Add 1st netcdf example based on watershed model #48
Workflow file for this run
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| name: GW3099 continuous integration | |
| on: | |
| # run at 6 AM UTC every day | |
| schedule: | |
| - cron: '0 6 * * *' | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - '**.md' | |
| pull_request: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - '**.md' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| 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 ruff | |
| run: pip install ruff | |
| - name: Lint | |
| run: ruff check . | |
| - name: Check format | |
| run: ruff format . --check | |
| install_env_linux: | |
| name: Install gw3099 environment on linux | |
| needs: lint | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: apt install | |
| run: | | |
| sudo apt-get install -y pkg-config petsc-dev libnetcdf-dev | |
| - name: list installed packages | |
| run: | | |
| pkg-config --list-all | grep petsc | |
| pkg-config --list-all | grep netcdf | |
| pkg-config --list-all | grep hdf | |
| - name: Install miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: "environment.yml" | |
| activate-environment: "gw3099" | |
| auto-activate-base: false | |
| - name: Update flopy mf6 classes | |
| run: | | |
| conda env list | |
| python -m flopy.mf6.utils.generate_classes --ref 'develop' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Clone MODFLOW repo | |
| run: | | |
| git clone --depth 1 --branch develop https://github.com/MODFLOW-USGS/modflow6.git | |
| - name: Build extended version of MODFLOW | |
| if: runner.os != 'Windows' | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false -Dextended=true --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Create symbolic links on Linux | |
| working-directory: modflow6 | |
| run: | | |
| ln -sf $(pwd)/bin/mf6 $CONDA_PREFIX/bin/mf6 | |
| ln -sf $(pwd)/bin/libmf6.so $CONDA_PREFIX/bin/libmf6.so | |
| - name: Test modflow installation | |
| if: runner.os != 'Windows' | |
| run: | | |
| which mf6 | |
| mf6 -v | |
| mf6 -co | |
| - name: Test notebooks | |
| working-directory: .scripts | |
| run: | | |
| python test_notebooks.py --script | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| install_env: | |
| name: Install gw3099 environment | |
| needs: lint | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["macos-latest", "windows-latest"] | |
| python-version: ["3.9", "3.10", "3.11"] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Update environment file | |
| working-directory: .scripts | |
| run: | | |
| python update_env_file.py | |
| - name: Install miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: "environment.yml" | |
| activate-environment: "gw3099" | |
| auto-activate-base: false | |
| - name: List netcdf version | |
| if: runner.os != 'Windows' | |
| run: | | |
| which nc-config | |
| nc-config --version | |
| pkg-config --libs netcdf | |
| pkg-config --libs netcdf-fortran | |
| - name: Update flopy mf6 classes | |
| run: | | |
| conda env list | |
| python -m flopy.mf6.utils.generate_classes --ref 'develop' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Update package config files | |
| if: (runner.os != 'Windows') | |
| working-directory: .scripts | |
| run: | | |
| python update_pc_files.py | |
| - name: Clone MODFLOW repo | |
| run: | | |
| git clone --depth 1 --branch develop https://github.com/MODFLOW-USGS/modflow6.git | |
| - name: Build extended version of MODFLOW | |
| if: runner.os != 'Windows' | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false -Dextended=true --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Create symbolic links on Linux | |
| if: runner.os == 'Linux' | |
| working-directory: modflow6 | |
| run: | | |
| ln -sf $(pwd)/bin/mf6 $CONDA_PREFIX/bin/mf6 | |
| ln -sf $(pwd)/bin/libmf6.so $CONDA_PREFIX/bin/libmf6.so | |
| - name: Create symbolic links on MacOS | |
| if: runner.os == 'macOS' | |
| working-directory: modflow6 | |
| run: | | |
| ln -sf $(pwd)/bin/mf6 $CONDA_PREFIX/bin/mf6 | |
| ln -sf $(pwd)/bin/libmf6.dylib $CONDA_PREFIX/bin/libmf6.dylib | |
| - name: Test modflow installation | |
| if: runner.os != 'Windows' | |
| run: | | |
| which mf6 | |
| mf6 -v | |
| mf6 -co | |
| - name: Get and test parallel MODFLOW on Windows | |
| if: runner.os == 'Windows' | |
| working-directory: modflow6/.mf6minsim | |
| run: | | |
| get-modflow --repo modflow6-nightly-build --ostag win64par :python | |
| mpiexec -n 1 mf6 -p | |
| mpiexec -n 2 mf6 -p | |
| - name: Test notebooks | |
| working-directory: .scripts | |
| run: | | |
| python test_notebooks.py | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| install_vizenv: | |
| name: Install viz environment | |
| needs: lint | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest", "windows-latest"] | |
| python-version: ["3.9", "3.10", "3.11"] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Install miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: 'environment-viz.yml' | |
| activate-environment: 'gw3099viz' | |
| auto-activate-base: false | |
| - name: Conda info | |
| run: | | |
| conda info | |
| conda list | |