fix(fixtures): fix model filtering by package

* get_packages() was called incorrectly in model-loading fixtures, fix it
* mention optional dependencies in README and make some minor corrections

README.md

@@ -16,46 +16,64 @@ Python tools for MODFLOW development and testing.
 - [Requirements](#requirements)
 - [Installation](#installation)
 - [Use cases](#use-cases)
+- [Quickstart](#quickstart)
 - [Documentation](#documentation)
 - [MODFLOW Resources](#modflow-resources)
 
 <!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 ## Requirements
 
-This package requires Python3.8+. Its only dependencies are `numpy` and `pytest`.
+This project requires Python3.8+. Its only core dependencies are `numpy` and `pytest`.
 
 ## Installation
 
-The package is available on PyPI and can be installed with pip:
+`modflow-devtools` is available on PyPI and can be installed with pip:
 
 ```shell
 pip install modflow-devtools
 ```
 
+This package pairs well with a few pytest plugins:
+
+- `pytest-cases`
+- `pytest-dotenv`
+- `pytest-xdist`
+
+These and a few other optional dependencies can be installed with:
+
+```shell
+pip install "modflow-devtools[test]"
+```
+
 To install from source and set up a development environment please see the [developer documentation](DEVELOPER.md).
 
 ## Use cases
 
 This package contains shared tools for developing and testing MODFLOW 6 and FloPy, including standalone utilities as well as `pytest` fixtures, CLI options, and test cases:
 
-- a `ZipFile` subclass preserving file attributes
-- variably-scoped `pytest` temporary directory fixtures
-- a `pytest` smoke test CLI option (to run a fast subset of cases)
-- a minimal `pytest` framework for reusing test functions and data
-- a `pytest_generate_tests` hook to load example/test model fixtures
+- a `ZipFile` subclass preserving file permissions ([more information here](https://stackoverflow.com/questions/39296101/python-zipfile-removes-execute-permissions-from-binaries))
+- a `pytest` CLI option for smoke testing (running a fast subset of cases)
+- a minimal `pytest-cases` framework for reusing test functions and data
+- a set of keepable `pytest` temporary directory fixtures for each scope
+- a set of fixtures to parametrize tests with models from external repos
+  - `MODFLOW-USGS/modflow6-examples`
+  - `MODFLOW-USGS/modflow6-testmodels`
+  - `MODFLOW-USGS/modflow6-largetestmodels`
 - a set of `pytest` markers to conditionally skip test cases based on
   - operating system
   - Python packages installed
   - executables available on the path
 
+## Quickstart
+
 To import `pytest` fixtures in a project consuming `modflow-devtools`, add the following to a `conftest.py` file in the project root:
 
 ```python
 pytest_plugins = [ "modflow_devtools.fixtures" ]
 ```
 
-Note that `pytest` requires this to be a top-level `conftest.py` living in your project root. Nested `conftest.py` files may override or extend this package's behavior.
+**Note**: `pytest` requires this to be a top-level `conftest.py` file. Nested `conftest.py` files may override or extend this package's fixtures.
 
 ## Documentation
 

docs/md/zip.md

@@ -1,3 +1,3 @@
 # `MFZipFile`
 
-Python's `ZipFile` doesn't preserve execute permissions. The `MFZipFile` subclass modifies `ZipFile.extract()` to do so, as per the recommendation [here](https://stackoverflow.com/questions/39296101/python-zipfile-removes-execute-permissions-from-binaries).
+Python's `ZipFile` doesn't preserve file permissions at extraction time. The `MFZipFile` subclass modifies `ZipFile.extract()` to do so, as per the recommendation [here](https://stackoverflow.com/questions/39296101/python-zipfile-removes-execute-permissions-from-binaries).

modflow_devtools/fixtures.py

@@ -6,12 +6,13 @@
 from typing import Dict, List, Optional
 
 import pytest
+
 from modflow_devtools.misc import (
-    get_model_paths,
     get_namefile_paths,
     get_packages,
 )
 
+
 # temporary directory fixtures
 
 
@@ -284,7 +285,7 @@ def get_examples():
                 for name, namefiles in examples.items():
                     ftypes = []
                     for namefile in namefiles:
-                        ftype = get_packages(namefile, packages_selected)
+                        ftype = get_packages(namefile)
                         if ftype not in ftypes:
                             ftypes += ftype
                     if len(ftypes) > 0:

modflow_devtools/misc.py

@@ -157,7 +157,7 @@ def get_packages(namefile_path: PathLike) -> List[str]:
 def has_package(namefile_path: PathLike, package: str) -> bool:
     """Determines whether the model with the given namefile contains the selected package"""
     packages = get_packages(namefile_path)
-    return package.lower in packages
+    return package.lower() in packages
 
 
 def get_namefile_paths(

modflow_devtools/test/test_misc.py

@@ -8,7 +8,7 @@
     get_model_paths,
     get_namefile_paths,
     get_packages,
-    set_dir,
+    set_dir, has_package,
 )
 
 
@@ -32,12 +32,21 @@ def test_set_dir(tmp_path):
 
 
 @pytest.mark.skipif(not any(_example_paths), reason="examples not found")
-def test_has_packages():
-    example_path = _example_paths[0]
-    packages = get_packages(example_path / "mfsim.nam")
+def test_get_packages():
+    namefile_path = _example_paths[0]
+    packages = get_packages(namefile_path / "mfsim.nam")
     assert set(packages) == {"tdis", "gwf", "ims"}
 
 
+@pytest.mark.skipif(not any(_example_paths), reason="examples not found")
+def test_has_package():
+    namefile_path = _example_paths[0] / "mfsim.nam"
+    assert has_package(namefile_path, "tdis")
+    assert has_package(namefile_path, "gwf")
+    assert has_package(namefile_path, "ims")
+    assert not has_package(namefile_path, "gwt")
+
+
 def get_expected_model_dirs(path, pattern="mfsim.nam") -> List[Path]:
     folders = []
     for root, dirs, files in os.walk(path):