Update black requirement from <=23.0,>=19.10b0 to >=19.10b0,<=24.8.0 …

…in the pip group across 1 directory (#291) * Update black requirement in the pip group across 1 directory Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. Updates `black` to 24.8.0 - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@19.10b0...24.8.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development dependency-group: pip ... Signed-off-by: dependabot[bot] <[email protected]> * fix lint error --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Ruge Li <[email protected]>
mesoscope · Oct 7, 2024 · 2ebc6ed · 2ebc6ed
1 parent bd9d6e1
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Showing 13 changed files with 47 additions and 44 deletions.
diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py
@@ -755,7 +755,10 @@ def add_ingredient_positions_to_plot(
                 )
                 # plot the sphere
                 if ingr.use_rbsphere:
-                    (ext_recipe, pts,) = ingr.getInterpolatedSphere(
+                    (
+                        ext_recipe,
+                        pts,
+                    ) = ingr.getInterpolatedSphere(
                         seed_ingredient_positions[-i - 1],
                         seed_ingredient_positions[-i],
                     )
@@ -857,9 +860,9 @@ def update_pairwise_distances(
                 ingr.name,
                 ingr2.name,
             ):
-                pairwise_distance_dict[seed_index][
-                    f"{ingr.name}_{ingr2.name}"
-                ] = self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
+                pairwise_distance_dict[seed_index][f"{ingr.name}_{ingr2.name}"] = (
+                    self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
+                )
 
         return pairwise_distance_dict
 

diff --git a/cellpack/autopack/DBRecipeHandler.py b/cellpack/autopack/DBRecipeHandler.py
@@ -201,13 +201,13 @@ def resolve_local_regions(self, local_data, recipe_data, db):
                 if not DataDoc.is_key(key_or_dict):
                     obj_item = local_data["regions"][region_name][index]["object"]
                     if DataDoc.is_key(obj_item):
-                        local_data["regions"][region_name][index][
-                            "object"
-                        ] = prep_recipe_data["objects"][obj_item]
+                        local_data["regions"][region_name][index]["object"] = (
+                            prep_recipe_data["objects"][obj_item]
+                        )
                     else:
-                        local_data["regions"][region_name][index][
-                            "object"
-                        ] = prep_recipe_data["objects"][obj_item["name"]]
+                        local_data["regions"][region_name][index]["object"] = (
+                            prep_recipe_data["objects"][obj_item["name"]]
+                        )
                     # replace reference in obj with actual data
                     obj_data = local_data["regions"][region_name][index]["object"]
                     self.resolve_object_data(obj_data, prep_recipe_data)
@@ -362,9 +362,9 @@ def convert_representation(doc, db):
                 and doc_value["packing"] is not None
             ):
                 position_value = doc_value["packing"]["positions"]
-                convert_doc["representations"]["packing"][
-                    "positions"
-                ] = ObjectDoc.convert_positions_in_representation(position_value)
+                convert_doc["representations"]["packing"]["positions"] = (
+                    ObjectDoc.convert_positions_in_representation(position_value)
+                )
         return convert_doc
 
     @staticmethod

diff --git a/cellpack/autopack/Environment.py b/cellpack/autopack/Environment.py
@@ -628,10 +628,10 @@ def resolve_gradient_data_objects(self, gradient_data):
         """
         # TODO: check if other modes need to be resolved
         if gradient_data["mode"] == "surface":
-            gradient_data["mode_settings"][
-                "object"
-            ] = self.get_compartment_object_by_name(
-                gradient_data["mode_settings"]["object"]
+            gradient_data["mode_settings"]["object"] = (
+                self.get_compartment_object_by_name(
+                    gradient_data["mode_settings"]["object"]
+                )
             )
         return gradient_data
 
@@ -2567,9 +2567,9 @@ def store_asJson(self, resultfilename=None, indent=True):
         if r:
             self.result_json["exteriorRecipe"] = OrderedDict()
             for ingr in r.ingredients:
-                self.result_json["exteriorRecipe"][
-                    ingr.composition_name
-                ] = self.dropOneIngrJson(ingr, self.result_json["exteriorRecipe"])
+                self.result_json["exteriorRecipe"][ingr.composition_name] = (
+                    self.dropOneIngrJson(ingr, self.result_json["exteriorRecipe"])
+                )
 
         # compartment ingr
         for orga in self.compartments:

diff --git a/cellpack/autopack/GeometryTools.py b/cellpack/autopack/GeometryTools.py
@@ -165,12 +165,7 @@ def region_2_integrand(self, theta, rho, d):
 
     def region_2(self, rho, d):
         # require scipy
-        i4 = (
-            d**3
-            / 6.0
-            * (rho**2 / d**2 - 1)
-            * (pi / 4 - self.region_1_2_theta(rho, d))
-        )
+        i4 = d**3 / 6.0 * (rho**2 / d**2 - 1) * (pi / 4 - self.region_1_2_theta(rho, d))
         i3 = (
             d**2
             * rho

diff --git a/cellpack/autopack/Graphics.py b/cellpack/autopack/Graphics.py
@@ -1523,9 +1523,9 @@ def displayCompartmentsIngredients(self):
                         elif self.vi.host == "dejavu":
                             self.orgaToMasterGeom[ingr] = ingr.mesh
                         elif self.vi.host == "softimage":
-                            self.orgaToMasterGeom[
-                                ingr
-                            ] = ingr.mesh  # self.getMasterInstance(polygon)
+                            self.orgaToMasterGeom[ingr] = (
+                                ingr.mesh
+                            )  # self.getMasterInstance(polygon)
                             # polygon already an instance from a different object\
 
                     j += 1

diff --git a/cellpack/autopack/ingredient/single_cube.py b/cellpack/autopack/ingredient/single_cube.py
@@ -366,9 +366,7 @@ def cube_surface_distance(
                     current_distance = numpy.sqrt(dist_x**2 + dist_y**2)
                 else:
                     # vertex is the closest
-                    current_distance = numpy.sqrt(
-                        dist_x**2 + dist_y**2 + dist_z**2
-                    )
+                    current_distance = numpy.sqrt(dist_x**2 + dist_y**2 + dist_z**2)
         return current_distance
 
     def get_signed_distance(

diff --git a/cellpack/autopack/ingredient/single_sphere.py b/cellpack/autopack/ingredient/single_sphere.py
@@ -188,7 +188,10 @@ def collision_jitter(
                 distance_to_packing_location - radius_of_ing_being_packed
             )
 
-            (insidePoints, newDistPoints,) = self.get_new_distances_and_inside_points(
+            (
+                insidePoints,
+                newDistPoints,
+            ) = self.get_new_distances_and_inside_points(
                 env,
                 jtrans,
                 rotMat,

diff --git a/cellpack/autopack/interface_objects/partners.py b/cellpack/autopack/interface_objects/partners.py
@@ -60,9 +60,11 @@ def __init__(self, partners):
                 partner["name"],
                 partner["position"] if "position" in partner else [0, 0, 0],
                 partner["weight"] if "weight" in partner else weight,
-                partner["binding_probability"]
-                if "binding_probability" in partner
-                else 1.0,
+                (
+                    partner["binding_probability"]
+                    if "binding_probability" in partner
+                    else 1.0
+                ),
             )
             self.all_partners.append(partner)
 

diff --git a/cellpack/autopack/loaders/recipe_loader.py b/cellpack/autopack/loaders/recipe_loader.py
@@ -252,9 +252,9 @@ def _load_json(self):
                         ):
                             node = {"include": compartment["from"]}
                             sub_recipe = self._request_sub_recipe(inode=node)
-                            recipe_data["compartments"][
-                                compartment["from"]
-                            ] = sub_recipe["compartments"]
+                            recipe_data["compartments"][compartment["from"]] = (
+                                sub_recipe["compartments"]
+                            )
                         continue
                     compartment_dict = recipe_data["compartments"][cname]
                     rep = None

diff --git a/cellpack/autopack/upy/colors.py b/cellpack/autopack/upy/colors.py
@@ -16,6 +16,7 @@
     You should have received a copy of the GNU General Public License
     along with upy.  If not, see <http://www.gnu.org/licenses/gpl-3.0.html>.
 """
+
 import numpy
 from math import floor
 

diff --git a/cellpack/autopack/upy/simularium/__init__.py b/cellpack/autopack/upy/simularium/__init__.py
@@ -16,5 +16,6 @@
     You should have received a copy of the GNU General Public License
     along with upy.  If not, see <http://www.gnu.org/licenses/gpl-3.0.html>.
 """
+
 # CRITICAL_DEPENDENCIES = ['blender','c4d']
 __revision__ = "01"
diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py
@@ -292,10 +292,10 @@ def save_Mixed_asJson(
                         "include": ing_filename,
                     }
                 else:
-                    env.jsondic["cytoplasme"]["ingredients"][
-                        ingr.composition_name
-                    ] = io_ingr.ingrJsonNode(
-                        ingr, result=result, kwds=kwds, transpose=transpose
+                    env.jsondic["cytoplasme"]["ingredients"][ingr.composition_name] = (
+                        io_ingr.ingrJsonNode(
+                            ingr, result=result, kwds=kwds, transpose=transpose
+                        )
                     )  # {"name":ingr.composition_name}
                     env.jsondic["cytoplasme"]["ingredients"][ingr.composition_name][
                         "name"

diff --git a/setup.py b/setup.py
@@ -13,7 +13,7 @@
 ]
 
 test_requirements = [
-    "black>=19.10b0, <=23.0",
+    "black>=19.10b0, <=24.8.0",
     "flake8>=3.8.3, <=6.0.0",
     "flake8-debugger>=3.2.1",
     "pytest>=5.4.3",