.io/",
"languages": {
"Python": 121140
},
"pushed_at": "2026-07-21T06:42:34Z",
"created_at": "2022-10-03T01:53:06Z",
"owner_type": "Organization",
"updated_at": "2026-07-21T07:25:38Z",
"description": "Accelerated, Python-only, single-cell integration benchmarking metrics",
"is_archived": false,
"is_disabled": false,
"license_spdx": "BSD-3-Clause",
"default_branch": "main",
"license_spdx_raw": "BSD-3-Clause",
"primary_language": "Python",
"significant_languages": [
"Python"
]
},
"owner": {
"blog": "https://www.weizmann.ac.il/immunology/yosef/",
"name": "Yosef Lab",
"type": "Organization",
"login": "YosefLab",
"company": null,
"location": "Israel",
"followers": 138,
"avatar_url": "https://avatars.githubusercontent.com/u/13837262?v=4",
"created_at": "2015-08-17T17:07:24Z",
"is_verified": null,
"public_repos": 73,
"account_age_days": 3991
},
"license": {
"state": "standard",
"spdx_id": "BSD-3-Clause",
"raw_spdx": "BSD-3-Clause",
"file_present": true,
"scorecard_found": true,
"profile_has_license": true
},
"activity": {
"releases": [
{
"tag": "v0.5.10",
"kind": "patch",
"published_at": "2026-07-13T07:05:47Z"
},
{
"tag": "v0.5.9",
"kind": "patch",
"published_at": "2026-02-26T08:11:41Z"
},
{
"tag": "v0.5.8",
"kind": "patch",
"published_at": "2026-02-06T09:57:47Z"
},
{
"tag": "v0.5.7",
"kind": "patch",
"published_at": "2025-09-14T07:22:28Z"
},
{
"tag": "v0.5.6",
"kind": "patch",
"published_at": "2025-07-08T12:30:38Z"
},
{
"tag": "v0.5.5",
"kind": "patch",
"published_at": "2025-06-03T11:04:57Z"
},
{
"tag": "v0.5.4",
"kind": "patch",
"published_at": "2025-04-23T06:16:28Z"
},
{
"tag": "v0.5.3",
"kind": "patch",
"published_at": "2025-02-17T10:04:09Z"
},
{
"tag": "v0.5.2",
"kind": "patch",
"published_at": "2025-02-12T22:19:04Z"
},
{
"tag": "v0.5.1",
"kind": "patch",
"published_at": "2024-02-23T22:18:26Z"
},
{
"tag": "v0.5.0",
"kind": "minor",
"published_at": "2024-01-04T18:38:46Z"
},
{
"tag": "0.4.1",
"kind": "patch",
"published_at": "2023-10-08T20:40:57Z"
},
{
"tag": "0.4.0",
"kind": "minor",
"published_at": "2023-09-18T22:46:24Z"
},
{
"tag": "0.3.3",
"kind": "patch",
"published_at": "2023-03-29T19:04:51Z"
},
{
"tag": "0.3.2",
"kind": "patch",
"published_at": "2023-03-13T17:27:13Z"
},
{
"tag": "0.3.1",
"kind": "patch",
"published_at": "2023-02-16T18:06:54Z"
},
{
"tag": "0.3.0",
"kind": "minor",
"published_at": "2023-02-16T17:08:49Z"
},
{
"tag": "0.2.0",
"kind": "minor",
"published_at": "2023-02-03T17:52:06Z"
},
{
"tag": "0.1.1",
"kind": "patch",
"published_at": "2023-01-04T18:51:35Z"
},
{
"tag": "0.1.0",
"kind": "minor",
"published_at": "2023-01-02T20:28:23Z"
},
{
"tag": "0.0.9",
"kind": "patch",
"published_at": "2022-12-17T03:45:40Z"
},
{
"tag": "0.0.8",
"kind": "patch",
"published_at": "2022-11-18T19:58:25Z"
},
{
"tag": "0.0.7",
"kind": "patch",
"published_at": "2022-10-31T20:27:52Z"
},
{
"tag": "0.0.6",
"kind": "patch",
"published_at": "2022-10-25T16:57:15Z"
},
{
"tag": "0.0.5",
"kind": "patch",
"published_at": "2022-10-25T05:44:14Z"
},
{
"tag": "0.0.4",
"kind": "patch",
"published_at": "2022-10-11T03:38:21Z"
},
{
"tag": "0.0.3",
"kind": "patch",
"published_at": "2022-10-10T03:05:41Z"
},
{
"tag": "0.0.2",
"kind": "patch",
"published_at": "2022-10-03T18:59:51Z"
},
{
"tag": "0.0.1",
"kind": "patch",
"published_at": "2022-10-03T18:52:05Z"
}
],
"recent_commits": [
{
"oid": "ad2afce6acfc09318f92c516e011e86b851413c3",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.21 → v0.15.22](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.21...v0.15.22)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#279)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-07-21T06:42:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d435d7aebefd6cfbb751973c70390fa4b564f396",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.20 → v0.15.21](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.20...v0.15.21)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#277)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-07-14T05:53:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "cdeaaa5fb041e17ea396712d3e854bce485b499b",
"body": null,
"is_bot": false,
"headline": "Also updated to codecov/codecov-action@v6",
"author_name": "ori-kron-wis",
"author_login": "ori-kron-wis",
"committed_at": "2026-07-13T07:19:33Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8a6a855f2bfdaead2408a7b041686882b4ab6c99",
"body": "* ci: update github workflows\n\n* also fixed anndata 0.13 and pandas 3 updated api",
"is_bot": false,
"headline": "ci: update github workflows (#276)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2026-07-13T07:01:18Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "132db5b6f11a7e71b64a20afb7b5dff72c371849",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.18 → v0.15.20](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.18...v0.15.20)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#275)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-06-30T07:07:23Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0be2f216852c3d26468409c1557f398d2fbfdee6",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.17 → v0.15.18](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.17...v0.15.18)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>\nCo-authored-by: Ori Kronfeld <ori.kronfeld@weizmann.ac.il>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#274)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-06-23T08:25:35Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d62345481a20066846c97921eb978812eacf8700",
"body": null,
"is_bot": false,
"headline": "Update Read the Docs configuration for new versions",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2026-06-23T07:47:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "851c8e606dad7fa43d2da2b085d997cc96bd49be",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.16 → v0.15.17](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.16...v0.15.17)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#272)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-06-16T05:52:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2d3ce834887d0f5fa4acf65d3e7457d68625879c",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.15 → v0.15.16](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.15...v0.15.16)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#271)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-06-09T06:17:19Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d9fb5f849d1a292e8e685a2ce1a9cf3415056f78",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.14 → v0.15.15](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.14...v0.15.15)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#270)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-06-02T06:12:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "80a0723085913cc5ac2c63df29ea53bee69df992",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.13 → v0.15.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.13...v0.15.14)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#269)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-05-25T20:58:34Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "494f1109b948d5a750a958342d72a44ed38f62b9",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.12 → v0.15.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.12...v0.15.13)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#268)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-05-19T06:27:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e15177d634797751a2328af2df06469d71d226b4",
"body": null,
"is_bot": false,
"headline": "Bump version from 0.5.9 to 0.5.10",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2026-05-12T13:23:58Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "778f4c1f5ff7915b05f7548c9d911b50df0c6a5f",
"body": "* [pre-commit.ci] pre-commit autoupdate\n\nupdates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.11 → v0.15.12](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.11...v0.15.12)\n\n* Added support for HarmonyPy V2\n\n---------\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>\nCo-authored-by: ori-kron-wis <ori.kronfeld@weizmann.ac.il>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#266)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-04-28T10:41:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6473ae23bc30c79e9c25380a0230508caa903cde",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.10 → v0.15.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.10...v0.15.11)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#265)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-04-23T07:15:38Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1fe209c1edea3699a6c4509355f866f7046a950e",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.9 → v0.15.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.9...v0.15.10)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#264)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-04-14T08:06:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f68d5b94c3e93e646fe6a0a7df1619ad1d345bf4",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.8 → v0.15.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.8...v0.15.9)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#263)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-04-09T09:58:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0006efa6ea7ab7409b0bc85757c1d55e883be669",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.7 → v0.15.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.7...v0.15.8)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#262)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-03-31T06:34:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "00661bb8cecfa4c4e9317721d1989ff015d34e1c",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.6 → v0.15.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.6...v0.15.7)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#261)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-03-24T08:10:10Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7bdb15a775053b080c109dc41956ed8492b13532",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.5 → v0.15.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.5...v0.15.6)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#260)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-03-17T07:36:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2c0ca5dd00c48e86ddd0904c543ac53875bf4a35",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.4 → v0.15.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.4...v0.15.5)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#258)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-03-09T21:25:18Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b381c920ef66d9ecd8410617d28c1432088e25d4",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.2 → v0.15.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.2...v0.15.4)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#257)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-03-03T06:46:43Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e22886e3053643a787903bdfc126a34ccd21cf03",
"body": "* Update changelog for kbet calculation fix\n\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\n\nfor more information, see https://pre-commit.ci\n\n---------\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": false,
"headline": "Update changelog for kbet calculation fix (#256)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2026-02-26T08:05:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8eea92fd04c562ca3a825a2c92ebeb4269ae49a0",
"body": null,
"is_bot": false,
"headline": "Update CHANGELOG for version 0.5.9",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2026-02-26T08:03:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "93991f066bd0525b0f5e90d4e508e61e5534417b",
"body": null,
"is_bot": false,
"headline": "Bump version from 0.5.8 to 0.5.9",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2026-02-26T07:51:01Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "35232e59464b4654cc11f761ece9d6ac5403f5ef",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.1 → v0.15.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.1...v0.15.2)\n- [github.com/kynan/nbstripout: 0.9.0 → 0.9.1](https://github.com/kynan/nbstripout/compare/0.9.0...0.9.1)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#255)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-02-24T07:48:26Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0f10ca89b52eb3727fe31cfb097e925d8ea7c966",
"body": null,
"is_bot": false,
"headline": "update kbet calc with new numpy (#254)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2026-02-22T15:18:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d89a8c2bb4175d13ca303804e4877a606c0d7fd5",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.15.0 → v0.15.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.0...v0.15.1)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#253)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-02-17T10:18:36Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7e4993376bc664f0062120784bdb348a6f7aaa02",
"body": "* [pre-commit.ci] pre-commit autoupdate\n\nupdates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.14 → v0.15.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.14...v0.15.0)\n\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\n\nfor more information, see https://pre-commit.ci\n\n---------\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#252)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-02-10T07:04:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "14c5e347b16f72381a92b74354a4e8119b862381",
"body": "Added citation information for scib-metrics and original benchmarking work.",
"is_bot": false,
"headline": "Update README with citation details",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2026-02-06T10:05:34Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0d554a96805c35ba3d228e5e1fd844361ba816d1",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.13 → v0.14.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.13...v0.14.14)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#251)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-01-26T21:30:40Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "24e35fb69c00b9ab729f432207315c6d5757501f",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.11 → v0.14.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.11...v0.14.13)\n- [github.com/kynan/nbstripout: 0.8.2 → 0.9.0](https://github.com/kynan/nbstripout/compare/0.8.2...0.9.0)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#250)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-01-21T07:32:34Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e8af0b306c1600d3cdf903454db711da3d22491a",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.10 → v0.14.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.10...v0.14.11)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#249)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2026-01-12T20:41:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f5a9530792caa50e34451065254f2ddb73bd0886",
"body": "* [pre-commit.ci] pre-commit autoupdate\n\nupdates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.8 → v0.14.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.8...v0.14.10)\n\n* Update pyproject.toml\n\n---------\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>\nCo-authored-by: Ori Kronfeld <ori.kronfeld@weizmann.ac.il>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#247)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-12-23T10:09:16Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "918e45a154130f20006044ce52aa10cba581e9b9",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.7 → v0.14.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.7...v0.14.8)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#246)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-12-08T21:41:26Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4ef9a52296238318433bfc9a10e59bf9076d0cc9",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.6 → v0.14.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.6...v0.14.7)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#245)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-12-02T07:29:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "366130096138df0484fe8fa8a179381410b43336",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.5 → v0.14.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.5...v0.14.6)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#244)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-11-25T07:20:26Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "66889d55020b9d54503d1e87936bf4e058b2b4f4",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.4 → v0.14.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.4...v0.14.5)\n- [github.com/kynan/nbstripout: 0.8.1 → 0.8.2](https://github.com/kynan/nbstripout/compare/0.8.1...0.8.2)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#243)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-11-18T09:54:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "db3df0b577cd75b80bf192371f17dfc8c81fb683",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.3 → v0.14.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.3...v0.14.4)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#242)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-11-11T07:51:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d709e227b19013cac48ecdb0cb15c8096fb1ffb8",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.2 → v0.14.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.2...v0.14.3)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#241)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-11-04T06:59:44Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c0b2d7f5bfd257932d6ad9659404b501f1939256",
"body": "* Added set seed for all leiden metric calcualtions options\n\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\n\nfor more information, see https://pre-commit.ci\n\n---------\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": false,
"headline": "Fix: set seed for Leiden clustering (#240)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-10-30T06:53:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0404e63b35e526132b29aefa607093df7feaa324",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.1 → v0.14.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.1...v0.14.2)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#239)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-10-28T12:31:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5f806c3ed539d6367770e34ff418c4d7235455bf",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.14.0 → v0.14.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.0...v0.14.1)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#238)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-10-21T06:04:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a3a8da40a5c58bf19789de58966fb0d638a6290a",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.13.2 → v0.14.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.2...v0.14.0)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#237)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-10-15T07:39:00Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "42107f2450943aba526db3dd23434f49fef8a1fa",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.13.1 → v0.13.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.1...v0.13.2)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#235)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-09-30T06:07:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e450f9a56259d0a7197b53d90014fdacc7a39fee",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.13.0 → v0.13.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.0...v0.13.1)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#233)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-09-25T05:34:33Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b82f1b916ec288ae6f1da67ce3fef512cd0adb9b",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.12 → v0.13.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.12...v0.13.0)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#230)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-09-16T09:56:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "83de2a79a04bdbbb1a4b77b40e18af6f48c5d0fd",
"body": "…es + moving to py313 (#229)\n\n* added solver selection to benchmarker for arpack stability issues\n\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\n\nfor more information, see https://pre-commit.ci\n\n* also removed py3.10 and added py3.13\n\n* update RTD python ver\n\n---------\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": false,
"headline": "feat: added solver selection to benchmarker for arpack stability issu…",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-09-14T07:17:26Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2c0b934b6272ae9d55a68bcbd9b4690f5e2d81c8",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.10 → v0.12.12](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.10...v0.12.12)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#228)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-09-09T06:23:57Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "177dd252658fc2af059c3c21769a8d3bf721b796",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.9 → v0.12.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.9...v0.12.10)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#227)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-09-01T06:32:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "06a1f2c8c10d24ddb7c05d2871dd6114fb588a6c",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.8 → v0.12.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.8...v0.12.9)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#226)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-08-19T05:57:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "bb473d4e03f0a37de93807dd44a0299c1ad8607a",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.7...v0.12.8)\n- [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#225)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-08-12T05:35:28Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "b9590642a65224e2888e28e0699e0b194ae8aefb",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.5 → v0.12.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.5...v0.12.7)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#223)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-08-05T06:10:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f872405579c9b954f70ff248b9965c58c965e6b7",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.4 → v0.12.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.4...v0.12.5)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#222)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-07-31T10:01:03Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a79ad9fc94abac002cc335868e9c606ab3db85b4",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.3 → v0.12.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.3...v0.12.4)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#221)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-07-22T10:26:25Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "4ec7832d385dbdcdc4b64f7826f413f831f5597c",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.2 → v0.12.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.2...v0.12.3)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#220)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-07-15T06:32:31Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "de7edbac0be6241c1229efee575730856d408e0f",
"body": "* adding BRAS to benchmarker\n\n* added to benchmarker\n\n* added a flag for _compute_neighbors\n\n* added a flag for _compute_neighbors\n\n* chanlog\n\n* chanlog",
"is_bot": false,
"headline": "feat: adding BRAS to benchmarker (#217)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-07-08T12:29:41Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "872d50eafba1d8a48958fc0d5ae620fb9fc3f9d0",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.1 → v0.12.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.1...v0.12.2)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#216)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-07-08T06:12:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a9695893012247252901167336e277906c548418",
"body": null,
"is_bot": false,
"headline": "min_max_scale=False should be default in .get_results (#215)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-07-07T12:39:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a639cbcb7f85c0a8ae7119a54c7bc6e0a7493f65",
"body": "This reverts commit 343cb8fca0500f38c134aac7e6d5dd40b8781dd1.\n\nCo-authored-by: Ori Kronfeld <ori.kronfeld@weizmann.ac.il>",
"is_bot": false,
"headline": "Revert \"Skip labels before loop (#180)\" (#213)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2025-07-07T12:25:22Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "51ad6873b90e960183848893625bc2793d74d303",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.12.0 → v0.12.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.0...v0.12.1)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#214)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-07-01T10:13:50Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "268cd9d5ae6c75f74677fc78bcbdb2f0ee3bfb24",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.13 → v0.12.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.13...v0.12.0)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#211)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-06-26T08:37:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e76555e2ff494f81cdc2652216622e8f83e7befa",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.12 → v0.11.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.12...v0.11.13)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#210)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-06-11T09:07:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "12b6f354ac0305c8c81859696ed57f7e3c75927c",
"body": "* Add fast BRAS implementation to scib-metrics package.\n\n* Fix edge cases for naive silhouette implementation, remove comment line and update CHANGELOG.md.\n\n* Apply suggestions from code review\r\n\r\nCorrected function referencing in CHANGELOG and docstrings.\n\nCo-authored-by: Adam Gayoso <adamgayoso@us\n[…]\nleased section.\n\n* Update pyproject.toml\n\n* Update CHANGELOG.md\n\n---------\n\nCo-authored-by: Adam Gayoso <adamgayoso@users.noreply.github.com>\nCo-authored-by: Ori Kronfeld <ori.kronfeld@weizmann.ac.il>",
"is_bot": false,
"headline": "Add fast BRAS implementation to scib-metrics package. (#197)",
"author_name": "prauten",
"author_login": "prauten",
"committed_at": "2025-06-03T11:01:59Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "649362c4154cf134a81a53a4491b7cc951a13911",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.11 → v0.11.12](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.11...v0.11.12)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#209)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-06-03T08:51:37Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "5d01bb46f4d2317b4b3379851c7202df5be36c68",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.10 → v0.11.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.10...v0.11.11)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#208)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-05-27T06:45:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "86df19892555a5acf827c86bd2321ebb3249db6e",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.8 → v0.11.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.8...v0.11.10)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#207)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-05-22T07:48:44Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "51cbe344f6ccbd61341362fca37148f7d720e021",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.7 → v0.11.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.7...v0.11.8)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#206)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-05-08T09:11:02Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2432e6c7fb0a1a47ccca677292282c038ba5b663",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.6 → v0.11.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.6...v0.11.7)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#204)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-04-29T06:33:45Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a4938c1ae21e09e79d21c180d2fab401bb0dbd85",
"body": "* update to bio_conservation_metrics, batch_correction_metrics deafult values\n\n* added log and test\n\n* typo",
"is_bot": false,
"headline": "fix: update default init values for benchmarker (#203)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-04-23T06:13:21Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "fc28c2a62276ca00c0ccc02f383187b77219cfe3",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.5 → v0.11.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.5...v0.11.6)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#202)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-04-23T05:55:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "1e8fab75307b6f954d5583431c1a61ea193601db",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.4 → v0.11.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.4...v0.11.5)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#201)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-04-20T07:39:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "c82456e8748f0798f8b1d3fac17f6e96cbbd9f59",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.2 → v0.11.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.2...v0.11.4)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#199)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-04-10T10:20:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "343cb8fca0500f38c134aac7e6d5dd40b8781dd1",
"body": "Co-authored-by: Adam Gayoso <adamgayoso@users.noreply.github.com>",
"is_bot": false,
"headline": "Skip labels before loop (#180)",
"author_name": "John Arevalo",
"author_login": "johnarevalo",
"committed_at": "2025-04-06T20:18:54Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2bc648d99a917fce319edb129c66c1de100b31a2",
"body": null,
"is_bot": false,
"headline": "Update CHANGELOG.md (#196)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-03-30T07:13:47Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "44ea38a16b7e08f310e8b4b02181a7e127867bc6",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.11.0 → v0.11.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.0...v0.11.2)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#195)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-03-28T13:42:53Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2471c5011a487b0aa4703945f47b4c17cfe7e1f5",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.9.9 → v0.11.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.9...v0.11.0)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#194)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-03-18T08:21:06Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "aef5a7686ca429dec0b6eb434410e41a28f8910e",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.9.7 → v0.9.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.7...v0.9.9)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#191)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-03-04T07:44:51Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "82d67b8e77389088b3c572f82a83de0ea3f436f4",
"body": "updates:\n- [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.9.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.9.6...v0.9.7)\n\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#190)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-02-25T07:40:03Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e4033d400b2e955a2086dda9b6a3535057c4e4c8",
"body": null,
"is_bot": false,
"headline": "Update pyproject.toml",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-02-17T10:03:43Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e22f3746c1fae1b1c176480802d392bf667968eb",
"body": null,
"is_bot": false,
"headline": "Update pyproject.toml",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-02-17T09:59:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "3b70c9850a46ab60ae9e71924a03e2b0eadf77e5",
"body": null,
"is_bot": false,
"headline": "Update _core.py (#189)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-02-17T09:52:07Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d7f3df76b796788a4d7b1a5a64e41dc0fd084bdf",
"body": "* [pre-commit.ci] pre-commit autoupdate\r\n\r\nupdates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.7.3 → v0.9.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.3...v0.9.6)\r\n- [github.com/kynan/nbstripout: 0.8.0 → 0.8.1](https://github.com/kynan/nbstripout/compare/0.8.0...0.8.1)\r\n\r\n* [pre-co\n[…]\nrmation, see https://pre-commit.ci\r\n\r\n---------\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>\r\nCo-authored-by: Ori Kronfeld <ori.kronfeld@weizmann.ac.il>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#185)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2025-02-12T22:17:21Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "721695c2350187a0ca5c4f0f579da2b4563b2f8b",
"body": "* added option for missing group of metrics and fill in with 0.5\r\n\r\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\r\n\r\nfor more information, see https://pre-commit.ci\r\n\r\n* tests fixes\r\n\r\n* tests fixes2\r\n\r\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\r\n\r\nfor more information, see https://pre-commit.ci\r\n\r\n* add changlog\r\n\r\n---------\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": false,
"headline": "feat: support scvi-tools scib-metric autotune (#188)",
"author_name": "Ori Kronfeld",
"author_login": "ori-kron-wis",
"committed_at": "2025-02-12T22:12:11Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "8cf4fafe422a7efcb501ca77efd3b47a2fb01d92",
"body": "updates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.7.2 → v0.7.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.2...v0.7.3)\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#184)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2024-11-18T07:57:13Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "d5f8a81ebe13d99d1b4ebc5ed5bfcc7a58c4f15f",
"body": "updates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.7.1 → v0.7.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.1...v0.7.2)\r\n- [github.com/kynan/nbstripout: 0.7.1 → 0.8.0](https://github.com/kynan/nbstripout/compare/0.7.1...0.8.0)\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#183)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2024-11-10T18:26:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "2ffccb4318ba985f2395c005064c225c4197f822",
"body": "* Update _lisi.py\r\n\r\n* Update _lisi.py\r\n\r\n* Update CHANGELOG.md\r\n\r\n* Update CHANGELOG.md",
"is_bot": false,
"headline": "Fix Lisi return type and docstring (#182)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-11-04T08:46:05Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "e31aa1cc7f8c6e8e3332369519aed7dfd6b1f15b",
"body": "… work with bio/batch separately. (#181)\n\n\r\n---------\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": false,
"headline": "Change behavior of None default metrics and allow results/plotting to…",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-11-04T08:01:59Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a2575daea1d0491d80090edef5b2fa21371ee01f",
"body": "updates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.7.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.7.1)\r\n- [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0)\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#178)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2024-10-30T08:51:32Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "876e8fd1f581e466482f33980769de0d779f039f",
"body": "* Add more ruff rules\r\n\r\n* remove bandit\r\n\r\n* Add FA\r\n\r\n* fixes\r\n\r\n* Remove D400",
"is_bot": false,
"headline": "Add more ruff rules (#177)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-09-01T16:12:20Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "f41e4325c7750857fe201384a4c5128adc6a8875",
"body": "updates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.6.1 → v0.6.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.1...v0.6.2)\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#176)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2024-08-29T07:02:29Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "ec7c55b20ac823615906c544eadf81bd65314e2c",
"body": "* Update _core.py\r\n\r\n* Update _lisi.py\r\n\r\n* Update sampling.py\r\n\r\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\r\n\r\nfor more information, see https://pre-commit.ci\r\n\r\n---------\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": false,
"headline": "Typing fixes (#174)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-08-22T08:12:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "6a2924f30dfc53146944cbece5fea264b25ae734",
"body": "* Update template to v0.4.0\r\n\r\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\r\n\r\nfor more information, see https://pre-commit.ci\r\n\r\n* Delete README.md.rej\r\n\r\n* Delete docs/conf.py.rej\r\n\r\n* Update README.md\r\n\r\n* Update pyproject.toml\r\n\r\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\r\n\n[…]\n----\r\n\r\nCo-authored-by: scverse-bot <None>\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>\r\nCo-authored-by: Adam Gayoso <adamgayoso@users.noreply.github.com>",
"is_bot": false,
"headline": "Update template to v0.4.0 (#165)",
"author_name": "scverse-bot",
"author_login": "scverse-bot",
"committed_at": "2024-08-22T08:03:01Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "081dff0dde6fa8e80ff06f5dc39a1bcae3f4b63a",
"body": "* Add seed to leiden clustering\r\n\r\n* Update _nmi_ari.py\r\n\r\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\r\n\r\nfor more information, see https://pre-commit.ci\r\n\r\n* Update test_metrics.py\r\n\r\n* [pre-commit.ci] auto fixes from pre-commit.com hooks\r\n\r\nfor more information, see https://pre-commit.c\n[…]\nit.ci] auto fixes from pre-commit.com hooks\r\n\r\nfor more information, see https://pre-commit.ci\r\n\r\n---------\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": false,
"headline": "Add seed to leiden clustering (#173)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-08-22T07:29:15Z",
"body_truncated": true,
"is_coding_agent": false
},
{
"oid": "c19679cc885287584f86e3b821266e0ec8b35d0a",
"body": "updates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.5.1 → v0.6.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.1...v0.6.1)\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>\r\nCo-authored-by: Adam Gayoso <adamgayoso@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#169)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2024-08-22T06:38:15Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "96cb2c07c00114e88ab316c1f10988c53f68d508",
"body": "* Fix warnings\r\n\r\n* Update _nmi_ari.py\r\n\r\n* Update _kbet.py\r\n\r\n* Update CHANGELOG.md",
"is_bot": false,
"headline": "Fix warnings (#171)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-08-21T21:08:08Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "a04c58f2ca2b1bfd544a503f8987000a739d8612",
"body": "* Fix kmeans test instability\r\n\r\n* Update test_neighbors.py\r\n\r\n* Update test_metrics.py\r\n\r\n* Update CHANGELOG.md",
"is_bot": false,
"headline": "Fix kmeans test instability (#172)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-08-21T20:57:52Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "7482c062883303c05ebe34f11180f08fafb69ff1",
"body": "* Use new scanpy umap connectivity fn in test\r\n\r\n* Update test_neighbors.py\r\n\r\n* Update CHANGELOG.md",
"is_bot": false,
"headline": "Use new scanpy umap connectivity fn in test (#170)",
"author_name": "Adam Gayoso",
"author_login": "adamgayoso",
"committed_at": "2024-08-21T20:22:27Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "0071da9d2216487727286916aa275b2c6ca844cb",
"body": "updates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.4.10 → v0.5.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.10...v0.5.1)\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#168)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2024-07-09T19:07:04Z",
"body_truncated": false,
"is_coding_agent": false
},
{
"oid": "88d0c7a8c1d50dad805b297053f3bf2c203bf83a",
"body": "updates:\r\n- [github.com/astral-sh/ruff-pre-commit: v0.4.9 → v0.4.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.9...v0.4.10)\r\n\r\nCo-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>",
"is_bot": true,
"headline": "[pre-commit.ci] pre-commit autoupdate (#167)",
"author_name": "pre-commit-ci[bot]",
"author_login": "pre-commit-ci[bot]",
"committed_at": "2024-06-25T16:38:14Z",
"body_truncated": false,
"is_coding_agent": false
}
],
"releases_count": 29,
"commits_last_year": 54,
"latest_release_at": "2026-07-13T07:05:47Z",
"latest_release_tag": "v0.5.10",
"releases_from_tags": false,
"days_since_last_push": 0,
"active_weeks_last_year": 38,
"days_since_latest_release": 8,
"mean_days_between_releases": 96.7
},
"community": {
"has_readme": true,
"has_license": true,
"has_description": true,
"has_contributing": true,
"health_percentage": 50,
"has_issue_template": false,
"has_code_of_conduct": false,
"has_pull_request_template": false
},
"ecosystem": {
"packages": [
{
"name": "scib-metrics",
"exists": true,
"license": null,
"keywords": [],
"ecosystem": "pypi",
"matches_repo": true,
"registry_url": "https://pypi.org/project/scib-metrics/",
"is_deprecated": false,
"latest_version": "0.5.10",
"repository_url": "https://github.com/yoseflab/scib-metrics",
"versions_count": 28,
"total_downloads": null,
"dependents_count": null,
"deprecation_note": null,
"maintainers_count": null,
"monthly_downloads": null,
"first_published_at": "2022-10-03T19:00:49.142781Z",
"latest_published_at": "2026-07-13T07:06:14.558760Z",
"latest_version_yanked": null,
"days_since_latest_publish": 8
}
]
},
"popularity": {
"forks": 22,
"stars": 96,
"watchers": 6,
"fork_history": {
"days": [
{
"date": "2023-04-14",
"count": 1
},
{
"date": "2023-05-02",
"count": 1
},
{
"date": "2023-06-06",
"count": 1
},
{
"date": "2023-08-23",
"count": 1
},
{
"date": "2023-09-14",
"count": 1
},
{
"date": "2023-09-19",
"count": 1
},
{
"date": "2024-02-22",
"count": 1
},
{
"date": "2024-03-08",
"count": 1
},
{
"date": "2024-04-10",
"count": 1
},
{
"date": "2024-09-03",
"count": 1
},
{
"date": "2024-09-06",
"count": 1
},
{
"date": "2024-12-04",
"count": 1
},
{
"date": "2025-02-04",
"count": 1
},
{
"date": "2025-03-31",
"count": 1
},
{
"date": "2025-04-14",
"count": 1
},
{
"date": "2025-04-21",
"count": 1
},
{
"date": "2025-08-15",
"count": 1
},
{
"date": "2025-10-06",
"count": 1
},
{
"date": "2025-11-04",
"count": 1
},
{
"date": "2025-12-16",
"count": 1
},
{
"date": "2026-04-07",
"count": 1
},
{
"date": "2026-05-16",
"count": 1
}
],
"complete": true,
"collected": 22,
"total_forks": 22
},
"star_history": {
"days": [
{
"date": "2022-10-25",
"count": 1
},
{
"date": "2022-10-26",
"count": 1
},
{
"date": "2022-11-02",
"count": 1
},
{
"date": "2022-11-03",
"count": 1
},
{
"date": "2022-11-14",
"count": 1
},
{
"date": "2023-02-03",
"count": 1
},
{
"date": "2023-02-10",
"count": 1
},
{
"date": "2023-03-08",
"count": 1
},
{
"date": "2023-03-14",
"count": 1
},
{
"date": "2023-04-05",
"count": 1
},
{
"date": "2023-04-26",
"count": 1
},
{
"date": "2023-05-25",
"count": 1
},
{
"date": "2023-06-20",
"count": 1
},
{
"date": "2023-08-02",
"count": 2
},
{
"date": "2023-08-03",
"count": 1
},
{
"date": "2023-08-07",
"count": 1
},
{
"date": "2023-09-19",
"count": 1
},
{
"date": "2023-09-21",
"count": 1
},
{
"date": "2023-09-24",
"count": 1
},
{
"date": "2023-09-25",
"count": 2
},
{
"date": "2023-10-17",
"count": 2
},
{
"date": "2023-12-11",
"count": 1
},
{
"date": "2023-12-12",
"count": 1
},
{
"date": "2023-12-13",
"count": 1
},
{
"date": "2024-01-03",
"count": 1
},
{
"date": "2024-01-04",
"count": 1
},
{
"date": "2024-02-12",
"count": 1
},
{
"date": "2024-02-22",
"count": 2
},
{
"date": "2024-02-27",
"count": 2
},
{
"date": "2024-03-13",
"count": 2
},
{
"date": "2024-03-30",
"count": 1
},
{
"date": "2024-04-10",
"count": 1
},
{
"date": "2024-04-17",
"count": 1
},
{
"date": "2024-05-26",
"count": 1
},
{
"date": "2024-07-11",
"count": 1
},
{
"date": "2024-07-25",
"count": 1
},
{
"date": "2024-08-07",
"count": 1
},
{
"date": "2024-08-17",
"count": 1
},
{
"date": "2024-09-04",
"count": 1
},
{
"date": "2024-10-04",
"count": 1
},
{
"date": "2024-10-17",
"count": 1
},
{
"date": "2024-11-02",
"count": 1
},
{
"date": "2024-11-09",
"count": 1
},
{
"date": "2024-12-04",
"count": 1
},
{
"date": "2024-12-11",
"count": 1
},
{
"date": "2024-12-25",
"count": 1
},
{
"date": "2025-01-07",
"count": 1
},
{
"date": "2025-02-04",
"count": 1
},
{
"date": "2025-03-26",
"count": 1
},
{
"date": "2025-03-27",
"count": 1
},
{
"date": "2025-04-21",
"count": 1
},
{
"date": "2025-04-24",
"count": 1
},
{
"date": "2025-05-27",
"count": 1
},
{
"date": "2025-06-16",
"count": 1
},
{
"date": "2025-07-01",
"count": 2
},
{
"date": "2025-07-30",
"count": 1
},
{
"date": "2025-08-06",
"count": 1
},
{
"date": "2025-08-07",
"count": 1
},
{
"date": "2025-08-11",
"count": 1
},
{
"date": "2025-08-12",
"count": 1
},
{
"date": "2025-08-19",
"count": 1
},
{
"date": "2025-08-24",
"count": 1
},
{
"date": "2025-09-03",
"count": 1
},
{
"date": "2025-09-07",
"count": 1
},
{
"date": "2025-09-10",
"count": 1
},
{
"date": "2025-10-20",
"count": 1
},
{
"date": "2025-10-22",
"count": 1
},
{
"date": "2025-10-29",
"count": 1
},
{
"date": "2025-11-03",
"count": 1
},
{
"date": "2025-11-14",
"count": 1
},
{
"date": "2025-11-22",
"count": 1
},
{
"date": "2025-11-25",
"count": 1
},
{
"date": "2026-01-06",
"count": 1
},
{
"date": "2026-01-13",
"count": 1
},
{
"date": "2026-01-18",
"count": 1
},
{
"date": "2026-01-21",
"count": 1
},
{
"date": "2026-01-27",
"count": 1
},
{
"date": "2026-01-30",
"count": 1
},
{
"date": "2026-02-11",
"count": 1
},
{
"date": "2026-02-27",
"count": 1
},
{
"date": "2026-03-05",
"count": 1
},
{
"date": "2026-03-15",
"count": 1
},
{
"date": "2026-04-03",
"count": 1
},
{
"date": "2026-04-15",
"count": 1
},
{
"date": "2026-05-16",
"count": 1
},
{
"date": "2026-06-18",
"count": 1
},
{
"date": "2026-07-08",
"count": 1
},
{
"date": "2026-07-09",
"count": 1
},
{
"date": "2026-07-21",
"count": 1
}
],
"complete": true,
"collected": 96,
"total_stars": 96
},
"open_issues_and_prs": 12
},
"ai_readiness": {
"has_nix": false,
"example_dirs": [
"notebooks"
],
"has_llms_txt": false,
"has_dockerfile": false,
"has_mcp_signal": false,
"bootstrap_files": [
"docs/Makefile"
],
"api_schema_files": [],
"has_devcontainer": false,
"typecheck_configs": [],
"toolchain_manifests": [],
"largest_source_bytes": 16779,
"source_files_sampled": 40,
"oversized_source_files": 0,
"agent_instruction_files": [],
"agent_instruction_max_bytes": null
},
"dependencies": {
"manifests": [
"pyproject.toml",
"setup.py"
],
"advisories": {
"error": "No resolved dependencies carried a version and a supported ecosystem",
"scope": "repository_graph",
"source": null,
"findings": [],
"collected": false,
"malicious": [],
"truncated": false,
"by_severity": {},
"advisory_count": 0,
"affected_count": 0,
"assessed_count": 0,
"malicious_count": 0,
"assessed_package": null,
"unassessed_count": 11,
"direct_affected_count": 0
},
"ecosystems": [
"pypi"
],
"dependencies": [
{
"name": "anndata",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "chex",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "jax",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "jaxlib",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "numpy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "pandas",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "scipy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "scikit-learn",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "scanpy",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=1.9"
},
{
"name": "rich",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "pynndescent",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "igraph",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">0.9.0"
},
{
"name": "matplotlib",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "plottable",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "tqdm",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": null
},
{
"name": "umap-learn",
"manifest": "pyproject.toml",
"ecosystem": "pypi",
"version_constraint": ">=0.5.0"
}
],
"all_dependencies": {
"error": null,
"source": "github-sbom",
"packages": [
{
"name": "igraph",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "scanpy",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "umap-learn",
"direct": true,
"version": null,
"ecosystem": "pypi"
},
{
"name": "numba",
"direct": false,
"version": null,
"ecosystem": "pypi"
},
{
"name": "pybtex-docutils",
"direct": false,
"version": null,
"ecosystem": "pypi"
},
{
"name": "scanpydoc",
"direct": false,
"version": null,
"ecosystem": "pypi"
},
{
"name": "scib",
"direct": false,
"version": null,
"ecosystem": "pypi"
},
{
"name": "sphinx",
"direct": false,
"version": null,
"ecosystem": "pypi"
},
{
"name": "sphinx-book-theme",
"direct": false,
"version": null,
"ecosystem": "pypi"
},
{
"name": "sphinxcontrib-bibtex",
"direct": false,
"version": null,
"ecosystem": "pypi"
},
{
"name": "twine",
"direct": false,
"version": null,
"ecosystem": "pypi"
}
],
"collected": true,
"truncated": false,
"total_count": 11,
"direct_count": 3,
"indirect_count": 8
}
},
"maintainership": {
"issues": {
"open_prs": 5,
"merged_prs": 203,
"open_issues": 7,
"closed_ratio": 0.873,
"closed_issues": 48,
"closed_unmerged_prs": 16
},
"bus_factor": 1,
"bot_contributors": 2,
"top_contributors": [
{
"type": "User",
"login": "adamgayoso",
"commits": 95,
"avatar_url": "https://avatars.githubusercontent.com/u/10859440?v=4"
},
{
"type": "User",
"login": "martinkim0",
"commits": 20,
"avatar_url": "https://avatars.githubusercontent.com/u/46072231?v=4"
},
{
"type": "User",
"login": "ori-kron-wis",
"commits": 18,
"avatar_url": "https://avatars.githubusercontent.com/u/175299014?v=4"
},
{
"type": "User",
"login": "scverse-bot",
"commits": 2,
"avatar_url": "https://avatars.githubusercontent.com/u/108668866?v=4"
},
{
"type": "User",
"login": "grst",
"commits": 1,
"avatar_url": "https://avatars.githubusercontent.com/u/7051479?v=4"
},
{
"type": "User",
"login": "johnarevalo",
"commits": 1,
"avatar_url": "https://avatars.githubusercontent.com/u/1301626?v=4"
},
{
"type": "User",
"login": "justjhong",
"commits": 1,
"avatar_url": "https://avatars.githubusercontent.com/u/14086852?v=4"
},
{
"type": "User",
"login": "Zethson",
"commits": 1,
"avatar_url": "https://avatars.githubusercontent.com/u/21954664?v=4"
},
{
"type": "User",
"login": "prauten",
"commits": 1,
"avatar_url": "https://avatars.githubusercontent.com/u/38099261?v=4"
}
],
"contributors_sampled": 9,
"top_contributor_share": 0.679
},
"quality_signals": {
"has_ci": true,
"has_tests": true,
"ci_workflows": [
"build.yaml",
"release.yaml",
"test_linux.yaml",
"test_linux_cuda.yaml",
"test_linux_pre.yaml",
"test_macos.yaml",
"test_macos_m1.yaml",
"test_windows.yaml"
],
"has_docs_dir": true,
"linter_configs": [],
"has_editorconfig": true,
"has_linter_config": true,
"has_precommit_config": true
},
"security_signals": {
"lockfiles": [],
"scorecard": {
"checks": [
{
"name": "Binary-Artifacts",
"score": 10,
"reason": "no binaries found in the repo",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#binary-artifacts"
},
{
"name": "Branch-Protection",
"score": 5,
"reason": "branch protection is not maximal on development and all release branches",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#branch-protection"
},
{
"name": "CI-Tests",
"score": 10,
"reason": "24 out of 24 merged PRs checked by a CI test -- score normalized to 10",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#ci-tests"
},
{
"name": "CII-Best-Practices",
"score": 0,
"reason": "no effort to earn an OpenSSF best practices badge detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#cii-best-practices"
},
{
"name": "Code-Review",
"score": 0,
"reason": "Found 0/9 approved changesets -- score normalized to 0",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#code-review"
},
{
"name": "Contributors",
"score": 10,
"reason": "project has 5 contributing companies or organizations",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#contributors"
},
{
"name": "Dangerous-Workflow",
"score": 10,
"reason": "no dangerous workflow patterns detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dangerous-workflow"
},
{
"name": "Dependency-Update-Tool",
"score": 0,
"reason": "no update tool detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#dependency-update-tool"
},
{
"name": "Fuzzing",
"score": 0,
"reason": "project is not fuzzed",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#fuzzing"
},
{
"name": "License",
"score": 10,
"reason": "license file detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#license"
},
{
"name": "Maintained",
"score": 10,
"reason": "15 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#maintained"
},
{
"name": "Packaging",
"score": 10,
"reason": "packaging workflow detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#packaging"
},
{
"name": "Pinned-Dependencies",
"score": 0,
"reason": "dependency not pinned by hash detected -- score normalized to 0",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#pinned-dependencies"
},
{
"name": "SAST",
"score": 0,
"reason": "SAST tool is not run on all commits -- score normalized to 0",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#sast"
},
{
"name": "Security-Policy",
"score": 0,
"reason": "security policy file not detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#security-policy"
},
{
"name": "Signed-Releases",
"score": null,
"reason": "no releases found",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#signed-releases"
},
{
"name": "Token-Permissions",
"score": 0,
"reason": "detected GitHub workflow tokens with excessive permissions",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#token-permissions"
},
{
"name": "Vulnerabilities",
"score": 10,
"reason": "0 existing vulnerabilities detected",
"documentation_url": "https://github.com/ossf/scorecard/blob/c395761df6afe1a69e476bc60a013a94bcbc153f/docs/checks.md#vulnerabilities"
}
],
"commit": "ad2afce6acfc09318f92c516e011e86b851413c3",
"ran_at": "2026-07-22T04:32:10Z",
"aggregate_score": 5,
"scorecard_version": "v5.5.0"
},
"has_codeql_workflow": false,
"has_security_policy": false,
"has_dependabot_config": false
},
"contribution_flow": {
"collected": true,
"ci_last_run_at": "2026-07-21T10:44:54Z",
"oldest_open_prs": [
{
"number": 83,
"created_at": "2023-02-16T17:58:42Z",
"last_comment_at": "2023-02-16T18:03:50Z",
"last_comment_author": "codecov"
},
{
"number": 259,
"created_at": "2026-03-10T16:23:03Z",
"last_comment_at": "2026-03-10T16:47:06Z",
"last_comment_author": "codecov"
},
{
"number": 267,
"created_at": "2026-05-16T21:36:30Z",
"last_comment_at": "2026-05-19T10:30:36Z",
"last_comment_author": "ori-kron-wis"
},
{
"number": 273,
"created_at": "2026-06-18T11:58:51Z",
"last_comment_at": "2026-06-23T08:24:02Z",
"last_comment_author": "codecov"
},
{
"number": 278,
"created_at": "2026-07-17T07:12:04Z",
"last_comment_at": null,
"last_comment_author": null
}
],
"last_merged_pr_at": "2026-07-21T06:42:32Z",
"ci_last_conclusion": null,
"oldest_open_issues": [
{
"number": 12,
"created_at": "2022-10-03T18:34:40Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 32,
"created_at": "2022-10-14T00:58:21Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 51,
"created_at": "2022-11-13T20:43:05Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 58,
"created_at": "2022-11-29T22:18:31Z",
"last_comment_at": "2025-10-08T09:32:27Z",
"last_comment_author": "jkobject"
},
{
"number": 62,
"created_at": "2022-12-09T20:09:00Z",
"last_comment_at": null,
"last_comment_author": null
},
{
"number": 100,
"created_at": "2023-08-10T13:42:43Z",
"last_comment_at": "2023-12-28T17:17:32Z",
"last_comment_author": "adamgayoso"
},
{
"number": 144,
"created_at": "2024-02-23T21:33:38Z",
"last_comment_at": null,
"last_comment_author": null
}
]
}
},
"config": {
"disabled_metrics": [],
"disabled_categories": [],
"disabled_components": {}
},
"source": {
"url": "https://github.com/YosefLab/scib-metrics",
"host": "github.com",
"name": "scib-metrics",
"owner": "YosefLab"
},
"metrics": {
"overall": {
"key": "overall",
"band": "good",
"name": "Overall health",
"note": null,
"notes": [],
"value": 73,
"inputs": {
"security": 50,
"vitality": 90,
"community": 58,
"governance": 68,
"engineering": 92
},
"components": []
},
"categories": [
{
"key": "vitality",
"band": "excellent",
"name": "Vitality",
"value": 90,
"weight": 0.22,
"metrics": [
{
"key": "development_activity",
"band": "excellent",
"name": "Development activity",
"note": null,
"notes": [],
"value": 88,
"inputs": {
"commits_last_year": 54,
"human_commit_share": 0.31,
"days_since_last_push": 0,
"active_weeks_last_year": 38
},
"components": [
{
"key": "push_recency",
"name": "Push recency",
"detail": "last push 0 days ago",
"points": 36,
"status": "met",
"details": [
{
"code": "push_recency",
"params": {
"days": 0
}
}
],
"max_points": 36
},
{
"key": "commit_cadence",
"name": "Commit cadence",
"detail": "38/52 weeks with commits",
"points": 26.3,
"status": "partial",
"details": [
{
"code": "commit_cadence_weeks",
"params": {
"weeks": 38
}
}
],
"max_points": 36
},
{
"key": "commit_volume",
"name": "Commit volume",
"detail": "54 commits in the last year",
"points": 15.6,
"status": "partial",
"details": [
{
"code": "commits_last_year",
"params": {
"count": 54
}
}
],
"max_points": 18
},
{
"key": "openssf_scorecard_maintained",
"name": "OpenSSF Scorecard: Maintained",
"detail": "15 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
},
{
"key": "release_discipline",
"band": "excellent",
"name": "Release discipline",
"note": "Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"openssf_scorecard_signed_releases"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 92,
"inputs": {
"releases_count": 29,
"latest_release_tag": "v0.5.10",
"releases_from_tags": false,
"days_since_latest_release": 8,
"mean_days_between_releases": 96.7
},
"components": [
{
"key": "ships_releases",
"name": "Ships releases",
"detail": "29 releases published",
"points": 27,
"status": "met",
"details": [
{
"code": "releases_published",
"params": {
"count": 29
}
}
],
"max_points": 27
},
{
"key": "release_recency",
"name": "Release recency",
"detail": "latest release 8 days ago",
"points": 36,
"status": "met",
"details": [
{
"code": "release_recency",
"params": {
"days": 8
}
}
],
"max_points": 36
},
{
"key": "release_cadence",
"name": "Release cadence",
"detail": "a release every ~96.7 days",
"points": 19.8,
"status": "partial",
"details": [
{
"code": "release_cadence",
"params": {
"gap": 96.7
}
}
],
"max_points": 27
},
{
"key": "openssf_scorecard_signed_releases",
"name": "OpenSSF Scorecard: Signed-Releases",
"detail": "no releases found",
"points": 0,
"status": "excluded",
"details": [
{
"code": "no_data",
"params": {}
}
],
"max_points": 10
}
]
},
{
"key": "abandonment",
"band": "excellent",
"name": "Abandonment",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"cap": null,
"state": "maintained",
"guards": [],
"signals": [],
"red_flag": false,
"multiplier_pct": 100,
"declared_reason": null,
"unverified_reason": null,
"unanswered_open_prs": null,
"unanswered_open_issues": null,
"days_since_last_merged_pr": null,
"days_since_last_human_commit": 8,
"days_since_last_human_commit_is_floor": false
},
"components": [
{
"key": "project_is_still_maintained",
"name": "Project is still maintained",
"detail": "last human commit 8 days ago",
"points": 100,
"status": "met",
"details": [
{
"code": "abandonment_maintained",
"params": {
"days": 8
}
}
],
"max_points": 100
}
]
}
],
"description": "Is the project alive — is code being written and are releases shipping?"
},
{
"key": "community",
"band": "moderate",
"name": "Community & Adoption",
"value": 58,
"weight": 0.18,
"metrics": [
{
"key": "popularity",
"band": "at_risk",
"name": "Popularity & adoption",
"note": null,
"notes": [],
"value": 47,
"inputs": {
"forks": 22,
"stars": 96,
"watchers": 6,
"growth_state": "unverified",
"growth_factor_pct": 100,
"growth_unverified_reason": "below_threshold"
},
"components": [
{
"key": "stars",
"name": "Stars",
"detail": "96 stars",
"points": 32.1,
"status": "partial",
"details": [
{
"code": "stars",
"params": {
"count": 96
}
}
],
"max_points": 60
},
{
"key": "forks",
"name": "Forks",
"detail": "22 forks",
"points": 11,
"status": "partial",
"details": [
{
"code": "forks",
"params": {
"count": 22
}
}
],
"max_points": 25
},
{
"key": "watchers",
"name": "Watchers",
"detail": "6 watchers",
"points": 3.9,
"status": "partial",
"details": [
{
"code": "watchers",
"params": {
"count": 6
}
}
],
"max_points": 15
}
]
},
{
"key": "community_health",
"band": "good",
"name": "Community health",
"note": null,
"notes": [],
"value": 70,
"inputs": {
"has_readme": true,
"has_license": true,
"has_contributing": true,
"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",
"name": "License",
"detail": "recognized license (BSD-3-Clause)",
"points": 22.5,
"status": "met",
"details": [
{
"code": "license_standard",
"params": {}
},
{
"code": "license_spdx",
"params": {
"spdx": "BSD-3-Clause"
}
}
],
"max_points": 22.5
},
{
"key": "contributing_guide",
"name": "CONTRIBUTING guide",
"detail": null,
"points": 18,
"status": "met",
"details": [],
"max_points": 18
},
{
"key": "code_of_conduct",
"name": "Code of conduct",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 13.5
},
{
"key": "issue_template",
"name": "Issue template",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.2
},
{
"key": "pr_template",
"name": "PR template",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 6.3
}
]
}
],
"description": "Does the project have users, downloads, attention, and a welcoming setup for contributors?"
},
{
"key": "governance",
"band": "moderate",
"name": "Sustainability & Governance",
"value": 68,
"weight": 0.24,
"metrics": [
{
"key": "maintainer_resilience",
"band": "at_risk",
"name": "Maintainer resilience (bus factor)",
"note": null,
"notes": [],
"value": 38,
"inputs": {
"bus_factor": 1,
"contributors_sampled": 9,
"top_contributor_share": 0.679
},
"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
}
}
],
"max_points": 54
},
{
"key": "commit_distribution",
"name": "Commit distribution",
"detail": "top contributor authored 68% of commits",
"points": 7.2,
"status": "partial",
"details": [
{
"code": "top_contributor_share",
"params": {
"share": 68
}
}
],
"max_points": 22.5
},
{
"key": "contributor_breadth",
"name": "Contributor breadth",
"detail": "9 contributors",
"points": 12.2,
"status": "partial",
"details": [
{
"code": "contributors_sampled",
"params": {
"count": 9
}
}
],
"max_points": 13.5
},
{
"key": "openssf_scorecard_contributors",
"name": "OpenSSF Scorecard: Contributors",
"detail": "project has 5 contributing companies or organizations",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
}
]
},
{
"key": "responsiveness",
"band": "good",
"name": "Issue & PR responsiveness",
"note": null,
"notes": [],
"value": 76,
"inputs": {
"merged_prs": 203,
"open_issues": 7,
"closed_issues": 48,
"issue_closed_ratio": 0.873,
"closed_unmerged_prs": 16
},
"components": [
{
"key": "issue_resolution",
"name": "Issue resolution",
"detail": "87% of issues closed",
"points": 40.8,
"status": "partial",
"details": [
{
"code": "issues_closed_share",
"params": {
"share": 87
}
}
],
"max_points": 46.75
},
{
"key": "pr_acceptance",
"name": "PR acceptance",
"detail": "203/219 decided PRs merged",
"points": 35.5,
"status": "partial",
"details": [
{
"code": "decided_prs_merged",
"params": {
"merged": 203,
"decided": 219
}
}
],
"max_points": 38.25
},
{
"key": "openssf_scorecard_code_review",
"name": "OpenSSF Scorecard: Code-Review",
"detail": "Found 0/9 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 15
}
]
},
{
"key": "stewardship",
"band": "good",
"name": "Ownership & stewardship",
"note": null,
"notes": [],
"value": 70,
"inputs": {
"followers": 138,
"owner_type": "Organization",
"is_verified": null,
"owner_login": "YosefLab",
"public_repos": 73,
"account_age_days": 3991
},
"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": "138 followers of YosefLab",
"points": 15.4,
"status": "partial",
"details": [
{
"code": "owner_followers",
"params": {
"count": 138,
"login": "YosefLab"
}
}
],
"max_points": 25
},
{
"key": "track_record",
"name": "Track record",
"detail": "73 public repos, account ~10 yr old",
"points": 25,
"status": "met",
"details": [
{
"code": "public_repos",
"params": {
"count": 73
}
},
{
"code": "account_age_years",
"params": {
"years": 10
}
}
],
"max_points": 25
}
]
},
{
"key": "package_maintenance",
"band": "excellent",
"name": "Package maintenance",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"packages": [
"scib-metrics"
],
"ecosystems": "pypi",
"any_deprecated": false,
"min_days_since_publish": 8
},
"components": [
{
"key": "published_resolvable",
"name": "Published & resolvable",
"detail": "1 package(s) on pypi",
"points": 25,
"status": "met",
"details": [
{
"code": "packages_published",
"params": {
"count": 1,
"ecosystems": "pypi"
}
}
],
"max_points": 25
},
{
"key": "publish_recency",
"name": "Publish recency",
"detail": "latest publish 8 days ago",
"points": 35,
"status": "met",
"details": [
{
"code": "publish_recency",
"params": {
"days": 8
}
}
],
"max_points": 35
},
{
"key": "version_history",
"name": "Version history",
"detail": "28 published versions",
"points": 20,
"status": "met",
"details": [
{
"code": "published_versions",
"params": {
"count": 28
}
}
],
"max_points": 20
},
{
"key": "not_deprecated",
"name": "Not deprecated",
"detail": "active, not deprecated or yanked",
"points": 20,
"status": "met",
"details": [
{
"code": "package_not_deprecated",
"params": {}
}
],
"max_points": 20
}
]
}
],
"description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
},
{
"key": "engineering",
"band": "excellent",
"name": "Engineering Quality",
"value": 92,
"weight": 0.2,
"metrics": [
{
"key": "engineering_practices",
"band": "excellent",
"name": "Engineering practices",
"note": null,
"notes": [],
"value": 100,
"inputs": {
"has_ci": true,
"has_tests": true,
"has_editorconfig": true,
"has_linter_config": true,
"has_precommit_config": true
},
"components": [
{
"key": "ci_workflows",
"name": "CI workflows",
"detail": "8 workflow(s)",
"points": 24,
"status": "met",
"details": [
{
"code": "ci_workflows",
"params": {
"count": 8
}
}
],
"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": 16,
"status": "met",
"details": [],
"max_points": 16
},
{
"key": "pre_commit_hooks",
"name": "Pre-commit hooks",
"detail": null,
"points": 9.6,
"status": "met",
"details": [],
"max_points": 9.6
},
{
"key": "editorconfig",
"name": ".editorconfig",
"detail": null,
"points": 6.4,
"status": "met",
"details": [],
"max_points": 6.4
},
{
"key": "openssf_scorecard_ci_tests",
"name": "OpenSSF Scorecard: CI-Tests",
"detail": "24 out of 24 merged PRs checked by a CI test -- score normalized to 10",
"points": 20,
"status": "met",
"details": [],
"max_points": 20
}
]
},
{
"key": "documentation",
"band": "good",
"name": "Documentation",
"note": null,
"notes": [],
"value": 80,
"inputs": {
"topics": [],
"has_wiki": false,
"homepage": "https://scib-metrics.readthedocs.io/",
"has_readme": true,
"has_docs_dir": true,
"has_description": true
},
"components": [
{
"key": "readme",
"name": "README",
"detail": null,
"points": 30,
"status": "met",
"details": [],
"max_points": 30
},
{
"key": "documentation_directory",
"name": "Documentation directory",
"detail": null,
"points": 25,
"status": "met",
"details": [],
"max_points": 25
},
{
"key": "documentation_homepage_site",
"name": "Documentation / homepage site",
"detail": "https://scib-metrics.readthedocs.io/",
"points": 15,
"status": "met",
"details": [],
"max_points": 15
},
{
"key": "repository_description",
"name": "Repository description",
"detail": null,
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "topics",
"name": "Topics",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
},
{
"key": "wiki",
"name": "Wiki",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
}
],
"description": "Are baseline engineering and documentation practices in place?"
},
{
"key": "security",
"band": "moderate",
"name": "Security",
"value": 50,
"weight": 0.16,
"metrics": [
{
"key": "security_posture",
"band": "moderate",
"name": "Security posture",
"note": "Excluded from scoring (no data or not applicable): Signed-Releases. Remaining weights renormalized.",
"notes": [
{
"code": "excluded_no_data",
"params": {
"components": [
"signed_releases"
]
}
},
{
"code": "weights_renormalized",
"params": {}
}
],
"value": 50,
"inputs": {
"source": "openssf_scorecard",
"checks_evaluated": 17,
"scorecard_version": "v5.5.0",
"checks_inconclusive": 1,
"scorecard_aggregate": 5
},
"components": [
{
"key": "binary_artifacts",
"name": "Binary-Artifacts",
"detail": "no binaries found in the repo",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "branch_protection",
"name": "Branch-Protection",
"detail": "branch protection is not maximal on development and all release branches",
"points": 3.8,
"status": "partial",
"details": [],
"max_points": 7.5
},
{
"key": "ci_tests",
"name": "CI-Tests",
"detail": "24 out of 24 merged PRs checked by a CI test -- score normalized to 10",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "cii_best_practices",
"name": "CII-Best-Practices",
"detail": "no effort to earn an OpenSSF best practices badge detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 2.5
},
{
"key": "code_review",
"name": "Code-Review",
"detail": "Found 0/9 approved changesets -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "contributors",
"name": "Contributors",
"detail": "project has 5 contributing companies or organizations",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "dangerous_workflow",
"name": "Dangerous-Workflow",
"detail": "no dangerous workflow patterns detected",
"points": 10,
"status": "met",
"details": [],
"max_points": 10
},
{
"key": "dependency_update_tool",
"name": "Dependency-Update-Tool",
"detail": "no update tool detected",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "fuzzing",
"name": "Fuzzing",
"detail": "project is not fuzzed",
"points": 0,
"status": "missed",
"details": [],
"max_points": 5
},
{
"key": "license",
"name": "License",
"detail": "license file detected",
"points": 2.5,
"status": "met",
"details": [],
"max_points": 2.5
},
{
"key": "maintained",
"name": "Maintained",
"detail": "15 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 10",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
},
{
"key": "packaging",
"name": "Packaging",
"detail": "packaging workflow detected",
"points": 5,
"status": "met",
"details": [],
"max_points": 5
},
{
"key": "pinned_dependencies",
"name": "Pinned-Dependencies",
"detail": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"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": "detected GitHub workflow tokens with excessive permissions",
"points": 0,
"status": "missed",
"details": [],
"max_points": 7.5
},
{
"key": "vulnerabilities",
"name": "Vulnerabilities",
"detail": "0 existing vulnerabilities detected",
"points": 7.5,
"status": "met",
"details": [],
"max_points": 7.5
}
]
},
{
"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": 15
},
"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": "at_risk",
"name": "AI Readiness",
"value": 47,
"weight": 0,
"metrics": [
{
"key": "ai_agent_context",
"band": "at_risk",
"name": "Agent context & guidance",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"has_llms_txt": false,
"legible_history_share": 0.742,
"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": "23 of 31 human commits state their intent (structured subject or explanatory body)",
"points": 39.6,
"status": "partial",
"details": [
{
"code": "legible_history",
"params": {
"legible": 23,
"sampled": 31
}
}
],
"max_points": 40
}
]
},
{
"key": "ai_verify_loop",
"band": "moderate",
"name": "Verify loop (build / test / typecheck)",
"note": null,
"notes": [],
"value": 51,
"inputs": {
"has_nix": false,
"has_tests": true,
"lockfiles": [],
"has_dockerfile": false,
"typed_language": false,
"bootstrap_files": [
"docs/Makefile"
],
"has_devcontainer": false,
"has_linter_config": true,
"typecheck_configs": [],
"agent_commit_share": 0,
"toolchain_manifests": [],
"dependency_bot_commit_share": 0
},
"components": [
{
"key": "one_command_bootstrap",
"name": "One-command bootstrap",
"detail": "docs/Makefile",
"points": 18,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "docs/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": 11,
"status": "met",
"details": [],
"max_points": 11
},
{
"key": "static_type_checking",
"name": "Static type checking",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"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": "dependency not pinned by hash detected -- score normalized to 0",
"points": 0,
"status": "missed",
"details": [],
"max_points": 10
}
]
},
{
"key": "ai_code_legibility",
"band": "moderate",
"name": "Code legibility for models",
"note": null,
"notes": [],
"value": 55,
"inputs": {
"primary_language": "Python",
"largest_source_bytes": 16779,
"source_files_sampled": 40,
"oversized_source_files": 0
},
"components": [
{
"key": "type_checkable_code",
"name": "Type-checkable code",
"detail": "Python without a type-check config",
"points": 0,
"status": "missed",
"details": [
{
"code": "no_typecheck_config_language",
"params": {
"language": "Python"
}
}
],
"max_points": 45
},
{
"key": "manageable_file_sizes",
"name": "Manageable file sizes",
"detail": "0/40 source files over 60KB",
"points": 55,
"status": "met",
"details": [
{
"code": "oversized_source_files",
"params": {
"kb": 60,
"sampled": 40,
"oversized": 0
}
}
],
"max_points": 55
}
]
},
{
"key": "ai_interfaces",
"band": "at_risk",
"name": "Machine-readable interfaces",
"note": null,
"notes": [],
"value": 40,
"inputs": {
"example_dirs": [
"notebooks"
],
"has_mcp_signal": false,
"api_schema_files": []
},
"components": [
{
"key": "api_schema_openapi_graphql_proto",
"name": "API schema (OpenAPI/GraphQL/proto)",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 40
},
{
"key": "mcp_server",
"name": "MCP server",
"detail": null,
"points": 0,
"status": "missed",
"details": [],
"max_points": 20
},
{
"key": "runnable_examples",
"name": "Runnable examples",
"detail": "notebooks",
"points": 40,
"status": "met",
"details": [
{
"code": "file_list",
"params": {
"files": "notebooks"
}
}
],
"max_points": 40
}
]
}
],
"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": [
"deps.dev does not index pypi:scib-metrics@0.5.10; advisories assessed against the repository dependency graph instead",
"No resolved dependencies carried a version and a supported ecosystem"
],
"report_type": "repository",
"generated_at": "2026-07-22T04:32:28.724905Z",
"schema_version": "0.26.0",
"badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/y/YosefLab/scib-metrics.svg",
"full_name": "YosefLab/scib-metrics",
"license_state": "standard",
"license_spdx": "BSD-3-Clause"
}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 v0.26.0 — full methodology · metrics wiki.
How one result sits in the wider record: aggregate statistics — PyPI.