fix(fixtures): fix package detection/selection

modflow_devtools/misc.py

@@ -1,6 +1,7 @@
 import importlib
 import socket
 import sys
+import traceback
 from contextlib import contextmanager
 from importlib import metadata
 from os import PathLike, chdir, environ, getcwd
@@ -118,20 +119,46 @@ def get_current_branch() -> str:
 
 def get_packages(namefile_path: PathLike) -> List[str]:
     """
-    Return a list of packages used by the model defined in the given namefile.
+    Return a list of packages used by the simulation or model defined in the given namefile.
+    The namefile may be for an entire simulation or for a GWF or GWT model. If a simulation
+    namefile is given, packages used in its component model namefiles will be included.
 
     Parameters
     ----------
     namefile_path : PathLike
-        path to MODFLOW 6 name file
+        path to MODFLOW 6 simulation or model name file
     Returns
     -------
-        list of package types
+        a list of packages used by the simulation or model
     """
-    with open(namefile_path, "r") as f:
-        lines = f.readlines()
 
-    ftypes = []
+    packages = []
+    path = Path(namefile_path).expanduser().absolute()
+    lines = open(path, "r").readlines()
+    gwf_lines = [l for l in lines if l.strip().lower().startswith("gwf6 ")]
+    gwt_lines = [l for l in lines if l.strip().lower().startswith("gwt6 ")]
+
+    def parse_model_namefile(line):
+        nf_path = [path.parent / s for s in line.split(" ") if s != ""][1]
+        if nf_path.suffix != ".nam":
+            raise ValueError(
+                f"Failed to parse GWF or GWT model namefile from simulation namefile line: {line}"
+            )
+        return nf_path
+
+    # load model namefiles
+    try:
+        for line in gwf_lines:
+            packages = (
+                packages + get_packages(parse_model_namefile(line)) + ["gwf"]
+            )
+        for line in gwt_lines:
+            packages = (
+                packages + get_packages(parse_model_namefile(line)) + ["gwt"]
+            )
+    except:
+        warn(f"Invalid namefile format: {traceback.format_exc()}")
+
     for line in lines:
         # Skip over blank and commented lines
         ll = line.strip().split()
@@ -149,9 +176,9 @@ def get_packages(namefile_path: PathLike) -> List[str]:
         # strip "6" from package name
         l = l.replace("6", "")
 
-        ftypes.append(l.lower())
+        packages.append(l.lower())
 
-    return list(set(ftypes))
+    return list(set(packages))
 
 
 def has_package(namefile_path: PathLike, package: str) -> bool:
@@ -179,7 +206,7 @@ def get_namefile_paths(
     if not Path(path).is_dir():
         return []
 
-    # find namefiles
+    # find simulation namefiles
     paths = [
         p
         for p in Path(path).rglob(

modflow_devtools/test/test_misc.py

@@ -1,4 +1,5 @@
 import os
+import shutil
 from os import environ
 from pathlib import Path
 from typing import List
@@ -24,6 +25,13 @@ def test_set_dir(tmp_path):
 if _repos_path is None:
     _repos_path = Path(__file__).parent.parent.parent.parent
 _repos_path = Path(_repos_path).expanduser().absolute()
+_testmodels_repo_path = _repos_path / "modflow6-testmodels"
+_testmodels_repo_paths_mf6 = sorted(
+    list((_testmodels_repo_path / "mf6").glob("test*"))
+)
+_testmodels_repo_paths_mf5to6 = sorted(
+    list((_testmodels_repo_path / "mf5to6").glob("test*"))
+)
 _largetestmodels_repo_path = _repos_path / "modflow6-largetestmodels"
 _largetestmodel_paths = sorted(list(_largetestmodels_repo_path.glob("test*")))
 _examples_repo_path = _repos_path / "modflow6-examples"
@@ -35,20 +43,68 @@ def test_set_dir(tmp_path):
 )
 
 
-@pytest.mark.skipif(not any(_example_paths), reason="examples not found")
+@pytest.mark.skipif(
+    not any(_testmodels_repo_paths_mf6), reason="mf6 test models not found"
+)
 def test_get_packages():
-    namefile_path = _example_paths[0]
-    packages = get_packages(namefile_path / "mfsim.nam")
-    assert set(packages) == {"tdis", "gwf", "ims"}
+    model_path = _testmodels_repo_paths_mf6[0]
+
+    # simulation namefile
+    namefile_path = model_path / "mfsim.nam"
+    packages = get_packages(namefile_path)
+    assert model_path.name == "test001a_Tharmonic"
+    assert set(packages) >= {"tdis", "gwf", "ims", "npf", "chd", "oc", "dis"}
+
+    # model namefile
+    namefile_path = model_path / "flow15.nam"
+    packages = get_packages(namefile_path)
+    assert model_path.name == "test001a_Tharmonic"
+    assert set(packages) >= {"npf", "chd", "oc", "dis"}
+    assert "tdis" not in packages
+    assert "gwf" not in packages
+    assert "ims" not in packages
+
+
+@pytest.mark.skipif(
+    not any(_testmodels_repo_paths_mf6), reason="mf6 test models not found"
+)
+def test_get_packages_fails_on_invalid_namefile(module_tmpdir):
+    model_path = _testmodels_repo_paths_mf6[0]
+    new_model_path = module_tmpdir / model_path.name
+    namefile_path = new_model_path / "mfsim.nam"
+    shutil.copytree(model_path, new_model_path)
+
+    # invalid gwf namefile reference - result should only contain packages from mfsim.nam
+    lines = open(namefile_path, "r").read().splitlines()
+    with open(namefile_path, "w") as f:
+        for line in lines:
+            if "GWF6" in line:
+                line = line.replace("GWF6", "GWF6  garbage")
+            f.write(line + os.linesep)
+    assert set(get_packages(namefile_path)) == {"gwf", "tdis", "ims"}
+
+    # entirely unparseable namefile - result should be empty
+    lines = open(namefile_path, "r").read().splitlines()
+    with open(namefile_path, "w") as f:
+        for _ in lines:
+            f.write("garbage" + os.linesep)
+    assert not any(get_packages(namefile_path))
 
 
 @pytest.mark.skipif(not any(_example_paths), reason="examples not found")
 def test_has_package():
-    namefile_path = _example_paths[0] / "mfsim.nam"
+    model_path = _testmodels_repo_paths_mf6[0]
+    namefile_path = model_path / "mfsim.nam"
+    assert model_path.name == "test001a_Tharmonic"
     assert has_package(namefile_path, "tdis")
     assert has_package(namefile_path, "gwf")
     assert has_package(namefile_path, "ims")
+    assert has_package(namefile_path, "npf")
+    assert has_package(namefile_path, "chd")
+    assert has_package(namefile_path, "oc")
+    assert has_package(namefile_path, "dis")
     assert not has_package(namefile_path, "gwt")
+    assert not has_package(namefile_path, "wel")
 
 
 def get_expected_model_dirs(path, pattern="mfsim.nam") -> List[Path]:
@@ -174,7 +230,5 @@ def test_get_namefile_paths_select_patterns():
 
 @pytest.mark.skipif(not any(_example_paths), reason="examples not found")
 def test_get_namefile_paths_select_packages():
-    paths = get_namefile_paths(
-        _examples_path, namefile="*.nam", packages=["wel"]
-    )
-    assert len(paths) == 64
+    paths = get_namefile_paths(_examples_path, packages=["wel"])
+    assert len(paths) == 43