refactor: apply Ruff-specific rule checks (#2377)

Apply Ruff-specific rule (RUF) checks 

* RUF002, RUFF003: ambiguous Unicode character
* RUF013: implicit optional
* RUF100: unused noqa
* RUF015: unnecessary iterable allocation for first element, i.e. use next()

.docs/Notebooks/groundwater_paper_example_1.py

@@ -17,7 +17,7 @@
 # ## Basic Flopy example
 #
 # From:
-# Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, https://doi.org/10.1111/gwat.12413.
+# Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733-739, https://doi.org/10.1111/gwat.12413.
 
 # Import the `modflow` and `utils` subpackages of FloPy and give them the aliases `fpm` and `fpu`, respectively
 

.docs/Notebooks/groundwater_paper_uspb_example.py

@@ -17,7 +17,7 @@
 # # Capture fraction example
 #
 # From:
-# Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, https://doi.org/10.1111/gwat.12413.
+# Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733-739, https://doi.org/10.1111/gwat.12413.
 
 # +
 import os

.docs/Notebooks/mfusg_zaidel_example.py

@@ -21,7 +21,7 @@
 #
 # One of the most challenging numerical cases for MODFLOW arises from drying-rewetting problems often associated with abrupt changes in the elevations of impervious base of a thin unconfined aquifer. This problem simulates a discontinuous water table configuration over a stairway impervious base and flow between constant-head boundaries in column 1 and 200. This problem is based on
 #
-# [Zaidel, J. (2013), Discontinuous Steady-State Analytical Solutions of the Boussinesq Equation and Their Numerical Representation by Modflow. Groundwater, 51: 952–959. doi: 10.1111/gwat.12019](https://doi.org/10.1111/gwat.12019)
+# [Zaidel, J. (2013), Discontinuous Steady-State Analytical Solutions of the Boussinesq Equation and Their Numerical Representation by Modflow. Groundwater, 51: 952-959. doi: 10.1111/gwat.12019](https://doi.org/10.1111/gwat.12019)
 #
 # The model consistes of a grid of 200 columns, 1 row, and 1 layer; a bottom altitude of ranging from 20 to 0 m; constant heads of 23 and 5 m in column 1 and 200, respectively; and a horizontal hydraulic conductivity of $1x10^{-4}$ m/d.  The discretization is 5 m in the row direction for all cells.
 #

.docs/Notebooks/mt3dms_sft_lkt_uzt_tutorial.py

@@ -421,7 +421,7 @@
 nlakes = int(np.max(LakArr))
 ipakcb = ipakcb  # From above
 theta = -1.0  # Implicit
-nssitr = 10  # Maximum number of iterations for Newton’s method
+nssitr = 10  # Maximum number of iterations for Newton's method
 sscncr = 1.000e-03  # Convergence criterion for equilibrium lake stage solution
 surfdep = 2.000e00  # Height of small topological variations in lake-bottom
 stages = 268.00  # Initial stage of each lake at the beginning of the run

.docs/Notebooks/uzf_example.py

@@ -19,7 +19,7 @@
 
 # # Unsaturated Zone Flow (UZF) Package demo
 # Demonstrates functionality of the flopy UZF module using the example from [Niswonger and others (2006)](https://pubs.usgs.gov/tm/2006/tm6a19/). This is the same as the SFR example problem from Prudic and others (2004;
-# p. 13–19), except the UZF package replaces the ET and RCH packages.
+# p. 13-19), except the UZF package replaces the ET and RCH packages.
 #
 # #### Problem description:
 #

.docs/create_rstfiles.py

@@ -98,7 +98,7 @@ def create_examples_rst():
             "mt3d": {"title": "MT3D and SEAWAT examples", "files": []},
             "2016gw-paper": {
                 "title": "Examples from Bakker and others (2016)",
-                "description": "Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, https://doi.org/10.1111/gwat.12413.",
+                "description": "Bakker, Mark, Post, Vincent, Langevin, C. D., Hughes, J. D., White, J. T., Starn, J. J. and Fienen, M. N., 2016, Scripting MODFLOW Model Development Using Python and FloPy: Groundwater, v. 54, p. 733–739, https://doi.org/10.1111/gwat.12413.",  # noqa: RUF001
                 "files": [],
             },
             "2023gw-paper": {

autotest/test_cbc_full3D.py

@@ -130,7 +130,7 @@ def test_cbc_full3D_mf6(function_tmpdir, path):
     sim.run_simulation()
 
     # get the groundwater model and determine the size of the model grid
-    gwf_name = list(sim.model_names)[0]
+    gwf_name = next(iter(sim.model_names))
     gwf = sim.get_model(gwf_name)
     nnodes, shape3d = gwf.modelgrid.nnodes, gwf.modelgrid.shape
 

autotest/test_grid.py

@@ -349,7 +349,7 @@ def test_structured_xyz_intersect(example_data_path):
 
 def test_vertex_xyz_intersect(example_data_path):
     sim = MFSimulation.load(sim_ws=example_data_path / "mf6" / "test003_gwfs_disv")
-    ml = sim.get_model(list(sim.model_names)[0])
+    ml = sim.get_model(next(iter(sim.model_names)))
     mg = ml.modelgrid
 
     assert mg.size == np.prod((mg.nlay, mg.ncpl))

autotest/test_zonbud_utility.py

@@ -320,7 +320,7 @@ def test_zonebudget_6(function_tmpdir, example_data_path):
 
     df = zb.get_dataframes()
 
-    assert list(df)[0] == "test_alias", "Alias testing failed"
+    assert next(iter(df)) == "test_alias", "Alias testing failed"
 
 
 @pytest.mark.mf6

flopy/export/metadata.py

@@ -76,11 +76,11 @@ def __init__(self, sciencebase_id, model):
             self.creator_institution
         )  # also in CF convention for global attributes
         self.project = self.sb["title"]
-        self.publisher_name = [
+        self.publisher_name = next(
             d.get("name")
             for d in self.sb["contacts"]
             if "publisher" in d.get("type").lower()
-        ][0]
+        )
         self.publisher_email = self.sb["provenance"]["linkProcess"].get("processedBy")
         # TODO: should publisher_url be obtained from linkReference?
         # publisher_url = self.sb['provenance']['linkProcess'].get('linkReference')
@@ -106,7 +106,7 @@ def __init__(self, sciencebase_id, model):
 
     def _get_xml_attribute(self, attr):
         try:
-            return list(self.xmlroot.iter(attr))[0].text
+            return next(iter(self.xmlroot.iter(attr))).text
         except:
             return None
 
@@ -116,9 +116,9 @@ def bounds(self):
 
     @property
     def creator(self):
-        return [
+        return next(
             d for d in self.sb["contacts"] if "point of contact" in d["type"].lower()
-        ][0]
+        )
 
     @property
     def creator_url(self):
@@ -181,7 +181,7 @@ def time_coverage(self):
         l = self.sb["dates"]
         tc = {}
         for t in ["start", "end"]:
-            tc[t] = [d.get("dateString") for d in l if t in d["type"].lower()][0]
+            tc[t] = next(d.get("dateString") for d in l if t in d["type"].lower())
         if not np.all(self.model_time.steady_state) and pd is not None:
             # replace with times from model reference
             tc["start"] = self.model_time.start_datetime

flopy/export/vtk.py

@@ -787,7 +787,7 @@ def add_transient_array(self, d, name=None, masked_values=None):
         if not self._vtk_geometry_set:
             self._set_vtk_grid_geometry()
 
-        k = list(d.keys())[0]
+        k = next(iter(d.keys()))
         transient = {}
         if isinstance(d[k], DataInterface):
             if d[k].data_type in (DataType.array2d, DataType.array3d):
@@ -937,7 +937,7 @@ def add_transient_vector(self, d, name, masked_values=None):
             self._set_vtk_grid_geometry()
 
         if self.__transient_data:
-            k = list(self.__transient_data.keys())[0]
+            k = next(iter(self.__transient_data.keys()))
             if len(d) != len(self.__transient_data[k]):
                 print(
                     "Transient vector not same size as transient arrays time "

flopy/mbase.py

@@ -1554,9 +1554,9 @@ def check(
                 if p.unit_number[i] != 0:
                     if p.unit_number[i] in package_units.values():
                         duplicate_units[p.name[i]] = p.unit_number[i]
-                        otherpackage = [
+                        otherpackage = next(
                             k for k, v in package_units.items() if v == p.unit_number[i]
-                        ][0]
+                        )
                         duplicate_units[otherpackage] = p.unit_number[i]
         if len(duplicate_units) > 0:
             for k, v in duplicate_units.items():

flopy/mfusg/mfusgcln.py

@@ -13,7 +13,7 @@
 Process for MODFLOW-USG, GSI Environmental, March, 2021
 
 Panday, Sorab, Langevin, C.D., Niswonger, R.G., Ibaraki, Motomu, and Hughes,
-J.D., 2013, MODFLOW–USG version 1: An unstructured grid version of MODFLOW
+J.D., 2013, MODFLOW-USG version 1: An unstructured grid version of MODFLOW
 for simulating groundwater flow and tightly coupled processes using a control
 volume finite-difference formulation: U.S. Geological Survey Techniques and
 Methods, book 6, chap. A45, 66 p.

flopy/modflow/mfmnw1.py

@@ -447,11 +447,11 @@ def _parse_5(f, itmp, qfrcmn_default=None, qfrcmx_default=None, qcut_default="")
         qfrcmn = 0.0
         qfrcmx = 0.0
         if "qcut" in linetxt:
-            txt = [t for t in line if "qcut" in t][0]
+            txt = next(t for t in line if "qcut" in t)
             qcut = txt
             line.remove(txt)
         elif "%cut" in linetxt:
-            txt = [t for t in line if "%cut" in t][0]
+            txt = next(t for t in line if "%cut" in t)
             qcut = txt
             line.remove(txt)
         if "qcut" in linetxt or "%cut" in linetxt:

flopy/modflow/mfmnw2.py

@@ -1085,7 +1085,7 @@ def __init__(
             if (
                 "k"
                 not in stress_period_data[
-                    list(stress_period_data.keys())[0]
+                    next(iter(stress_period_data.keys()))
                 ].dtype.names
             ):
                 self._add_kij_to_stress_period_data()

flopy/modflow/mfrch.py

@@ -193,7 +193,7 @@ def check(
         # check for unusually high or low values of mean R/T
         hk_package = {"UPW", "LPF"}.intersection(set(self.parent.get_package_list()))
         if len(hk_package) > 0 and self.parent.structured:
-            pkg = list(hk_package)[0]
+            pkg = next(iter(hk_package))
 
             # handle quasi-3D layers
             # (ugly, would be nice to put this else where in a general function)

flopy/modflow/mfuzf1.py

@@ -552,7 +552,7 @@ def __init__(
         # Dataset 9, 11, 13 and 15 will be written automatically in the
         # write_file function
         # Data Set 10
-        # [FINF (NCOL, NROW)] – U2DREL
+        # [FINF (NCOL, NROW)] - U2DREL
 
         self.finf = Transient2d(model, (nrow, ncol), np.float32, finf, name="finf")
         if ietflg > 0:

flopy/plot/crosssection.py

@@ -93,7 +93,7 @@ def __init__(
         else:
             self.ax = ax
 
-        onkey = list(line.keys())[0]
+        onkey = next(iter(line.keys()))
         self.__geographic_xpts = None
 
         # un-translate model grid into model coordinates
@@ -199,7 +199,7 @@ def __init__(
             self.xypts[node] = points
 
         if len(self.xypts) < 2:
-            if len(list(self.xypts.values())[0]) < 2:
+            if len(next(iter(self.xypts.values()))) < 2:
                 s = (
                     "cross-section cannot be created\n."
                     " less than 2 points intersect the model grid\n"

flopy/utils/compare.py

@@ -1083,8 +1083,8 @@ def compare_concentrations(
 
 
 def compare_stages(
-    namefile1: Union[str, os.PathLike] = None,
-    namefile2: Union[str, os.PathLike] = None,
+    namefile1: Optional[Union[str, os.PathLike]] = None,
+    namefile2: Optional[Union[str, os.PathLike]] = None,
     files1: Optional[Union[str, os.PathLike, list[Union[str, os.PathLike]]]] = None,
     files2: Optional[Union[str, os.PathLike, list[Union[str, os.PathLike]]]] = None,
     htol=0.001,
@@ -1295,8 +1295,8 @@ def compare_stages(
 
 
 def compare(
-    namefile1: Union[str, os.PathLike] = None,
-    namefile2: Union[str, os.PathLike] = None,
+    namefile1: Optional[Union[str, os.PathLike]] = None,
+    namefile2: Optional[Union[str, os.PathLike]] = None,
     precision="auto",
     max_cumpd=0.01,
     max_incpd=0.01,

flopy/utils/gridintersect.py

@@ -459,9 +459,10 @@ def _intersect_point_shapely(
             for ishp, cid in zip(ixresult, qcellids):
                 points = []
                 for pnt in shapely.get_parts(ishp):
-                    if tuple(pnt.coords)[0] not in parsed:
+                    next_pnt = next(iter(pnt.coords))
+                    if next_pnt not in parsed:
                         points.append(pnt)
-                    parsed.append(tuple(pnt.coords)[0])
+                    parsed.append(next_pnt)
 
                 if len(points) > 1:
                     keep_pts.append(shapely.MultiPoint(points))

flopy/utils/mfreadnam.py

@@ -11,7 +11,7 @@
 import os
 from os import PathLike
 from pathlib import Path, PurePosixPath, PureWindowsPath
-from typing import Union
+from typing import Optional, Union
 
 
 class NamData:
@@ -295,9 +295,9 @@ def attribs_from_namfile_header(namefile):
 
 def get_entries_from_namefile(
     path: Union[str, PathLike],
-    ftype: str = None,
-    unit: int = None,
-    extension: str = None,
+    ftype: Optional[str] = None,
+    unit: Optional[int] = None,
+    extension: Optional[str] = None,
 ) -> list[tuple]:
     """Get entries from an MF6 namefile. Can select using FTYPE, UNIT, or file
     extension.
@@ -481,7 +481,7 @@ def get_mf6_nper(tdisfile):
     """
     with open(tdisfile) as f:
         lines = f.readlines()
-    line = [line for line in lines if "NPER" in line.upper()][0]
+    line = next(line for line in lines if "NPER" in line.upper())
     nper = line.strip().split()[1]
     return nper
 

flopy/utils/utils_def.py

@@ -123,10 +123,10 @@ def get_pak_vals_shape(model, vals):
     if nrow is None:  # unstructured
         if isinstance(vals, dict):
             try:  # check for iterable
-                _ = (v for v in list(vals.values())[0])
+                _ = (v for v in next(iter(vals.values())))
             except:
                 return (1, ncol[0])  # default to layer 1 node count
-            return np.array(list(vals.values())[0], ndmin=2).shape
+            return np.array(next(iter(vals.values())), ndmin=2).shape
         else:
             # check for single iterable
             try:

pyproject.toml

@@ -139,6 +139,7 @@ select = [
     "F",    # Pyflakes
     "I001", # isort - unsorted-imports
     # "ISC001",  # implicitly concatenated string literals
+    "RUF",  # Ruff-specific rules
 ]
 ignore = [
     "E402", # module level import not at top of file
@@ -151,11 +152,14 @@ ignore = [
     "F524", # `.format` missing argument(s) for placeholder(s)
     "F811", # Redefinition of unused variable
     "F841", # local variable assigned but never used
+    "RUF005", # collection literal concatenation
+    "RUF012", # mutable class default
+    "RUF017", # quadratic-list-summation
 ]
 
 [tool.ruff.lint.per-file-ignores]
 ".docs/**/*.py" = ["E501"]
-"flopy/mf6/**/*.py" = ["C4", "E501", "F821", "ISC001"]
+"flopy/mf6/**/*.py" = ["C4", "E", "F", "ISC", "RUF"]
 
 [tool.codespell]
 skip = "cliff.toml,./examples/data/*"