feat(GWE, PRT): updates for GWE and PRT support

.github/workflows/ci.yml

@@ -176,10 +176,16 @@ jobs:
         shell: bash
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+
+      - name: Checkout mf6-examples
+        uses: actions/checkout@v4
+        with:
+          repository: MODFLOW-USGS/modflow6-examples
+          path: modflow6-examples
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
@@ -190,15 +196,33 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://[email protected]/Deltares/xmipy@develop
           pip install git+https://[email protected]/MODFLOW-USGS/modflow-devtools@develop
+          pip install git+https://[email protected]/modflowpy/flopy@develop
           pip install .[test]
 
+
+
+      - name: update flopy for mf6-examples
+        run: |
+          get-modflow :flopy
+          python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
+
+      - name: Install modflow6 for modflow6-examples
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          path: ${{ github.workspace }}/modflow6-examples/autotest
+
+      - name: Build mf6-examples
+        working-directory: modflow6-examples/autotest
+        run: |
+          pytest -v -n=auto --init test_scripts.py
+
       - name: Install modflow6 nightly build
         uses: modflowpy/install-modflow-action@v1
         with:
           path: ${{ github.workspace }}/autotest
           repo: modflow6-nightly-build
-      
+
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}
-        run: pytest -v -n auto -m "mf6 and not extensions"
+        run: pytest -v -n=auto test_mf6_examples.py --mf6-examples-path=../modflow6-examples/examples

autotest/conftest.py

@@ -33,21 +33,37 @@ def get_mf6_examples_path() -> Path:
         __mf6_examples_lock.release()
 
 
+def pytest_addoption(parser):
+    parser.addoption("--mf6-examples-path", action="store", default=None)
+
+
 def is_nested(namfile) -> bool:
     p = Path(namfile)
     if not p.is_file() or not p.name.endswith(".nam"):
         raise ValueError(f"Expected a namfile path, got {p}")
-
     return p.parent.parent.name != __mf6_examples
 
 
 def pytest_generate_tests(metafunc):
     # examples to skip:
     #   - ex-gwtgwt-mt3dms-p10: https://github.com/MODFLOW-USGS/modflow6/pull/1008
-    exclude = ["ex-gwt-gwtgwt-mt3dms-p10"]
+    option_value = metafunc.config.option.mf6_examples_path
+    t = metafunc.fixturenames
+    if (
+        "mf6_example_namfiles" in metafunc.fixturenames
+        and option_value is not None
+    ):
+        mf6_examples_path = Path(option_value)
+        global __mf6_examples
+        __mf6_examples = str(mf6_examples_path.name)
+    else:
+        mf6_examples_path = get_mf6_examples_path()
+
+    # grouping...
+    exclude = ["ex-gwt-gwtgwt-mt3dms-p10", "mp7-p02", "mp7-p04"]
     namfiles = [
         str(p)
-        for p in get_mf6_examples_path().rglob("mfsim.nam")
+        for p in mf6_examples_path.rglob("mfsim.nam")
         if not any(e in str(p) for e in exclude)
     ]
 
@@ -72,9 +88,20 @@ def simulation_name_from_model_path(p):
         for model_name, model_namfiles in groupby(
             namfiles, key=simulation_name_from_model_path
         ):
-            models = sorted(
-                list(model_namfiles)
-            )  # sort in alphabetical order (gwf < gwt)
+            models = []
+            model_namfiles = list(model_namfiles)
+            if len(model_namfiles) > 1:
+                # trap gwf models as first set of models
+                idxs = [
+                    ix for ix, _ in enumerate(model_namfiles) if "gwf" in _
+                ]
+                if len(idxs) > 0:
+                    for ix in idxs[::-1]:
+                        models.append(model_namfiles.pop(ix))
+
+            models += list(
+                sorted(model_namfiles)
+            )  # sort remaining models in alphabetical order (gwe < gwt < prt)
             simulations.append(models)
             print(
                 f"Simulation {model_name} has {len(models)} model(s):\n"

modflowapi/extensions/apiexchange.py

@@ -16,5 +16,9 @@ class ApiExchange(ApiMbase):
     """
 
     def __init__(self, mf6, name):
-        pkg_types = {"gwf-gwf": ListPackage, "gwt-gwt": ListPackage}
+        pkg_types = {
+            "gwf-gwf": ListPackage,
+            "gwt-gwt": ListPackage,
+            "gwe-gwe": ListPackage,
+        }
         super().__init__(mf6, name, pkg_types)

modflowapi/extensions/apimodel.py

@@ -165,11 +165,18 @@ def __init__(self, mf6, name):
             "sto": ArrayPackage,
             "wel": ListPackage,
             # gwt
-            "adv": ArrayPackage,
+            "dsp": ArrayPackage,
             "cnc": ListPackage,
             "ist": ArrayPackage,
             "mst": ArrayPackage,
             "src": ListPackage,
+            # gwe
+            "cnd": ArrayPackage,
+            "est": ArrayPackage,
+            "cpt": ListPackage,
+            "esl": ListPackage,
+            # prt
+            "mip": ArrayPackage,
         }
 
         self.allow_convergence = True

modflowapi/extensions/apisimulation.py

@@ -308,13 +308,21 @@ def load(mf6):
 
                 solution_names.append(t[0])
 
+        idp_names = [i for i in mf6.get_value("__INPUT__/SIM/NAM/SLNMNAMES")]
+        solution_types = [
+            i[:-1].lower()
+            for ix, i in enumerate(mf6.get_value("__INPUT__/SIM/NAM/SLNTYPE"))
+            if idp_names[ix]
+        ]
+
         tmpmdl = ApiMbase(mf6, "", {})
         solution_names = list(set(solution_names))
         solution_dict = {}
         for name in solution_names:
             sid_var_addr = mf6.get_var_address("ID", name)
             sid = mf6.get_value(sid_var_addr)[0]
-            sln = ApiSlnPackage(tmpmdl, name)
+            slntype = solution_types[sid - 1]
+            sln = ApiSlnPackage(tmpmdl, name, pkg_type=slntype)
             solution_dict[sid] = sln
 
         solutions = solution_dict

modflowapi/extensions/pakbase.py

@@ -91,8 +91,29 @@
         "auxname_cst",
         "auxvar",
     ],
+    # gwe model
+    "cnd": ["alh", "alv", "ath1", "ath2", "atv", "kts"],
+    "est": ["porosity", "decay", "cps", "rhos"],
+    "cpt": [
+        "maxbound",
+        "nbound",
+        "nodelist",
+        ("bound", ("temp",)),
+        "naux",
+        "auxname_cst",
+        "auxvar",
+    ],
+    "esl": [
+        "maxbound",
+        "nbound",
+        "nodelist",
+        ("bound", ("senerrate",)),
+        "naux",
+        "auxname_cst",
+        "auxvar",
+    ],
     # gwt model
-    "adv": ["diffc", "alh", "alv", "ath1", "ath2", "atv"],
+    "dsp": ["diffc", "alh", "alv", "ath1", "ath2", "atv"],
     "cnc": [
         "maxbound",
         "nbound",
@@ -121,9 +142,12 @@
         "auxname_cst",
         "auxvar",
     ],
+    # prt model
+    "mip": ["porosity", "retfactor", "izone"],
     # exchange model
-    "gwf-gwf": ["nexg", "nodem1", "nodem2", "cl1", "cl2", "ihc"],
-    "gwt-gwt": ["nexg", "nodem1", "nodem2", "cl1", "cl2", "ihc"],
+    "gwf-gwf": ["nexg", "nodem1", "nodem2", "cl1", "cl2", "ihc", "hwva"],
+    "gwt-gwt": ["nexg", "nodem1", "nodem2", "cl1", "cl2", "ihc", "hwva"],
+    "gwe-gwe": ["nexg", "nodem1", "nodem2", "cl1", "cl2", "ihc", "hwva"],
     # simulation
     "ats": [
         "maxats",
@@ -147,7 +171,7 @@
         "tsmult",
     ],
     # solution package
-    "sln": [
+    "sln-ims": [
         "mxiter",
         "dvclose",
         "gamma",
@@ -170,6 +194,10 @@
         "iscl",
         "iord",
     ],
+    "sln-ems": [
+        "icnvg",
+        "ttsoln",
+    ],
 }
 
 
@@ -599,6 +627,10 @@ def __setattr__(self, item, value):
         elif item in self._variables._ptrs:
             self._variables.set_value(item, value)
 
+        elif item in ("mxiter",):
+            # hack for sln-ems
+            super().__setattr__(item, value)
+
         else:
             raise AttributeError(f"{item}")
 
@@ -690,21 +722,26 @@ class ApiSlnPackage(ScalarPackage):
         package name (in the mf6 variables)
     sim_package : bool
         boolean flag for simulation level packages. Ex. TDIS, IMS
+    sln_type : str
+        ackronymn for the solution package type, default is "ims"
     """
 
-    def __init__(self, sim, pkg_name):
+    def __init__(self, sim, pkg_name, pkg_type="ims"):
         from .apimodel import ApiMbase
 
-        super().__init__(sim, "sln", pkg_name, sim_package=True)
+        super().__init__(sim, f"sln-{pkg_type}", pkg_name, sim_package=True)
 
-        mdl = ApiMbase(
-            sim.mf6, pkg_name.upper(), pkg_types={"ims": ScalarPackage}
-        )
-        imslin = ScalarPackage(mdl, "ims", "IMSLINEAR")
-        for key, ptr in imslin._variables._ptrs.items():
-            if key in self._variables._ptrs:
-                key = f"{imslin.pkg_type}_{key}".lower()
-            self._variables._ptrs[key] = ptr
+        if pkg_type in ("ims",):
+            mdl = ApiMbase(
+                sim.mf6, pkg_name.upper(), pkg_types={pkg_type: ScalarPackage}
+            )
+            imslin = ScalarPackage(mdl, "ims", "IMSLINEAR")
+            for key, ptr in imslin._variables._ptrs.items():
+                if key in self._variables._ptrs:
+                    key = f"{imslin.pkg_type}_{key}".lower()
+                self._variables._ptrs[key] = ptr
+        else:
+            self.mxiter = 10
 
 
 def package_factory(pkg_type, basepackage):

pyproject.toml

@@ -46,6 +46,13 @@ test = [
     "pytest!=8.1.0",
     "pytest-order",
     "pytest-xdist",
+    "GitPython",
+    "pooch",
+    "scipy",
+    "pyshp",
+    "shapely",
+    "rasterio",
+    "rasterstats"
 ]
 lint = [
     "ruff",