continuous-integration-pip.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: CI

on:
  push:
    branches: [master]
  pull_request:
    branches: [master, 'v?.?*']

jobs:
  code_lint:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.8]

    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install flake8
      - name: Lint with flake8
        run: |
          # stop the build if there are Python syntax errors or undefined names
          flake8 . --count --select=B,C,E,F,W,T,N8 --ignore=E402 --max-line-length=88 --show-source --statistics --exclude="examples/* *.npy docs/* *.pyx *.pxd"
          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
          flake8 . --count --exit-zero --max-complexity=8 --max-line-length=88 --statistics --exclude="examples/* *.npy docs/* *.pyx *.pxd"
  testing_unix:
    needs: [code_lint]
    strategy:
      matrix:
        os: ["ubuntu-latest", "macos-latest"]
        python-version: [3.7, 3.8, 3.9, "3.10"]
    runs-on: ${{ matrix.os }}

    steps:
      - name: Checkout
        uses: actions/checkout@v3

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install linux system dependencies
        if: startsWith(matrix.os, 'ubuntu')
        run: sudo apt-get install --yes libopenblas-dev libfftw3-dev

      - name: check gcc version on linux system
        if: startsWith(matrix.os, 'ubuntu')
        run: gcc -v

      - name: Install macos system dependencies
        if: startsWith(matrix.os, 'mac')
        run: brew install openblas fftw

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install pytest cython setuptools pytest-cov sympy sybil
          pip install -r requirements.txt
      - name: Build and install package from source
        run: python setup.py develop

      - name: Test with pytest
        run: pytest --cov=./ --cov-report=xml

      - name: Upload coverage
        uses: codecov/codecov-action@v3.1.1

  # build_windows_test:
  #   needs: [code_lint]
  #   strategy:
  #     matrix:
  #       os: ["windows-latest"]
  #       python-version: [3.6, 3.7]
  #   runs-on: ${{ matrix.os }}

  #   env:
  #     LIB: "C:\\Miniconda\\Library\\lib"
  #     INCLUDE: "C:\\Miniconda\\Library\\include;C:\\Miniconda\\Library\\include\\openblas"
  #     MRSIM_LIB: "C:\\Miniconda\\Library\\lib"
  #   steps:
  #     - name: Checkout
  #       uses: actions/checkout@v3

  #     - name: Set up Python ${{ matrix.python-version }}
  #       uses: actions/setup-python@v4
  #       with:
  #         python-version: ${{ matrix.python-version }}

  #     - name: Install windows dependencies
  #       run: |
  #         C:\Miniconda\Scripts\conda install -c conda-forge openblas fftw

  #     - name: Install package dependencies
  #       run: |
  #         python -m pip install --upgrade pip
  #         pip install pytest cython setuptools pytest-cov sympy
  #         pip install -r requirements.txt

  #     - name: Build and install package from source
  #       run: python setup.py develop

  #     - name: Test with pytest
  #       run: pytest --cov=./ --cov-report=xml

  #     - name: Upload coverage
  #       uses: codecov/codecov-action@v3.1.1

  testing_windows:
    needs: [code_lint]
    strategy:
      matrix:
        python-version: [3.7, 3.8, 3.9, "3.10"]
    runs-on: "windows-latest"

    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Setup Miniconda
        uses: conda-incubator/setup-miniconda@v2
        env:
          ACTIONS_ALLOW_UNSECURE_COMMANDS: "true"
        with:
          auto-update-conda: true
          auto-activate-base: false
          miniconda-version: "latest"
          python-version: ${{ matrix.python-version }}
          environment-file: environment-dev.yml
          activate-environment: mrsimulator-dev
      - run: |
          conda --version
          which python
      - name: Build and install package from source
        shell: pwsh
        run: |
          conda --version
          which python
          python setup.py develop
      - name: Test with pytest
        shell: pwsh
        run: pytest --cov=./ --cov-report=xml
      - name: Upload coverage
        uses: codecov/codecov-action@v3.1.1