docs: add note about bcftools version for merging to annotaTR #295
Workflow file for this run
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| name: Tests | |
| on: [pull_request, workflow_call] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| tests: | |
| name: ${{ matrix.session }} / ${{ matrix.python }} / ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { python: "3.7", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.8", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.9", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.10", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.11", os: "ubuntu-latest", session: "tests" } | |
| - { python: "3.12", os: "ubuntu-latest", session: "tests" } | |
| # - { python: "3.11", os: "windows-latest", session: "tests" } | |
| - { python: "3.8", os: "macos-13", session: "tests" } | |
| - { python: "3.9", os: "macos-latest", session: "tests" } | |
| - { python: "3.8", os: "ubuntu-latest", session: "size" } | |
| - { python: "3.8", os: "ubuntu-latest", session: "coverage" } | |
| env: | |
| NOXSESSION: ${{ matrix.session }} | |
| FORCE_COLOR: "1" | |
| PRE_COMMIT_COLOR: "always" | |
| steps: | |
| - name: Check out the repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: trtools | |
| auto-activate-base: false | |
| miniforge-version: latest | |
| use-mamba: true | |
| - name: Get Date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Cache Conda env | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: | |
| conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('dev-env.yml') }}-${{ env.CACHE_NUMBER }} | |
| env: | |
| # Increase this value to reset cache if dev-env.yml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache | |
| - name: Install dev environment | |
| run: | |
| mamba env update -n trtools -f dev-env.yml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Try to build trtools | |
| shell: bash -el {0} | |
| run: | | |
| poetry build --no-ansi | |
| - name: Check distribution size | |
| if: matrix.session == 'size' | |
| run: | | |
| du -csh dist/* | |
| tar -ztvf dist/*.tar.gz | |
| # check that the generated dist/ directory does not exceed 0.3 MB | |
| # if this check fails, it's because you forgot to list large files in the "exclude" section of our pyproject.toml | |
| # https://python-poetry.org/docs/pyproject/#include-and-exclude | |
| [ $(du -b dist | cut -f1) -lt 300000 ] | |
| - name: Check code coverage | |
| if: matrix.session == 'coverage' | |
| shell: bash -el {0} | |
| run: | | |
| export NOXSESSION=tests | |
| # check that code coverage is not lower than specific percent | |
| nox --verbose --python=${{ matrix.python }} -- --cov=. --cov-report=term-missing --cov-fail-under=94 | |
| - name: Run tests with nox | |
| if: matrix.session == 'tests' | |
| shell: bash -el {0} | |
| run: | | |
| nox --verbose --python=${{ matrix.python }} | |
| large-files: | |
| name: File sizes | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the repository | |
| uses: actions/checkout@v4 | |
| - name: Check for large files | |
| uses: ppremk/[email protected] | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} # Optional | |
| filesizelimit: 500000b | |
| labelName: large-files |