diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml index 50299769..c0cb58d1 100644 --- a/.github/workflows/python-package-conda.yml +++ b/.github/workflows/python-package-conda.yml @@ -52,22 +52,26 @@ jobs: steps: - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + - uses: conda-incubator/setup-miniconda@v2 with: + auto-update-conda: true python-version: ${{ matrix.python-version }} - name: Install dependencies + shell: bash -l {0} run: | - # $CONDA is an environment variable pointing to the root of the miniconda directory - $CONDA/bin/conda install --name base pip click numpy "scipy>=1.3.1" pep8 flake8 coverage future six "pandas>=0.20.0" nose h5py>=2.2.0 cython - # pip install anndata + conda create --yes -n env_name python=${{ matrix.python-version }} + conda activate env_name + conda install -y pip click numpy "scipy>=1.3.1" pep8 flake8 coverage future six "pandas>=0.20.0" nose h5py>=2.2.0 cython + pip install anndata - name: Tests + shell: bash -l {0} run: | - conda install pytest - which python - pytest + conda activate env_name + conda install -y pytest + which python pip install -e . --no-deps + make test biom show-install-info for table in examples/*hdf5.biom; do echo ${table}; biom validate-table -i ${table}; done for table in examples/*table.biom; do echo ${table}; biom validate-table -i ${table}; done;