Test with modflow6 release and nightly, add test.common module

.github/workflows/CI.yml

@@ -17,6 +17,7 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest, macos-latest, windows-latest]
+        modflow6-repo: [modflow6, modflow6-nightly-build]
 
     steps:
       - uses: actions/checkout@v4
@@ -26,14 +27,16 @@ jobs:
           python-version: "${{ matrix.python-version }}"
       - name: Setup Fortran
         uses: fortran-lang/setup-fortran@v1
+      - name: Install MODFLOW 6
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          repo: ${{ matrix.modflow6-repo }}
       - name: Install test dependencies
         run: |
           pip install -e ".[tests]"
-      - name: Test with pytest
-        # The flag -s stops pytest from capturing output
-        # This is necessary until proper error reporting is implemented by Modflow
+      - name: Run tests with MODFLOW 6 release
         run: |
-          pytest -vs --cov=xmipy --cov-report=xml tests/
+          pytest -v --cov=xmipy --cov-report=xml
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:

pyproject.toml

@@ -31,6 +31,9 @@ docs = ["pdoc"]
 Documentation = "https://deltares.github.io/xmipy/xmipy.html"
 Source = "https://github.com/Deltares/xmipy"
 
+[tool.hatch.build.targets.wheel]
+packages = ["xmipy"]
+
 [tool.hatch.version]
 path = "xmipy/__init__.py"
 
@@ -50,6 +53,9 @@ disallow_untyped_defs = true
 no_implicit_reexport = true
 warn_return_any = true
 
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
 [tool.ruff]
 select = [
     "ARG",

tests/common.py

@@ -0,0 +1,45 @@
+"""Common functions for tests. For pytest fixtures, see conftest.py."""
+
+import os
+import platform
+import shutil
+from pathlib import Path
+
+
+def get_libmf6() -> Path:
+    """Get libmf6 based on environment variable or PATH with mf6.
+
+    To specify directly, set the environment variable `LIBMF6` to the path of
+    the library to test.
+
+    Otherwise, check for the environment variable `MODFLOW_BIN_PATH` as used by
+    modflowpy/install-modflow-action to find the mf6 executable.
+
+    Lastly, find the mf6 executable from the PATH environment, and
+    try to find the library in the same directory as the executable.
+    """
+    if "LIBMF6" in os.environ:
+        lib_path = Path(os.environ["LIBMF6"])
+    else:
+        if "MODFLOW_BIN_PATH" in os.environ:
+            mf6 = shutil.which("mf6", path=os.environ["MODFLOW_BIN_PATH"])
+        else:
+            mf6 = shutil.which("mf6")
+        if mf6 is None:
+            raise FileNotFoundError("cannot find mf6 on PATH")
+        mf6 = Path(mf6)
+        sysinfo = platform.system()
+        if sysinfo == "Windows":
+            lib_path = mf6.parent / "libmf6.dll"
+        elif sysinfo == "Linux":
+            lib_path = mf6.parent / "libmf6.so"
+        elif sysinfo == "Darwin":
+            lib_path = mf6.parent / "libmf6.dylib"
+        else:
+            raise NotImplementedError(f"system not supported: {sysinfo}")
+    if lib_path.exists():
+        return lib_path
+    raise FileNotFoundError(f"{lib_path} not found")
+
+
+libmf6_path = get_libmf6()

tests/conftest.py

@@ -1,4 +1,5 @@
-import platform
+"""Fixtures for pytest. Other common functions are in common.py."""
+
 from dataclasses import dataclass
 from typing import Any, List, Tuple
 
@@ -9,22 +10,20 @@
 
 from xmipy import XmiWrapper
 
+from .common import libmf6_path
 
-@pytest.fixture(scope="session")
-def modflow_lib_path(tmp_path_factory):
-    tmp_path = tmp_path_factory.getbasetemp()
-    sysinfo = platform.system()
-    if sysinfo == "Windows":
-        lib_path = tmp_path / "libmf6.dll"
-    elif sysinfo == "Linux":
-        lib_path = tmp_path / "libmf6.so"
-    elif sysinfo == "Darwin":
-        lib_path = tmp_path / "libmf6.dylib"
-    else:
-        raise RuntimeError(f"system not supported: {sysinfo}")
 
-    flopy.utils.get_modflow(bindir=str(tmp_path), repo="modflow6-nightly-build")
-    return str(lib_path)
+def pytest_report_header(config, start_path, startdir):
+    """Show report header at top of pytest output.
+
+    https://docs.pytest.org/reference/reference.html#pytest.hookspec.pytest_report_header
+    """
+    return f"libmf6: {libmf6_path}"
+
+
+@pytest.fixture(scope="session")
+def modflow_lib_path():
+    return libmf6_path
 
 
 @dataclass
@@ -40,7 +39,7 @@ class FlopyDis:
 
 
 @pytest.fixture(scope="function")
-def flopy_dis(tmp_path):
+def flopy_dis(tmp_path, modflow_lib_path):
     sim_path = str(tmp_path)
     sim = flopy.mf6.MFSimulation(
         sim_name="TEST_SIM_DIS",
@@ -97,7 +96,7 @@ def flopy_dis_mf6(flopy_dis, modflow_lib_path, request):
 
 
 @pytest.fixture(scope="function")
-def flopy_dis_idomain(tmp_path):
+def flopy_dis_idomain(tmp_path, modflow_lib_path):
     sim_path = str(tmp_path)
     sim = flopy.mf6.MFSimulation(
         sim_name="TEST_SIM_DIS", version="mf6", sim_ws=sim_path
@@ -167,6 +166,15 @@ def flopy_disu(tmp_path):
     flopy.mf6.ModflowTdis(sim, time_units="DAYS", nper=2, perioddata=flopy_disu.tdis_rc)
     flopy.mf6.ModflowIms(sim)
     gwf = flopy.mf6.ModflowGwf(sim, modelname=flopy_disu.model_name, save_flows=True)
+    # fmt: off
+    ja = [0, 1, 3, 1, 0, 2, 4, 2, 1, 5, 3, 0, 4, 6, 4, 1, 3,
+          5, 7, 5, 2, 4, 8, 6, 3, 7, 7, 4, 6, 8, 8, 5, 7]
+    # fmt: on
+    zero_locs = [0, 3, 7, 10, 14, 19, 23, 26, 30]
+    hwva = np.full(33, 1.0)
+    hwva[zero_locs] = 0.0
+    cl12 = np.full(33, 0.5)
+    cl12[zero_locs] = 0.0
     flopy.mf6.ModflowGwfdisu(
         gwf,
         nodes=9,
@@ -176,112 +184,10 @@ def flopy_disu(tmp_path):
         bot=[-2.0],
         area=np.full(9, 1.0),
         iac=[3, 4, 3, 4, 5, 4, 3, 4, 3],
-        ja=[
-            0,
-            1,
-            3,
-            1,
-            0,
-            2,
-            4,
-            2,
-            1,
-            5,
-            3,
-            0,
-            4,
-            6,
-            4,
-            1,
-            3,
-            5,
-            7,
-            5,
-            2,
-            4,
-            8,
-            6,
-            3,
-            7,
-            7,
-            4,
-            6,
-            8,
-            8,
-            5,
-            7,
-        ],
+        ja=ja,
         ihc=[1],
-        cl12=[
-            0,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-            0.5,
-            0,
-            0.5,
-            0.5,
-        ],
-        hwva=[
-            0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-            1.0,
-            0,
-            1.0,
-            1.0,
-        ],
+        cl12=cl12,
+        hwva=hwva,
         vertices=[
             [0, 0.0, 0.0],
             [1, 0.0, 1.0],
@@ -326,7 +232,7 @@ class FlopyGwfSto:
 
 
 @pytest.fixture(scope="function")
-def flopy_gwf_sto(tmp_path):
+def flopy_gwf_sto(tmp_path, modflow_lib_path):
     sim_path = str(tmp_path)
     sim = flopy.mf6.MFSimulation(
         sim_name="TEST_SIM_DIS", version="mf6", sim_ws=sim_path