cyclops/.github/workflows/code_checks.yml at main · VectorInstitute/cyclops · GitHub

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name: code checks

on:
  push:
    branches:
      - main
    paths:
      - .pre-commit-config.yaml
      - .github/workflows/code_checks.yml
      - '**.py'
      - uv.lock
      - pyproject.toml
      - '**.ipynb'
  pull_request:
    branches:
      - main
    paths:
      - .pre-commit-config.yaml
      - .github/workflows/code_checks.yml
      - '**.py'
      - uv.lock
      - pyproject.toml
      - '**.ipynb'

jobs:
  run-code-check:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v7.0.1
      - name: Install uv
        uses: astral-sh/setup-uv@v9.0.0
        with:
          enable-cache: true
          python-version: '3.11'
      - name: Install dependencies and check code
        run: |
          uv sync --no-default-groups --group test --all-extras
          source .venv/bin/activate
          pre-commit run --all-files
      - name: pip-audit (gh-action-pip-audit)
        uses: pypa/gh-action-pip-audit@v1.1.0
        with:
          virtual-environment: .venv/
          # The ignored vulnerabilities below cannot be fixed while alibi and
          # alibi-detect cap pillow (<11) and transformers (<5), cycquery
          # caps pyarrow (<18), and pybtex needs pkg_resources (removed in
          # setuptools 81+). Revisit when those libraries relax their
          # constraints.
          ignore-vulns: |
            GHSA-pg7h-5qx3-wjr3
            PYSEC-2026-3447
            PYSEC-2026-165
            PYSEC-2026-2249
            PYSEC-2026-2250
            PYSEC-2026-2252
            PYSEC-2026-2253
            PYSEC-2026-2254
            PYSEC-2026-2255
            PYSEC-2026-2256
            PYSEC-2026-2257
            PYSEC-2026-2874
            PYSEC-2026-3451
            PYSEC-2026-3453
            PYSEC-2026-3454
            PYSEC-2026-3493
            PYSEC-2026-3494
            PYSEC-2026-3495
            PYSEC-2026-3496
            PYSEC-2026-113
            PYSEC-2025-217
            PYSEC-2026-2288
            PYSEC-2026-2289
            PYSEC-2026-2290