fix ruff errors

mesa_geo/geoagent.py

@@ -110,7 +110,9 @@ def __init__(self, agent_class, model=None, crs=None, agent_kwargs=None):
 
         if agent_kwargs and "unique_id" in agent_kwargs:
             agent_kwargs.remove("unique_id")
-            warnings.warn("Unique_id should not be in the agent_kwargs")
+            warnings.warn(
+                "Unique_id should not be in the agent_kwargs", UserWarning, stacklevel=2
+            )
 
         self.agent_class = agent_class
         self.model = model
@@ -219,7 +221,10 @@ def from_file(self, filename, unique_id="index", set_attributes=True):
         return agents
 
     def from_GeoJSON(
-        self, GeoJSON, unique_id="index", set_attributes=True  # noqa: N803
+        self,
+        GeoJSON,  # noqa: N803
+        unique_id="index",
+        set_attributes=True,
     ):
         """
         Create agents from a GeoJSON object or string. CRS is set to epsg:4326.
@@ -230,7 +235,7 @@ def from_GeoJSON(
         :param set_attributes: Set agent attributes from GeoDataFrame columns. Default True.
         """
 
-        gj = json.loads(GeoJSON) if type(GeoJSON) is str else GeoJSON
+        gj = json.loads(GeoJSON) if isinstance(GeoJSON, str) else GeoJSON
 
         gdf = gpd.GeoDataFrame.from_features(gj)
         # epsg:4326 is the CRS for all GeoJSON: https://datatracker.ietf.org/doc/html/rfc7946#section-4

mesa_geo/geospace.py

@@ -131,7 +131,9 @@ def add_layer(self, layer: ImageLayer | RasterLayer | gpd.GeoDataFrame) -> None:
                     f"Converting {layer.__class__.__name__} from crs {layer.crs.to_string()} "
                     f"to the crs of {self.__class__.__name__} - {self.crs.to_string()}. "
                     "Please check your crs settings if this is unintended, or set `GeoSpace.warn_crs_conversion` "
-                    "to `False` to suppress this warning message."
+                    "to `False` to suppress this warning message.",
+                    UserWarning,
+                    stacklevel=2,
                 )
             layer.to_crs(self.crs, inplace=True)
         self._total_bounds = None
@@ -145,7 +147,9 @@ def _check_agent(self, agent):
                         f"Converting {agent.__class__.__name__} from crs {agent.crs.to_string()} "
                         f"to the crs of {self.__class__.__name__} - {self.crs.to_string()}. "
                         "Please check your crs settings if this is unintended, or set `GeoSpace.warn_crs_conversion` "
-                        "to `False` to suppress this warning message."
+                        "to `False` to suppress this warning message.",
+                        UserWarning,
+                        stacklevel=2,
                     )
                 agent.to_crs(self.crs, inplace=True)
         else:

mesa_geo/raster_layers.py

@@ -694,4 +694,4 @@ def from_file(cls, image_file) -> ImageLayer:
             return obj
 
     def __repr__(self) -> str:
-        return f"{self.__class__.__name__}(crs={self.crs}, total_bounds={self.total_bounds}, values={repr(self.values)})"
+        return f"{self.__class__.__name__}(crs={self.crs}, total_bounds={self.total_bounds}, values={self.values!r})"

pyproject.toml

@@ -47,7 +47,11 @@ extend-ignore = [
     "PGH004", # Use specific rule codes when using `noqa` TODO
     "B905", # `zip()` without an explicit `strict=` parameter
     "N802", # Function name should be lowercase
-    "N999", # Invalid module name
+    "N999",  # Invalid module name. We should revisit this in the future, TODO
+    "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar` TODO
+    "S310",  # Audit URL open for permitted schemes. Allowing use of `file:` or custom schemes is often unexpected.
+    "S603",  # `subprocess` call: check for execution of untrusted input
+    "ISC001",  # ruff format asks to disable this feature
 ]
 extend-exclude = ["docs", "build"]
 # Hardcode to Python 3.8.

tests/test_GeoSpace.py

@@ -88,7 +88,7 @@ def test_add_agents_with_different_crs(self):
 
     def test_remove_agent(self):
         self.geo_space.add_agents(self.agents)
-        agent_to_remove = random.choice(self.agents)
+        agent_to_remove = random.choice(self.agents)  # noqa: S311
         self.geo_space.remove_agent(agent_to_remove)
         remaining_agent_idx = {agent.unique_id for agent in self.geo_space.agents}
 
@@ -121,7 +121,7 @@ def test_add_vector_layer(self):
 
     def test_get_neighbors_within_distance(self):
         self.geo_space.add_agents(self.agents)
-        agent_to_check = random.choice(self.agents)
+        agent_to_check = random.choice(self.agents)  # noqa: S311
 
         neighbors = list(
             self.geo_space.get_neighbors_within_distance(
@@ -175,9 +175,9 @@ def test_get_relation_within(self):
             list(self.geo_space.get_relation(self.agents[0], relation="within")), []
         )
         self.geo_space.add_agents(self.polygon_agent)
-        within_agent = list(
+        within_agent = next(
             self.geo_space.get_relation(self.agents[0], relation="within")
-        )[0]
+        )
         self.assertEqual(within_agent.unique_id, self.polygon_agent.unique_id)
 
     def test_get_relation_touches(self):
@@ -196,9 +196,9 @@ def test_get_relation_touches(self):
             1,
         )
         self.assertEqual(
-            list(self.geo_space.get_relation(self.polygon_agent, relation="touches"))[
-                0
-            ].unique_id,
+            next(
+                self.geo_space.get_relation(self.polygon_agent, relation="touches")
+            ).unique_id,
             self.touching_agent.unique_id,
         )