scverse/scvi-tools
Grade a repo

85

/ 100

GradeB

Well engineered. The main gaps are a contributing guide and a reproducible setup.

Top 26% of 5,156 graded repos

Deep probabilistic analysis of single-cell and spatial omics data

Documentation78
Engineering81
Health98
Python1,724BSD-3-Clause1d ago

Top fixes

Highest-impact changes first, ranked by point weight

10 to address
  1. 1
    Tests18pt

    Wire your tests to a documented command (e.g. a test script in your build config) so the suite is reproducible.

  2. 2
    CI/CD14pt

    Add a lint step to catch style issues automatically.

  3. 3
    CI/CD14pt

    Add `tsc --noEmit`, `mypy`, or `cargo check` to catch type errors before they merge.

  4. 4
    README12pt

    Add CI/build status badges from shields.io or your CI provider to signal project health.

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Scorecard

Every check, grouped by category and sorted worst-first

Documentation

78

Contributing guide5pt0

No CONTRIBUTING.md found (−47 pts base + up to −53 pts more for content).

→ Add a CONTRIBUTING.md telling newcomers how to get involved. Include setup, code style, test, and PR instructions.

README12pt90

README is present.

Install and run instructions9pt90

README documents how to install the project.

License6pt100

Licensed under BSD-3-Clause.

Engineering

81

Reproducibility6pt22

No dependency lockfile found (−70 pts).

→ Commit poetry.lock, uv.lock, pdm.lock, Pipfile.lock, conda-lock.yml, or another lockfile for your Python dependency manager.

Tests18pt85

Test files detected (conftest.py).

CI/CD14pt85

CI is configured (.github/workflows/build_image_base.yaml).

Linting and formatting5pt100

Linter or formatter configured (.editorconfig).

Issue and PR templates6pt100

Issue or PR templates present.

Project health

98

Dependency manifest6pt93

Dependency manifest found (pyproject.toml).

Repository metadata5pt100

Repository has a description.

Activity5pt100

Actively maintained (pushed within the last month).

Housekeeping3pt100

.gitignore present.

Repository health signals

Activity, community, and responsiveness at scan time

Activity

  • 19 / 51
    Commits (30d / 90d)
  • 483
    Forks
  • 98
    Releaseslatest 5y ago

Community

  • 87% - Good
    Community health
  • 3 bus factor
    authors own >50% of commits
  • 1,724
    Watchers

Responsiveness

  • <1h
    Median issue response
  • <1h
    Median PR merge time
  • 25
    Open issues
Repository files19 root entries
  • .github
    Good: CI is configured (.github/workflows/build_image_base.yaml).
    Good: Dependabot configured for github-actions.
    Good: Issue or PR templates present.
  • .vscode
  • docs
  • src
  • tests
  • .codecov.yaml
  • .cruft.json
  • .editorconfig
    Good: Linter or formatter configured (.editorconfig).
  • .gitignore
    Good: .gitignore present.
  • .gitmodules
  • .pre-commit-config.yaml
  • .readthedocs.yaml
  • biome.jsonc
  • CHANGELOG.md
  • conftest.py
    Good: Test files detected (conftest.py).
  • Dockerfile
    Good: Environment pinned via Dockerfile.
  • LICENSE
    Good: Licensed under BSD-3-Clause.
  • pyproject.toml
    Good: Dependency manifest found (pyproject.toml).
  • README.md
    Good: README is present.
    Good: README is well structured with multiple sections.
    Good: README includes screenshots or visuals. Great for first impressions.
    Good: README has code examples.
    Good: README links to a live demo or deployed app.
    Issue: No status badges in the README (−10 pts).Fix: Add CI/build status badges from shields.io or your CI provider to signal project health.
    Good: README documents how to install the project.
    Good: README documents how to run the project.
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