chore: add codespell configuration and check with lint CI job (#2369)

Add configuration for codespell, to check spelling, with suggested changes. Also add this check to the "Lint" job, and fix a few outstanding typos since last done with #2160.

.github/workflows/commit.yml

@@ -70,6 +70,9 @@ jobs:
       - name: Check format
         run: ruff format . --check
 
+      - name: Check spelling
+        run: codespell
+
       - name: Check CITATION.cff
         run: |
           cffconvert --validate

DEVELOPER.md

@@ -221,7 +221,7 @@ The `section` attribute assigns the example to a group within the rendered docum
 
 **Note**: Examples are rendered into a thumbnail gallery view by [nbsphinx](https://github.com/spatialaudio/nbsphinx) when the [online documentation](https://flopy.readthedocs.io/en/latest/) is built. At least one plot/visualization is recommended in order to provide a thumbnail for each example notebook in the [Examples gallery](https://flopy.readthedocs.io/en/latest/notebooks.html)gallery.
 
-**Note**: Thumbnails for the examples gallery are generated automatically from the notebook header (typically the first line, begining with a single '#'), and by default, the last plot generated. Thumbnails can be customized to use any plot in the notebook, or an external image, as described [here](https://nbsphinx.readthedocs.io/en/0.9.1/subdir/gallery.html).
+**Note**: Thumbnails for the examples gallery are generated automatically from the notebook header (typically the first line, beginning with a single '#'), and by default, the last plot generated. Thumbnails can be customized to use any plot in the notebook, or an external image, as described [here](https://nbsphinx.readthedocs.io/en/0.9.1/subdir/gallery.html).
 
 Each example should create and (attempt to) dispose of its own isolated temporary workspace. On Windows, Python's `TemporaryDirectory` can raise permissions errors, so cleanup is trapped with `try/except`. Some scripts also accept a `--quiet` flag, curtailing verbose output, and a `--keep` option to specify a working directory of the user's choice.
 
@@ -289,7 +289,7 @@ This should complete in under a minute on most machines. Smoke testing aims to c
 
 ### Writing tests
 
-Test functions and files should be named informatively, with related tests grouped in the same file. The test suite runs on GitHub Actions in parallel, so tests should not access the working space of other tests, example scripts, tutorials or notebooks. A number of shared test fixtures are [imported](conftest.py) from [`modflow-devtools`](https://github.com/MODFLOW-USGS/modflow-devtools). These include keepable temporary directory fixtures and miscellanous utilities (see `modflow-devtools` repository README for more information on fixture usage). New tests should use these facilities where possible. See also the [contribution guidelines](CONTRIBUTING.md) before submitting a pull request.
+Test functions and files should be named informatively, with related tests grouped in the same file. The test suite runs on GitHub Actions in parallel, so tests should not access the working space of other tests, example scripts, tutorials or notebooks. A number of shared test fixtures are [imported](conftest.py) from [`modflow-devtools`](https://github.com/MODFLOW-USGS/modflow-devtools). These include keepable temporary directory fixtures and miscellaneous utilities (see `modflow-devtools` repository README for more information on fixture usage). New tests should use these facilities where possible. See also the [contribution guidelines](CONTRIBUTING.md) before submitting a pull request.
 
 ### Debugging tests
 

autotest/test_gridgen.py

@@ -714,7 +714,7 @@ def test_gridgen(function_tmpdir):
     g6.add_refinement_features(rfpoly, "polygon", 3, range(nlay))
     gu.add_refinement_features(rfpoly, "polygon", 3, range(nlay))
 
-    # inactivate parts of mfusg layer 2 to test vertical-pass-through option
+    # deactivate parts of mfusg layer 2 to test vertical-pass-through option
     xmin = 0 * delr
     xmax = 18 * delr
     ymin = 0 * delc

autotest/test_mbase.py

@@ -65,7 +65,7 @@ def test_resolve_exe_by_rel_path(function_tmpdir, use_ext, forgive):
         assert actual.lower() == expected
         assert which(actual)
 
-        # check behavior if exe DNE
+        # check behavior if exe does not exist
         with pytest.warns(UserWarning) if forgive else pytest.raises(FileNotFoundError):
             assert not resolve_exe("../bin/mf2005", forgive)
 

autotest/test_modflow.py

@@ -277,14 +277,14 @@ def test_exe_selection(example_data_path, function_tmpdir):
         == exe_name
     )
 
-    # init/load should warn if exe DNE
+    # init/load should warn if exe does not exist
     exe_name = "not_an_exe"
     with pytest.warns(UserWarning):
         ml = Modflow(exe_name=exe_name)
     with pytest.warns(UserWarning):
         ml = Modflow.load(namfile_path, exe_name=exe_name, model_ws=model_path)
 
-    # run should error if exe DNE
+    # run should error if exe does not exist
     ml = Modflow.load(namfile_path, exe_name=exe_name, model_ws=model_path)
     ml.change_model_ws(function_tmpdir)
     ml.write_input()

autotest/test_uzf.py

@@ -625,15 +625,15 @@ def test_uzf_negative_iuzfopt(function_tmpdir):
 
 
 def test_optionsblock_auxillary_typo():
-    # Incorrect: auxillary
+    # Incorrect: auxillary  # codespell:ignore
     #   Correct: auxiliary
     options = OptionBlock("", ModflowWel, block=True)
     assert options.auxiliary == []
     with pytest.deprecated_call():
-        assert options.auxillary == []
+        assert options.auxillary == []  # codespell:ignore
     with pytest.deprecated_call():
-        options.auxillary = ["aux", "iface"]
+        options.auxillary = ["aux", "iface"]  # codespell:ignore
     assert options.auxiliary == ["aux", "iface"]
     options.auxiliary = []
     with pytest.deprecated_call():
-        assert options.auxillary == []
+        assert options.auxillary == []  # codespell:ignore

flopy/discretization/unstructuredgrid.py

@@ -618,12 +618,12 @@ def neighbors(self, node=None, **kwargs):
         reset = kwargs.pop("reset", False)
         if method == "iac":
             if self._neighbors is None or reset:
-                neighors = {}
+                neighbors = {}
                 idx0 = 0
                 for node, ia in enumerate(self._iac):
                     idx1 = idx0 + ia
-                    neighors[node] = list(self._ja[idx0 + 1 : idx1])
-                self._neighbors = neighors
+                    neighbors[node] = list(self._ja[idx0 + 1 : idx1])
+                self._neighbors = neighbors
             if node is not None:
                 return self._neighbors[node]
             else:

flopy/discretization/vertexgrid.py

@@ -222,7 +222,7 @@ def grid_lines(self):
         if self.cell1d is not None:
             close_cell = False
 
-        # go through each cell and create a line segement for each face
+        # go through each cell and create a line segment for each face
         lines = []
         ncpl = len(xgrid)
         for icpl in range(ncpl):

flopy/mf6/data/mfdatautil.py

@@ -15,7 +15,7 @@ def iterable(obj, any_iterator=False):
     if any_iterator:
         try:
             my_iter = iter(obj)
-        except TypeError as te:
+        except TypeError:
             return False
         return True
     else:

flopy/mf6/utils/lakpak_utils.py

@@ -40,7 +40,7 @@ def get_lak_connections(modelgrid, lake_map, idomain=None, bedleak=None):
     Returns
     -------
     idomain : ndarry
-        idomain adjusted to inactivate cells with lakes
+        idomain adjusted to deactivate cells with lakes
     connection_dict : dict
         dictionary with the zero-based lake number keys and number of
         connections in a lake values

flopy/modpath/mp6bas.py

@@ -28,7 +28,7 @@ class Modpath6Bas(Package):
     hdry : float
         Head value assigned to dry cells (default is -8888.).
     def_face_ct : int
-        Number fo default iface codes to read (default is 0).
+        Number of default iface codes to read (default is 0).
     bud_label : str or list of strs
         MODFLOW budget item to which a default iface is assigned.
     def_iface : int or list of ints

flopy/plot/crosssection.py

@@ -185,7 +185,7 @@ def __init__(
         self.xypts = plotutil.UnstructuredPlotUtilities.filter_line_segments(
             self.xypts, threshold=min_segment_length
         )
-        # need to ensure that the ordering of verticies in xypts is correct
+        # need to ensure that the ordering of vertices in xypts is correct
         # based on the projection. In certain cases vertices need to be sorted
         # for the specific "projection"
         for node, points in self.xypts.items():
@@ -933,7 +933,7 @@ def plot_centers(
             optional numpy nd.array of size modelgrid.nnodes
         s : None, float, numpy array
             optional point size parameter
-        masked_values : None, iteratable
+        masked_values : None, iterable
             optional list, tuple, or np array of array (a) values to mask
         inactive : bool
             boolean flag to include inactive cell centers in the plot.

flopy/plot/map.py

@@ -629,7 +629,7 @@ def plot_centers(
             optional numpy nd.array of size modelgrid.nnodes
         s : None, float, numpy array
             optional point size parameter
-        masked_values : None, iteratable
+        masked_values : None, iterable
             optional list, tuple, or np array of array (a) values to mask
         inactive : bool
             boolean flag to include inactive cell centers in the plot.

flopy/utils/lgrutil.py

@@ -589,7 +589,7 @@ def to_disv_gridprops(self):
         used to create a disv grid (instead of a separate parent
         and child representation).  The gridprops dictionary can
         be unpacked into the flopy.mf6.Modflowdisv() constructor
-        and flopy.discretization.VertexGrid() contructor.
+        and flopy.discretization.VertexGrid() constructor.
 
         Note that export capability will only work if the parent
         and child models have corresponding layers.
@@ -964,7 +964,7 @@ def get_disv_gridprops(self):
         used to create a disv grid (instead of a separate parent
         and child representation).  The gridprops dictionary can
         be unpacked into the flopy.mf6.Modflowdisv() constructor
-        and flopy.discretization.VertexGrid() contructor.
+        and flopy.discretization.VertexGrid() constructor.
 
         Note that export capability will only work if the parent
         and child models have corresponding layers.

flopy/utils/optionblock.py

@@ -59,10 +59,10 @@ def __init__(self, options_line, package, block=True):
         self._set_attributes()
 
     def __getattr__(self, key):
-        if key == "auxillary":  # catch typo from older version
+        if key == "auxillary":  # catch typo from older version - codespell:ignore
             key = "auxiliary"
             warnings.warn(
-                "the atttribute 'auxillary' is deprecated, use 'auxiliary' instead",
+                "the attribute 'auxillary' is deprecated, use 'auxiliary' instead",
                 category=DeprecationWarning,
             )
         return super().__getattribute__(key)
@@ -159,10 +159,10 @@ def __setattr__(self, key, value):
                 is consistent with the attribute data type
 
         """
-        if key == "auxillary":  # catch typo from older version
+        if key == "auxillary":  # catch typo from older version - codespell:ignore
             key = "auxiliary"
             warnings.warn(
-                "the atttribute 'auxillary' is deprecated, use 'auxiliary' instead",
+                "the attribute 'auxillary' is deprecated, use 'auxiliary' instead",
                 category=DeprecationWarning,
             )
 

pyproject.toml

@@ -39,6 +39,7 @@ dynamic = ["version", "readme"]
 dev = ["flopy[lint,test,optional,doc]"]
 lint = [
     "cffconvert",
+    "codespell[toml] >=2.2.2",
     "ruff"
 ]
 test = [
@@ -159,3 +160,28 @@ ignore = [
 [tool.ruff.lint.per-file-ignores]
 ".docs/**/*.py" = ["E501"]
 "flopy/mf6/**/*.py" = ["E501", "ISC001"]
+
+[tool.codespell]
+skip = "cliff.toml,./examples/data/*"
+ignore-words-list = [
+    "alltime",
+    "dum",
+    "inout",
+    "intot",
+    "delt",
+    "gage",
+    "gages",
+    "datbase",
+    "wel",
+    "nam",
+    "lke",
+    "ist",
+    "ninj",
+    "drob",
+    "thck",
+    "vor",
+    "yur",
+    "localy",
+    "vertx",
+    "nd",
+]