Required checks passing
19%
3 of 16 scored
Failing
13
required checks
Unreadable
0
needs more permissions
Single-cell epigenomics analysis tools
- Default branch
main- PyPI
- snapatac2 2.10.0
Template
| Check | Tier | Detail | Fix | |
|---|---|---|---|---|
| ✗ |
Uses cookiecutter-scverse
template/cruft — .cruft.json exists and names the scverse template |
required | No .cruft.json — repo was not generated from the template |
open |
| – |
Template up to date
template/up-to-date — .cruft.json commit matches the latest cookiecutter-scverse release |
required | Does not apply to this repository | |
| ✗ |
src layout + hatchling
template/src-layout — Builds with hatchling from a src/ layout |
recommended | build backend is maturin | open |
| – |
pre-commit.ci enabled
template/pre-commit-ci — pre-commit.ci runs on pull requests |
recommended | Does not apply to this repository | |
| ✗ |
codecov configured
template/codecov — A codecov config or a codecov check run exists |
recommended | No codecov config file and no codecov check run | open |
| ✓ |
Default branch is main
template/default-branch — The default branch is called main |
recommended | Default branch is main |
open |
| ✓ |
Listed in packages.json
template/packages-json — Listed in scverse.org's ecosystem index, under a category the dashboard knows |
informational | Listed under core-framework | open |
Documentation
| Check | Tier | Detail | Fix | |
|---|---|---|---|---|
| ✗ |
.readthedocs.yaml present
docs/readthedocs-yaml — A .readthedocs.yaml build config is committed |
required | No .readthedocs.yaml |
open |
| – |
RTD project points here
docs/rtd-linked — The Read the Docs project of the same slug builds *this* repository |
required | Does not apply to this repository | |
| – |
≥2 core devs on RTD
docs/rtd-core-devs — At least two scverse core devs can administer the RTD project |
required | Does not apply to this repository | |
| – |
Docs on *.scverse.org
docs/scverse-domain — Documentation is served from <package>.scverse.org, not readthedocs.io |
required | Does not apply to this repository | |
| – |
Stable RTD build passed
docs/rtd-build — The most recent build of the stable version succeeded |
recommended | Does not apply to this repository |
Packaging
| Check | Tier | Detail | Fix | |
|---|---|---|---|---|
| ✗ |
PyPI project owned by scverse
packaging/pypi-org — ownership.organization on PyPI is the scverse org |
required | Not owned by a PyPI organization | open |
| ✓ |
Trusted publishing
packaging/trusted-publishing — The latest release carries PEP 740 attestations naming this repo's workflow |
required | 2.10.0 published by scverse/SnapATAC2/.github/workflows/test_python.yml |
open |
| ✗ |
Release workflow hardened
packaging/release-workflow — Publishes via pypa/gh-action-pypi-publish with id-token: write, no password, in an environment |
required | job publish is not bound to an environment |
open |
| ✗ |
SPEC 0 minimum Python
packaging/spec0-python — requires-python has dropped the Python versions SPEC 0 has dropped |
required | requires-python = ">=3.12, <3.15" still allows 3.12; SPEC 0 is at 3.13 |
open |
| ✓ |
Immutable releases enabled
packaging/immutable-releases — The repository has immutable releases turned on |
required | Immutable releases enabled | open |
| ✓ |
Recent releases immutable
packaging/releases-immutable — The last few published releases are actually marked immutable |
recommended | All of the last 1 releases are immutable | open |
| ✗ |
`pypi` environment protected
packaging/pypi-environment — A deployment environment named pypi exists and has protection rules |
recommended | No pypi environment (found: github-pages, pypi_password) |
open |
| – |
Tag matches PyPI version
packaging/version-sync — The newest GitHub release tag matches the newest PyPI version |
recommended | No published GitHub releases |
Supply chain
| Check | Tier | Detail | Fix | |
|---|---|---|---|---|
| – |
Integration tests passing
integration/upstream-tests — This package's test suite passes in scverse/integration-testing against upstream core packages |
required | Does not apply to this repository | |
| ✗ |
Actions pinned to SHA
security/actions-pinned — Every uses: names a full 40-character commit SHA |
required | 17 of 17 unpinned: actions/checkout@v4, actions/checkout@v5, actions/download-artifact@v4 and 9 more | open |
| – |
pre-commit revs pinned
security/precommit-pinned — Every rev: in .pre-commit-config.yaml is a commit SHA |
recommended | Does not apply to this repository | |
| ✗ |
zizmor audit is clean
security/zizmor-clean — A zizmor audit of every workflow, action and Dependabot config reports no findings |
required | 44 findings in 7 files, online: archived-uses, artipacked, excessive-permissions and 4 more | open |
| ✗ |
Dependabot configured
security/dependabot — .github/dependabot.yml covers both the github-actions and pre-commit ecosystems |
required | No .github/dependabot.yml (needs github-actions) |
open |
| ✗ |
No open Dependabot alerts
security/dependabot-alerts — No unresolved Dependabot security alerts |
recommended | 2 open alerts, 1 high or critical | open |
| ✓ |
Secret scanning + push protection
security/secret-scanning — Secret scanning and push protection are both enabled |
recommended | Secret scanning and push protection enabled | open |
| ✓ |
Private vulnerability reporting
security/private-vuln-reporting — Researchers can report vulnerabilities privately |
recommended | Private vulnerability reporting enabled | open |
| ✗ |
Minimal workflow permissions
security/workflow-permissions — Every workflow declares a top-level permissions:, and the repo default is read-only |
required | 4 of 4 lack permissions:: nightly.yml, test_python.yml, test_rust.yml and 1 more |
open |
| ✗ |
checkout without credentials
security/persist-credentials — actions/checkout steps set persist-credentials: false (zizmor artipacked) |
recommended | 3 of 3 keep credentials: nightly.yml:check-for-new-commits, wheels.yml:build_wheels, wheels.yml:make_sdist | open |
| ✓ |
No unsafe pull_request_target
security/dangerous-triggers — pull_request_target does not check out untrusted PR code (zizmor dangerous-triggers) |
recommended | No workflow uses pull_request_target |
open |
| ✗ |
SECURITY.md
security/security-md — A security policy exists, in this repo or via the org's .github repo |
recommended | No security policy | open |
Branch protection
| Check | Tier | Detail | Fix | |
|---|---|---|---|---|
| ✗ |
Default branch protected
branch/protected — Neither force-pushes nor deletion are allowed on the default branch |
required | main is not protected at all |
open |
| ✗ |
Requires a pull request
branch/requires-pr — Changes to the default branch must go through a pull request |
required | Direct pushes to the default branch are allowed | open |
| ✗ |
Requires ≥1 approving review
branch/requires-review — A pull request needs at least one approving review to merge |
required | No review requirement | open |
| ✗ |
Requires status checks
branch/status-checks — At least one status check must pass before merging |
recommended | No required status checks | open |
Governance
| Check | Tier | Detail | Fix | |
|---|---|---|---|---|
| ✓ |
OSI license
governance/license — The repo carries a recognised OSI-approved license |
required | MIT | open |
| ✗ |
GPL-free dependencies
governance/gpl-free — No runtime dependency, direct or transitive, is GPL-licensed, unless the repo is GPL itself |
required | igraph (GNU General Public License (GPL)) |
open |
| ✓ |
Description, homepage, topic
governance/description-topics — The repo has a description, a homepage and the scverse topic |
recommended | Described, linked and tagged (2 topics) | open |
| ✓ |
Actively maintained
governance/maintained — Pushed to within the last year |
informational | Last push 51 days ago | open |