topiary/.github/workflows/python-app.yml at main · harmslab/topiary · GitHub

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: topiary

on:
  push:
    branches: [ main   ]
  pull_request:
    branches: [ main   ]

concurrency:
  group: topiary-ci-group
  cancel-in-progress: false

jobs:
  build-nix:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      max-parallel: 1
      matrix:
        os: [ubuntu-latest,macos-latest]
        python-version: ['3.11', '3.12', '3.13']

    steps:
    - name: checkout
      uses: actions/checkout@v4

    - name: set up miniconda
      uses: conda-incubator/setup-miniconda@v3
      with:
        activate-environment: topiary
        environment-file: environment.yml
        channel-priority: strict
        python-version: ${{ matrix.python-version }}
        auto-activate-base: false
        miniconda-version: "latest"

    - name: get dependency hashes
      id: get-hashes
      shell: bash
      run: |
        GENERAX_HASH=$(git ls-remote https://github.com/harmslab/generax.git HEAD | awk '{print $1}')
        RAXML_HASH=$(git ls-remote https://github.com/harmslab/raxml-ng.git HEAD | awk '{print $1}')
        echo "generax_hash=$GENERAX_HASH" >> $GITHUB_OUTPUT
        echo "raxml_hash=$RAXML_HASH" >> $GITHUB_OUTPUT

    - name: cache generax
      id: cache-generax
      uses: actions/cache@v4
      with:
        path: bin-cache/generax
        key: ${{ runner.os }}-generax-${{ steps.get-hashes.outputs.generax_hash }}

    - name: cache raxml-ng
      id: cache-raxml
      uses: actions/cache@v4
      with:
        path: bin-cache/raxml-ng
        key: ${{ runner.os }}-raxml-${{ steps.get-hashes.outputs.raxml_hash }}

    - name: install topiary
      shell: bash -l {0}
      run: |
        # platform specific packages
        conda install -c conda-forge cmake
        python -m pip install .[dev] -vv
        python -m pip install coverage flake8 pytest genbadge[tests] pytest-mock

        # Ensure bin-cache exists
        mkdir -p bin-cache

        # compile generax if not cached
        if [ ! -f bin-cache/generax ]; then
            cd dependencies
            conda run -n topiary bash compile-generax.sh
            cp $CONDA_PREFIX/bin/generax ../bin-cache/
            cd ..
        else
            cp bin-cache/generax $CONDA_PREFIX/bin/
        fi

        # compile raxml if not cached
        if [ ! -f bin-cache/raxml-ng ]; then
            cd dependencies
            conda run -n topiary bash compile-raxml-ng.sh
            cp $CONDA_PREFIX/bin/raxml-ng ../bin-cache/
            cd ..
        else
            cp bin-cache/raxml-ng $CONDA_PREFIX/bin/
        fi

    - name: run flake8
      shell: bash -l {0}
      run: |
        flake8 src/topiary tests --count --select=E9,F63,F7,F82 --show-source --statistics

    - name: run pytest
      shell: bash -l {0}
      env:
        TOPIARY_MPI_OVERSUBSCRIBE: "1"
      run: |
        pytest tests/ --run-raxml --run-generax --run-blast