msibi-sample/.github/workflows/CI.yaml at main · kassonlab/msibi-sample · GitHub

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name: CI

on:
  push:
    branches:
      - "main"
  pull_request:
    branches:
      - "main"
  schedule:
    - cron:  "0 0 * * *"

jobs:
  test:
    if: github.event.pull_request.draft == false
    name: MSIBI Tests (python)
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
        python-version: ["3.10", "3.11", "3.12"]

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v5
        name: Checkout Branch / Pull Request

      - name: Install Mamba
        uses: mamba-org/setup-micromamba@v2
        with:
          environment-file: environment-dev.yml
          create-args: >-
            python=${{ matrix.python-version }}

      - name: Install Package
        run: python -m build && pip install dist/*.whl

      - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
        run: python -m pytest -v --cov=msibi --cov-report=xml --cov-append --cov-config=setup.cfg --color yes --pyargs msibi

      - name: Upload Coverage Report
        uses: codecov/codecov-action@v5
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          name: MSIBI-Coverage
          verbose: true

  arch-test:
    if: github.event.pull_request.draft == false
    name: MSIBI Tests (arch)
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macOS-latest, ubuntu-latest]
        python-version: ["3.13"]

    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v5
        name: Checkout Branch / Pull Request

      - name: Install Mamba
        uses: mamba-org/setup-micromamba@v2
        with:
          environment-file: environment-dev.yml
          create-args: >-
            python=${{ matrix.python-version }}

      - name: Install Package
        run: python -m build && pip install dist/*.whl

      - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }})
        run: python -m pytest -v --color yes --pyargs msibi

  wsl-test:
    if: github.event.pull_request.draft == false
    name: MSIBI Tests (WSL)
    runs-on: windows-latest

    steps:
      - uses: actions/checkout@v4
        name: Checkout Branch / Pull Request

      - uses: Vampire/setup-wsl@v5
        with:
          distribution: Ubuntu-24.04
          wsl-shell-user: runner
        name: Set up WSL

      - name: Install MSIBI and run pytest
        shell: wsl-bash {0}
        run: |
          wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -O $HOME/Miniforge3.sh
          bash $HOME/Miniforge3.sh -b -p $HOME/miniforge
          echo 'export PATH=$HOME/miniforge/bin:$PATH' >> ~/.bashrc
          export PATH=$HOME/miniforge/bin:$PATH
          source ~/.bashrc
          source $HOME/miniforge/etc/profile.d/conda.sh
          mamba update -n base --all -y
          mamba env create -f environment-dev.yml python=3.12 -y
          conda activate msibi-dev
          pip install -e . --prefix=$HOME/tmp_egginfo --no-build-isolation
          python -m pytest -v --color yes