diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index c8146bc5..1d793e98 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -36,15 +36,22 @@ jobs: # - torch: 1.9.0 # torchvision: 0.10.0 # python-version: 3.9 + # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell + defaults: + run: + shell: bash -l {0} steps: - name: Checkout repository - uses: actions/checkout@v2 - # See: https://github.com/marketplace/actions/setup-conda - - name: Setup anaconda - uses: s-weigand/setup-conda@v1 + uses: actions/checkout@v3 + # See: https://github.com/marketplace/actions/setup-miniconda + - name: Setup miniconda + uses: conda-incubator/setup-miniconda@v2 with: + auto-update-conda: true + miniforge-variant: Mambaforge + channels: "conda-forge, salilab, pytorch, pyg" python-version: ${{ matrix.python-version }} - conda-channels: "conda-forge, salilab, pytorch, pyg" + use-mamba: true #- name: Set up Python ${{ matrix.python-version }} # uses: actions/setup-python@v2 # with: diff --git a/.github/workflows/code-style.yaml b/.github/workflows/code-style.yaml index 400fec73..964f278f 100644 --- a/.github/workflows/code-style.yaml +++ b/.github/workflows/code-style.yaml @@ -9,7 +9,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Install Python uses: actions/setup-python@v2 diff --git a/.github/workflows/code-tests-docker.yaml b/.github/workflows/code-tests-docker.yaml index 93c5eeae..e483b30a 100644 --- a/.github/workflows/code-tests-docker.yaml +++ b/.github/workflows/code-tests-docker.yaml @@ -6,17 +6,23 @@ jobs: code-tests-docker: name: Run code tests (docker) runs-on: "ubuntu-latest" + defaults: + run: + shell: bash -l {0} steps: - name: Checkout repository - uses: actions/checkout@v2 - - # See: https://github.com/marketplace/actions/setup-conda - - name: Setup anaconda - uses: s-weigand/setup-conda@v1 + uses: actions/checkout@v3 + # See: https://github.com/marketplace/actions/setup-miniconda + - name: Setup miniconda + uses: conda-incubator/setup-miniconda@v2 with: + auto-update-conda: true + miniforge-variant: Mambaforge + channels: conda-forge python-version: 3.8 - conda-channels: "conda-forge" + use-mamba: true + # # Build cache of environment # - name: Cache conda environment diff --git a/.github/workflows/minimal__install.yaml b/.github/workflows/minimal__install.yaml index f05e0092..27f4d5ca 100644 --- a/.github/workflows/minimal__install.yaml +++ b/.github/workflows/minimal__install.yaml @@ -18,19 +18,26 @@ on: jobs: build_cpu: runs-on: ubuntu-latest + # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell + defaults: + run: + shell: bash -l {0} + strategy: matrix: python-version: [3.7, 3.8, 3.9, 3.11] steps: - name: Checkout repository - uses: actions/checkout@v2 - # See: https://github.com/marketplace/actions/setup-conda - - name: Setup anaconda - uses: s-weigand/setup-conda@v1 + uses: actions/checkout@v3 + # See: https://github.com/marketplace/actions/setup-miniconda + - name: Setup miniconda + uses: conda-incubator/setup-miniconda@v2 with: + auto-update-conda: true + miniforge-variant: Mambaforge + conda-channels: conda-forge python-version: ${{ matrix.python-version }} - conda-channels: "conda-forge" - + use-mamba: true - name: Install Graphein run: pip install -e . - name: Install Extras