update defaults for ncaa parameterization #201
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| name: Test and deploy code | |
| on: [push] | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.8", "3.9", "3.10"] | |
| defaults: # Needed for conda | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| submodules: true | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| miniforge-variant: Mambaforge | |
| channels: acellera,conda-forge,defaults | |
| - name: Install HTMD conda deps # psfgen should not be included by default in HTMD due to licensing | |
| run: | | |
| mamba install --file package/htmd-deps/DEPENDENCIES python=${{ matrix.python-version }} -y | |
| - name: Install pip dependencies | |
| run: | | |
| pip install flake8 pytest | |
| pip install . | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test | |
| run: | | |
| export HTMD_NONINTERACTIVE=1 | |
| pytest --verbose --durations=10 ./htmd/ | |
| deploy: | |
| if: startsWith(github.event.ref, 'refs/tags/') | |
| needs: test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: writedeps | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| uses-mamba: true | |
| miniforge-variant: Mambaforge | |
| channels: acellera,conda-forge,defaults | |
| - name: Dump exact dependencies yaml file | |
| shell: bash -l {0} | |
| run: | | |
| mamba install --file package/htmd-deps/DEPENDENCIES python=${{ matrix.python-version }} -y | |
| python package/htmd-deps/write_meta_yaml.py package/htmd-deps | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: true | |
| activate-environment: build | |
| python-version: ${{ matrix.python-version }} | |
| uses-mamba: true | |
| miniforge-variant: Mambaforge | |
| - name: Build htmd-deps conda package | |
| shell: bash -l {0} | |
| run: | | |
| export TAG_DESCRIBE=$(git describe) | |
| export BUILD_VERSION=$(echo $TAG_DESCRIBE | sed 's/-/ /g' | awk '{print $1}') | |
| mamba install anaconda-client conda-build python=${{ matrix.python-version }} boa | |
| conda mambabuild --python ${{ matrix.python-version }} package/htmd-deps --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
| - name: Build htmd conda package | |
| shell: bash -l {0} | |
| run: | | |
| export TAG_DESCRIBE=$(git describe) | |
| export BUILD_VERSION=$(echo $TAG_DESCRIBE | sed 's/-/ /g' | awk '{print $1}') | |
| conda mambabuild --python ${{ matrix.python-version }} package/htmd --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge | |
| - name: Upload to conda | |
| shell: bash -l {0} | |
| run: | | |
| anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/htmd-*.tar.bz2 |