feat(idm): initial netcdf integration

.github/workflows/ci.yml

@@ -566,4 +566,134 @@ jobs:
         with:
           name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }}
           path: modflow6/autotest/.failed
-
+
+  netcdf_test:
+    name: NetCDF testing
+    needs:
+      - lint
+      - build
+      - smoke_test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-22.04, macos-12 ] #, windows-2022 ]
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      FC: gfortran
+      FC_V: 12
+    steps:
+
+      - name: Checkout modflow6
+        uses: actions/checkout@v4
+        with:
+          path: modflow6
+
+      - name: Setup ${{ env.FC }} ${{ env.FC_V }}
+        uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: gcc
+          version: ${{ env.FC_V }}
+
+      - name: Cache PETSc
+        id: cache-petsc
+        uses: actions/cache@v4
+        with:
+          path: petsc
+          key: ${{ runner.os }}-petsc
+
+      - name: Clone PETSc
+        if: runner.os != 'Windows' && steps.cache-petsc.outputs.cache-hit != 'true'
+        run: git clone -b release https://gitlab.com/petsc/petsc.git petsc
+
+      - name: Configure environment
+        if: runner.os == 'Linux'
+        run: |
+          echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/linux-gnu/lib/pkgconfig" >> $GITHUB_ENV
+          echo "$GITHUB_WORKSPACE/petsc/linux-gnu/bin" >> $GITHUB_PATH
+
+      - name: Configure environment
+        if: runner.os == 'macOS'
+        run: |
+          echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/lib/pkgconfig" >> $GITHUB_ENV
+          echo "$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/bin" >> $GITHUB_PATH
+
+      - name: Configure PETSc
+        if: runner.os == 'Linux'
+        working-directory: petsc
+        run: |
+          sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi
+          sudo make all
+
+      - name: Configure PETSc
+        if: runner.os == 'macOS'
+        working-directory: petsc
+        run: |
+          sudo ./configure PETSC_DIR="$GITHUB_WORKSPACE/petsc" PETSC_ARCH=arch-darwin-gcc-debug --download-fblaslapack --download-openmpi
+          sudo make all
+
+      - name: Install netcdf
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install build-essential \
+            libnetcdf-dev \
+            libnetcdff-dev \
+            netcdf-bin
+          nc-config --all
+          nf-config --all
+
+      - name: Install netcdf
+        if: runner.os == 'macOS'
+        run: |
+          bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+          brew install netcdf-fortran
+          brew install gcc
+          nc-config --all
+          nf-config
+
+      - name: Setup Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: modflow6/environment-nctest.yml
+          create-args: >-
+            netcdf4
+          init-shell: >-
+            bash
+            powershell
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Build modflow6
+        working-directory: modflow6
+        run: |
+          meson setup builddir -Ddebug=false -Dextended=true --prefix=$(pwd) --libdir=bin
+          meson install -C builddir
+          meson test --verbose --no-rebuild -C builddir
+
+      - name: Show Meson logs
+        if: failure()
+        working-directory: modflow6
+        run: cat builddir/meson-logs/meson-log.txt
+
+      - name: Get executables
+        working-directory: modflow6/autotest
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: pytest -v --durations 0 get_exes.py
+
+      - name: Test programs (netcdf)
+        working-directory: modflow6/autotest
+        env:
+          REPOS_PATH: ${{ github.workspace }}
+        run: |
+          pytest -v -n auto -m netcdf --netcdf --parallel --durations 0 --keep-failed .failed
+
+      - name: Upload failed test output
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: failed-${{ matrix.os }}-${{ env.FC }}-${{ env.FC_V }}
+          path: modflow6/autotest/.failed

autotest/conftest.py

@@ -119,13 +119,25 @@ def pytest_addoption(parser):
         default=False,
         help="include parallel test cases",
     )
+    parser.addoption(
+        "--netcdf",
+        action="store_true",
+        default=False,
+        help="include netcdf test cases",
+    )
 
 
 def pytest_collection_modifyitems(config, items):
-    if config.getoption("--parallel"):
-        # --parallel given in cli: do not skip parallel tests
-        return
-    skip_parallel = pytest.mark.skip(reason="need --parallel option to run")
-    for item in items:
-        if "parallel" in item.keywords:
-            item.add_marker(skip_parallel)
+    if not config.getoption("--parallel"):
+        skip_parallel = pytest.mark.skip(
+            reason="need --parallel option to run"
+        )
+        for item in items:
+            if "parallel" in item.keywords:
+                item.add_marker(skip_parallel)
+
+    if not config.getoption("--netcdf"):
+        skip_netcdf = pytest.mark.skip(reason="need --netcdf option to run")
+        for item in items:
+            if "netcdf" in item.keywords:
+                item.add_marker(skip_netcdf)

autotest/framework.py

@@ -118,7 +118,9 @@ def run_parallel(workspace, target, ncpus) -> Tuple[bool, List[str]]:
     return success, buff
 
 
-def write_input(*sims, overwrite: bool = True, verbose: bool = True):
+def write_input(
+    *sims, overwrite: bool = True, verbose: bool = True, netcdf: bool = False
+):
     """
     Write input files for `flopy.mf6.MFSimulation` or `flopy.mbase.BaseModel`.
 
@@ -149,7 +151,10 @@ def write_input(*sims, overwrite: bool = True, verbose: bool = True):
                 print(
                     f"Writing mf6 simulation '{sim.name}' to: {sim.sim_path}"
                 )
-            sim.write_simulation()
+            if netcdf:
+                sim.write_simulation(write_netcdf=True)
+            else:
+                sim.write_simulation()
         elif isinstance(sim, flopy.mbase.BaseModel):
             workspace = Path(sim.model_ws)
             if any(workspace.glob("*")) and not overwrite:
@@ -232,6 +237,7 @@ def __init__(
         check: Optional[Callable] = None,
         compare: Optional[str] = "auto",
         parallel=False,
+        netcdf=False,
         ncpus=1,
         htol=None,
         rclose=None,
@@ -251,6 +257,7 @@ def __init__(
         self.build = build
         self.check = check
         self.parallel = parallel
+        self.netcdf = netcdf
         self.ncpus = [ncpus] if isinstance(ncpus, int) else ncpus
         self.api_func = api_func
         self.compare = compare
@@ -704,7 +711,12 @@ def run(self):
             if len(self.ncpus) == 1 and nsims:
                 self.ncpus = list(repeat(self.ncpus[0], nsims))
 
-            write_input(*sims, overwrite=self.overwrite, verbose=self.verbose)
+            write_input(
+                *sims,
+                overwrite=self.overwrite,
+                verbose=self.verbose,
+                netcdf=self.netcdf,
+            )
         else:
             self.sims = [MFSimulation.load(sim_ws=self.workspace)]
             self.buffs = [None]

autotest/pytest.ini

@@ -16,3 +16,4 @@ markers =
     lak: tests for lake package
     maw: tests for multi-aquifer well package
     parallel: test relying on a parallel (MPI+PETSc) build
+    netcdf: test relying on a netcdf (NetCDF-FORTRAN) build

autotest/test_gwf_auxvars.py

@@ -11,7 +11,7 @@
 auxvar2 = 102.0
 
 
-def build_models(idx, test):
+def build_models(idx, test, netcdf=None):
     nlay, nrow, ncol = 1, 10, 10
     nper = 3
     perlen = [1.0, 1.0, 1.0]
@@ -70,14 +70,22 @@ def build_models(idx, test):
         delc=delc,
         top=90.0,
         botm=0.0,
+        filename=f"{name}.nc" if netcdf else f"{name}.dis",
     )
 
     # initial conditions
-    ic = flopy.mf6.ModflowGwfic(gwf, strt=strt)
+    ic = flopy.mf6.ModflowGwfic(
+        gwf, strt=strt, filename=f"{name}.nc" if netcdf else f"{name}.ic"
+    )
 
     # node property flow
     npf = flopy.mf6.ModflowGwfnpf(
-        gwf, save_flows=True, icelltype=1, k=1.0, k33=0.01
+        gwf,
+        save_flows=True,
+        icelltype=1,
+        k=1.0,
+        k33=0.01,
+        filename=f"{name}.nc" if netcdf else f"{name}.npf",
     )
     # storage
     sto = flopy.mf6.ModflowGwfsto(
@@ -100,7 +108,7 @@ def build_models(idx, test):
         gwf,
         stress_period_data=chdspdict,
         save_flows=False,
-        filename=f"{name}.chd",
+        filename=f"{name}.nc" if netcdf else f"{name}.chd",
     )
 
     # MAW
@@ -298,12 +306,16 @@ def check_output(idx, test):
 
 
 @pytest.mark.parametrize("idx, name", enumerate(cases))
-def test_mf6model(idx, name, function_tmpdir, targets):
+@pytest.mark.parametrize(
+    "netcdf", [0, pytest.param(1, marks=pytest.mark.netcdf)]
+)
+def test_mf6model(idx, name, function_tmpdir, targets, netcdf):
     test = TestFramework(
         name=name,
         workspace=function_tmpdir,
-        build=lambda t: build_models(idx, t),
+        build=lambda t: build_models(idx, t, netcdf),
         check=lambda t: check_output(idx, t),
         targets=targets,
+        netcdf=netcdf,
     )
     test.run()

autotest/test_gwf_bnd_negative_cond.py

@@ -25,7 +25,7 @@
 ]
 
 
-def build_models(idx, test):
+def build_models(idx, test, netcdf=None):
     # static model data
     # temporal discretization
     nper = 1
@@ -87,21 +87,32 @@ def build_models(idx, test):
         delc=delc,
         top=top,
         botm=botm,
+        filename=f"{name}.nc" if netcdf else f"{name}.dis",
     )
 
     # initial conditions
-    ic = flopy.mf6.ModflowGwfic(gwf, strt=strt)
+    ic = flopy.mf6.ModflowGwfic(
+        gwf, strt=strt, filename=f"{name}.nc" if netcdf else f"{name}.ic"
+    )
 
     # node property flow
-    npf = flopy.mf6.ModflowGwfnpf(gwf, icelltype=0, k=hk)
+    npf = flopy.mf6.ModflowGwfnpf(
+        gwf,
+        icelltype=0,
+        k=hk,
+        filename=f"{name}.nc" if netcdf else f"{name}.npf",
+    )
 
     # chd files
     # chd data
     spd = [
         [(0, 0, 0), 1.0],
     ]
     chd = flopy.mf6.modflow.ModflowGwfchd(
-        gwf, stress_period_data=spd, pname="chd-1"
+        gwf,
+        stress_period_data=spd,
+        pname="chd-1",
+        filename=f"{name}.nc" if netcdf else f"{name}.chd",
     )
 
     bnd_loc = (0, 0, 1)
@@ -117,20 +128,23 @@ def build_models(idx, test):
             auxiliary=["mult"],
             auxmultname="mult",
             stress_period_data=[(bnd_loc, top, cond, mult)],
+            filename=f"{name}.nc" if netcdf else f"{name}.drn",
         )
     elif name.startswith("riv"):
         riv = flopy.mf6.ModflowGwfriv(
             gwf,
             auxiliary=["mult"],
             auxmultname="mult",
             stress_period_data=[(bnd_loc, 1.0, cond, top, mult)],
+            filename=f"{name}.nc" if netcdf else f"{name}.riv",
         )
     elif name.startswith("ghb"):
         ghb = flopy.mf6.ModflowGwfghb(
             gwf,
             auxiliary=["mult"],
             auxmultname="mult",
             stress_period_data=[(bnd_loc, top, cond, mult)],
+            filename=f"{name}.nc" if netcdf else f"{name}.ghb",
         )
 
     return sim
@@ -169,13 +183,17 @@ def check_output(idx, test):
 
 
 @pytest.mark.parametrize("idx, name", enumerate(cases))
-def test_mf6model(idx, name, function_tmpdir, targets):
+@pytest.mark.parametrize(
+    "netcdf", [0, pytest.param(1, marks=pytest.mark.netcdf)]
+)
+def test_mf6model(idx, name, function_tmpdir, targets, netcdf):
     test = TestFramework(
         name=name,
         workspace=function_tmpdir,
         targets=targets,
-        build=lambda t: build_models(idx, t),
+        build=lambda t: build_models(idx, t, netcdf),
         check=lambda t: check_output(idx, t),
+        netcdf=netcdf,
         xfail=True,
     )
     test.run()