ci.yaml

name: CI
on:
  push:
    branches:
      - "*"
      - "!v[0-9]+.[0-9]+.[0-9]+*"
  pull_request:
    branches:
      - "*"
      - "!v[0-9]+.[0-9]+.[0-9]+*"

  workflow_dispatch:
    inputs:
      debug_enabled:
        type: boolean
        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
        required: false
        default: false

jobs:

  pyws_setup:
    name: standard installation
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
    defaults:
      run:
        shell: bash
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"

      - name: Upgrade pip and install build and twine
        run: |
          python -m pip install --upgrade pip
          pip install wheel build 'twine<5.0.0' 'importlib_metadata<=7.0.1' 'setuptools<=72.2.0' 'numpy<2.0'

      - name: Base installation
        run: |
          pip --verbose install .

      - name: Print pyhmn version
        run: |
          python -c "import pywatershed; print(pywatershed.__version__)"

      - name: Build pywatershed, check dist outputs
        run: |
          python -m build
          twine check --strict dist/*

  pyws_lint:
    name: linting
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
    defaults:
      run:
        shell: bash
    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"

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

      - name: Version info
        run: |
          pip -V
          pip list

      - name: Lint
        run: ruff check .

      - name: Format
        run: ruff format --check .

  test:
    name: ${{ matrix.os }} py${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      fail-fast: false
      matrix:
        os: [ "ubuntu-latest", "macos-latest", "windows-latest" ]
        python-version: ["3.10", "3.11"]

    steps:

      - name: Free Disk Space (Ubuntu)
        if: runner.os == 'Linux'
        uses: jlumbroso/free-disk-space@main
        with:
          tool-cache: false
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          docker-images: true
          swap-storage: true

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

      - name: Setup tmate session
        uses: mxschmitt/action-tmate@v3
        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}

      - name: Set environment variables
        run: |
          echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
          echo "PYWS_FORTRAN=false" >> $GITHUB_ENV
          cat .mf6_ci_ref_remote  >> $GITHUB_ENV

      - name: Enforce MF6 ref and remote merge to main
        if: github.base_ref == 'main'
        run: |
          echo Merge commit: GITHUB_BASE_REF = $GITHUB_BASE_REF
          req_ref=develop  # if not develop, submit an issue
          echo $MF6_REF
          if [[ "$MF6_REF" != "$req_ref" ]]; then exit 1; fi
          req_remote=MODFLOW-USGS/modflow6
          echo $MF6_REMOTE
          if [[ "$MF6_REMOTE" != "$req_remote" ]]; then echo "bad mf6 remote in .mf6_ci_ref_remote"; exit 1; fi

      - name: Setup gfortran
        uses: fortran-lang/setup-fortran@v1
        with:
          compiler: gcc
          version: 11

      - name: Link gfortran dylibs on Mac
        if: runner.os == 'macOS'
        run: .github/scripts/symlink_gfortran_mac.sh

      - name: Install Dependencies via Micromamba
        uses: mamba-org/setup-micromamba@v1.9.0
        with:
          micromamba-version: '1.5.10-0'
          log-level: debug
          environment-file: environment.yml
          cache-environment: true
          cache-downloads: true
          create-args: >-
            python=${{matrix.python-version}}

      - name: Checkout MODFLOW 6
        uses: actions/checkout@v4
        with:
          repository: ${{ env.MF6_REMOTE }}
          ref: ${{ env.MF6_REF }}
          path: modflow6

      - name: Update flopy MODFLOW 6 classes
        working-directory: modflow6/autotest
        run: |
          python update_flopy.py

      - name: Install mf6 nightly build binaries
        uses: modflowpy/install-modflow-action@v1
        with:
          repo: modflow6-nightly-build

      - name: Install pywatershed
        run: |
          pip install .

      - name: Version info
        run: |
          pip -V
          pip list

      - name: Get GIS files for tests
        run: |
          python pywatershed/utils/gis_files.py

      - name: domainless - run tests not requiring domain data
        working-directory: autotest
        run: pytest
          -m domainless
          -n=auto
          -vv
          --durations=0
          --cov=pywatershed
          --cov-report=xml
          --junitxml=pytest_domainless.xml

      - name: sagehen_5yr_no_cascades - generate and manage test data domain, run PRMS and convert csv output to NetCDF
        working-directory: autotest
        run: |
          python generate_test_data.py \
            -n=auto --domain=sagehen_5yr --control_pattern=sagehen_no_cascades.control \
            --remove_prms_csvs --remove_prms_output_dirs

      - name: sagehen_5yr_no_cascades - list netcdf input files
        working-directory: test_data
        run: |
          find sagehen_5yr/output_no_cascades -name '*.nc'

      - name: sagehen_5yr_no_cascades - pywatershed tests
        working-directory: autotest
        run: pytest
          -vv
          -rs
          -n=auto
          -m "not domainless"
          --domain=sagehen_5yr
          --control_pattern=sagehen_no_cascades.control
          --durations=0
          --cov=pywatershed
          --cov-report=xml
          --junitxml=pytest_sagehen_5yr_no_cascades.xml

      - name: hru_1_nhm - generate and manage test data domain, run PRMS and convert csv output to NetCDF
        working-directory: autotest
        run: |
          python generate_test_data.py \
            -n=auto --domain=hru_1 --control_pattern=nhm.control \
            --remove_prms_csvs --remove_prms_output_dirs

      - name: hru_1_nhm - list netcdf input files
        working-directory: test_data
        run: |
          find hru_1/output -name '*.nc'

      - name: hru_1_nhm - pywatershed tests
        working-directory: autotest
        run: pytest
          -vv
          -rs
          -n=auto
          -m "not domainless"
          --domain=hru_1
          --control_pattern=nhm.control
          --durations=0
          --cov=pywatershed
          --cov-report=xml
          --junitxml=pytest_hru_1_nhm.xml

      - name: drb_2yr with and without dprst and obsin - generate and manage test data
        working-directory: autotest
        run: |
          python generate_test_data.py \
            -n=auto --domain=drb_2yr \
            --remove_prms_csvs --remove_prms_output_dirs

      - name: drb_2yr_nhm - list netcdf input files
        working-directory: test_data
        run: |
          find drb_2yr/output -name '*.nc'

      - name: drb_2yr_no_dprst - list netcdf input files
        working-directory: test_data
        run: |
          find drb_2yr/output_no_dprst -name '*.nc'

      - name: drb_2yr_nhm - pywatershed tests
        working-directory: autotest
        run: pytest
          -vv
          -rs
          -n=auto
          -m "not domainless"
          --domain=drb_2yr
          --control_pattern=nhm.control
          --durations=0
          --cov=pywatershed
          --cov-report=xml
          --junitxml=pytest_drb_2yr_nhm.xml

      # Specific tests not redundant with dprst
      - name: drb_2yr_no_dprst - pywatershed tests
        working-directory: autotest
        run: pytest
          test_prms_runoff.py
          test_prms_soilzone.py
          test_prms_groundwater.py
          test_prms_above_snow.py
          test_prms_below_snow.py
          -vv
          -rs
          -n=auto
          -m "not domainless"
          --domain=drb_2yr
          --control_pattern=no_dprst
          --durations=0
          --cov=pywatershed
          --cov-report=xml
          --junitxml=pytest_drb_2yr_no_dprst.xml

      # Specific tests not redundant with dprst
      - name: drb_2yr_obsin - pywatershed tests
        working-directory: autotest
        run: pytest
          test_obsin_flow_node.py
          -vv
          -n=0
          -m "not domainless"
          --domain=drb_2yr
          --control_pattern=nhm_obsin.control
          --durations=0
          --cov=pywatershed
          --cov-report=xml
          --junitxml=pytest_drb_2yr_no_dprst.xml


      - name: ucb_2yr_nhm - generate and manage test data
        working-directory: autotest
        run: |
          python generate_test_data.py \
            -n=auto --domain=ucb_2yr --control_pattern=nhm.control \
            --remove_prms_csvs --remove_prms_output_dirs

      - name: ucb_2yr_nhm - list netcdf input files
        working-directory: test_data
        run: |
          find ucb_2yr/output -name '*.nc'

      - name: ucb_2yr_nhm - pywatershed tests
        working-directory: autotest
        run: pytest
          -vv
          -n=auto
          -m "not domainless"
          --domain=ucb_2yr
          --control_pattern=nhm.control
          --durations=0
          --cov=pywatershed
          --cov-report=xml
          --junitxml=pytest_ucb_2yr_nhm.xml

      - name: Upload test results
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: Test results for ${{ runner.os }}-${{ matrix.python-version }}
          path: |
            ./autotest/pytest_hru_1_nhm.xml
            ./autotest/pytest_drb_2yr_nhm.xml
            ./autotest/pytest_drb_2yr_no_dprst.xml
            ./autotest/pytest_ucb_2yr_nhm.xml

      - name: Upload code coverage to Codecov
        uses: codecov/codecov-action@v3
        with:
          file: ./autotest/coverage.xml  # should be just the ucb result
          # flags: unittests
          env_vars: RUNNER_OS,PYTHON_VERSION
          # name: codecov-umbrella
          fail_ci_if_error: false
          version: "v0.1.15"