Refactor tests, adding a common module (#138)

* Refactor tests, adding a common module

* Update pixi lockfile

* Install MODFLOW 6 via modflowpy/install-modflow-action@v1

* Only install modflow6 release

* Add nightly in matrix

* Change test_get_value_int_scalar to check with NROW, which has rank=0

* Only use modflow6-nightly-build

.github/workflows/CI.yml

@@ -29,6 +29,10 @@ jobs:
         uses: prefix-dev/setup-pixi@v0.6.0
         with:
           manifest-path: pyproject.toml
+      - name: Install MODFLOW 6
+        uses: modflowpy/install-modflow-action@v1
+        with:
+          repo: modflow6-nightly-build
       - name: Test with pytest
         run: pixi run tests-ci
         env: 

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"
 
@@ -56,8 +59,8 @@ twine = "*"
 # Tests
 # The flag -s stops pytest from capturing output
 # This is necessary until proper error reporting is implemented by Modflow
-tests-ci = "pytest -vs --cov=xmipy --cov-report=xml tests/"
-tests = "pytest tests/"
+tests-ci = "pytest --cov=xmipy --cov-report=xml"
+tests = "pytest"
 
 # Docs
 docs = "pdoc -o docs/ xmipy"
@@ -90,6 +93,10 @@ py311 = ["py311"]
 py310 = ["py310"]
 py39 = ["py39"]
 
+[tool.pytest.ini_options]
+addopts = "-vs"
+testpaths = ["tests"]
+
 [tool.mypy]
 exclude = ["tests"]
 warn_unused_configs = true
@@ -106,7 +113,7 @@ disallow_untyped_defs = true
 no_implicit_reexport = true
 warn_return_any = true
 
-[tool.ruff]
+[tool.ruff.lint]
 select = [
     "ARG",
     "B",

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 := os.environ.get("MODFLOW_BIN_PATH"):
+            mf6 = shutil.which("mf6", path=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 +10,19 @@
 
 from xmipy import XmiWrapper
 
+from .common import libmf6_path
+
+
+def pytest_report_header(**kwargs):  # noqa: ARG001
+    """Show report header at top of pytest output.
+    https://docs.pytest.org/en/stable/reference/reference.html#pytest.hookspec.pytest_report_header
+    """
+    return f"libmf6: {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)
+@pytest.fixture(scope="session")
+def modflow_lib_path():
+    return libmf6_path
 
 
 @dataclass
@@ -167,6 +165,15 @@ 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 +183,10 @@ 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],

tests/test_mf6_dis_bmi.py

@@ -299,7 +299,7 @@ def test_get_value_int_scalar(flopy_dis_idomain_mf6):
     mf6.initialize()
 
     # get scalar variable:
-    id_tag = next(var for var in mf6.get_output_var_names() if var.endswith("/ID"))
+    id_tag = next(var for var in mf6.get_output_var_names() if var.endswith("/NROW"))
     assert mf6.get_var_rank(id_tag) == 0
 
     # compare with value in MODFLOW memory: