[black-command] fixes

conftest.py

@@ -30,16 +30,23 @@ def pytest_addoption(parser):
     Lets options be passed to test functions.
     """
     parser.addoption(
-        "--with-answer-testing", action="store_true", default=False,
+        "--with-answer-testing",
+        action="store_true",
+        default=False,
     )
     parser.addoption(
-        "--answer-store", action="store_true", default=False,
+        "--answer-store",
+        action="store_true",
+        default=False,
     )
     parser.addoption(
-        "--answer-big-data", action="store_true", default=False,
+        "--answer-big-data",
+        action="store_true",
+        default=False,
     )
     parser.addoption(
-        "--save-answer-arrays", action="store_true",
+        "--save-answer-arrays",
+        action="store_true",
     )
 
 

doc/source/cookbook/multiplot_phaseplot.py

@@ -23,7 +23,15 @@
     # Load the data and create a single plot
     ds = yt.load("enzo_tiny_cosmology/DD00%2d/DD00%2d" % (SnapNum, SnapNum))
     ad = ds.all_data()
-    p = yt.PhasePlot(ad, "density", "temperature", ["cell_mass",], weight_field=None)
+    p = yt.PhasePlot(
+        ad,
+        "density",
+        "temperature",
+        [
+            "cell_mass",
+        ],
+        weight_field=None,
+    )
 
     # Ensure the axes and colorbar limits match for all plots
     p.set_xlim(1.0e-32, 8.0e-26)

doc/source/cookbook/particle_filter_sfr.py

@@ -23,7 +23,11 @@ def formed_star(pfilter, data):
 
 time_range = [0, 5e8]  # years
 n_bins = 1000
-hist, bins = np.histogram(formation_time, bins=n_bins, range=time_range,)
+hist, bins = np.histogram(
+    formation_time,
+    bins=n_bins,
+    range=time_range,
+)
 inds = np.digitize(formation_time, bins=bins)
 time = (bins[:-1] + bins[1:]) / 2
 

setup.py

@@ -112,7 +112,9 @@
         ],
         keywords="astronomy astrophysics visualization " + "amr adaptivemeshrefinement",
         entry_points={
-            "console_scripts": ["yt = yt.utilities.command_line:run_main",],
+            "console_scripts": [
+                "yt = yt.utilities.command_line:run_main",
+            ],
             "nose.plugins.0.10": [
                 "answer-testing = yt.utilities.answer_testing.framework:AnswerTesting"
             ],

yt/data_objects/construction_data_containers.py

@@ -685,7 +685,11 @@ def to_xarray(self, fields=None):
         coords = {}
         for f in fields or self.field_data.keys():
             data[f] = {
-                "dims": ("x", "y", "z",),
+                "dims": (
+                    "x",
+                    "y",
+                    "z",
+                ),
                 "data": self[f],
                 "attrs": {"units": str(self[f].uq)},
             }

yt/data_objects/data_containers.py

@@ -713,74 +713,74 @@ def create_firefly_object(
         dataset_name="yt",
     ):
         r"""This function links a region of data stored in a yt dataset
-            to the Python frontend API for [Firefly](github.com/ageller/Firefly),
-            a browser-based particle visualization platform.
-
-            Parameters
-            ----------
-            path_to_firefly : string
-                The (ideally) absolute path to the direction containing the index.html
-                file of Firefly.
-
-            fields_to_include : array_like of strings
-                A list of fields that you want to include in your
-                Firefly visualization for on-the-fly filtering and
-                colormapping.
-
-            default_decimation_factor : integer
-                The factor by which you want to decimate each particle group
-                by (e.g. if there are 1e7 total particles in your simulation
-                you might want to set this to 100 at first). Randomly samples
-                your data like `shuffled_data[::decimation_factor]` so as to
-                not overtax a system. This is adjustable on a per particle group
-                basis by changing the returned reader's
-                `reader.particleGroup[i].decimation_factor` before calling
-                `reader.dumpToJSON()`.
-
-            velocity_units : string
-                The units that the velocity should be converted to in order to
-                show streamlines in Firefly. Defaults to km/s.
-
-            coordinate_units: string
-                The units that the coordinates should be converted to. Defaults to
-                kpc.
-
-            show_unused_fields: boolean
-                A flag to optionally print the fields that are available, in the
-                dataset but were not explicitly requested to be tracked.
-
-            dataset_name: string
-                The name of the subdirectory the JSON files will be stored in
-                (and the name that will appear in startup.json and in the dropdown
-                menu at startup). e.g. `yt` -> json files will appear in
-                `Firefly/data/yt`.
-
-            Returns
-            -------
-            reader : firefly_api.reader.Reader object
-                A reader object from the firefly_api, configured
-                to output
-
-            Examples
-            --------
-
-                >>> ramses_ds = yt.load(
-                ...     "/Users/agurvich/Desktop/yt_workshop/"+
-                ...     "DICEGalaxyDisk_nonCosmological/output_00002/info_00002.txt")
-
-                >>> region = ramses_ds.sphere(ramses_ds.domain_center,(1000,'kpc'))
-
-                >>> reader = region.create_firefly_object(
-                ...     path_to_firefly="/Users/agurvich/research/repos/Firefly",
-                ...     fields_to_include=[
-                ...     'particle_extra_field_1',
-                ...     'particle_extra_field_2'],
-                ...     fields_units = ['dimensionless','dimensionless'],
-                ...     dataset_name = 'IsoGalaxyRamses')
-
-                >>> reader.options['color']['io']=[1,1,0,1]
-                >>> reader.particleGroups[0].decimation_factor=100
-                >>> reader.dumpToJSON()
+        to the Python frontend API for [Firefly](github.com/ageller/Firefly),
+        a browser-based particle visualization platform.
+
+        Parameters
+        ----------
+        path_to_firefly : string
+            The (ideally) absolute path to the direction containing the index.html
+            file of Firefly.
+
+        fields_to_include : array_like of strings
+            A list of fields that you want to include in your
+            Firefly visualization for on-the-fly filtering and
+            colormapping.
+
+        default_decimation_factor : integer
+            The factor by which you want to decimate each particle group
+            by (e.g. if there are 1e7 total particles in your simulation
+            you might want to set this to 100 at first). Randomly samples
+            your data like `shuffled_data[::decimation_factor]` so as to
+            not overtax a system. This is adjustable on a per particle group
+            basis by changing the returned reader's
+            `reader.particleGroup[i].decimation_factor` before calling
+            `reader.dumpToJSON()`.
+
+        velocity_units : string
+            The units that the velocity should be converted to in order to
+            show streamlines in Firefly. Defaults to km/s.
+
+        coordinate_units: string
+            The units that the coordinates should be converted to. Defaults to
+            kpc.
+
+        show_unused_fields: boolean
+            A flag to optionally print the fields that are available, in the
+            dataset but were not explicitly requested to be tracked.
+
+        dataset_name: string
+            The name of the subdirectory the JSON files will be stored in
+            (and the name that will appear in startup.json and in the dropdown
+            menu at startup). e.g. `yt` -> json files will appear in
+            `Firefly/data/yt`.
+
+        Returns
+        -------
+        reader : firefly_api.reader.Reader object
+            A reader object from the firefly_api, configured
+            to output
+
+        Examples
+        --------
+
+            >>> ramses_ds = yt.load(
+            ...     "/Users/agurvich/Desktop/yt_workshop/"+
+            ...     "DICEGalaxyDisk_nonCosmological/output_00002/info_00002.txt")
+
+            >>> region = ramses_ds.sphere(ramses_ds.domain_center,(1000,'kpc'))
+
+            >>> reader = region.create_firefly_object(
+            ...     path_to_firefly="/Users/agurvich/research/repos/Firefly",
+            ...     fields_to_include=[
+            ...     'particle_extra_field_1',
+            ...     'particle_extra_field_2'],
+            ...     fields_units = ['dimensionless','dimensionless'],
+            ...     dataset_name = 'IsoGalaxyRamses')
+
+            >>> reader.options['color']['io']=[1,1,0,1]
+            >>> reader.particleGroups[0].decimation_factor=100
+            >>> reader.dumpToJSON()
         """
 
         ## attempt to import firefly_api

yt/data_objects/static_output.py

@@ -1505,7 +1505,8 @@ def add_field(self, name, function, sampling_type, **kwargs):
         # Handle the case where the field has already been added.
         if not override and name in self.field_info:
             mylog.warning(
-                "Field %s already exists. To override use `force_override=True`.", name,
+                "Field %s already exists. To override use `force_override=True`.",
+                name,
             )
 
         self.field_info.add_field(name, function, sampling_type, **kwargs)

yt/fields/field_functions.py

@@ -20,7 +20,9 @@ def get_radius(data, field_prefix, ftype):
         # This will coerce the units, so we don't need to worry that we copied
         # it from a cm**2 array.
         np.subtract(
-            data[ftype, f"{field_prefix}{ax}"].in_base(unit_system.name), center[i], r,
+            data[ftype, f"{field_prefix}{ax}"].in_base(unit_system.name),
+            center[i],
+            r,
         )
         if data.ds.periodicity[i]:
             np.abs(r, r)

yt/fields/field_info_container.py

@@ -168,8 +168,18 @@ def setup_smoothed_fields(self, ptype, num_neighbors=64, ftype="gas"):
                 uni_alias_name = alias_name.replace("particle_position_", "")
             elif "particle_" in alias_name:
                 uni_alias_name = alias_name.replace("particle_", "")
-            new_aliases.append(((ftype, uni_alias_name), (ptype, alias_name),))
-            new_aliases.append(((ptype, uni_alias_name), (ptype, alias_name),))
+            new_aliases.append(
+                (
+                    (ftype, uni_alias_name),
+                    (ptype, alias_name),
+                )
+            )
+            new_aliases.append(
+                (
+                    (ptype, uni_alias_name),
+                    (ptype, alias_name),
+                )
+            )
             for alias, source in new_aliases:
                 self.alias(alias, source)
 

yt/fields/local_fields.py

@@ -23,7 +23,8 @@ def add_field(self, name, function, sampling_type, **kwargs):
         # Handle the case where the field has already been added.
         if not override and name in self:
             mylog.warning(
-                "Field %s already exists. To override use `force_override=True`.", name,
+                "Field %s already exists. To override use `force_override=True`.",
+                name,
             )
 
         return super(LocalFieldInfoContainer, self).add_field(

yt/fields/tests/test_sph_fields.py

@@ -20,7 +20,10 @@
 
 load_kwargs = defaultdict(dict)
 load_kwargs.update(
-    {isothermal_h5: iso_kwargs, isothermal_bin: iso_kwargs,}
+    {
+        isothermal_h5: iso_kwargs,
+        isothermal_bin: iso_kwargs,
+    }
 )
 
 gas_fields_to_particle_fields = {

yt/frontends/adaptahop/data_structures.py

@@ -39,7 +39,13 @@ def _setup_filenames(self):
             ]
         else:
             self.data_files = [
-                cls(self.dataset, self.io, self.dataset.parameter_filename, 0, None,)
+                cls(
+                    self.dataset,
+                    self.io,
+                    self.dataset.parameter_filename,
+                    0,
+                    None,
+                )
             ]
 
 

yt/frontends/art/data_structures.py

@@ -882,10 +882,10 @@ def _count_art_octs(self, f, offset, MinLev, MaxLevelNow):
 
     def _read_amr_level(self, oct_handler):
         """Open the oct file, read in octs level-by-level.
-           For each oct, only the position, index, level and domain
-           are needed - its position in the octree is found automatically.
-           The most important is finding all the information to feed
-           oct_handler.add
+        For each oct, only the position, index, level and domain
+        are needed - its position in the octree is found automatically.
+        The most important is finding all the information to feed
+        oct_handler.add
         """
         self.level_offsets
         f = open(self.ds._file_amr, "rb")

yt/frontends/art/io.py

@@ -280,7 +280,14 @@ def _yield_coordinates(self, data_file):
 
 def _determine_field_size(pf, field, lspecies, ptmax):
     pbool = np.zeros(len(lspecies), dtype="bool")
-    idxas = np.concatenate(([0,], lspecies[:-1]))
+    idxas = np.concatenate(
+        (
+            [
+                0,
+            ],
+            lspecies[:-1],
+        )
+    )
     idxbs = lspecies
     if "specie" in field:
         index = int(field.replace("specie", ""))

yt/frontends/athena_pp/data_structures.py

@@ -318,7 +318,8 @@ def _parse_parameter_file(self):
         self._field_map = {}
         k = 0
         for dname, num_var in zip(
-            self._handle.attrs["DatasetNames"], self._handle.attrs["NumVariables"],
+            self._handle.attrs["DatasetNames"],
+            self._handle.attrs["NumVariables"],
         ):
             for j in range(num_var):
                 fname = self._handle.attrs["VariableNames"][k].decode("ascii", "ignore")

yt/frontends/boxlib/data_structures.py

@@ -552,9 +552,7 @@ def _initialize_grid_arrays(self):
         self.grid_start_index = np.zeros((self.num_grids, 3), "int64")
 
     def _initialize_state_variables(self):
-        """override to not re-initialize num_grids in AMRHierarchy.__init__
-
-        """
+        """override to not re-initialize num_grids in AMRHierarchy.__init__"""
         self._parallel_locking = False
         self._data_file = None
         self._data_mode = None
@@ -995,9 +993,7 @@ def _read_particles(self):
             self._read_particle_file(self.particle_filename)
 
     def _read_particle_file(self, fn):
-        """actually reads the orion particle data file itself.
-
-        """
+        """actually reads the orion particle data file itself."""
         if not os.path.exists(fn):
             return
         with open(fn, "r") as f:

yt/frontends/eagle/fields.py

@@ -133,8 +133,7 @@ def __init__(self, ds, field_list, slice_info=None):
         )
 
     def _create_ion_density_func(self, ftype, ion):
-        """ returns a function that calculates the ion density of a particle.
-        """
+        """returns a function that calculates the ion density of a particle."""
 
         def _ion_density(field, data):