Genome class to handle fasta files and chromsizes throughout package #272
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: Test | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| schedule: | |
| - cron: "0 5 1,15 * *" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # TensorFlow Test Cases | |
| - os: ubuntu-latest | |
| python: "3.9" | |
| backend: "tensorflow" | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| backend: "tensorflow" | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| backend: "tensorflow" | |
| pip-flags: "--pre" | |
| name: "TensorFlow PRE-RELEASE DEPENDENCIES" | |
| # PyTorch Test Cases | |
| - os: ubuntu-latest | |
| python: "3.9" | |
| backend: "pytorch" | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| backend: "pytorch" | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| backend: "pytorch" | |
| pip-flags: "--pre" | |
| name: "PyTorch PRE-RELEASE DEPENDENCIES" | |
| name: ${{ matrix.name }} Python ${{ matrix.python }} Backend ${{ matrix.backend }} | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| BACKEND: ${{ matrix.backend }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: "pip" | |
| cache-dependency-path: "**/pyproject.toml" | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| - name: Install dependencies for ${{ matrix.backend }} | |
| run: | | |
| if [ "${{ matrix.backend }}" = "tensorflow" ]; then | |
| pip install ${{ matrix.pip-flags }} "tensorflow" ".[dev,test]"; | |
| elif [ "${{ matrix.backend }}" = "pytorch" ]; then | |
| pip install ${{ matrix.pip-flags }} "torch" ".[dev,test]"; | |
| fi | |
| - name: Run tests | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| run: | | |
| coverage run -m pytest -v --color=yes | |
| - name: Report coverage | |
| run: | | |
| coverage report | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: aertslab/CREsted |