CI-test.yml

# This workflow will reformat all python files with yapf

name: CI-test

on:
#  push:
#    branches:
#      - main
  workflow_dispatch:


permissions:
  contents: read

jobs:
  build_and_test:
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-latest, macos-13]
        # macos-latest should be added later as soon as libsbml support is back up
        python-version: ['3.9', '3.10', '3.11', '3.12']
        package-manager: ['pip','conda','conda_env']
#        exclude:
#        - os: macos-latest
#          package-manager: 'pip'
    steps:
      - uses: actions/checkout@v4
      - name: Cache Conda packages
        uses: actions/cache@v4
        with:
          path: |
            ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ hashFiles('**/environment.yml') }}
          restore-keys: |
            ${{ runner.os }}-conda-
      - name: Cache pip packages
        uses: actions/cache@v4
        with:
          path: |
            ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Java Setup
        uses: actions/setup-java@v4
        with:
          distribution: 'temurin' # See 'Supported distributions' for available options
          java-version: '17'
      - name: Set JAVA_HOME for mac OS
        if: runner.os == 'macOS'
        run: export JAVA_HOME=$(/usr/libexec/java_home)
      - name: Set up Conda Environment with Micromamba (conda environment test)
        if: matrix.package-manager == 'conda_env'
        uses: mamba-org/setup-micromamba@v1
        with:
          micromamba-version: '1.5.8-0'
          environment-file: environment.yml
          create-args: >-
            python=${{ matrix.python-version }}
          post-cleanup: 'none'
      - name: Build for PyPI (if pip)
        if: matrix.package-manager == 'pip'
        run: |
          pip install setuptools wheel
          python setup.py sdist bdist_wheel
      - name: Install package using pip
        if: matrix.package-manager == 'pip'
        run: pip install ./dist/*.whl
      - name: Install gurobi (pip)
        if: matrix.package-manager == 'pip'
        run: |
          pip install gurobipy
      - name: Install cplex (pip)
        if: matrix.package-manager == 'pip' && runner.os != 'macOS' && matrix.python-version != '3.12' && matrix.python-version != '3.13'
        run: |
          pip install cplex
      - name: Install pytest (pip)
        if: matrix.package-manager == 'pip'
        run: |
          pip install pytest pytest-timeout
      - name: Set up Conda Environment with Micromamba
        if: matrix.package-manager == 'conda'
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-name: straindesign
          micromamba-version: latest
          create-args: >-
            python=${{ matrix.python-version }}
          post-cleanup: 'none'
      - name: Activate Micromamba environment
        if: matrix.package-manager == 'conda'
        run: |
          micromamba activate straindesign
      - name: Build for Conda (if conda)
        if: matrix.package-manager == 'conda'
        run: |
          micromamba install anaconda-client conda-build
          run: rm -rf conda-bld
          conda build conda-recipe/. -c conda-forge --croot conda-bld --output-folder ./build
      - name: Install package using conda
        if: matrix.package-manager == 'conda'
        run: |
          conda install straindesign -c ./build
      - name: Install gurobi (conda)
        if: matrix.package-manager == 'conda'
        run: |
          micromamba install -c gurobi gurobi
      - name: Install cplex (conda)
        if: matrix.package-manager == 'conda' && matrix.python-version != '3.12' && matrix.python-version != '3.13'
        run: |
          micromamba install -c ibmdecisionoptimization cplex
      - name: Install scip (conda)
        if: matrix.package-manager == 'conda' && matrix.python-version != '3.12' && matrix.python-version != '3.13'
        run: |
          micromamba install -c conda-forge pyscipopt scip
      - name: Install pytest (conda)
        if: matrix.package-manager == 'conda'
        run: |
          micromamba install pytest pytest-timeout
      - name: Test with pytest
        if: matrix.package-manager == 'conda' || matrix.package-manager == 'pip'
        run: pytest tests -v --log-cli-level=INFO