scverse/scvi-tools
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A well-known project done right. Strong docs and solid engineering throughout.

Top 22% of 5,156 graded repos

Deep probabilistic analysis of single-cell and spatial omics data

Documentation78
Engineering85
Health98
Python1,650BSD-3-Clause1mo ago

Top fixes

Highest-impact changes first, ranked by point weight

9 to address
  1. 1
    CI/CD14pt

    Add a lint step to catch style issues automatically.

  2. 2
    CI/CD14pt

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

  3. 3
    README12pt

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

  4. 4
    Install and run instructions9pt

    Add a .env.example listing all required environment variables so contributors know what to set up.

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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

85

Reproducibility6pt10

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.

CI/CD14pt85

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

Tests18pt100

Test files detected (conftest.py).

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

  • -
    Commits (30d / 90d)
  • 465
    Forks
  • 94
    Releaseslatest 5y ago

Community

  • -
    Community health
  • -
    authors own >50% of commits
  • 1,650
    Watchers

Responsiveness

  • <1h
    Median issue response
  • <1h
    Median PR merge time
  • 28
    Open issues
Repository files17 root entries
  • .github
    Good: CI is configured (.github/workflows/build_image_base.yaml).
    Good: Issue or PR templates present.
  • docs
  • src
  • tests
  • .codecov.yaml
  • .editorconfig
    Good: Linter or formatter configured (.editorconfig).
  • .gitignore
    Good: .gitignore present.
  • .gitmodules
  • .markdownlint.yaml
  • .pre-commit-config.yaml
  • .readthedocs.yaml
  • 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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