diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index dc8a68e9..e25704ec 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -43,9 +43,6 @@ jobs: - os: ubuntu-latest python-version: "3.9" gromacs-version: "2021.1" - - os: macos-latest - python-version: "3.9" - gromacs-version: "2021.1" - os: macos-latest python-version: "3.10" gromacs-version: "2021.1" @@ -57,38 +54,32 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: conda-incubator/setup-miniconda@v2 + - name: mamba environment and package installation + uses: mamba-org/provision-with-micromamba@main with: - python-version: ${{ matrix.python-version }} - auto-update-conda: true - mamba-version: "*" - channels: conda-forge,bioconda,defaults - channel-priority: true - show-channel-urls: true + environment-file: devtools/conda-envs/test_env.yaml + channel-priority: "flexible" + cache-downloads: true + cache-env: true + extra-specs: | + python=${{ matrix.python-version }} - - name: Conda info - run: | - conda info - conda list - conda config --show-sources - conda config --show - - - name: Python version + - name: Python version information run: | python -c "import sys; print(sys.version)" - - name: Install package dependencies + - name: micromamba environment information run: | - mamba install six numpy scipy matplotlib-base pandas scikit-learn pyyaml "mdanalysis>=2" numkit gromacswrapper "alchemlyb<2" - - - name: Install pytest+plugins and pybol + micromamba info + micromamba list + + - name: Install pybol (fixture staging tool) run: | - mamba install pytest pytest-pep8 pytest-cov codecov python -m pip install pybol - name: Install GROMACS (${{ matrix.gromacs-version }}) run: | - mamba install 'gromacs==${{ matrix.gromacs-version }}' pocl + micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl - name: Install package (with no dependencies) run: | diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml new file mode 100644 index 00000000..5544ee54 --- /dev/null +++ b/devtools/conda-envs/test_env.yaml @@ -0,0 +1,23 @@ +name: test +channels: +- conda-forge +- bioconda +dependencies: +- python +- six +- numpy +- scipy +- matplotlib-base +- pandas +- scikit-learn +- pyyaml +- mdanalysis >=2 +- numkit +- gromacswrapper +- alchemlyb <2 + + # Testing +- pytest +- pytest-pep8 +- pytest-cov +- codecov \ No newline at end of file