Merge pull request #36 from MODFLOW-USGS/v0.1.0

Release 0.1.0

HISTORY.md

@@ -1,3 +1,9 @@
+### Version 0.1.0
+
+#### Refactoring
+
+* [refactor(fixtures)](https://github.com/modflowpy/flopy/commit/23593df7fb427d6de1d33f9aa408697d2536e473): Fix/refactor model-loading fixtures (#33). Committed by w-bonelli on 2022-12-29.
+
 ### Version 0.0.8
 
 #### Bug fixes

README.md

@@ -1,6 +1,6 @@
 # MODFLOW developer tools
 
-### Version 0.0.8 — release candidate
+### Version 0.1.0 — release candidate
 [![GitHub tag](https://img.shields.io/github/tag/MODFLOW-USGS/modflow-devtools.svg)](https://github.com/MODFLOW-USGS/modflow-devtools/tags/latest)
 [![PyPI Version](https://img.shields.io/pypi/v/modflow-devtools.png)](https://pypi.python.org/pypi/modflow-devtools)
 [![PyPI Versions](https://img.shields.io/pypi/pyversions/modflow-devtools.png)](https://pypi.python.org/pypi/modflow-devtools)

docs/conf.py

@@ -8,7 +8,7 @@
 
 project = 'modflow-devtools'
 author = 'MODFLOW Team'
-release = 0.0.8
+release = 0.1.0
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/md/fixtures.md

@@ -2,7 +2,7 @@
 
 Several `pytest` fixtures are provided to help with testing.
 
-## Keepable temporary directory fixtures
+## Keepable temporary directories
 
 Tests often need to exercise code that reads from and/or writes to disk. The test harness may also need to create test data during setup and clean up the filesystem on teardown. Temporary directories are built into `pytest` via the [`tmp_path`](https://docs.pytest.org/en/latest/how-to/tmp_path.html#the-tmp-path-fixture) and `tmp_path_factory` fixtures.
 
@@ -40,9 +40,9 @@ pytest --keep <path>
 
 There is also a `--keep-failed <path>` option which preserves outputs only from failing test cases.
 
-## Model-loading fixtures
+## Loading example models
 
-Fixtures are provided to load models from the MODFLOW 6 example and test model repositories and feed them to test functions. Models can be loaded from:
+Fixtures are provided to find and enumerate models from the MODFLOW 6 example and test model repositories and feed them to test functions. Models can be loaded from:
 
 - [`MODFLOW-USGS/modflow6-examples`](https://github.com/MODFLOW-USGS/modflow6-examples)
 - [`MODFLOW-USGS/modflow6-testmodels`](https://github.com/MODFLOW-USGS/modflow6-testmodels)
@@ -61,14 +61,15 @@ To use these fixtures, the environment variable `REPOS_PATH` must point to the l
 
 ### Test models
 
-The `test_model_mf5to6`, `test_model_mf6` and `large_test_model` fixtures are each a `Path` to the directory containing the model's namefile. For instance, to load `mf5to6` models from the [`MODFLOW-USGS/modflow6-testmodels`](https://github.com/MODFLOW-USGS/modflow6-testmodels) repository:
+The `test_model_mf5to6`, `test_model_mf6` and `large_test_model` fixtures are each a `Path` to the model's namefile. For example:, to load `mf5to6` models from the  repository:
 
 ```python
-def test_mf5to6_model(testmodel_mf5to6):
-    assert testmodel_mf5to6.is_dir()
+def test_mf5to6_model(test_model_mf5to6):
+    assert test_model_mf5to6.is_file()
+    assert test_model_mf5to6.suffix == ".nam"
 ```
 
-This test function will be parametrized with all `mf5to6` models found in the `testmodels` repository (likewise for `mf6` models, and for large test models in their own repository).
+This test function will be parametrized with all `mf5to6` models found in the [`MODFLOW-USGS/modflow6-testmodels`](https://github.com/MODFLOW-USGS/modflow6-testmodels).
 
 ### Example scenarios
 
@@ -87,4 +88,13 @@ def test_example_scenario(tmp_path, example_scenario):
         model_ws.mkdir()
         # load and run model
         # ...
-```
+```
+
+### Utility functions
+
+Model-loading fixtures use a set of utility functions to find and enumerate models. These functions can be imported from `modflow_devtools.misc` for use in other contexts:
+
+- `get_model_dir_paths()`
+- `get_namefile_paths()`
+
+See this project's test suite for usage examples.

modflow_devtools/__init__.py

@@ -1,6 +1,6 @@
 __author__ = "Joseph D. Hughes"
 __date__ = "Dec 29, 2022"
-__version__ = "0.0.8"
+__version__ = "0.1.0"
 __maintainer__ = "Joseph D. Hughes"
 __email__ = "[email protected]"
 __status__ = "Production"

modflow_devtools/fixtures.py

@@ -6,7 +6,11 @@
 from typing import Dict, List, Optional
 
 import pytest
-from modflow_devtools.misc import get_model_paths, get_packages
+from modflow_devtools.misc import (
+    get_model_dir_paths,
+    get_namefile_paths,
+    get_packages,
+)
 
 # temporary directory fixtures
 
@@ -174,7 +178,7 @@ def pytest_generate_tests(metafunc):
     key = "test_model_mf6"
     if key in metafunc.fixturenames:
         models = (
-            get_model_paths(
+            get_namefile_paths(
                 Path(repos_path) / "modflow6-testmodels" / "mf6",
                 prefix="test",
                 excluded=["test205_gwtbuy-henrytidal"],
@@ -184,12 +188,12 @@ def pytest_generate_tests(metafunc):
             if repos_path
             else []
         )
-        metafunc.parametrize(key, models, ids=[m.name for m in models])
+        metafunc.parametrize(key, models, ids=[str(m) for m in models])
 
     key = "test_model_mf5to6"
     if key in metafunc.fixturenames:
         models = (
-            get_model_paths(
+            get_namefile_paths(
                 Path(repos_path) / "modflow6-testmodels" / "mf5to6",
                 prefix="test",
                 namefile="*.nam",
@@ -200,23 +204,23 @@ def pytest_generate_tests(metafunc):
             if repos_path
             else []
         )
-        metafunc.parametrize(key, models, ids=[m.name for m in models])
+        metafunc.parametrize(key, models, ids=[str(m) for m in models])
 
     key = "large_test_model"
     if key in metafunc.fixturenames:
         models = (
-            get_model_paths(
+            get_namefile_paths(
                 Path(repos_path) / "modflow6-largetestmodels",
                 prefix="test",
-                namefile="*.nam",
+                namefile="mfsim.nam",
                 excluded=[],
                 selected=models_selected,
                 packages=packages_selected,
             )
             if repos_path
             else []
         )
-        metafunc.parametrize(key, models, ids=[m.name for m in models])
+        metafunc.parametrize(key, models, ids=[str(m) for m in models])
 
     key = "example_scenario"
     if key in metafunc.fixturenames:

modflow_devtools/misc.py

@@ -160,66 +160,87 @@ def has_package(namefile_path: PathLike, package: str) -> bool:
     return package.lower in packages
 
 
-def get_model_paths(
+def get_namefile_paths(
     path: PathLike,
     prefix: str = None,
     namefile: str = "mfsim.nam",
     excluded=None,
     selected=None,
     packages=None,
-) -> List[Path]:
+):
     """
-    Find models recursively in the given location.
-    Models can be filtered or excluded by pattern,
-    filtered by packages used or naming convention
-    for namefiles, or by parent folder name prefix.
-    The path to the model folder (i.e., the folder
-    containing the model's namefile) is returned.
+    Find namefiles recursively in the given location.
+    Namefiles can be filtered or excluded by pattern,
+    by parent directory name prefix or pattern, or by
+    packages used.
     """
 
     # if path doesn't exist, return empty list
     if not Path(path).is_dir():
         return []
 
-    # find namfiles
-    namfile_paths = [
+    # find namefiles
+    paths = [
         p
         for p in Path(path).rglob(
             f"{prefix}*/**/{namefile}" if prefix else namefile
         )
     ]
 
     # remove excluded
-    namfile_paths = [
+    paths = [
         p
-        for p in namfile_paths
+        for p in paths
         if (not excluded or not any(e in str(p) for e in excluded))
     ]
 
     # filter by package
     if packages:
         filtered = []
-        for nfp in namfile_paths:
+        for nfp in paths:
             nf_pkgs = get_packages(nfp)
             shared = set(nf_pkgs).intersection(
                 set([p.lower() for p in packages])
             )
             if any(shared):
                 filtered.append(nfp)
-        namfile_paths = filtered
-
-    # get model folder paths
-    model_paths = [p.parent for p in namfile_paths]
+        paths = filtered
 
     # filter by model name
     if selected:
-        model_paths = [
-            model
-            for model in model_paths
-            if any(s in model.name for s in selected)
+        paths = [
+            namfile_path
+            for (namfile_path, model_path) in zip(
+                paths, [p.parent for p in paths]
+            )
+            if any(s in model_path.name for s in selected)
         ]
 
-    return sorted(model_paths)
+    return sorted(paths)
+
+
+def get_model_dir_paths(
+    path: PathLike,
+    prefix: str = None,
+    namefile: str = "mfsim.nam",
+    excluded=None,
+    selected=None,
+    packages=None,
+) -> List[Path]:
+    """
+    Find model directories recursively in the given location.
+    A model directory is any directory containing one or more
+    namefiles. Model directories can be filtered or excluded,
+    by prefix, pattern, namefile name, or packages used.
+    """
+
+    namefile_paths = get_namefile_paths(
+        path, prefix, namefile, excluded, selected, packages
+    )
+    model_paths = sorted(
+        list(set([p.parent for p in namefile_paths if p.parent.name]))
+    )
+    return model_paths
 
 
 def is_connected(hostname):

modflow_devtools/test/test_fixtures.py

@@ -249,16 +249,18 @@ def test_example_scenario(example_scenario):
 
 def test_test_model_mf6(test_model_mf6):
     assert isinstance(test_model_mf6, Path)
-    assert (test_model_mf6 / "mfsim.nam").is_file()
+    assert test_model_mf6.is_file()
+    assert test_model_mf6.name == "mfsim.nam"
 
 
 def test_test_model_mf5to6(test_model_mf5to6):
     assert isinstance(test_model_mf5to6, Path)
-    assert any(list(test_model_mf5to6.glob("*.nam")))
+    assert test_model_mf5to6.is_file()
+    assert test_model_mf5to6.suffix == ".nam"
 
 
 def test_large_test_model(large_test_model):
+    print(large_test_model)
     assert isinstance(large_test_model, Path)
-    assert (large_test_model / "mfsim.nam").is_file() or any(
-        list(large_test_model.glob("*.nam"))
-    )
+    assert large_test_model.is_file()
+    assert large_test_model.suffix == ".nam"