Apply more ruff linting

pyproject.toml

@@ -20,7 +20,7 @@ matplotlib = "^3.7.2"
 [tool.poetry.group.dev.dependencies]
 black = "^24.3.0"
 isort = "^5.12.0"
-mypy = "^1.3.0"
+mypy = "^1.10.0"
 pylint = "^2.16.2"
 pytest = "^7.3.0"
 pytest-cov = "^4.0.0"
@@ -60,6 +60,7 @@ namespace_packages = true
 module = [
     "matplotlib.*",
     "pandas.*",
+    "ruamel.*",
     "simulariumio.*",
     "skimage.*",
 ]

src/arcade_collection/output/parse_cells_file.py

@@ -42,9 +42,12 @@ def parse_cells_file(tar: tarfile.TarFile, regions: list[str]) -> pd.DataFrame:
     all_cells: list[list[str | int]] = []
 
     for member in tar.getmembers():
-        tick = int(member.name.replace(".CELLS.json", "").split("_")[-1])
-
         extracted_member = tar.extractfile(member)
+
+        if extracted_member is None:
+            continue
+
+        tick = int(member.name.replace(".CELLS.json", "").split("_")[-1])
         cells_json = json.loads(extracted_member.read().decode("utf-8"))
 
         cells = [parse_cell_tick(tick, cell, regions) for cell in cells_json]

src/arcade_collection/output/parse_growth_file.py

@@ -50,6 +50,10 @@ def parse_growth_file(tar: tarfile.TarFile) -> pd.DataFrame:
 
     for member in tar.getmembers():
         extracted_member = tar.extractfile(member)
+
+        if extracted_member is None:
+            continue
+
         extracted_json = json.loads(extracted_member.read().decode("utf-8"))
 
         seed = extracted_json["seed"]

src/arcade_collection/output/parse_locations_file.py

@@ -46,9 +46,12 @@ def parse_locations_file(tar: tarfile.TarFile, regions: list[str]) -> pd.DataFra
     all_locations: list[list[str | int]] = []
 
     for member in tar.getmembers():
-        tick = int(member.name.replace(".LOCATIONS.json", "").split("_")[-1])
-
         extracted_member = tar.extractfile(member)
+
+        if extracted_member is None:
+            continue
+
+        tick = int(member.name.replace(".LOCATIONS.json", "").split("_")[-1])
         locations_json = json.loads(extracted_member.read().decode("utf-8"))
 
         locations = [parse_location_tick(tick, cell, regions) for cell in locations_json]

tests/arcade_collection/output/test_parse_cells_file.py

@@ -22,8 +22,8 @@ def test_parse_cells_file_without_regions(self):
             second_member_mock.name: second_member_mock,
         }
 
-        tar_mock.getmembers.return_value = contents.values()
-        tar_mock.extractfile.side_effect = lambda member: contents.get(member.name, None)
+        tar_mock.getmembers.return_value = [*list(contents.values()), None]
+        tar_mock.extractfile.side_effect = lambda m: None if m is None else contents[m.name]
 
         first_member_contents = [
             {
@@ -97,8 +97,8 @@ def test_parse_cells_file_with_regions(self):
             second_member_mock.name: second_member_mock,
         }
 
-        tar_mock.getmembers.return_value = contents.values()
-        tar_mock.extractfile.side_effect = lambda member: contents.get(member.name, None)
+        tar_mock.getmembers.return_value = [*list(contents.values()), None]
+        tar_mock.extractfile.side_effect = lambda m: None if m is None else contents[m.name]
 
         first_member_contents = [
             {

tests/arcade_collection/output/test_parse_growth_file.py

@@ -27,8 +27,10 @@ def test_parse_growth_file(self):
             second_member_mock.name: second_member_mock,
         }
 
-        tar_mock.getmembers.return_value = contents.values()
-        tar_mock.extractfile.side_effect = lambda member: contents.get(member.name, None)
+        tar_mock.getmembers.return_value = [*list(contents.values()), None]
+        tar_mock.extractfile.side_effect = lambda member: (
+            None if member is None else contents[member.name]
+        )
 
         first_member_contents = {
             "seed": 0,

tests/arcade_collection/output/test_parse_locations_file.py

@@ -22,8 +22,8 @@ def test_parse_locations_file_without_regions(self):
             second_member_mock.name: second_member_mock,
         }
 
-        tar_mock.getmembers.return_value = contents.values()
-        tar_mock.extractfile.side_effect = lambda member: contents.get(member.name, None)
+        tar_mock.getmembers.return_value = [*list(contents.values()), None]
+        tar_mock.extractfile.side_effect = lambda m: None if m is None else contents[m.name]
 
         first_member_contents = [
             {
@@ -96,8 +96,8 @@ def test_parse_locations_file_with_regions(self):
             second_member_mock.name: second_member_mock,
         }
 
-        tar_mock.getmembers.return_value = contents.values()
-        tar_mock.extractfile.side_effect = lambda member: contents.get(member.name, None)
+        tar_mock.getmembers.return_value = [*list(contents.values()), None]
+        tar_mock.extractfile.side_effect = lambda m: None if m is None else contents[m.name]
 
         first_member_contents = [
             {