Bump dependency versions (#77)

* Bump setuptools (67.4.0 -> 70.3.0)

* Bump zipp (3.14.0 -> 3.19.2)

* Bump prefect (2.16.1 -> 2.19.8)

* Bump jinja2 (3.1.3 -> 3.1.4)

* Bump idna (3.4 -> 3.7)

* Bump black (22.12.0 -> 24.4.2)

* Bump certifi (2024.2.2 -> 2024.7.4)

* Bump pillow (10.2.0 -> 10.4.0)

* Bump requests (2.31.0 -> 2.32.3)

* Bump urllib3 (2.2.1 -> 2.2.2)

* Bump pydantic (1.10.5 -> 2.8.2)

* Fix linting errors

pyproject.toml

@@ -18,7 +18,7 @@ simulariumio = "^1.7.0"
 matplotlib = "^3.7.2"
 
 [tool.poetry.group.dev.dependencies]
-black = "^22.12.0"
+black = "^24.3.0"
 isort = "^5.12.0"
 mypy = "^1.3.0"
 pylint = "^2.16.2"

src/arcade_collection/convert/convert_to_simularium_shapes.py

@@ -109,7 +109,7 @@ def format_patch_for_shapes(
                 graph_tar, series_key, frame, "GRAPH", field="graph"
             )
 
-            for (from_node, to_node, edge) in graph_timepoint:
+            for from_node, to_node, edge in graph_timepoint:
                 edge_type, radius, _, _, _, _, flow = edge
 
                 name = f"VASCULATURE##{'UNDEFINED' if isnan(flow) else EDGE_TYPES[edge_type + 2]}"

src/arcade_collection/output/parse_growth_file.py

@@ -121,7 +121,7 @@ def parse_growth_timepoint(timepoint: dict, seed: int) -> list:
     parsed_data = []
     time = timepoint["time"]
 
-    for (location, cells) in timepoint["cells"]:
+    for location, cells in timepoint["cells"]:
         u, v, w, z = location
 
         for cell in cells:

tests/arcade_collection/output/test_convert_model_units.py

@@ -51,3 +51,7 @@ def test_estimate_spatial_resolution_invalid_spatiall_key(self):
         self.assertEqual(1, estimate_spatial_resolution(f"{ds_key}_B_C"))
         self.assertEqual(1, estimate_spatial_resolution(f"A_{ds_key}_C"))
         self.assertEqual(1, estimate_spatial_resolution(f"A_B_{ds_key}"))
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/arcade_collection/output/test_parse_growth_file.py

@@ -123,3 +123,7 @@ def test_parse_growth_timepoint(self):
 
         expected_df = pd.DataFrame(expected_dict)
         self.assertTrue(expected_df.equals(returned_df))
+
+
+if __name__ == "__main__":
+    unittest.main()