python-package.yml

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

name: PSAMM

on:
  push:
    branches: [ master, release ]
  pull_request:
    branches: [ master, release ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.7", "3.8", "3.9"]
        solver: ["qsoptex", "glpk", "nosolver"]
    env:
      PSAMM_SOLVER: ${{ matrix.solver }}
    steps:
    - uses: actions/checkout@v3
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        sudo apt-get install libgmp-dev
        sudo apt-get install libgmp10
        python -m pip install --upgrade pip
        python -m pip install flake8 pytest
        pip install .
        pip install biopython
        pip install libchebipy
        if echo ${{ matrix.solver }} | grep -q "glpk"; then
          pip install swiglpk;
        fi
        if echo ${{ matrix.solver }} | grep -q "qsoptex"; then
          if [ ! -f "src" ]; then
            mkdir src;
          fi;
          pip install cython;
          if [ ! -f "src/python-qsoptex" ]; then
            ( cd src/;
              git clone https://github.com/jonls/qsopt-ex.git;
              ./qsopt-ex/bootstrap;
              echo "$GITHUB_WORKSPACE"
              ./qsopt-ex/configure --prefix="${GITHUB_WORKSPACE}/src/qsopt-ex";
              make install;
              git clone https://github.com/jonls/python-qsoptex.git;
              export QSOPTEX_INCLUDE_DIR=${GITHUB_WORKSPACE}/src/qsopt-ex/include/
              export QSOPTEX_LIBRARY_DIR=${GITHUB_WORKSPACE}/src/qsopt-ex/lib/
              cd python-qsoptex/;
              ./setup.py install;
              cd ../.. );
          fi;
          pip install python-qsoptex;
        fi;
    - name: Lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source \
            --statistics --exclude ${GITHUB_WORKSPACE}/psamm/tests \
            --ignore E226,D101,D102,D103,D104,D203,W503,W504,N814,E722,N804
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 \
            --statistics
    - name: Test with pytest
      run: |
        if echo ${{ matrix.solver }} | grep -q "qsoptex"; then
          export CPATH="${GITHUB_WORKSPACE}/src/qsopt-ex/include:$CPATH";
          export LIBRARY_PATH="${GITHUB_WORKSPACE}/src/qsopt-ex/lib:$LIBRARY_PATH";
          export LD_LIBRARY_PATH="${GITHUB_WORKSPACE}/src/qsopt-ex/lib:$LD_LIBRARY_PATH";
        fi;
        pytest --ignore=src