diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index a90873fa..84a54393 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -70,7 +70,7 @@ jobs: steps: - uses: actions/checkout@v3 - - name: micromamba environment and package installation (Python ${{ matrix.python-version }}) + - name: micromamba package and testing environment installation (Python ${{ matrix.python-version }}, GROMACS ${{ matrix.gromacs-version }}) uses: mamba-org/setup-micromamba@v1 with: environment-file: ci/conda-envs/test_env.yaml @@ -83,6 +83,7 @@ jobs: cache-environment: true create-args: >- python=${{ matrix.python-version }}.*=*_cpython + gromacs==${{ matrix.gromacs-version }} - name: Python version information ${{ matrix.python-version }} run: | @@ -93,17 +94,8 @@ jobs: micromamba info micromamba list cat /proc/cpuinfo || (/usr/sbin/system_profiler SPHardwareDataType; /usr/sbin/sysctl -a | grep machdep.cpu) - - - name: Install pytest and plugins - run: | - micromamba install pytest pytest-pep8 pytest-cov codecov - - - name: Install GROMACS (${{ matrix.gromacs-version }}) - # UGLY HACK/FIX (probably to issues with bioconda packages) - # - For 3.9, micromamba insists on using pypy 3.9 (and --py-pin does not help). - # We can't freeze because then it's not possible to install older GROMACS versions from bioconda. - run: | - micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl numkit python=${{ matrix.python-version }}.*=*_cpython + micromamba list | grep gromacs | grep ${{ matrix.gromacs-version }} + micromamba list | grep python | grep ${{ matrix.python-version }} - name: Install package (with no dependencies) run: | diff --git a/ci/conda-envs/test_env.yaml b/ci/conda-envs/test_env.yaml index 3222e3d5..0bdbb4ac 100644 --- a/ci/conda-envs/test_env.yaml +++ b/ci/conda-envs/test_env.yaml @@ -1,10 +1,16 @@ -name: test +# it is important to install gromacs together with everything else to ensure correct dependency resolution +name: gromacs_wrapper channels: - conda-forge dependencies: -- python -- numpy>=1.0 - matplotlib -- pandas>=0.17 - numkit>=1.0 +- numpy>=1.0 +- pandas>=0.17 +- pocl - setuptools +# dev tools +- codecov +- pytest +- pytest-cov +- pytest-pep8