CI.yaml

name: CI

on:
  push:
    branches:
      - 'master'
      - 'pymbar4'
      - 'gha'
  pull_request:
    branches:
      - 'master'
      - 'pymbar4'
      - 'gha'
  schedule:
    # Nightly Tests
    - cron: '0 0 * * *'

jobs:

  test:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macOS-latest, ubuntu-latest, windows-latest]
        python-version: ["3.8", "3.11", "3.12"]  # Check against oldest and newest versions
        jax: ["", "_jax"]
        exclude:  # Skip win + jax
          - jax: "_jax"
            os: windows-latest
    env:
      PYVER: ${{ matrix.python-version }}
      CI_OS: ${{ matrix.os }}
      PACKAGE: "pymbar"

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

    - name: Additional info about the build
      shell: bash
      run: |
        uname -a
        df -h
        ulimit -a

    - name: Setup Conda via Mamba
      uses: mamba-org/setup-micromamba@v1
      with:
        environment-file: devtools/conda-envs/test_env${{ matrix.jax }}.yaml
        environment-name: test
        condarc: |
          channels:
            - conda-forge
            - defaults
        create-args: >-
          python=${{ matrix.python-version }}

    - name: Install package
      shell: bash -l {0}
      run: |
        python -m pip install . --no-deps
        micromamba list

    - name: Run tests (pytest)
      shell: bash -l {0}
      run: |
        pytest -v --cov=$PACKAGE --cov-report=xml --color=yes --doctest-modules $PACKAGE/

    - name: Run examples
      shell: bash -l {0}
      run: |
        ### constant-force-optical-trap
        cd examples/constant-force-optical-trap
        python extract-data.py
        python force-bias-optical-trap.py
        ### harmonic-oscillators
        cd ../harmonic-oscillators
        python harmonic-oscillators.py
        python harmonic-oscillators-distributions.py
        cd ../heat-capacity
        python heat-capacity.py -b 2
        ### parallel-tempering-2dfes
        cd ../parallel-tempering-2dfes
        python parallel-tempering-2dfes.py
        ### umbrella-sampling-fes
        cd ../umbrella-sampling-fes
        python umbrella-sampling.py
        python umbrella-sampling-advanced-fes.py

    - name: CodeCov
      uses: codecov/codecov-action@v1
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml
        flags: unittests
        yml: ./.codecov.yml

  lint-format:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.8]
    env:
      PACKAGE: "pymbar"

    steps:
    - name: Checkout the code
      uses: actions/checkout@v1

    - name: Setup Conda via Mamba
      uses: mamba-org/provision-with-micromamba@main
      with:
        environment-file: devtools/conda-envs/test_env.yaml
        environment-name: test
        channels: conda-forge,defaults
        extra-specs: |
          python=${{ matrix.python-version }}

    - name: Install linter and formatter
      shell: bash -l {0}
      run: |
        micromamba install pylint black

    - name: Run pylint
      shell: bash -l {0}
      run: |
        pylint $PACKAGE/

    # Black has a default --exclude which reads .gitignore.
    # Black's --exclude and --extend-exclude are single specified RegEx patterns and overwrite if multi-marked.
    - name: Run black check
      shell: bash -l {0}
      if: always()
      run: |
        black --check -l 99 $PACKAGE/ examples/ --extend-exclude "$PACKAGE/_version.py"