chore: reformat Python code with line length = 88 (#57)

Reformat Python code with a maximum line length of 88 characters to better represent the code. See modflowpy/flopy#2362 for a related PR with rational and discussion. Also change some of Ruff's configuration: - Remove target-version, since it was outdated and is automatically evaluated from pyproject.toml - Remove include so that Ruff will work globally in this repo - Remove extend-include since "*.ipynb" files are already included by default
MODFLOW-USGS · Nov 20, 2024 · 4cee570 · 4cee570
1 parent 7fb6b67
commit 4cee570
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Showing 13 changed files with 35 additions and 116 deletions.
diff --git a/autotest/conftest.py b/autotest/conftest.py
@@ -49,10 +49,7 @@ def pytest_generate_tests(metafunc):
     #   - ex-gwtgwt-mt3dms-p10: https://github.com/MODFLOW-USGS/modflow6/pull/1008
     option_value = metafunc.config.option.mf6_examples_path
     t = metafunc.fixturenames
-    if (
-        "mf6_example_namfiles" in metafunc.fixturenames
-        and option_value is not None
-    ):
+    if "mf6_example_namfiles" in metafunc.fixturenames and option_value is not None:
         mf6_examples_path = Path(option_value)
         global __mf6_examples
         __mf6_examples = str(mf6_examples_path.name)
@@ -97,9 +94,7 @@ def simulation_name_from_model_path(p):
             model_namfiles = list(model_namfiles)
             if len(model_namfiles) > 1:
                 # trap gwf models as first set of models
-                idxs = [
-                    ix for ix, _ in enumerate(model_namfiles) if "gwf" in _
-                ]
+                idxs = [ix for ix, _ in enumerate(model_namfiles) if "gwf" in _]
                 if len(idxs) > 0:
                     for ix in idxs[::-1]:
                         models.append(model_namfiles.pop(ix))
@@ -125,6 +120,4 @@ def simulation_name_from_model_namfiles(mnams):
                 namfile.parent.parent if is_nested(namfile) else namfile.parent
             ).name
 
-        metafunc.parametrize(
-            key, simulations, ids=simulation_name_from_model_namfiles
-        )
+        metafunc.parametrize(key, simulations, ids=simulation_name_from_model_namfiles)
diff --git a/autotest/test_interface.py b/autotest/test_interface.py
@@ -98,9 +98,7 @@ def callback(sim, step):
 
             rch = model.rch
             if len(rch) != 2:
-                raise AssertionError(
-                    "ApiModel object not returning multiple packages"
-                )
+                raise AssertionError("ApiModel object not returning multiple packages")
 
             idomain = dis.idomain.values
             if not isinstance(idomain, np.ndarray):
@@ -193,9 +191,7 @@ def callback(sim, step):
 
             chd = model.chd
             if len(chd) != 2:
-                raise AssertionError(
-                    "ApiModel object not returning multiple packages"
-                )
+                raise AssertionError("ApiModel object not returning multiple packages")
 
             top = dis.top.values
             if not isinstance(top, np.ndarray):
@@ -347,9 +343,7 @@ def callback(sim, step):
         if step == Callbacks.timestep_start:
             if sim.kstp == 1:
                 if delt0 == sim.delt:
-                    raise AssertionError(
-                        "ATS routines not reducing timestep length"
-                    )
+                    raise AssertionError("ATS routines not reducing timestep length")
 
         name = "ats0"
         sim_pth = data_pth / name

diff --git a/autotest/test_mf6_examples.py b/autotest/test_mf6_examples.py
@@ -46,9 +46,7 @@ def run_models():
             # (e.g. 'mf6gwf') because coupled models refer to each other with
             # relative paths
             wrkdir = (
-                Path(function_tmpdir / model_path.name)
-                if nested
-                else function_tmpdir
+                Path(function_tmpdir / model_path.name) if nested else function_tmpdir
             )
             try:
                 run_simulation(dll, wrkdir, callback, verbose=True)

diff --git a/examples/notebooks/Head_Monitor_Example.ipynb b/examples/notebooks/Head_Monitor_Example.ipynb
@@ -104,9 +104,7 @@
     "        fig, ax = plt.subplots(figsize=(8, 8))\n",
     "        self.fig = fig\n",
     "        self.ax = ax\n",
-    "        self.pmv = PlotMapView(\n",
-    "            modelgrid=self.modelgrid, ax=ax, layer=self.layer\n",
-    "        )\n",
+    "        self.pmv = PlotMapView(modelgrid=self.modelgrid, ax=ax, layer=self.layer)\n",
     "        grid = self.pmv.plot_grid()\n",
     "        idm = self.pmv.plot_inactive()\n",
     "        initial = np.full(self.modelgrid.shape, np.nan)\n",

diff --git a/examples/notebooks/MODFLOW-API_extensions_objects.ipynb b/examples/notebooks/MODFLOW-API_extensions_objects.ipynb
@@ -778,9 +778,7 @@
     "            spd[\"recharge\"] += 0.40 * sim.kper\n",
     "\n",
     "    if callback_step == Callbacks.timestep_start:\n",
-    "        print(\n",
-    "            f\"updating wel flux: stress_period={ml.kper}, timestep={ml.kstp}\"\n",
-    "        )\n",
+    "        print(f\"updating wel flux: stress_period={ml.kper}, timestep={ml.kstp}\")\n",
     "        ml.wel.stress_period_data[\"q\"] -= ml.kstp * 1.5\n",
     "\n",
     "    if callback_step == Callbacks.iteration_start:\n",

diff --git a/examples/notebooks/Quickstart.ipynb b/examples/notebooks/Quickstart.ipynb
@@ -97,9 +97,7 @@
     "            spd[\"recharge\"] += 0.40 * sim.kper\n",
     "\n",
     "    if callback_step == Callbacks.timestep_start:\n",
-    "        print(\n",
-    "            f\"updating wel flux: stress_period={ml.kper}, timestep={ml.kstp}\"\n",
-    "        )\n",
+    "        print(f\"updating wel flux: stress_period={ml.kper}, timestep={ml.kstp}\")\n",
     "        ml.wel.stress_period_data[\"q\"] -= ml.kstp * 1.5\n",
     "\n",
     "    if callback_step == Callbacks.iteration_start:\n",

diff --git a/modflowapi/extensions/apimodel.py b/modflowapi/extensions/apimodel.py
@@ -100,9 +100,7 @@ def _create_package_list(self):
             package = package(basepackage, self, pkg_type, adj_pkg_name)
             self.package_dict[pkg_name.lower()] = package
 
-    def get_package(
-        self, pkg_name
-    ) -> ListPackage or ArrayPackage or AdvancedPackage:
+    def get_package(self, pkg_name) -> ListPackage or ArrayPackage or AdvancedPackage:
         """
         Method to get a package
 
@@ -115,9 +113,7 @@ def get_package(
         if pkg_name in self.package_dict:
             return self.package_dict[pkg_name]
 
-        raise KeyError(
-            f"{pkg_name} is not a valid package name for this model"
-        )
+        raise KeyError(f"{pkg_name} is not a valid package name for this model")
 
 
 class ApiModel(ApiMbase):
@@ -148,9 +144,7 @@ def __init__(self, mf6, name):
             self.dis_type = "disu"
             self.dis_name = "DIS"
         else:
-            raise AssertionError(
-                f"Unrecognized discretization type {grid_type}"
-            )
+            raise AssertionError(f"Unrecognized discretization type {grid_type}")
 
         pkg_types = {
             "dis": ArrayPackage,
@@ -192,10 +186,7 @@ def __repr__(self):
         s = f"{self.name}, "
         shape = self.shape
         if self.dis_type == "dis":
-            s += (
-                f"{shape[0]} Layer, {shape[1]} Row, {shape[2]} "
-                f"Column model\n"
-            )
+            s += f"{shape[0]} Layer, {shape[1]} Row, {shape[2]} Column model\n"
 
         elif self.dis_type == "disu":
             if len(shape) == 2:
@@ -319,9 +310,7 @@ def shape(self):
                 if var_addr in ivn:
                     shape.append(self.mf6.get_value(var_addr)[0])
             if not shape:
-                var_addr = self.mf6.get_var_address(
-                    "NODES", self.name, self.dis_name
-                )
+                var_addr = self.mf6.get_var_address("NODES", self.name, self.dis_name)
                 shape.append(self.mf6.get_value(var_addr)[0])
             self._shape = tuple(shape)
         return self._shape

diff --git a/modflowapi/extensions/apisimulation.py b/modflowapi/extensions/apisimulation.py
@@ -221,9 +221,7 @@ def get_model(self, model_id=None):
             model name (ex. "GWF_1") or subcomponent id (ex. 1)
         """
         if model_id is None:
-            model_id = int(
-                min([model.subcomponent_id for model in self.models])
-            )
+            model_id = int(min([model.subcomponent_id for model in self.models]))
 
         if isinstance(model_id, int):
             for model in self.models:
@@ -329,9 +327,7 @@ def load(mf6):
 
         # TDIS package construction
         tdis_constructor = package_factory("tdis", ScalarPackage)
-        tdis = tdis_constructor(
-            ScalarPackage, tmpmdl, "tdis", "tdis", sim_package=True
-        )
+        tdis = tdis_constructor(ScalarPackage, tmpmdl, "tdis", "tdis", sim_package=True)
 
         ats = None
         # ATS package construction
@@ -346,9 +342,7 @@ def load(mf6):
         # get the exchanges
         exchange_names = []
         for variable in variables:
-            if variable.startswith("GWF-GWF") or variable.startswith(
-                "GWT-GWT"
-            ):
+            if variable.startswith("GWF-GWF") or variable.startswith("GWT-GWT"):
                 exchange_name = variable.split("/")[0]
                 if exchange_name not in exchange_names:
                     exchange_names.append(exchange_name)

diff --git a/modflowapi/extensions/data.py b/modflowapi/extensions/data.py
@@ -237,27 +237,19 @@ def _recarray_to_ptr(self, recarray):
 
         for name in recarray.dtype.names:
             if name in self._nodevars:
-                multi_index = tuple(
-                    np.array([list(i) for i in recarray[name]]).T
-                )
-                nodes = np.ravel_multi_index(
-                    multi_index, self.parent.model.shape
-                )
+                multi_index = tuple(np.array([list(i) for i in recarray[name]]).T)
+                nodes = np.ravel_multi_index(multi_index, self.parent.model.shape)
                 recarray[name] = self.parent.model.usertonode[nodes] + 1
 
             if name in self.parent._bound_vars:
                 if "bound" in self._ptrs:
                     # Block slated for deprecation after IDM inclusion
                     idx = self.parent._bound_vars.index(name)
                     bname = "bound"
-                    self._ptrs[bname][0 : self._nbound[0], idx] = recarray[
-                        name
-                    ]
+                    self._ptrs[bname][0 : self._nbound[0], idx] = recarray[name]
                 elif self.parent._idm_enabled:
                     # new IDM simplification
-                    self._ptrs[name][0 : self._nbound[0]] = recarray[
-                        name
-                    ].ravel()
+                    self._ptrs[name][0 : self._nbound[0]] = recarray[name].ravel()
                 else:
                     pass
             elif name in self._auxnames:
@@ -569,9 +561,7 @@ def set_array(self, item, array):
         if item in self._ptrs:
             self._ptrs[item].values = array
         else:
-            raise KeyError(
-                f"{item} is not a valid variable name for this package"
-            )
+            raise KeyError(f"{item} is not a valid variable name for this package")
 
 
 class AdvancedInput(object):
@@ -631,13 +621,9 @@ def get_variable(self, name, model=None, package=None):
                 )
         else:
             if self.parent is not None:
-                var_addr = self.mf6.get_var_address(
-                    name.upper(), self.parent.pkg_name
-                )
+                var_addr = self.mf6.get_var_address(name.upper(), self.parent.pkg_name)
             else:
-                var_addr = self.mf6.get_var_address(
-                    name.upper(), package.upper()
-                )
+                var_addr = self.mf6.get_var_address(name.upper(), package.upper())
 
         try:
             values = self.mf6.get_value_ptr(var_addr)

diff --git a/modflowapi/extensions/pakbase.py b/modflowapi/extensions/pakbase.py
@@ -258,9 +258,7 @@ def __init__(self, model, pkg_type, pkg_name, child_type, sim_package):
 
                 if sim_package:
                     var_addrs.append(
-                        self.model.mf6.get_var_address(
-                            var.upper(), self.pkg_name
-                        )
+                        self.model.mf6.get_var_address(var.upper(), self.pkg_name)
                     )
                 else:
                     var_addrs.append(
@@ -335,8 +333,7 @@ def get_advanced_var(self, name):
         name = name.lower()
         if name not in self.advanced_vars:
             raise AssertionError(
-                f"{name} is not accessible as an advanced "
-                f"variable for this package"
+                f"{name} is not accessible as an advanced variable for this package"
             )
 
         values = self._variables_adv.get_variable(name)
@@ -432,9 +429,7 @@ class ListPackage(PackageBase):
     """
 
     def __init__(self, model, pkg_type, pkg_name, sim_package=False):
-        super().__init__(
-            model, pkg_type, pkg_name.upper(), "list", sim_package
-        )
+        super().__init__(model, pkg_type, pkg_name.upper(), "list", sim_package)
 
         self._variables = ListInput(self)
 
@@ -497,9 +492,7 @@ class ArrayPackage(PackageBase):
     """
 
     def __init__(self, model, pkg_type, pkg_name, sim_package=False):
-        super().__init__(
-            model, pkg_type, pkg_name.upper(), "array", sim_package
-        )
+        super().__init__(model, pkg_type, pkg_name.upper(), "array", sim_package)
 
         self._variables = ArrayInput(self)
 
@@ -595,9 +588,7 @@ class ScalarPackage(PackageBase):
     """
 
     def __init__(self, model, pkg_type, pkg_name, sim_package=False):
-        super().__init__(
-            model, pkg_type, pkg_name.upper(), "scalar", sim_package
-        )
+        super().__init__(model, pkg_type, pkg_name.upper(), "scalar", sim_package)
 
         self._variables = ScalarInput(self)
 
@@ -697,9 +688,7 @@ class AdvancedPackage(PackageBase):
     """
 
     def __init__(self, model, pkg_type, pkg_name, sim_package=False):
-        super().__init__(
-            model, pkg_type, pkg_name.upper(), "advanced", sim_package
-        )
+        super().__init__(model, pkg_type, pkg_name.upper(), "advanced", sim_package)
 
     def __repr__(self):
         s = f"{self.pkg_type.upper()} Package: {self.pkg_name} \n"

diff --git a/modflowapi/extensions/runner.py b/modflowapi/extensions/runner.py
@@ -64,10 +64,7 @@ def run_simulation(dll, sim_path, callback, verbose=False, _develop=False):
         mf6.prepare_time_step(dt)
 
         if verbose:
-            print(
-                f"Solving: Stress Period {sim.kper + 1}; "
-                f"Timestep {sim.kstp + 1}"
-            )
+            print(f"Solving: Stress Period {sim.kper + 1}; Timestep {sim.kstp + 1}")
 
         for sol_id, slnobj in sorted(sim.solutions.items()):
             models = {}

diff --git a/pyproject.toml b/pyproject.toml
@@ -70,18 +70,7 @@ version = {attr = "modflowapi.version.__version__"}
 include = ["modflowapi", "modflowapi.*"]
 
 [tool.ruff]
-target-version = "py38"
-line-length = 79
-include = [
-    "pyproject.toml",
-    "modflowapi/**/*.py",
-    "autotest/**/*.py",
-    "examples/**/*.py",
-    "scripts/**/*.py",
-]
-extend-include = [
-    "examples/**/*.ipynb"
-]
+line-length = 88
 
 [tool.ruff.lint]
 select = ["F", "E", "I001"]

diff --git a/scripts/update_version.py b/scripts/update_version.py
@@ -33,9 +33,7 @@ def update_version_py(timestamp: datetime, version: Version):
             f"# {_project_name} version file automatically "
             + f"created using...{basename(__file__)}\n"
         )
-        f.write(
-            "# created on..." + f"{timestamp.strftime('%B %d, %Y %H:%M:%S')}\n"
-        )
+        f.write(f"# created on...{timestamp.strftime('%B %d, %Y %H:%M:%S')}\n")
         f.write(f'__version__ = "{version}"\n')
     log_update(_version_py_path, version)
 
@@ -109,7 +107,5 @@ def update_version(
     else:
         update_version(
             timestamp=datetime.now(),
-            version=(
-                Version(args.version) if args.version else _current_version
-            ),
+            version=(Version(args.version) if args.version else _current_version),
         )