python-package.yml

name: CI

on:
  push:
  pull_request:

jobs:
  python:

    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.12", "3.11", "3.10", "3.9"]
        os: [ubuntu-latest, macos-12, macos-14]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install
      run: |
        pip install .
    - name: Test with pytest
      run: |
        pip install pytest
        pytest -v
    - name: Pyflakes
      run: |
        pip install --upgrade pyflakes
        pyflakes MDRefine
    - name: Pylint
      run: |
        pip install --upgrade  pylint
        pylint -E MDRefine
    - name: Flake8
      run: |
        pip install --upgrade flake8
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 MDRefine bin --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | tee flake8_report.txt
    - name: Upload flake8_report.txt to artifact
      if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }}
      uses: actions/upload-artifact@v3
      with:
        path: flake8_report.txt
        name: flake8_report
    - name: Doc
      if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }}
      run: |
        pip install --upgrade pdoc3 jupyter nbconvert
        pdoc3 -f --html -o doc/ MDRefine
        ( cd Examples && ./render.sh )
        mkdir doc/examples
        cp Examples/*html doc/examples/
        ( sudo apt-get install tree && cd doc/examples && tree -H '.' -L 1 --noreport --charset utf-8 > index.html )
        ( sudo apt-get install pandoc texlive-xetex && pdoc3 -f --pdf MDRefine > MDRefine.md && pandoc --metadata=title:"MDRefine Documentation" --from=markdown+abbreviations+tex_math_single_backslash --pdf-engine=xelatex --toc --toc-depth=4 --output=doc/MDRefine.pdf MDRefine.md )
    - name: Upload doc to artifact
      if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' }}
      uses: actions/upload-artifact@v3
      with:
        path: doc
        name: doc

    - name: Deploy PyPI
      if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' && startsWith(github.ref, 'refs/tags/') }}
      env:
        MDREFINE_PYPI: ${{ secrets.MDREFINE_PYPI }}
      run: |
        pip install twine setuptools
        python setup.py sdist
        python -m twine upload -u __token__ -p "$MDREFINE_PYPI" dist/*.tar.gz


  conda:

    strategy:
      matrix:
        os: [ubuntu-latest, macos-12, macos-14]
    
    runs-on: ${{ matrix.os }}

    steps:
    - uses: actions/checkout@v4
    - name: Install conda
      run: |
        curl -LO https://raw.githubusercontent.com/GiovanniBussi/conda-ci/master/conda-ci
        source ./conda-ci install
        source ./conda-ci install-conda-build
    - name: Build
      run: |
        source activate base
        python make_conda_recipe.py
        export CPU_COUNT=2
        conda-build -c conda-forge conda
        rm -fr MDRefine # make sure this is not imported by mistake in tests
    - name: Test 3.9
      run: |
        source activate base
        conda create -n py39 -c conda-forge -c local python=3.9 MDRefine pytest
        source activate py39
        pytest -v
    - name: Test 3.10
      run: |
        source activate base
        conda create -n py310 -c conda-forge -c local python=3.10 MDRefine pytest
        source activate py310
        pytest -v
    - name: Test 3.11
      run: |
        source activate base
        conda create -n py311 -c conda-forge -c local python=3.11 MDRefine pytest
        source activate py311
        pytest -v
    - name: Test 3.12
      run: |
        source activate base
        conda create -n py312 -c conda-forge -c local python=3.12 MDRefine pytest
        source activate py312
        pytest -v
    - name: Deploy conda
      if: ${{ matrix.os == 'ubuntu-latest' && startsWith(github.ref, 'refs/tags/') }}
      #env:
      #  CONDA_UPLOAD_TOKEN: ${{ secrets.CONDA_UPLOAD_TOKEN }}
      run: |
        #TODO
        #source activate base
        #anaconda -t $CONDA_UPLOAD_TOKEN upload -u bussilab -l main $CONDA_PREFIX/conda-bld/*/py-bussilab*.tar.bz2 --force