commit.yml

name: FloPy continuous integration
on:
  push:
    branches:
      - master
      - develop
      - ci-diagnose*
      - notebooks
  pull_request:
    branches:
      - master
      - develop
jobs:
  build:
    name: Build
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash
    timeout-minutes: 10
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
          cache: 'pip'
          cache-dependency-path: pyproject.toml

      - name: Install Python dependencies
        run: |
          pip install --upgrade pip
          pip install build twine
          pip install .
          python -c "import flopy; print(f'{flopy.__version__}')"

      - name: Build package
        run: |
          python -m build
      - name: Check package
        run: |
          twine check --strict dist/*

  lint:
    name: Lint
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash
    timeout-minutes: 10

    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
          cache: 'pip'
          cache-dependency-path: pyproject.toml

      - name: Install Python dependencies
        run: |
          pip install .
          pip install ".[lint]"

      - name: Run isort
        run: |
          echo "if isort check fails update isort using"
          echo "  pip install isort --upgrade"
          echo "and run"
          echo "  isort ./flopy"
          echo "and then commit the changes."
          isort --check --diff ./flopy

      - name: Run black
        run: |
          echo "if black check fails update black using"
          echo "  pip install black --upgrade"
          echo "and run"
          echo "  black ./flopy"
          echo "and then commit the changes."
          black --check --diff ./flopy

      - name: Run flake8
        run: |
          flake8 --count --show-source --exit-zero ./flopy

      - name: Run pylint
        run: |
          pylint --jobs=2 --errors-only --exit-zero ./flopy

      - name: Check CITATION.cff
        run: |
          cffconvert --validate
          cffconvert -f apalike
          cffconvert -f bibtex

  smoke:
    name: Smoke test
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash
    timeout-minutes: 10
    env:
      PYTHON_VERSION: 3.8

    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ env.PYTHON_VERSION }}
          cache: 'pip'
          cache-dependency-path: pyproject.toml

      - name: Install Python dependencies
        run: |
          pip install --upgrade pip
          pip install .
          pip install ".[test,optional]"
      
      - name: Install Modflow executables
        uses: modflowpy/install-modflow-action@v1
      
      - name: Smoke test
        working-directory: autotest
        run: pytest -v -n=auto --smoke --cov=flopy --cov-report=xml --durations=0 --keep-failed=.failed
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Upload failed test outputs
        uses: actions/upload-artifact@v3
        if: failure()
        with:
          name: failed-smoke-${{ runner.os }}-${{ env.PYTHON_VERSION }}
          path: ./autotest/.failed/**
      
      - name: Upload coverage
        if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
        uses: codecov/codecov-action@v3
        with:
          files: ./autotest/coverage.xml

  test:
    name: Test
    needs: smoke
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ ubuntu-latest, macos-latest, windows-latest ]
        python-version: [ 3.8, 3.9, "3.10", "3.11" ]
        exclude:
          # avoid shutil.copytree infinite recursion bug
          # https://github.com/python/cpython/pull/17098
          - python-version: '3.8.0'
    defaults:
      run:
        shell: bash
    timeout-minutes: 45
    steps:

      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Setup Python
        if: runner.os != 'Windows'
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
          cache-dependency-path: pyproject.toml

      - name: Install Python dependencies
        if: runner.os != 'Windows'
        run: |
          pip install --upgrade pip
          pip install .
          pip install ".[test, optional]"

      - name: Setup Micromamba
        if: runner.os == 'Windows'
        uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: etc/environment.yml
          cache-environment: true
          cache-downloads: true
          create-args: >-
            python=${{ matrix.python-version }}
          init-shell: >-
            bash
            powershell

      - name: Install Python dependencies
        shell: bash -l {0}
        if: runner.os == 'Windows'
        run: |
          pip install xmipy
          pip install .

      - name: Install Modflow-related executables
        uses: modflowpy/install-modflow-action@v1

      - name: Install Modflow dev build executables
        uses: modflowpy/install-modflow-action@v1
        with:
          repo: modflow6-nightly-build

      - name: Update FloPy packages
        if: runner.os != 'Windows'
        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup

      - name: Update FloPy packages
        if: runner.os == 'Windows'
        shell: bash -l {0}
        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup

      - name: Run tests
        if: runner.os != 'Windows'
        working-directory: ./autotest
        run: |
          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
          coverage report
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Run tests
        if: runner.os == 'Windows'
        shell: bash -l {0}
        working-directory: ./autotest
        run: |
          pytest -v -m="not example and not regression" -n=auto --cov=flopy --cov-append --cov-report=xml --durations=0 --keep-failed=.failed --dist loadfile
          coverage report
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Upload failed test outputs
        uses: actions/upload-artifact@v3
        if: failure()
        with:
          name: failed-${{ matrix.os }}-${{ matrix.python-version }}
          path: |
            ./autotest/.failed/**

      - name: Upload coverage
        if: github.repository_owner == 'modflowpy' && (github.event_name == 'push' || github.event_name == 'pull_request')
        uses: codecov/codecov-action@v3
        with:
          files: ./autotest/coverage.xml