fix(PrtFmiType): accommodate 0s in nodelist #2148
Workflow file for this run
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| name: MODFLOW 6 continuous integration | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.pdf' | |
| - '**.tex' | |
| - '**.jpg' | |
| - '**.jpeg' | |
| - '**.png' | |
| - '**.bbl' | |
| - '**.bib' | |
| - 'doc/**.dat' | |
| - 'doc/**.ipynb' | |
| - 'doc/**.py' | |
| - 'doc/**.sh' | |
| - 'doc/**.xlsx' | |
| - '.hpc/**' | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| paths-ignore: | |
| - '**.md' | |
| - '**.pdf' | |
| - '**.tex' | |
| - '**.jpg' | |
| - '**.jpeg' | |
| - '**.png' | |
| - '**.bbl' | |
| - '**.bib' | |
| - 'doc/**.dat' | |
| - 'doc/**.ipynb' | |
| - 'doc/**.py' | |
| - 'doc/**.sh' | |
| - 'doc/**.xlsx' | |
| - '.hpc/**' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| PIXI_BETA_WARNING_OFF: true | |
| jobs: | |
| lint: | |
| name: Check format | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout MF6 | |
| uses: actions/checkout@v4 | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| - name: Check Fortran source formatting | |
| run: pixi run check-format | |
| - name: Check MSVS project files | |
| run: pixi run check-vfproj | |
| - name: Check python lint | |
| run: pixi run check-python-lint | |
| - name: Check python format | |
| run: pixi run check-python-format | |
| - name: Check CITATION.cff | |
| uses: dieghernan/cff-validator@v3 | |
| build: | |
| name: Build | |
| runs-on: ubuntu-22.04 | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout MF6 | |
| uses: actions/checkout@v4 | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| - name: Setup MF6 | |
| run: pixi run setup -Dwerror=true builddir | |
| - name: Build MF6 | |
| run: pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test MF6 | |
| run: pixi run test builddir | |
| smoke_test: | |
| name: Smoke test | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout MF6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout test-drive | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: fortran-lang/test-drive | |
| path: test-drive | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Build test-drive | |
| working-directory: test-drive | |
| run: | | |
| pixi run --manifest-path=../modflow6/pixi.toml meson setup builddir --prefix=$(pwd) --libdir=lib | |
| pixi run --manifest-path=../modflow6/pixi.toml meson install -C builddir | |
| echo "PKG_CONFIG_PATH=$(pwd)/lib/pkgconfig:$PKG_CONFIG_PATH" >> $GITHUB_ENV | |
| - name: Build MF6 | |
| working-directory: modflow6 | |
| run: | | |
| pixi run setup builddir | |
| pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test MF6 | |
| working-directory: modflow6 | |
| run: pixi run test builddir | |
| - name: Update flopy | |
| working-directory: modflow6 | |
| run: pixi run update-flopy | |
| - name: Get executables | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run get-exes | |
| - name: Test MF6 | |
| working-directory: modflow6 | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pixi run autotest -m "not slow and not regression and not developmode" | |
| else | |
| pixi run autotest --smoke | |
| fi | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-smoke-${{ runner.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| test_gfortran: | |
| name: Test GNU fortran | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: macos-12 | |
| debug: false | |
| - os: macos-14 | |
| debug: false | |
| - os: macos-14 | |
| debug: true | |
| - os: ubuntu-22.04 | |
| debug: false | |
| - os: ubuntu-22.04 | |
| debug: true | |
| - os: windows-2022 | |
| debug: false | |
| defaults: | |
| run: | |
| shell: bash | |
| env: | |
| FC: gfortran | |
| FC_V: 13 | |
| steps: | |
| - name: Checkout MF6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout test models | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Checkout examples | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-examples | |
| path: modflow6-examples | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: gcc | |
| version: ${{ env.FC_V }} | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Set LDFLAGS (macOS) | |
| if: matrix.os == 'macos-14' | |
| run: | | |
| os_ver=$(sw_vers -productVersion | cut -d'.' -f1) | |
| if (( "$os_ver" > 12 )); then | |
| ldflags="$LDFLAGS -Wl,-ld_classic" | |
| echo "LDFLAGS=$ldflags" >> $GITHUB_ENV | |
| fi | |
| - name: Build MF6 | |
| working-directory: modflow6 | |
| run: | | |
| setupargs="" | |
| if [[ "${{ matrix.debug }}" == "true" ]]; then | |
| setupargs="-Ddebug=true -Doptimization=0" | |
| elif [[ "${{ matrix.os }}" == "macos-14" ]]; then | |
| setupargs="-Doptimization=1" | |
| fi | |
| pixi run setup builddir $setupargs | |
| pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test MF6 | |
| working-directory: modflow6 | |
| run: pixi run test builddir | |
| - name: Update flopy | |
| working-directory: modflow6 | |
| run: pixi run update-flopy | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run get-exes | |
| - name: Test MF6 | |
| working-directory: modflow6 | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| markers="" | |
| if [[ "${{ github.ref_name }}" == "master" ]]; then | |
| markers="not large and not developmode" | |
| else | |
| markers="not large" | |
| fi | |
| filters="" | |
| if [[ "${{ matrix.os }}" == "macos-14" ]]; then | |
| # comparison fails on macos-14 with optimization=1 | |
| filters="not test028_sfr_rewet" | |
| fi | |
| pixi run autotest -m "$markers" -k "$filters" | |
| - name: Install executables | |
| if: runner.os == 'Linux' | |
| uses: modflowpy/install-modflow-action@v1 | |
| - name: Test examples | |
| if: runner.os == 'Linux' | |
| working-directory: modflow6 | |
| shell: pixi run bash -e {0} | |
| run: | | |
| cp bin/mf6 ~/.local/bin/modflow/ | |
| cp bin/libmf6.so ~/.local/bin/modflow/ | |
| cd ../modflow6-examples/autotest | |
| pytest -v -n auto test_scripts.py | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| - name: Checkout usgslatex | |
| if: runner.os == 'Linux' | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/usgslatex | |
| path: usgslatex | |
| - name: Install TeX Live | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt install texlive-science \ | |
| texlive-latex-extra \ | |
| texlive-font-utils \ | |
| texlive-fonts-recommended \ | |
| texlive-fonts-extra | |
| - name: Install USGS LaTeX style files and Univers font | |
| if: runner.os == 'Linux' | |
| working-directory: usgslatex/usgsLaTeX | |
| run: sudo ./install.sh --all-users | |
| - name: Test distribution scripts | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run test-dist-scripts | |
| test_intel_fortran: | |
| name: Test Intel fortran | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| FC: intel-classic | |
| FC_V: "2021.7" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-22.04, macos-12, windows-2022] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Free disk space (Ubuntu) | |
| if: runner.os == 'Linux' | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: true | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - name: Checkout MF6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout test models | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Checkout examples | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-examples | |
| path: modflow6-examples | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Setup ${{ env.FC }} ${{ env.FC_V }} | |
| uses: fortran-lang/setup-fortran@v1 | |
| with: | |
| compiler: ${{ env.FC }} | |
| version: ${{ env.FC_V }} | |
| - name: Update version files | |
| working-directory: modflow6 | |
| run: pixi run update-version | |
| - name: Build MF6 | |
| working-directory: modflow6 | |
| run: | | |
| pixi run setup builddir | |
| pixi run build builddir | |
| - name: Show build log | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Unit test MF6 | |
| working-directory: modflow6 | |
| run: pixi run test builddir | |
| - name: Update flopy | |
| working-directory: modflow6 | |
| run: pixi run update-flopy | |
| - name: Get executables | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run get-exes | |
| - name: Test MF6 | |
| working-directory: modflow6 | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pixi run autotest -m "not large and not developmode" | |
| else | |
| pixi run autotest -m "not large" | |
| fi | |
| - name: Install executables | |
| if: runner.os == 'Linux' | |
| uses: modflowpy/install-modflow-action@v1 | |
| - name: Test examples | |
| if: runner.os == 'Linux' | |
| working-directory: modflow6 | |
| shell: pixi run bash -e {0} | |
| run: | | |
| cp bin/mf6 ~/.local/bin/modflow/ | |
| cp bin/libmf6.so ~/.local/bin/modflow/ | |
| cd ../modflow6-examples/autotest | |
| pytest -v -n auto test_scripts.py | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }} | |
| path: modflow6/autotest/.failed | |
| - name: Test scripts | |
| working-directory: modflow6 | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pixi run test-dist-scripts | |
| parallel_test: | |
| name: Parallel testing | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-13, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout MF6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Checkout test models | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Set LDFLAGS (macOS) | |
| if: matrix.os == 'macos-13' | |
| run: | | |
| os_ver=$(sw_vers -productVersion | cut -d'.' -f1) | |
| if (( "$os_ver" > 12 )); then | |
| ldflags="$LDFLAGS -Wl,-ld_classic" | |
| echo "LDFLAGS=$ldflags" >> $GITHUB_ENV | |
| fi | |
| - name: Test parallel MF6 | |
| if: runner.os != 'Windows' | |
| uses: ./modflow6/.github/actions/test-par | |
| - name: Test parallel MF6 (Windows) | |
| if: runner.os == 'Windows' | |
| uses: ./modflow6/.github/actions/test-par-win | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }} | |
| path: modflow6/autotest/.failed | |
| extended_test: | |
| name: Extended executable testing | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-13 ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Checkout MF6 | |
| uses: actions/checkout@v4 | |
| with: | |
| path: modflow6 | |
| - name: Setup pixi | |
| uses: prefix-dev/[email protected] | |
| with: | |
| pixi-version: v0.24.2 | |
| manifest-path: "modflow6/pixi.toml" | |
| - name: Custom pixi install | |
| working-directory: modflow6 | |
| run: pixi run install | |
| - name: Install additional netcdf testing packages | |
| working-directory: modflow6 | |
| run: pixi run pip install xugrid xarray netcdf4 | |
| - name: Set LDFLAGS (macOS) | |
| if: matrix.os == 'macos-13' | |
| run: | | |
| os_ver=$(sw_vers -productVersion | cut -d'.' -f1) | |
| if (( "$os_ver" > 12 )); then | |
| ldflags="$LDFLAGS -Wl,-ld_classic" | |
| echo "LDFLAGS=$ldflags" >> $GITHUB_ENV | |
| fi | |
| - name: Test extended MF6 | |
| uses: ./modflow6/.github/actions/test-extended | |
| - name: Upload failed test output | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: failed-${{ matrix.os }} | |
| path: modflow6/autotest/.failed |