chore: fix mypy issues

pyproject.toml

@@ -241,8 +241,14 @@ plugins = [
     "pydantic.mypy"
 ]
 
-
 # mypy per-module options:
 [[tool.mypy.overrides]]
-module = ["placholder.dummy.*"]
+module = [
+    "kiara_plugin.streamlit.*",
+    "networkx.*",
+    "pyarrow.*",
+    "pyvis.*",
+    "ruamel.*",
+    "streamlit.*"
+]
 ignore_missing_imports = true

src/kiara_plugin/network_analysis/data_types.py

@@ -62,6 +62,11 @@ def parse_python_obj(self, data: Any) -> NetworkData:
                 augment_tables=False,
             )
 
+        if not isinstance(data, NetworkData):
+            raise KiaraException(
+                f"Can't parse object to network data: invalid type '{type(data)}'."
+            )
+
         return data
 
     def _validate(cls, value: Any) -> None:

src/kiara_plugin/network_analysis/models/__init__.py

@@ -255,7 +255,7 @@ def from_filtered_nodes(
 
         node_columns = [NODE_ID_COLUMN_NAME, LABEL_COLUMN_NAME]
         for column_name, metadata in network_data.nodes.column_metadata.items():
-            attr_prop: Union[None, NetworkNodeAttributeMetadata] = metadata.get(
+            attr_prop: Union[None, NetworkNodeAttributeMetadata] = metadata.get(  # type: ignore
                 ATTRIBUTE_PROPERTY_KEY, None
             )
             if attr_prop is None or not attr_prop.computed_attribute:
@@ -271,7 +271,7 @@ def from_filtered_nodes(
         edges_table = network_data.edges.arrow_table  # noqa
         edge_columns = [SOURCE_COLUMN_NAME, TARGET_COLUMN_NAME]
         for column_name, metadata in network_data.edges.column_metadata.items():
-            attr_prop = metadata.get(ATTRIBUTE_PROPERTY_KEY, None)
+            attr_prop = metadata.get(ATTRIBUTE_PROPERTY_KEY, None)  # type: ignore
             if attr_prop is None or not attr_prop.computed_attribute:
                 edge_columns.append(column_name)
 
@@ -390,7 +390,7 @@ def _calculate_node_attributes(
         if incl_node_attributes is False:
             node_attr_names: List[str] = [NODE_ID_COLUMN_NAME, LABEL_COLUMN_NAME]
         else:
-            all_node_attr_names = self.nodes.column_names
+            all_node_attr_names: List[str] = self.nodes.column_names  # type: ignore
             if incl_node_attributes is True:
                 node_attr_names = [NODE_ID_COLUMN_NAME]
                 node_attr_names.extend((x for x in all_node_attr_names if x != NODE_ID_COLUMN_NAME))  # type: ignore
@@ -598,7 +598,7 @@ def add_edge(_source: int, _target: int, **attrs):
         )
 
         if attach_node_id_map:
-            graph.attrs = {"node_id_map": node_map}
+            graph.attrs = {"node_id_map": node_map}  # type: ignore
 
         return graph
 

src/kiara_plugin/network_analysis/models/inputs.py

@@ -14,7 +14,7 @@ class AttributeMapStrategy(KiaraModel):
 
     @model_validator(mode="before")
     @classmethod
-    def validate(cls, values: Dict[str, Any]):
+    def pre_validate_model(cls, values: Dict[str, Any]):
 
         if len(values) == 1 and DEFAULT_MODEL_KEY in values.keys():
 

src/kiara_plugin/network_analysis/modules/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from typing import Any, Dict, List, Union
+from typing import Any, Dict, List, Mapping, Union
 
 from kiara.api import KiaraModule, ValueMap, ValueMapSchema
 from kiara.exceptions import KiaraProcessingException
@@ -28,7 +28,7 @@ class RedefineNetworkEdgesModule(KiaraModule):
     def create_inputs_schema(
         self,
     ) -> ValueMapSchema:
-        result = {
+        result: Mapping[str, Mapping[str, Any]] = {
             "network_data": {
                 "type": "network_data",
                 "doc": "The network data to flatten.",

src/kiara_plugin/network_analysis/modules/components.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from typing import Any, Dict
+from typing import TYPE_CHECKING, Any, Dict
 
 from kiara.api import KiaraModule, ValueMap, ValueMapSchema
 from kiara.exceptions import KiaraException
@@ -11,6 +11,9 @@
 from kiara_plugin.network_analysis.models import NetworkData
 from kiara_plugin.network_analysis.models.metadata import NetworkNodeAttributeMetadata
 
+if TYPE_CHECKING:
+    from kiara.models import KiaraModel
+
 KIARA_METADATA = {
     "authors": [
         {"name": "Lena Jaskov", "email": "helena.jaskov@uni.lu"},
@@ -86,9 +89,9 @@ def process(self, inputs: ValueMap, outputs: ValueMap):
             omit_self_loops=False,
             attach_node_id_map=True,
         )
-        undir_components = rx.connected_components(undir_graph)
+        undir_components = rx.connected_components(undir_graph)  # type: ignore
 
-        nodes_columns_metadata = {
+        nodes_columns_metadata: Dict[str, Dict[str, KiaraModel]] = {
             COMPONENT_ID_COLUMN_NAME: {
                 ATTRIBUTE_PROPERTY_KEY: COMPONENT_COLUMN_METADATA
             }
@@ -115,7 +118,7 @@ def process(self, inputs: ValueMap, outputs: ValueMap):
 
         number_of_components = len(undir_components)
         is_connected = False
-        node_id_map = undir_graph.attrs["node_id_map"]
+        node_id_map = undir_graph.attrs["node_id_map"]  # type: ignore
 
         node_components = {}
         for idx, component in enumerate(
@@ -192,9 +195,9 @@ def process(self, inputs, outputs) -> None:
             attach_node_id_map=True,
         )
 
-        node_id_map = undir_graph.attrs["node_id_map"]
+        node_id_map = undir_graph.attrs["node_id_map"]  # type: ignore
 
-        cut_points = rx.articulation_points(undir_graph)
+        cut_points = rx.articulation_points(undir_graph)  # type: ignore
         translated_cut_points = [node_id_map[x] for x in cut_points]
         if not cut_points:
             raise NotImplementedError()
@@ -208,7 +211,7 @@ def process(self, inputs, outputs) -> None:
             IS_CUTPOINT_COLUMN_NAME, pa.array(cut_points_column, type=pa.bool_())
         )
 
-        nodes_columns_metadata = {
+        nodes_columns_metadata: Dict[str, Dict[str, KiaraModel]] = {
             IS_CUTPOINT_COLUMN_NAME: {
                 ATTRIBUTE_PROPERTY_KEY: CUT_POINTS_COLUMN_METADATA
             }

src/kiara_plugin/network_analysis/utils.py

@@ -162,7 +162,7 @@ def extract_networkx_edges_as_table(
 
 def augment_nodes_table_with_connection_counts(
     nodes_table: Union["pa.Table", "pl.DataFrame"],
-    edges_table: Union["pa.Table", "pl.Dataframe"],
+    edges_table: Union["pa.Table", "pl.DataFrame"],
 ) -> "pa.Table":
 
     import duckdb