Upgrading dependencies

cellpack/autopack/Analysis.py

@@ -4,6 +4,7 @@
 
 @author: ludo
 """
+
 import concurrent.futures
 import json
 import logging

cellpack/autopack/BaseGrid.py

@@ -35,6 +35,7 @@
 ###############################################################################
 @author: Ludovic Autin, Graham Johnson,  & Michel Sanner
 """
+
 import logging
 import numpy
 from scipy import spatial

cellpack/autopack/GeometryTools.py

@@ -13,6 +13,7 @@
 http://crowsandcats.blogspot.com/2013/04/cube-sphere-intersection-volume.html
 Copyright ©  Andrew White
 """
+
 import math
 import numpy as np
 

cellpack/autopack/IOutils.py

@@ -4,6 +4,7 @@
 
 @author: Ludovic Autin
 """
+
 import json
 import os
 import pickle

cellpack/autopack/MeshStore.py

@@ -281,15 +281,15 @@ def get_smallest_radius(self, geomname, center):
         mesh = self.get_object(geomname)
         if mesh is not None:
             query = trimesh.proximity.ProximityQuery(mesh)
-            (_, distance, _) = query.on_surface([center])
+            _, distance, _ = query.on_surface([center])
             return distance[0]
         return 1.0
 
     def get_normal(self, geomname, point_pos):
         mesh = self.get_object(geomname)
         if mesh is not None:
             query = trimesh.proximity.ProximityQuery(mesh)
-            (distance, triangle_ids) = query.vertex([point_pos])
+            distance, triangle_ids = query.vertex([point_pos])
             triangle_id = triangle_ids[0]
             return mesh.vertex_normals[triangle_id]
 

cellpack/autopack/Serializable.py

@@ -4,10 +4,10 @@
 
 @author: ludo
 """
+
 # serializabl;e class for auopack recipe
 import json
 
-
 # toDO class Assambly for nesting of protein quaternary structure.
 # class sAssambly
 #    static_id=0

cellpack/autopack/__init__.py

@@ -34,6 +34,7 @@
 AF
 @author: Ludovic Autin with editing by Graham Johnson
 """
+
 import getpass
 import json
 import logging

cellpack/autopack/ingredient/Ingredient.py

@@ -1619,10 +1619,10 @@ def attempt_to_pack_at_grid_location(
             # TODO: make this work for ingredients other than single spheres
 
             success = True
-            (jtrans, rotMatj) = self.get_new_jitter_location_and_rotation(
+            jtrans, rotMatj = self.get_new_jitter_location_and_rotation(
                 env, target_grid_point_position, rotation_matrix
             )
-            (insidePoints, newDistPoints) = self.pack_at_grid_pt_location(
+            insidePoints, newDistPoints = self.pack_at_grid_pt_location(
                 env,
                 jtrans,
                 rotMatj,

cellpack/autopack/interface_objects/__init__.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Interface classes for cellpack. These are to establish data structures."""
+
 from .default_values import (  # noqa: F401
     default_recipe_values,
 )

cellpack/autopack/transformation.py

@@ -185,6 +185,7 @@
 True
 
 """
+
 from __future__ import division, print_function
 
 

cellpack/autopack/upy/hostHelper.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 math
 import os
 import random

cellpack/autopack/writers/__init__.py

@@ -2,7 +2,6 @@
 
 """Write out data for cellpack."""
 
-
 import json
 import os
 from collections import OrderedDict

cellpack/tests/archive/test_gradient_data.py

@@ -7,6 +7,7 @@
 Docs: https://docs.pytest.org/en/latest/example/simple.html
     https://docs.pytest.org/en/latest/plugins.html#requiring-loading-plugins-in-a-test-module-or-conftest-file
 """
+
 import pytest
 from cellpack.autopack.interface_objects.archive.gradient_data import GradientData
 

cellpack/tests/test_partners.py

@@ -6,6 +6,7 @@
 Docs: https://docs.pytest.org/en/latest/
       https://docs.pytest.org/en/latest/goodpractices.html#conventions-for-python-test-discovery
 """
+
 import pytest
 from cellpack.autopack.ingredient.agent import Agent
 from cellpack.autopack.interface_objects import Partners

cellpack/tests/test_recipe_loader.py

@@ -4,6 +4,7 @@
 Docs: https://docs.pytest.org/en/latest/example/simple.html
     https://docs.pytest.org/en/latest/plugins.html#requiring-loading-plugins-in-a-test-module-or-conftest-file
 """
+
 import pytest
 from cellpack.autopack.loaders.recipe_loader import RecipeLoader
 

cellpack/tests/test_recipe_version_migration.py

@@ -5,6 +5,7 @@
 Docs: https://docs.pytest.org/en/latest/example/simple.html
     https://docs.pytest.org/en/latest/plugins.html#requiring-loading-plugins-in-a-test-module-or-conftest-file
 """
+
 from math import pi
 from unittest.mock import MagicMock
 import pytest

pyproject.toml

@@ -125,6 +125,7 @@ source-exclude = [
 ]
 
 [tool.black]
+target-version = ["py311"]
 line-length = 88
 
 [tool.isort]