refactor: fix long lines to resolve check E501 (#2368)

This refactor resolves long line checks. See ruff check code E501 for more.

autotest/conftest.py

@@ -71,8 +71,8 @@ def close_plot(request):
 
 @pytest.fixture(scope="session", autouse=True)
 def patch_macos_ci_matplotlib():
-    # use noninteractive matplotlib backend if in Mac OS CI to avoid pytest-xdist node failure
-    # e.g. https://github.com/modflowpy/flopy/runs/7748574375?check_suite_focus=true#step:9:57
+    # use noninteractive matplotlib backend if in Mac OS CI to avoid pytest-xdist
+    # node failure
     if is_in_ci() and system().lower() == "darwin":
         import matplotlib
 
@@ -86,7 +86,7 @@ def patch_macos_ci_matplotlib():
 def pytest_runtest_makereport(item, call):
     # this is necessary so temp dir fixtures can
     # inspect test results and check for failure
-    # (see https://doc.pytest.org/en/latest/example/simple.html#making-test-result-information-available-in-fixtures)
+    # (see https://doc.pytest.org/en/latest/example/simple.html#making-test-result-information-available-in-fixtures)  # noqa
 
     outcome = yield
     rep = outcome.get_result()
@@ -101,16 +101,18 @@ def pytest_addoption(parser):
         "--show-plots",
         action="store_true",
         default=False,
-        help="Show any figure windows created by test cases. (Useful to display plots for visual inspection, "
-        "but automated tests should probably also check patch collections or figure & axis properties.)",
+        help="Show any figure windows created by test cases. (Useful to display "
+        "plots for visual inspection, but automated tests should probably also "
+        "check patch collections or figure & axis properties.)",
     )
 
     # for test_generate_classes.py
     parser.addoption(
         "--ref",
         action="append",
         type=str,
-        help="Include extra refs to test. Useful for testing branches on a fork, e.g. <your GitHub username>/modflow6/<your branch>.",
+        help="Include extra refs to test. Useful for testing branches on a fork, "
+        "e.g. <your GitHub username>/modflow6/<your branch>.",
     )
 
 

autotest/regression/test_mf6.py

@@ -4085,7 +4085,8 @@ def test006_gwf3(function_tmpdir, example_data_path):
     save_folder.mkdir()
     sim.set_sim_path(save_folder)
 
-    # write with "copy_external_files" turned off so external files do not get copied to new location
+    # write with "copy_external_files" turned off so external files
+    # do not get copied to new location
     sim.write_simulation(ext_file_action=ExtFileAction.copy_none)
 
     # store strt in an external binary file

autotest/regression/test_modflow.py

@@ -377,7 +377,8 @@ def test_mf2005_lake(function_tmpdir, namfile, mf2005_test_path):
 
     fn0 = join(ws, Path(namfile).name)
 
-    # write free format files - won't run without resetting to free format - evt external file issue
+    # write free format files -
+    # won't run without resetting to free format - evt external file issue
     m.free_format_input = True
 
     # rewrite files

autotest/test_cellbudgetfile.py

@@ -114,7 +114,7 @@ def test_cellbudgetfile_build_index_compact(example_data_path):
         52,
     )
     assert list_recorddict[-1] == (
-        (1, 1097, b"FLOW LOWER FACE ", 20, 40, -3, 1, 1.0, 1.0, 1097.0, b"", b"", b"", b""),
+        (1, 1097, b"FLOW LOWER FACE ", 20, 40, -3, 1, 1.0, 1.0, 1097.0, b"", b"", b"", b""),  # noqa
         42648784,
     )
     # fmt: on
@@ -209,7 +209,7 @@ def test_cellbudgetfile_build_index_mf6(example_data_path):
     assert list_recorddict[-1] == (
         (120, 4, b"             EVT", 10, 15, -3, 6,
          0.08333333333333333, 10.000000000000002, 30.99999999999983,
-         b"GWF_1           ", b"GWF_1           ", b"GWF_1           ", b"EVT             "),
+         b"GWF_1           ", b"GWF_1           ", b"GWF_1           ", b"EVT             "),  # noqa
         13414144,
     )
     # fmt: on
@@ -515,11 +515,10 @@ def test_cellbudgetfile_readrecord(example_data_path):
         for idx, kk in enumerate(kstpkper):
             t0 = v.get_data(kstpkper=kk, text=record.strip())[0]
             t1 = v.get_data(idx=indices[idx], text=record)[0]
-            assert np.array_equal(
-                t0, t1
-            ), "binary budget item {0} read using kstpkper != binary budget item {0} read using idx".format(
-                record
-            )
+            assert np.array_equal(t0, t1), (
+                "binary budget item {0} read using kstpkper != "
+                "binary budget item {0} read using idx"
+            ).format(record)
 
     # idx can be either an int or a list of ints
     s9 = v.get_data(idx=9)
@@ -577,11 +576,10 @@ def test_cellbudgetfile_readrecord_waux(example_data_path):
         for idx, kk in enumerate(kstpkper):
             t0 = v.get_data(kstpkper=kk, text=record.strip())[0]
             t1 = v.get_data(idx=indices[idx], text=record)[0]
-            assert np.array_equal(
-                t0, t1
-            ), "binary budget item {0} read using kstpkper != binary budget item {0} read using idx".format(
-                record
-            )
+            assert np.array_equal(t0, t1), (
+                "binary budget item {0} read using kstpkper != "
+                "binary budget item {0} read using idx"
+            ).format(record)
     v.close()
 
 

autotest/test_export.py

@@ -1600,7 +1600,8 @@ def test_vtk_pathline(function_tmpdir, example_data_path):
 
 
 def grid2disvgrid(nrow, ncol):
-    """Simple function to create disv verts and iverts for a regular grid of size nrow, ncol"""
+    """Simple function to create disv verts and iverts for a regular grid of
+    size nrow, ncol"""
 
     def lower_left_point(i, j, ncol):
         return i * (ncol + 1) + j

autotest/test_get_modflow.py

@@ -20,9 +20,11 @@
 flopy_dir = get_project_root_path()
 get_modflow_script = flopy_dir / "flopy" / "utils" / "get_modflow.py"
 bindir_options = {
-    "flopy": Path(expandvars(r"%LOCALAPPDATA%\flopy")) / "bin"
-    if system() == "Windows"
-    else Path.home() / ".local" / "share" / "flopy" / "bin",
+    "flopy": (
+        Path(expandvars(r"%LOCALAPPDATA%\flopy")) / "bin"
+        if system() == "Windows"
+        else Path.home() / ".local" / "share" / "flopy" / "bin"
+    ),
     "python": Path(sys.prefix) / ("Scripts" if system() == "Windows" else "bin"),
     "home": Path.home() / ".local" / "bin",
 }

autotest/test_grid.py

@@ -33,6 +33,12 @@
     import pyproj
 
 
+epsg_3070_proj4_str = (
+    "+proj=tmerc +lat_0=0 +lon_0=-90 +k=0.9996 +x_0=520000 "
+    "+y_0=-4480000 +datum=NAD83 +units=m +no_defs "
+)
+
+
 @pytest.fixture
 def minimal_unstructured_grid_info():
     d = {
@@ -579,10 +585,7 @@ def test_unstructured_from_gridspec_comments(example_data_path):
         (None, None),
         (26916, "EPSG:26916"),
         ("epsg:5070", "EPSG:5070"),
-        (
-            "+proj=tmerc +lat_0=0 +lon_0=-90 +k=0.9996 +x_0=520000 +y_0=-4480000 +datum=NAD83 +units=m +no_defs ",
-            "EPSG:3070",
-        ),
+        (epsg_3070_proj4_str, "EPSG:3070"),
         pytest.param(4269, None, marks=pytest.mark.xfail),
     ),
 )
@@ -649,10 +652,7 @@ def do_checks(g):
         (None, None),
         (26916, "EPSG:26916"),
         ("epsg:5070", "EPSG:5070"),
-        (
-            "+proj=tmerc +lat_0=0 +lon_0=-90 +k=0.9996 +x_0=520000 +y_0=-4480000 +datum=NAD83 +units=m +no_defs ",
-            "EPSG:3070",
-        ),
+        (epsg_3070_proj4_str, "EPSG:3070"),
         ("ESRI:102733", "ESRI:102733"),
         pytest.param(4269, None, marks=pytest.mark.xfail),
     ),

autotest/test_lgr.py

@@ -84,7 +84,9 @@ def singleModel(
     # Variables for the BAS package
     ibound = np.ones((nlay, nrow, ncol), dtype=np.int32)
     if iChild > 0:
-        iBndBnd = 59  # code for child cell to be linked to parent; value assigned to ibflg in the LGR-data
+        # code for child cell to be linked to parent;
+        # value assigned to ibflg in the LGR-data
+        iBndBnd = 59
     else:
         iBndBnd = -1
     ibound[:, 0, :] = iBndBnd

autotest/test_mf6.py

@@ -838,9 +838,10 @@ def test_binary_read(function_tmpdir):
             bf, data_shape, data_size, np.float64, modelgrid
         )[0]
 
-        assert np.allclose(
-            arr, arr2
-        ), f"Binary read for layered structured failed with {'Path' if isinstance(binfile, Path) else 'str'}"
+        assert np.allclose(arr, arr2), (
+            "Binary read for layered structured failed with "
+            + ("Path" if isinstance(binfile, Path) else "str")
+        )
 
     binfile = function_tmpdir / "structured_flat.hds"
     with open(binfile, "wb") as foo:
@@ -2335,7 +2336,8 @@ def test_remove_model(function_tmpdir, example_data_path):
     files = list(function_tmpdir.glob("*"))
     assert not any("model2" in f.name for f in files)
 
-    # there should be no model or solver entry for the child model in the simulation namefile
+    # there should be no model or solver entry for the child model
+    # in the simulation namefile
     lines = open(function_tmpdir / "mfsim.nam").readlines()
     lines = [l.lower().strip() for l in lines]
     assert not any("model2" in l for l in lines)

autotest/test_model_splitter.py

@@ -1295,5 +1295,6 @@ def build_gwt_model(sim, gwtname, rch_package):
             diff = np.nansum(diff)
             if diff > 10.25:
                 raise AssertionError(
-                    f"Difference between output arrays: {diff :.2f} greater than tolerance"
+                    "Difference between output arrays: "
+                    f"{diff :.2f} greater than tolerance"
                 )

autotest/test_modflow.py

@@ -94,7 +94,7 @@ def test_modflow_load(namfile, example_data_path):
         pytest.param(
             _example_data_path / "freyberg_multilayer_transient" / "freyberg.nam",
             {
-                "proj4": "+proj=utm +zone=14 +ellps=WGS84 +datum=WGS84 +units=m +no_defs",
+                "proj4": "+proj=utm +zone=14 +ellps=WGS84 +datum=WGS84 +units=m +no_defs",  # noqa
                 "angrot": 15.0,
                 "xoffset": 622241.1904510253,
                 "yoffset": 3343617.741737109,
@@ -1225,7 +1225,8 @@ def test_load_with_list_reader(function_tmpdir):
     ["recarray", "dataframe", "dict_of_recarray", "dict_of_dataframe"],
 )
 def test_pkg_data_containers(function_tmpdir, container):
-    """Test various containers for package data (list, ndarray, recarray, dataframe, dict of such)"""
+    """Test various containers for package data
+    (list, ndarray, recarray, dataframe, dict of such)"""
 
     nlay = 1
     nrow = 10

autotest/test_mp6.py

@@ -682,7 +682,8 @@ def test_data_pass_no_modflow(function_tmpdir, alt):
 @pytest.mark.parametrize("alt", [True, False])
 def test_data_pass_with_modflow(function_tmpdir, alt):
     """
-    test that user specified head files etc. are preferred over files from the modflow model
+    test that user specified head files etc. are preferred
+    over files from the modflow model
     """
 
     ml, ctx = get_mf2005_model("data_pass", function_tmpdir, alt)
@@ -760,7 +761,8 @@ def test_data_pass_with_modflow(function_tmpdir, alt):
 @pytest.mark.parametrize("alt", [True, False])
 def test_just_from_model(function_tmpdir, alt):
     """
-    test that user specified head files etc. are preferred over files from the modflow model
+    test that user specified head files etc. are preferred
+    over files from the modflow model
     """
 
     ml, ctx = get_mf2005_model("data_pass", function_tmpdir, alt)

autotest/test_particlegroup.py

@@ -44,7 +44,8 @@ def test_pgroup_release_data():
     )
     assert type(pgrd2.releaseinterval) == type(ripg2), (
         f"mp7: pgroup with releaseoption 2 returned "
-        f"type(releaseinterval)={type(pgrd2.releaseinterval)}. Should remain as {type(ripg2)}"
+        f"type(releaseinterval)={type(pgrd2.releaseinterval)}. "
+        f"Should remain as {type(ripg2)}"
     )
     assert len(pgrd3.releasetimes) == nripg3, (
         f"mp7: pgroup with releaseoption 3 returned "

autotest/test_plot_cross_section.py

@@ -84,7 +84,8 @@ def test_cross_section_bc_UZF_3lay(example_data_path):
 
 def structured_square_grid(side: int = 10, thick: int = 10):
     """
-    Creates a basic 1-layer structured grid with the given thickness and number of cells per side
+    Creates a basic 1-layer structured grid with the given thickness and number of
+    cells per side
     Parameters
     ----------
     side : The number of cells per side

autotest/test_specific_discharge.py

@@ -485,7 +485,7 @@ def specific_discharge_comprehensive(function_tmpdir):
 
 @pytest.mark.mf6
 @pytest.mark.xfail(
-    reason="occasional Unexpected collection type: <class 'matplotlib.collections.LineCollection'>"
+    reason="occasional Unexpected collection type: <class 'matplotlib.collections.LineCollection'>"  # noqa
 )
 def test_specific_discharge_mf6(mf6_model):
     # build and run MODFLOW 6 model

autotest/test_template_writer.py

@@ -56,7 +56,8 @@ def test_tpl_layered(function_tmpdir):
     partype = "hk"
     parname = "HK_LAYER_1-3"
 
-    # Span indicates that the hk parameter applies as a multiplier to layers 0 and 2 (MODFLOW layers 1 and 3)
+    # Span indicates that the hk parameter applies as a multiplier to layers 0 and 2
+    # (MODFLOW layers 1 and 3)
     span = {"layers": [0, 2]}
 
     # These parameters have not affect yet, but may in the future

autotest/test_uzf.py

@@ -213,7 +213,8 @@ def test_create_uzf(function_tmpdir, mf2005_test_path, uzf_test_path):
                 for i, a in enumerate(a1):
                     assert a == l2[i]
 
-    # load uzf test problem for nwt model with 'nwt_11_fmt'-style options and 'open/close' array types
+    # load uzf test problem for nwt model with 'nwt_11_fmt'-style options
+    # and 'open/close' array types
     tpth = uzf_test_path / "load_uzf_for_nwt"
     [shutil.copy(os.path.join(tpth, f), os.path.join(ws, f)) for f in os.listdir(tpth)]
     m3 = Modflow("UZFtest3", version="mfnwt", verbose=True)

flopy/discretization/grid.py

@@ -871,7 +871,7 @@ def map_polygons(self):
 
     def get_lni(self, nodes):
         """
-        Get the layer index and within-layer node index (both 0-based) for the given nodes
+        Get the 0-based layer index and within-layer node index for the given nodes
 
         Parameters
         ----------

flopy/discretization/unstructuredgrid.py

@@ -1177,7 +1177,8 @@ def split_line():
                 verts_provided = len(line) - 6
                 if verts_declared != verts_provided:
                     raise ValueError(
-                        f"Cell {nn} declares {verts_declared} vertices but provides {verts_provided}"
+                        f"Cell {nn} declares {verts_declared} vertices "
+                        f"but provides {verts_provided}"
                     )
 
                 verts = [int(vert) - 1 for vert in line[6 : 6 + verts_declared]]

flopy/export/metadata.py

@@ -82,7 +82,10 @@ def __init__(self, sciencebase_id, model):
             if "publisher" in d.get("type").lower()
         ][0]
         self.publisher_email = self.sb["provenance"]["linkProcess"].get("processedBy")
-        self.publisher_url = "https://www2.usgs.gov/water/"  # self.sb['provenance']['linkProcess'].get('linkReference')
+        # TODO: should publisher_url be obtained from linkReference?
+        # publisher_url = self.sb['provenance']['linkProcess'].get('linkReference')
+        publisher_url = "https://www2.usgs.gov/water/"
+        self.publisher_url = publisher_url
         self.geospatial_bounds_crs = "EPSG:4326"
         self.geospatial_lat_min = self.bounds.get("minY")
         self.geospatial_lat_max = self.bounds.get("maxY")

flopy/export/netcdf.py

@@ -877,7 +877,8 @@ def initialize_file(self, time_values=None):
                 delc.comments = (
                     "This is the row spacing that applied to the UNROTATED grid. "
                     "This grid HAS been rotated before being saved to NetCDF. "
-                    "To compute the unrotated grid, use the origin point and this array."
+                    "To compute the unrotated grid, use the origin point and "
+                    "this array."
                 )
 
             # delr
@@ -893,7 +894,8 @@ def initialize_file(self, time_values=None):
                 delr.comments = (
                     "This is the col spacing that applied to the UNROTATED grid. "
                     "This grid HAS been rotated before being saved to NetCDF. "
-                    "To compute the unrotated grid, use the origin point and this array."
+                    "To compute the unrotated grid, use the origin point and "
+                    "this array."
                 )
 
         # Workaround for CF/CDM.
@@ -1267,7 +1269,8 @@ def add_sciencebase_metadata(self, id, check=True):
             return md
 
     def _check_vs_sciencebase(self, md):
-        """Check that model bounds read from flopy are consistent with those in ScienceBase."""
+        """Check that model bounds read from flopy are consistent with
+        those in ScienceBase."""
         xmin, ymin, xmax, ymax = self.bounds
         tol = 1e-5
         assert md.geospatial_lon_min - xmin < tol

flopy/export/shapefile_utils.py

@@ -326,7 +326,8 @@ def model_attributes_to_shapefile(
                     if a.array.shape == horz_shape:
                         if hasattr(a, "shape"):
                             if a.shape[1] is None:  # usg unstructured Util3d
-                                # return a flattened array, with a.name[0] (a per-layer list)
+                                # return a flattened array,
+                                # with a.name[0] (a per-layer list)
                                 array_dict[a.name[0]] = a.array
                             else:
                                 array_dict[a.name] = a.array