Merge pull request #11 from cabb99/main #232
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| name: CI | |
| on: | |
| # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming | |
| # Existing codes likely still have "master" as the primary branch | |
| # Both are tracked here to keep legacy and new codes working | |
| push: | |
| branches: | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "main" | |
| # schedule: | |
| # Nightly tests run on master by default: | |
| # Scheduled workflows run on the latest commit on the default or base branch. | |
| # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | |
| # - cron: "0 0 * * *" | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| #os: [macOS-latest, ubuntu-latest, windows-latest] | |
| #python-version: [3.8, 3.9, "3.10"] | |
| os: [ubuntu-latest] | |
| python-version: [3.8, 3.9, "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Install hmmer | |
| run: | | |
| wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz | |
| tar zxf hmmer-3.4.tar.gz | |
| cd hmmer-3.4 | |
| ./configure | |
| make | |
| make check | |
| sudo make install | |
| cd .. | |
| - name: checkout source | |
| uses: actions/checkout@v2 | |
| # with: | |
| # path: main | |
| # - name: Generate lfs file list | |
| # run: git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id | |
| # - name: Restore lfs cache | |
| # uses: actions/cache@v2 | |
| # id: lfs-cache | |
| # with: | |
| # path: .git/lfs | |
| # key: ${{ runner.os }}-lfs-${{ hashFiles('.lfs-assets-id') }}-v1 | |
| # - name: Pull lfs files | |
| # run: git lfs pull | |
| # - name: Change to main directory | |
| # run: | | |
| # cd main | |
| # pwd | |
| # More info on options: https://github.com/conda-incubator/setup-miniconda | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| channels: conda-forge, defaults, bioconda | |
| activate-environment: test | |
| auto-update-conda: false | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| # - name: Change to root directory | |
| # run: | | |
| # cd main | |
| # pwd | |
| #Install numpy first | |
| - name: Install numpy | |
| run: | | |
| conda install "numpy<2" | |
| #Install pydca | |
| - name: Check out pydca | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: cabb99/pydca | |
| path: pydca_dir | |
| - name: Install pydca | |
| run: | | |
| cd pydca_dir | |
| echo "numpy<2" > constraints.txt | |
| conda run -n test pip install -r requirements.txt -c constraints.txt | |
| conda run -n test python -m pip install . --no-deps | |
| conda list | |
| cd .. | |
| pwd | |
| conda run -n test python -c "import sys; print(sys.executable); print('\n'.join(sys.path))" | |
| conda run -n test python -c "import pydca; print('pydca is installed and importable')" | |
| conda run -n test pip freeze | grep pydca | |
| - name: Install package | |
| # conda setup requires this special shell | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c conda-forge --file requirements.txt | |
| python -m pip install . --no-deps | |
| conda list | |
| - name: Install pdbfixer | |
| # conda setup requires this special shell | |
| shell: bash -l {0} | |
| run: | | |
| conda install -c conda-forge pdbfixer | |
| - name: Run tests | |
| # conda setup requires this special shell | |
| shell: bash -l {0} | |
| run: | | |
| python -c "import sys; print(sys.executable); print('\n'.join(sys.path))" | |
| python -c "import pydca; print('pydca is installed and importable')" | |
| pip freeze | grep pydca | |
| pytest -v --cov=frustratometer --cov-report=xml --color=yes tests/ | |
| - name: CodeCov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |