feat: add --chunk-size parameter to simgenotype
#409
This file contains 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: Tests | |
| on: [pull_request, workflow_call] | |
| jobs: | |
| tests: | |
| name: ${{ matrix.session }} ${{ matrix.python }} / ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { python: "3.9", os: "ubuntu-latest", session: "lint" } | |
| - { 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: "3.13", os: "ubuntu-latest", session: "tests" } | |
| # - { python: "3.11", os: "windows-latest", session: "tests" } | |
| - { python: "3.9", os: "macos-13", session: "tests" } | |
| - { python: "3.12", os: "macos-latest", session: "tests" } | |
| - { python: "3.9", os: "ubuntu-latest", session: "size" } | |
| env: | |
| NOXSESSION: ${{ matrix.session }} | |
| FORCE_COLOR: "1" | |
| PRE_COMMIT_COLOR: "always" | |
| steps: | |
| - name: Check out the repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Miniforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: haptools | |
| auto-activate-base: false | |
| miniforge-version: latest | |
| use-mamba: true | |
| conda-remove-defaults: "true" | |
| - name: Get Date | |
| id: get-date | |
| run: echo "today=$(/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 haptools -f dev-env.yml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Try to build haptools | |
| shell: bash -el {0} | |
| run: | | |
| poetry build --no-ansi | |
| - name: Check distribution size | |
| if: matrix.session == 'size' | |
| run: | | |
| du -csh dist/* | |
| # 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 a "tool.poetry.exclude" section of our pyproject.toml | |
| # https://python-poetry.org/docs/pyproject/#include-and-exclude | |
| [ $(du -b dist | cut -f1) -lt 300000 ] | |
| - name: Run tests with nox | |
| if: matrix.session != 'size' | |
| shell: bash -el {0} | |
| run: | | |
| nox --verbose --python=${{ matrix.python }} | |
| # - name: Upload coverage data | |
| # if: always() && matrix.session == 'tests' | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: coverage-data | |
| # path: ".coverage.*" | |
| 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/lfs-warning@v3.3 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} # Optional | |
| filesizelimit: 500000b | |
| labelName: large-files |