Flatgfa filesystem restructure #174
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| test-py: | |
| name: test Python tools | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| # Set up and use uv. | |
| - uses: actions/cache@v4 | |
| id: cache-uv | |
| with: | |
| path: ~/.cache/uv | |
| key: ${{ runner.os }}-python-${{ matrix.python-version }}-uv | |
| - name: Create and activate virtualenv with uv | |
| run: | | |
| curl -LsSf https://astral.sh/uv/install.sh | sh | |
| uv venv | |
| echo "VIRTUAL_ENV=.venv" >> $GITHUB_ENV | |
| echo "$PWD/.venv/bin" >> $GITHUB_PATH | |
| - name: Install Python tools | |
| run: uv pip install -r requirements.txt | |
| # Set up for tests. | |
| - name: Install Turnt | |
| run: uv pip install turnt | |
| - name: Problem matcher | |
| run: echo '::add-matcher::.github/tap-matcher.json' | |
| - name: Fetch test data | |
| run: make fetch SMALL=1 | |
| - name: Pull odgi container | |
| run: | | |
| docker pull quay.io/biocontainers/odgi:0.8.6--py310hdf79db3_1 | |
| docker tag quay.io/biocontainers/odgi:0.8.6--py310hdf79db3_1 odgi | |
| - name: Install odgi alias | |
| run: | | |
| mkdir -p $HOME/.local/bin | |
| cp .github/odgi.sh $HOME/.local/bin/odgi | |
| chmod a+x $HOME/.local/bin/odgi | |
| # Test slow_odgi. | |
| - name: Set up for slow_odgi tests | |
| run: make -C slow_odgi setup oracles SMALL=1 | |
| - name: Test slow_odgi | |
| run: make -C slow_odgi test SMALL=1 | |
| test-parser: | |
| name: test DSL parser | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions-rust-lang/setup-rust-toolchain@v1 | |
| - run: cargo install runt | |
| - run: cargo build | |
| working-directory: ./pollen | |
| - run: runt -v | |
| working-directory: ./pollen | |
| test-flatgfa: | |
| name: test FlatGFA | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions-rust-lang/setup-rust-toolchain@v1 | |
| # Install slow-odgi. | |
| - uses: actions/cache@v4 | |
| id: cache-uv | |
| with: | |
| path: ~/.cache/uv | |
| key: ${{ runner.os }}-python-${{ matrix.python-version }}-uv | |
| - name: Create and activate virtualenv with uv | |
| run: | | |
| curl -LsSf https://astral.sh/uv/install.sh | sh | |
| uv venv | |
| echo "VIRTUAL_ENV=.venv" >> $GITHUB_ENV | |
| echo "$PWD/.venv/bin" >> $GITHUB_PATH | |
| - name: Install Python tools | |
| run: uv pip install -r requirements.txt | |
| # Install odgi | |
| - name: Pull odgi container | |
| run: | | |
| docker pull quay.io/biocontainers/odgi:0.8.6--py310hdf79db3_1 | |
| docker tag quay.io/biocontainers/odgi:0.8.6--py310hdf79db3_1 odgi | |
| - name: Install odgi alias | |
| run: | | |
| mkdir -p $HOME/.local/bin | |
| cp .github/odgi.sh $HOME/.local/bin/odgi | |
| chmod a+x $HOME/.local/bin/odgi | |
| # Install Turnt. | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install Turnt | |
| run: pip install turnt | |
| - name: Problem matcher | |
| run: echo '::add-matcher::.github/tap-matcher.json' | |
| # We need the test data. | |
| - name: Fetch test data | |
| run: make fetch SMALL=1 | |
| # Build and test. | |
| - run: cargo build | |
| working-directory: ./flatgfa | |
| - run: cargo test | |
| working-directory: ./flatgfa | |
| - run: make test-flatgfa |