refactor: apply suggestions from pyupgrade (#2361)

This PR refactors the codebase with Ruff's pyupgrade check, based on pyupgrade. Not all suggestions are applied, and some manual edits were applied in addition to the affected code. Removing target-version from the ruff options allows this to be automatically evaluated from pyproject.toml.

The rules that were applied include:

- UP004 (useless-object-inheritance)
- UP006 (non-pep585-annotation) - see PEP 585 for details; this was not applied to get_modflow.py to maintain it's compatibility for older Python versions in stand-alone mode
- UP018 (native-literals)
- UP034 (extraneous-parentheses)
- UP035 (deprecated-import)

Meanwhile, these rules were somewhat ignored:

- UP031,UP032: related to upgrading to f-strings. Ignored since these could involve much more string and message related refactoring to adjacent code. However, a few upgraded f-strings are upgraded where it looks simple, and in user-facing docs.
- UP015: for redundant file modes. Kept default file modes (e.g. open(..., "r") to keep it more clear, e.g. when a file pointer object is left open for reading (and then closed many lines further down, as is often done with legacy flopy code)

.docs/groundwater_paper/scripts/uspb_capture.py

@@ -104,15 +104,9 @@ def cf_model(model, k, i, j, base, Q=-100):
 # write some summary information
 fs.write(f"Problem size: {nrow} rows and {ncol} columns.\n")
 fs.write(
-    "Capture fraction analysis performed every {} rows and columns.\n".format(
-        nstep
-    )
-)
-fs.write(
-    "Maximum number of analyses: {} rows and {} columns.\n".format(
-        nrow2, ncol2
-    )
+    f"Capture fraction analysis performed every {nstep} rows and columns.\n"
 )
+fs.write(f"Maximum number of analyses: {nrow2} rows and {ncol2} columns.\n")
 
 # create array to store capture fraction data (subset of model)
 cf_array = np.empty((10, nrow2, ncol2), dtype=float)
@@ -131,9 +125,7 @@ def cf_model(model, k, i, j, base, Q=-100):
         if ibound[i, j] < 1:
             sys.stdout.write(".")
         else:
-            line = "\nrow {} of {} - col {} of {}\n".format(
-                icnt + 1, nrow2, jcnt + 1, ncol2
-            )
+            line = f"\nrow {icnt + 1} of {nrow2} - col {jcnt + 1} of {ncol2}\n"
             fs.write(line)
             sys.stdout.write(line)
             s0 = time.time()

.docs/groundwater_paper/scripts/uspb_capture_par.py

@@ -106,9 +106,7 @@ def copy_files(ml, nproc):
                 os.makedirs(cf_pths[idx])
             filelist = [f for f in os.listdir(cf_pths[0])]
             sys.stdout.write(
-                "copying files from {} to {}\n".format(
-                    cf_pths[0], cf_pths[idx]
-                )
+                f"copying files from {cf_pths[0]} to {cf_pths[idx]}\n"
             )
             for f in filelist:
                 if os.path.splitext(f)[1].lower() in exclude:
@@ -179,9 +177,7 @@ def cf_model(imod, ion, nmax, k, i, j, Qt, base, hdry):
     sys.stdout.write(f"  model number {imod} working directory: {pth}\n")
     make_well(pth, k, i, j, Qt)
     success, elt = run_model(pth)
-    line = "\nModel run: {} of {} (model number {})\n".format(
-        ion + 1, nmax, imod
-    )
+    line = f"\nModel run: {ion + 1} of {nmax} (model number {imod})\n"
     line += f"  row {i + 1} - col {j + 1}\n"
     line += f"  {elt}\n"
     # get the results
@@ -211,14 +207,12 @@ def cf_model(imod, ion, nmax, k, i, j, Qt, base, hdry):
                     ]
                     v[idx] = ((v1.sum() + v2.sum() + v3.sum()) - base) / (-Qt)
         except:
-            line += " Error: Model run: {} of {} (model number {}) - ".format(
-                ion + 1, nmax, imod
-            )
+            line += f" Error: Model run: {ion + 1} of {nmax} (model number {imod}) - "
             line += "could not process model results.\n"
             v[:] = np.nan
     else:
-        line += " Error: Model run: {} of {} (model number {}) ".format(
-            ion + 1, nmax, imod
+        line += (
+            f" Error: Model run: {ion + 1} of {nmax} (model number {imod}) "
         )
         line += "did not execute successfully\n"
         v[:] = np.nan
@@ -232,15 +226,11 @@ def doit():
     ncores = mp.cpu_count()
     if nproc > ncores:
         sys.stdout.write(
-            "Requested {} cores but only {} cores are available.\n\n\n".format(
-                nproc, ncores
-            )
+            f"Requested {nproc} cores but only {ncores} cores are available.\n\n\n"
         )
     else:
         sys.stdout.write(
-            "Requested {} cores and {} cores are available.\n\n\n".format(
-                nproc, ncores
-            )
+            f"Requested {nproc} cores and {ncores} cores are available.\n\n\n"
         )
 
     # paths
@@ -275,14 +265,10 @@ def doit():
     # write some summary information
     fs.write(f"Problem size: {nrow} rows and {ncol} columns.\n")
     fs.write(
-        "Capture fraction analysis performed every {} rows and columns.\n".format(
-            nstep
-        )
+        f"Capture fraction analysis performed every {nstep} rows and columns.\n"
     )
     fs.write(
-        "Maximum number of analyses: {} rows and {} columns.\n".format(
-            nrow2, ncol2
-        )
+        f"Maximum number of analyses: {nrow2} rows and {ncol2} columns.\n"
     )
 
     # create array to store capture fraction data (subset of model)
@@ -359,9 +345,7 @@ def doit():
             f"USPB_capture_fraction_{nstep:02d}_{idx + 1:02d}.dat",
         )
         sys.stdout.write(
-            "saving capture fraction data to...{}\n".format(
-                os.path.basename(fn)
-            )
+            f"saving capture fraction data to...{os.path.basename(fn)}\n"
         )
         np.savetxt(fn, cf_array[idx, :, :], delimiter=" ")
 

autotest/conftest.py

@@ -2,7 +2,6 @@
 from importlib import metadata
 from pathlib import Path
 from platform import system
-from typing import List
 
 import matplotlib.pyplot as plt
 import pytest
@@ -52,7 +51,7 @@ def flopy_data_path() -> Path:
 
 
 @pytest.fixture(scope="session")
-def example_shapefiles(example_data_path) -> List[Path]:
+def example_shapefiles(example_data_path) -> list[Path]:
     return [f.resolve() for f in (example_data_path / "prj_test").glob("*")]
 
 

autotest/test_export.py

@@ -2,7 +2,6 @@
 import os
 import shutil
 from pathlib import Path
-from typing import List
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -56,7 +55,7 @@
     import pyproj
 
 
-def namfiles() -> List[Path]:
+def namfiles() -> list[Path]:
     mf2005_path = get_example_data_path() / "mf2005_test"
     return list(mf2005_path.rglob("*.nam"))
 
@@ -998,9 +997,10 @@ def test_export_mf6_shp(function_tmpdir):
     # Compare exported riv shapefiles
     riv.export(function_tmpdir / "riv.shp")
     riv6.export(function_tmpdir / "riv6.shp")
-    with Reader(function_tmpdir / "riv.shp") as riv_shp, Reader(
-        function_tmpdir / "riv6.shp"
-    ) as riv6_shp:
+    with (
+        Reader(function_tmpdir / "riv.shp") as riv_shp,
+        Reader(function_tmpdir / "riv6.shp") as riv6_shp,
+    ):
         assert list(riv_shp.shapeRecord(-1).record) == list(
             riv6_shp.shapeRecord(-1).record
         )

autotest/test_generate_classes.py

@@ -1,9 +1,9 @@
 import sys
+from collections.abc import Iterable
 from os import environ
 from pathlib import Path
 from platform import system
 from pprint import pprint
-from typing import Iterable
 from warnings import warn
 
 import pytest

autotest/test_lake_connections.py

@@ -503,8 +503,8 @@ def test_embedded_lak_prudic(example_data_path):
     nlay = 8  # Number of layers
     nrow = 36  # Number of rows
     ncol = 23  # Number of columns
-    delr = float(405.665)  # Column width ($ft$)
-    delc = float(403.717)  # Row width ($ft$)
+    delr = 405.665  # Column width ($ft$)
+    delc = 403.717  # Row width ($ft$)
     delv = 15.0  # Layer thickness ($ft$)
     top = 100.0  # Top of the model ($ft$)
 
@@ -606,8 +606,8 @@ def test_embedded_lak_prudic_mixed(example_data_path):
     nlay = 8  # Number of layers
     nrow = 36  # Number of rows
     ncol = 23  # Number of columns
-    delr = float(405.665)  # Column width ($ft$)
-    delc = float(403.717)  # Row width ($ft$)
+    delr = 405.665  # Column width ($ft$)
+    delc = 403.717  # Row width ($ft$)
     delv = 15.0  # Layer thickness ($ft$)
     top = 100.0  # Top of the model ($ft$)
 

autotest/test_mbase.py

@@ -66,8 +66,10 @@ def test_resolve_exe_by_rel_path(function_tmpdir, use_ext, forgive):
         assert which(actual)
 
         # check behavior if exe DNE
-        with pytest.warns(UserWarning) if forgive else pytest.raises(
-            FileNotFoundError
+        with (
+            pytest.warns(UserWarning)
+            if forgive
+            else pytest.raises(FileNotFoundError)
         ):
             assert not resolve_exe("../bin/mf2005", forgive)
 

autotest/test_modflow.py

@@ -3,7 +3,6 @@
 import os
 import shutil
 from pathlib import Path
-from typing import Dict
 
 import numpy as np
 import pandas as pd

autotest/test_mp7.py

@@ -877,7 +877,7 @@ def test_mp7bas_porosity(ex01_mf6_model, porosity_type):
         # Initialize porosity array based on dim of dis.botm
         # lay_1=0.35, lay_2=0.30, lay_3=0.25
         porosity = np.array([[[0.35]], [[0.30]], [[0.25]]]) * np.ones(
-            (gwf.dis.botm.array.shape)
+            gwf.dis.botm.array.shape
         )
         # Diversify porosity values, adjust both halves of the model
         porosity[:, :, : porosity.shape[2] // 2] -= 0.05

flopy/export/netcdf.py

@@ -219,8 +219,8 @@ def __init__(
         self.log("initializing attributes")
         self.nc_crs_str = "epsg:4326"
         self.nc_crs_longname = "https://www.opengis.net/def/crs/EPSG/0/4326"
-        self.nc_semi_major = float(6378137.0)
-        self.nc_inverse_flat = float(298.257223563)
+        self.nc_semi_major = 6378137.0
+        self.nc_inverse_flat = 298.257223563
 
         self.global_attributes = {}
         self.global_attributes["namefile"] = self.model.namefile

flopy/export/shapefile_utils.py

@@ -10,7 +10,7 @@
 import sys
 import warnings
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import Optional, Union
 from warnings import warn
 
 import numpy as np
@@ -489,7 +489,7 @@ def shape_attr_name(name, length=6, keep_layer=False):
     return n
 
 
-def enforce_10ch_limit(names: List[str], warnings: bool = True) -> List[str]:
+def enforce_10ch_limit(names: list[str], warnings: bool = True) -> list[str]:
     """Enforce 10 character limit for fieldnames.
     Add suffix for duplicate names starting at 0.
 

flopy/mbase.py

@@ -17,7 +17,7 @@
 from pathlib import Path
 from shutil import which
 from subprocess import PIPE, STDOUT, Popen
-from typing import List, Optional, Tuple, Union
+from typing import Optional, Union
 from warnings import warn
 
 import numpy as np
@@ -1395,7 +1395,7 @@ def run_model(
         pause=False,
         report=False,
         normal_msg="normal termination",
-    ) -> Tuple[bool, List[str]]:
+    ) -> tuple[bool, list[str]]:
         """
         This method will run the model using subprocess.Popen.
 
@@ -1667,7 +1667,7 @@ def run_model(
     use_async=False,
     cargs=None,
     custom_print=None,
-) -> Tuple[bool, List[str]]:
+) -> tuple[bool, list[str]]:
     """
     Run the model using subprocess.Popen, optionally collecting stdout and printing
     timestamped progress. Model workspace, namefile, executable to use, and several

flopy/mf6/mfpackage.py

@@ -259,7 +259,7 @@ def write_header(self, fd):
             if len(self.data_items) > 1:
                 for data_item in self.data_items[1:]:
                     entry = data_item.get_file_entry(values_only=True)
-                    fd.write("%s" % (entry.rstrip()))
+                    fd.write(str(entry).rstrip())
         if self.get_comment().text:
             fd.write(" ")
             self.get_comment().write(fd)

flopy/mf6/mfsimbase.py

@@ -4,7 +4,7 @@
 import sys
 import warnings
 from pathlib import Path
-from typing import List, Optional, Union, cast
+from typing import Optional, Union, cast
 
 import numpy as np
 
@@ -1255,12 +1255,12 @@ def load_package(
         return package
 
     def register_ims_package(
-        self, solution_file: MFPackage, model_list: Union[str, List[str]]
+        self, solution_file: MFPackage, model_list: Union[str, list[str]]
     ):
         self.register_solution_package(solution_file, model_list)
 
     def register_solution_package(
-        self, solution_file: MFPackage, model_list: Union[str, List[str]]
+        self, solution_file: MFPackage, model_list: Union[str, list[str]]
     ):
         """
         Register a solution package with the simulation.
@@ -2642,7 +2642,7 @@ def _is_in_solution_group(self, item, index, any_idx_after=False):
 
     def plot(
         self,
-        model_list: Optional[Union[str, List[str]]] = None,
+        model_list: Optional[Union[str, list[str]]] = None,
         SelPackList=None,
         **kwargs,
     ):

flopy/mf6/utils/model_splitter.py

@@ -117,7 +117,7 @@
 }
 
 
-class Mf6Splitter(object):
+class Mf6Splitter:
     """
     A class for splitting a single model into a multi-model simulation
 
@@ -2493,7 +2493,7 @@ def _remap_obs(self, package, mapped_data, remapper, pkg_type=None):
                         for mkey, model in self._model_dict.items():
                             idx = np.asarray(new_model2 == mkey).nonzero()
                             tmp_node = new_node2[idx]
-                            cidx = np.asarray((tmp_node != None)).nonzero()  # noqa: E711
+                            cidx = np.asarray(tmp_node != None).nonzero()  # noqa: E711
                             tmp_cellid = model.modelgrid.get_lrc(
                                 tmp_node[cidx].to_list()
                             )

flopy/mfusg/mfusgdisu.py

@@ -546,8 +546,8 @@ def load(cls, f, model, ext_unit_dict=None, check=True):
 
         if model.version != "mfusg":
             print(
-                "Warning: model version was reset from '{}' to 'mfusg' "
-                "in order to load a DISU file".format(model.version)
+                f"Warning: model version was reset from '{model.version}' "
+                "to 'mfusg' in order to load a DISU file"
             )
             model.version = "mfusg"
 

flopy/mfusg/mfusgsms.py

@@ -434,8 +434,8 @@ def load(cls, f, model, ext_unit_dict=None):
 
         if model.version != "mfusg":
             print(
-                "Warning: model version was reset from '{}' to 'mfusg' "
-                "in order to load a SMS file".format(model.version)
+                f"Warning: model version was reset from '{model.version}' "
+                "to 'mfusg' in order to load a SMS file"
             )
             model.version = "mfusg"