Merge branch 'master' into dev #82
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| name: Integration Tests & Code Style | |
| on: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| branches: [ master, dev ] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| - name: Install dependencies | |
| run: | | |
| $CONDA/bin/conda env update --file environment.yml --name base | |
| - name: Lint with flake8 | |
| run: | | |
| $CONDA/bin/flake8 src/marbel/ | |
| - name: Run tests with pytest | |
| run: | | |
| $CONDA/bin/pytest tests --ignore ./tests/test_functional.py --doctest-modules --cov=src/marbel --cov-report=xml | |
| - name: Convert coverage to lcov format | |
| run: | | |
| $CONDA/bin/coverage lcov | |
| # - name: Send coverage report to Coveralls | |
| # uses: coverallsapp/github-action@master | |
| # with: | |
| # github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # path-to-lcov: "coverage.lcov" | |
| simulate-data: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| - name: Create conda env | |
| run: | | |
| conda create -n marbel python=3.10 r-base | |
| - name: Install the package | |
| run: | | |
| pip install -e . | |
| - name: Simulate reads | |
| run: | | |
| marbel --n-species 10 --n-orthogroups 200 --n-samples 5 10 --library-size 10000 --outdir run_spec10_orth200_samp5-10/ | |
| - name: Archive simulation results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: simulated data | |
| path: run_spec10_orth200_samp5-10 | |
| tests-functional: | |
| needs: simulate-data | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout Repo | |
| uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| - name: Create conda test-env | |
| run: | | |
| conda create -n marbel-tests scikit-bio | |
| - name: Download simulated data | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: simulated data | |
| path: run_spec10_orth200_samp5-10/ | |
| - name: Execute functional tests | |
| run: | | |
| conda init | |
| eval "$(conda shell.bash hook)" | |
| conda activate marbel-tests | |
| python tests/test_functional.py run_spec10_orth200_samp5-10/ |