Rename fold_change column to log2_fold_change (deprecate alias) #198
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: "CI" | |
| on: [push, pull_request] | |
| jobs: | |
| all_jobs: | |
| runs-on: ubuntu-latest | |
| needs: [formatting, type-checking, pytest, semver-check] | |
| if: always() | |
| steps: | |
| - name: Complete | |
| run: | | |
| if [[ "${{ contains(needs.*.result, 'failure') }}" == "true" ]]; then | |
| echo "One or more required jobs failed." | |
| exit 1 | |
| fi | |
| echo "Complete" | |
| semver-check: | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'pull_request' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: check version bump | |
| run: | | |
| BASE_VERSION=$(git show origin/${{ github.base_ref }}:pyproject.toml \ | |
| | python3 -c "import sys, tomllib; print(tomllib.load(sys.stdin.buffer)['project']['version'])") | |
| PR_VERSION=$(python3 -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['version'])") | |
| echo "Base version: $BASE_VERSION" | |
| echo "PR version: $PR_VERSION" | |
| if [ -z "$BASE_VERSION" ] || [ -z "$PR_VERSION" ]; then | |
| echo "ERROR: failed to parse version from pyproject.toml" | |
| exit 1 | |
| fi | |
| if [ "$BASE_VERSION" = "$PR_VERSION" ]; then | |
| echo "ERROR: version in pyproject.toml ($PR_VERSION) must be bumped before merging." | |
| exit 1 | |
| fi | |
| install-job: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.13", "3.12", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: install uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: "pyproject.toml" | |
| python-version: ${{ matrix.python-version }} | |
| - name: install dependencies | |
| run: | | |
| uv sync --all-extras --dev | |
| formatting: | |
| runs-on: ubuntu-latest | |
| needs: [install-job] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: install uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: "pyproject.toml" | |
| python-version: "3.13" | |
| - name: install dependencies | |
| run: | | |
| uv sync --all-extras --dev | |
| - name: run formatting | |
| run: | | |
| uv run ruff format --check | |
| type-checking: | |
| runs-on: ubuntu-latest | |
| needs: [install-job] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: install uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: "pyproject.toml" | |
| python-version: "3.13" | |
| - name: install dependencies | |
| run: | | |
| uv sync --all-extras --dev | |
| - name: run type checking | |
| run: | | |
| uv run ty check | |
| pytest: | |
| runs-on: ubuntu-latest | |
| needs: [install-job] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: install uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: "pyproject.toml" | |
| python-version: "3.13" | |
| - name: install dependencies | |
| run: | | |
| uv sync --all-extras --dev | |
| - name: run pytest | |
| run: | | |
| uv run pytest -v |