chore: reformat Python code with line length = 88 (MODFLOW-USGS#2056)

This PR reformats Python code with a maximum line length of 88 characters to better represent the code. Note that a related repo MODFLOW-USGS/modflow6-examples already uses the default line length of 88.

See modflowpy/flopy#2362 for a related PR with rational and discussion.

This PR was automated using these Ruff commands (including quick fixes to ISC001):

ruff format
ruff check --select ISC001 --fix
ruff format

autotest/build_exes.py

@@ -23,9 +23,7 @@ def test_meson_build(bin_path):
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        "Rebuild local development version of MODFLOW 6"
-    )
+    parser = argparse.ArgumentParser("Rebuild local development version of MODFLOW 6")
     parser.add_argument(
         "-p", "--path", help="path to bin directory", default=top_bin_path
     )

autotest/common_regression.py

@@ -487,9 +487,7 @@ def get_regression_files(
             for extension in extensions:
                 if file_name.lower().endswith(extension):
                     files0.append(fpth0)
-                    fpth1 = os.path.join(
-                        workspace, "mf6_regression", file_name
-                    )
+                    fpth1 = os.path.join(workspace, "mf6_regression", file_name)
                     files1.append(fpth1)
                     break
     return files0, files1
@@ -579,9 +577,7 @@ def setup_model(namefile, dst, remove_existing=True, extrafiles=None):
             print(f"{srcf} does not exist")
 
 
-def setup_mf6(
-    src, dst, mfnamefile="mfsim.nam", extrafiles=None, remove_existing=True
-):
+def setup_mf6(src, dst, mfnamefile="mfsim.nam", extrafiles=None, remove_existing=True):
     """
     Setup an MF6 simulation test, copying input files from the source
     to the destination workspace.
@@ -664,9 +660,7 @@ def setup_mf6(
     return mf6inp, mf6outp
 
 
-def setup_mf6_comparison(
-    src, dst, cmp_exe="mf6", overwrite=True, verbose=False
-):
+def setup_mf6_comparison(src, dst, cmp_exe="mf6", overwrite=True, verbose=False):
     """Setup an output comparison for MODFLOW 6 simulation.
 
     Parameters

autotest/conftest.py

@@ -129,9 +129,7 @@ def pytest_addoption(parser):
 
 def pytest_collection_modifyitems(config, items):
     if not config.getoption("--parallel"):
-        skip_parallel = pytest.mark.skip(
-            reason="need --parallel option to run"
-        )
+        skip_parallel = pytest.mark.skip(reason="need --parallel option to run")
         for item in items:
             if "parallel" in item.keywords:
                 item.add_marker(skip_parallel)

autotest/cross_section_functions.py

@@ -127,10 +127,7 @@ def wetted_area(
 
             # write to screen
             if verbose:
-                print(
-                    f"{idx}->{idx + 1} ({x0},{x1}) - "
-                    f"perimeter={x1 - x0} - area={a}"
-                )
+                print(f"{idx}->{idx + 1} ({x0},{x1}) - perimeter={x1 - x0} - area={a}")
 
     return area
 
@@ -199,9 +196,7 @@ def is_neighb_vert(x, h, idx):
 
     # Assess left neighbor first
     if idx > 0:
-        if (
-            cnt > 2
-        ):  # only x-sections w/ 3 or more pts may host a vertical side
+        if cnt > 2:  # only x-sections w/ 3 or more pts may host a vertical side
             idxm1 = idx - 1
             if x[idxm1] == x[idx] and h[idxm1] != h[idx]:
                 leftvert = True

autotest/framework.py

@@ -91,9 +91,7 @@ def run_parallel(workspace, target, ncpus) -> Tuple[bool, List[str]]:
     if get_ostag() in ["win64"]:
         mpiexec_cmd = ["mpiexec", "-np", str(ncpus), target, "-p"]
     else:
-        mpiexec_cmd = (
-            ["mpiexec"] + oversubscribed + ["-np", str(ncpus), target, "-p"]
-        )
+        mpiexec_cmd = ["mpiexec"] + oversubscribed + ["-np", str(ncpus), target, "-p"]
 
     proc = Popen(mpiexec_cmd, stdout=PIPE, stderr=STDOUT, cwd=workspace)
 
@@ -145,19 +143,15 @@ def write_input(*sims, overwrite: bool = True, verbose: bool = True):
                 warn("Workspace is not empty, not writing input files")
                 return
             if verbose:
-                print(
-                    f"Writing mf6 simulation '{sim.name}' to: {sim.sim_path}"
-                )
+                print(f"Writing mf6 simulation '{sim.name}' to: {sim.sim_path}")
             sim.write_simulation()
         elif isinstance(sim, flopy.mbase.BaseModel):
             workspace = Path(sim.model_ws)
             if any(workspace.glob("*")) and not overwrite:
                 warn("Workspace is not empty, not writing input files")
                 return
             if verbose:
-                print(
-                    f"Writing {type(sim)} model '{sim.name}' to: {sim.model_ws}"
-                )
+                print(f"Writing {type(sim)} model '{sim.name}' to: {sim.model_ws}")
             sim.write_input()
         else:
             raise ValueError(f"Unsupported simulation/model type: {type(sim)}")
@@ -316,9 +310,7 @@ def _compare_heads(
                 file1 = files1[i]
                 ext = os.path.splitext(file1)[1][1:].lower()
                 outfile = os.path.splitext(os.path.basename(file1))[0]
-                outfile = os.path.join(
-                    self.workspace, outfile + "." + ext + ".cmp.out"
-                )
+                outfile = os.path.join(self.workspace, outfile + "." + ext + ".cmp.out")
                 file2 = None if files2 is None else files2[i]
 
                 # set exfile
@@ -356,9 +348,7 @@ def _compare_heads(
         extension = "hds"
         for i, (fpth0, fpth1) in enumerate(zip(files0, files1)):
             outfile = os.path.splitext(os.path.basename(fpth0))[0]
-            outfile = os.path.join(
-                self.workspace, outfile + f".{extension}.cmp.out"
-            )
+            outfile = os.path.join(self.workspace, outfile + f".{extension}.cmp.out")
             success = compare_heads(
                 None,
                 None,
@@ -388,9 +378,7 @@ def _compare_concentrations(self, extensions="ucn", htol=0.001) -> bool:
         extension = "ucn"
         for i, (fpth0, fpth1) in enumerate(zip(files0, files1)):
             outfile = os.path.splitext(os.path.basename(fpth0))[0]
-            outfile = os.path.join(
-                self.workspace, outfile + f".{extension}.cmp.out"
-            )
+            outfile = os.path.join(self.workspace, outfile + f".{extension}.cmp.out")
             success = compare_heads(
                 None,
                 None,
@@ -422,23 +410,17 @@ def _compare_budgets(self, extensions="cbc", rclose=0.001) -> bool:
                 f"{EXTTEXT[extension]} comparison {i + 1}",
                 f"{self.name} ({os.path.basename(fpth0)})",
             )
-            success = self._compare_budget_files(
-                extension, fpth0, fpth1, rclose
-            )
+            success = self._compare_budget_files(extension, fpth0, fpth1, rclose)
             if not success:
                 return False
         return True
 
-    def _compare_budget_files(
-        self, extension, fpth0, fpth1, rclose=0.001
-    ) -> bool:
+    def _compare_budget_files(self, extension, fpth0, fpth1, rclose=0.001) -> bool:
         success = True
         if os.stat(fpth0).st_size * os.stat(fpth0).st_size == 0:
             return success, ""
         outfile = os.path.splitext(os.path.basename(fpth0))[0]
-        outfile = os.path.join(
-            self.workspace, outfile + f".{extension}.cmp.out"
-        )
+        outfile = os.path.join(self.workspace, outfile + f".{extension}.cmp.out")
         fcmp = open(outfile, "w")
         fcmp.write("Performing CELL-BY-CELL to CELL-BY-CELL comparison\n")
         fcmp.write(f"{fpth0}\n")
@@ -608,9 +590,7 @@ def _run_sim_or_model(
             elif "mf6" in target.name:
                 # parallel test if configured
                 if self.parallel and ncpus > 1:
-                    print(
-                        f"Parallel test {self.name} on {self.ncpus} processes"
-                    )
+                    print(f"Parallel test {self.name} on {self.ncpus} processes")
                     try:
                         success, buff = run_parallel(workspace, target, ncpus)
                     except Exception:
@@ -641,9 +621,7 @@ def _run_sim_or_model(
                 try:
                     nf_ext = ".mpsim" if "mp7" in target.name else ".nam"
                     namefile = next(iter(workspace.glob(f"*{nf_ext}")), None)
-                    assert (
-                        namefile
-                    ), f"Control file with extension {nf_ext} not found"
+                    assert namefile, f"Control file with extension {nf_ext} not found"
                     success, buff = flopy.run_model(
                         target, namefile, workspace, report=True
                     )
@@ -660,9 +638,7 @@ def _run_sim_or_model(
 
         except Exception:
             success = False
-            warn(
-                f"Unhandled error in comparison model {self.name}:\n{format_exc()}"
-            )
+            warn(f"Unhandled error in comparison model {self.name}:\n{format_exc()}")
 
         return success, buff
 
@@ -701,21 +677,15 @@ def run(self):
         else:
             self.sims = [MFSimulation.load(sim_ws=self.workspace)]
             self.buffs = [None]
-            assert (
-                len(self.xfail) == 1
-            ), "Invalid xfail: expected a single boolean"
-            assert (
-                len(self.ncpus) == 1
-            ), "Invalid ncpus: expected a single integer"
+            assert len(self.xfail) == 1, "Invalid xfail: expected a single boolean"
+            assert len(self.ncpus) == 1, "Invalid ncpus: expected a single integer"
 
         # run models/simulations
         for i, sim_or_model in enumerate(self.sims):
             tgts = self.targets
             workspace = get_workspace(sim_or_model)
             exe_path = (
-                Path(sim_or_model.exe_name)
-                if sim_or_model.exe_name
-                else tgts["mf6"]
+                Path(sim_or_model.exe_name) if sim_or_model.exe_name else tgts["mf6"]
             )
             target = (
                 exe_path
@@ -724,9 +694,7 @@ def run(self):
             )
             xfail = self.xfail[i]
             ncpus = self.ncpus[i]
-            success, buff = self._run_sim_or_model(
-                workspace, target, xfail, ncpus
-            )
+            success, buff = self._run_sim_or_model(workspace, target, xfail, ncpus)
             self.buffs[i] = buff  # store model output for assertions later
             assert success, (
                 f"{'Simulation' if 'mf6' in str(target) else 'Model'} "
@@ -736,9 +704,7 @@ def run(self):
         # setup and run comparison model(s), if enabled
         if self.compare:
             # get expected output files from main simulation
-            _, self.outp = get_mf6_files(
-                self.workspace / "mfsim.nam", self.verbose
-            )
+            _, self.outp = get_mf6_files(self.workspace / "mfsim.nam", self.verbose)
 
             # try to autodetect comparison type if enabled
             if self.compare == "auto":
@@ -774,9 +740,7 @@ def run(self):
                         workspace = self.workspace / self.compare
                         success, _ = self._run_sim_or_model(
                             workspace,
-                            self.targets.get(
-                                self.compare, self.targets["mf6"]
-                            ),
+                            self.targets.get(self.compare, self.targets["mf6"]),
                         )
                         assert success, f"Comparison model failed: {workspace}"
 

autotest/get_exes.py

@@ -41,13 +41,9 @@ def test_rebuild_release(rebuilt_bin_path: Path):
     print(f"Rebuilding and installing last release to: {rebuilt_bin_path}")
     release = get_release(repository)
     assets = release["assets"]
-    asset = next(
-        iter([a for a in assets if a["name"] == get_asset_name(a)]), None
-    )
+    asset = next(iter([a for a in assets if a["name"] == get_asset_name(a)]), None)
     if not asset:
-        warn(
-            f"Couldn't find asset for OS {get_ostag()}, available assets:\n{assets}"
-        )
+        warn(f"Couldn't find asset for OS {get_ostag()}, available assets:\n{assets}")
 
     with TemporaryDirectory() as td:
         # download the release
@@ -59,9 +55,7 @@ def test_rebuild_release(rebuilt_bin_path: Path):
         )
 
         # update IDEVELOPMODE
-        source_files_path = (
-            download_path / asset["name"].replace(".zip", "") / "src"
-        )
+        source_files_path = download_path / asset["name"].replace(".zip", "") / "src"
         version_file_path = source_files_path / "Utilities" / "version.f90"
         with open(version_file_path) as f:
             lines = f.read().splitlines()
@@ -89,9 +83,7 @@ def test_get_executables(downloaded_bin_path: Path):
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        "Get executables needed for MODFLOW 6 testing"
-    )
+    parser = argparse.ArgumentParser("Get executables needed for MODFLOW 6 testing")
     parser.add_argument("-p", "--path", help="path to top-level bin directory")
     args = parser.parse_args()
     bin_path = Path(args.path).resolve() if args.path else top_bin_path

autotest/test_chf_dfw.py

@@ -48,9 +48,7 @@ def build_models(idx, test):
         outer_dvclose=1.0e-7,
         inner_dvclose=1.0e-8,
     )
-    chf = flopy.mf6.ModflowChf(
-        sim, modelname=name, save_flows=True, print_flows=True
-    )
+    chf = flopy.mf6.ModflowChf(sim, modelname=name, save_flows=True, print_flows=True)
 
     dx = 1000.0
     nreach = 3

autotest/test_chf_dfw_beg2022.py

@@ -219,9 +219,7 @@ def make_plot(test, mfsim):
     x = df_mfswr["TOTTIME"] - 86400.0
     x = x / 60.0 / 60.0
     ax.plot(x, -df_mfswr["QCRFLOW"], "go:", mfc="none", label="MODFLOW-SWR")
-    ax.plot(
-        times / 60.0 / 60.0, qoutflow, "bo:", mfc="none", label="MODFLOW 6"
-    )
+    ax.plot(times / 60.0 / 60.0, qoutflow, "bo:", mfc="none", label="MODFLOW 6")
     ax.set_xlim(0, 24.0)
     ax.set_ylim(19, 26)
     plt.xlabel("time, in hours")

autotest/test_chf_dfw_bowl.py

@@ -250,10 +250,7 @@ def check_output(idx, test):
     for v in stage_all[-1].flatten():
         print(f"{v:18.8f},")
 
-    msg = (
-        "Simulated stage does not match with the answer "
-        "stored from a previous run."
-    )
+    msg = "Simulated stage does not match with the answer stored from a previous run."
     assert np.allclose(stage_all[-1].flatten(), stage_answer, atol=1.0e-5), msg
 
 

autotest/test_chf_dfw_loop.py

@@ -251,18 +251,10 @@ def build_models(idx, test):
     )
 
     xfraction = (
-        [0.0, 10.0, 20.0, 30.0]
-        + [0, 20.0, 40.0, 60.0]
-        + [0.0, 15.0, 30.0, 45.0]
-    )
-    height = (
-        [10.0, 0.0, 0.0, 10.0]
-        + [20.0, 0.0, 0.0, 20.0]
-        + [15.0, 0.0, 0.0, 15.0]
-    )
-    mannfraction = (
-        [1.0, 1.0, 1.0, 1.0] + [1.0, 1.0, 1.0, 1.0] + [1.0, 1.0, 1.0, 1.0]
+        [0.0, 10.0, 20.0, 30.0] + [0, 20.0, 40.0, 60.0] + [0.0, 15.0, 30.0, 45.0]
     )
+    height = [10.0, 0.0, 0.0, 10.0] + [20.0, 0.0, 0.0, 20.0] + [15.0, 0.0, 0.0, 15.0]
+    mannfraction = [1.0, 1.0, 1.0, 1.0] + [1.0, 1.0, 1.0, 1.0] + [1.0, 1.0, 1.0, 1.0]
 
     cxsdata = list(zip(xfraction, height, mannfraction))
     cxs = flopy.mf6.ModflowChfcxs(
@@ -398,12 +390,8 @@ def make_plot(test):
         lw=0.0,
         label="MF6 Gauge 5",
     )
-    ax.plot(
-        answer_flow["TOTIME"], answer_flow["FLOW45"], "b-", label="SWR Gauge 4"
-    )
-    ax.plot(
-        answer_flow["TOTIME"], answer_flow["FLOW56"], "g-", label="SWR Gauge 5"
-    )
+    ax.plot(answer_flow["TOTIME"], answer_flow["FLOW45"], "b-", label="SWR Gauge 4")
+    ax.plot(answer_flow["TOTIME"], answer_flow["FLOW56"], "g-", label="SWR Gauge 5")
     # ax.plot(obsvals["time"], answer["STAGE0000000014"], marker="o", mfc="none", mec="k", lw=0., label="swr")
     ax.set_xscale("log")
     plt.xlabel("time, in seconds")

autotest/test_chf_dis.py

@@ -170,21 +170,13 @@ def check_grb_disv1d(fpth):
     ), "grb botm not correct"
     cellx = np.linspace(dx / 2, nreach * dx - dx / 2, nreach)
     celly = np.zeros(nreach)
-    assert np.allclose(
-        grb._datadict["CELLX"], cellx.flatten()
-    ), "cellx is not right"
-    assert np.allclose(
-        grb._datadict["CELLY"], celly.flatten()
-    ), "celly is not right"
-    assert (
-        grb._datadict["IAVERT"].shape[0] == nodes + 1
-    ), "iavert size not right"
+    assert np.allclose(grb._datadict["CELLX"], cellx.flatten()), "cellx is not right"
+    assert np.allclose(grb._datadict["CELLY"], celly.flatten()), "celly is not right"
+    assert grb._datadict["IAVERT"].shape[0] == nodes + 1, "iavert size not right"
     assert (
         grb._datadict["IAVERT"][-1] - 1 == grb._datadict["JAVERT"].shape[0]
     ), "javert size not right"
-    assert (
-        grb.ia.shape[0] == grb.ncells + 1
-    ), "ia in grb file is not correct size"
+    assert grb.ia.shape[0] == grb.ncells + 1, "ia in grb file is not correct size"
     assert grb.ja.shape[0] == grb.nja, "ja in grb file is not corect size"
     assert np.allclose(
         grb.idomain.reshape((nodes,)), idomain.reshape((nodes,))