fixing warnings on types, syntax

nexus_constructor/json/load_from_json.py

@@ -1,6 +1,6 @@
 import json
 from json import JSONDecodeError
-from typing import Dict, Optional, Tuple, Union
+from typing import Dict, Optional, Tuple, Union, cast
 
 from nexus_constructor.common_attrs import (
     NX_CLASSES_WITH_PLACEHOLDERS,
@@ -71,7 +71,7 @@
 
 class JSONReader:
     def __init__(self):
-        self.entry_node: Group = None
+        self.entry_node: Group = cast(Group, None)
         self.model = Model()
         self.sample_name: str = ""
         self.warnings = JsonWarningsContainer()
@@ -114,8 +114,11 @@ def _set_components_depends_on(self):
             except KeyError:
                 self.warnings.append(
                     TransformDependencyMissing(
-                        f"Component {component_name} depends on {depends_on_id.transform_name} in component "
-                        f"{depends_on_id.component_name}, but that transform was not successfully loaded from the JSON"
+                        f"Component {component_name} depends on "
+                        + (depends_on_id.transform_name if depends_on_id is not None else "Unknown")
+                        + " in component "
+                        + (depends_on_id.component_name if depends_on_id is not None else "Unknown")
+                        + ", but that transform was not successfully loaded from the JSON"
                     )
                 )
 
@@ -139,9 +142,11 @@ def _set_transforms_depends_on(self):
             except KeyError:
                 self.warnings.append(
                     TransformDependencyMissing(
-                        f"Transformation {transform_id.transform_name} in component {transform_id.component_name} "
-                        f"depends on {depends_on_id.transform_name} in component {depends_on_id.component_name}, "
-                        f"but that transform was not successfully loaded from the JSON"
+                        f"Transformation {transform_id.transform_name} in component {transform_id.component_name} depends on "
+                        + (depends_on_id.transform_name if depends_on_id is not None else "Unknown")
+                        + " in component "
+                        + (depends_on_id.component_name if depends_on_id is not None else "Unknown")
+                        + ", but that transform was not successfully loaded from the JSON"
                     )
                 )
 
@@ -199,14 +204,14 @@ def load_model_from_json(self, filename: str) -> bool:
             return self._load_from_json_dict(json_dict)
 
     def _load_from_json_dict(self, json_dict: Dict) -> bool:
-        self.entry_node = self._read_json_object(json_dict[CommonKeys.CHILDREN][0])
+        self.entry_node = cast(Group, self._read_json_object(json_dict[CommonKeys.CHILDREN][0]))
         self.model.entry.attributes = self.entry_node.attributes
         for child in self.entry_node.children:
             if isinstance(child, (Dataset, Link, FileWriter, Group)):
                 self.model.entry[child.name] = child
             else:
                 self.model.entry.children.append(child)
-            child.parent_node = self.model.entry
+            child.parent_node = cast(str, self.model.entry)
         self._set_transforms_depends_on()
         self._set_components_depends_on()
         self._append_transformations_to_nx_group()
@@ -231,16 +236,16 @@ def _replace_placeholder(self, placeholder: str):
             }
         return None
 
-    def _read_json_object(self, json_object: Dict, parent_node: Group = None):
+    def _read_json_object(self, json_object: Dict, parent_node: Group = cast(Group, None)):
         """
         Tries to create a component based on the contents of the JSON file.
         :param json_object: A component from the JSON dictionary.
         :param parent_name: The name of the parent object. Used for warning messages if something goes wrong.
         """
-        nexus_object: Union[Group, FileWriterModule] = None
+        nexus_object: Union[Group, FileWriterModule] = cast(Group, None)
         use_placeholder = False
         if isinstance(json_object, str) and json_object in PLACEHOLDER_WITH_NX_CLASSES:
-            json_object = self._replace_placeholder(json_object)
+            json_object = cast(Dict, self._replace_placeholder(json_object))
             if not json_object:
                 return
             use_placeholder = True
@@ -253,13 +258,13 @@ def _read_json_object(self, json_object: Dict, parent_node: Group = None):
             except KeyError:
                 self._add_object_warning(CommonKeys.NAME, parent_node)
                 return None
-            nx_class = _find_nx_class(json_object.get(CommonKeys.ATTRIBUTES))
+            nx_class = _find_nx_class(cast(list, json_object.get(CommonKeys.ATTRIBUTES)))
             if nx_class == SAMPLE_CLASS_NAME:
                 self.sample_name = name
             if not self._validate_nx_class(name, nx_class):
                 self._add_object_warning(f"valid Nexus class {nx_class}", parent_node)
             if nx_class in COMPONENT_TYPES:
-                nexus_object = Component(name=name, parent_node=parent_node)
+                nexus_object = Component(name=name, parent_node=cast(str, parent_node))
                 children_dict = json_object[CommonKeys.CHILDREN]
                 self._add_transform_and_shape_to_component(nexus_object, children_dict)
                 self.model.append_component(nexus_object)
@@ -282,12 +287,12 @@ def _read_json_object(self, json_object: Dict, parent_node: Group = None):
             ) and json_object[NodeType.CONFIG][
                 CommonKeys.NAME
             ] == CommonAttrs.DEPENDS_ON:
-                nexus_object = None
+                nexus_object = cast(Group, None)
             elif module_type in [x.value for x in WriterModules]:
                 nexus_object = create_fw_module_object(
                     module_type, json_object[NodeType.CONFIG], parent_node
                 )
-                nexus_object.parent_node = parent_node
+                nexus_object.parent_node = cast(str, parent_node)
             else:
                 self._add_object_warning("valid module type", parent_node)
                 return None
@@ -376,7 +381,7 @@ def _add_transform_and_shape_to_component(self, component, children_dict):
         )
         transformation_reader.add_transformations_to_component()
         self.warnings += transformation_reader.warnings
-        depends_on = _find_depends_on_path(children_dict, component.name)
+        depends_on: str = cast(str, _find_depends_on_path(children_dict, component.name))
         if depends_on not in [".", "", None]:
             if depends_on[0] != "/":
                 #   we are always in the NXtransformations group but the path could be anything

nexus_constructor/json/transformation_reader.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any, Dict, List, Optional, Tuple, Union, cast
 
 from PySide6.QtGui import QVector3D
 
@@ -127,7 +127,7 @@ def _get_transformation_attribute(
         self,
         attribute_name: Union[str, List[str]],
         json_transformation: dict,
-        transform_name: str = None,
+        transform_name: str = "",
         failure_value: Any = None,
     ) -> Any:
         """
@@ -323,15 +323,14 @@ def _create_transformations(self, json_transformations: list):
                 angle_or_magnitude = 0.0
             else:
                 continue
-            temp_depends_on = None
 
             transform = self.parent_component._create_and_add_transform(
                 name=name,
-                transformation_type=transformation_type,
+                transformation_type=cast(str, transformation_type),
                 angle_or_magnitude=angle_or_magnitude,
                 units=units,
                 vector=QVector3D(*vector),
-                depends_on=temp_depends_on,
+                depends_on=cast(Transformation, None),
                 values=values,
             )
             offset = self._find_attribute_in_list(CommonAttrs.OFFSET, name, attributes)

nexus_constructor/model/component.py

@@ -88,6 +88,8 @@ class Component(Group):
     has_link = attr.ib(type=bool, default=None)
     component_info: "ComponentInfo" = None
     stored_transforms: list = None
+    name: str = None
+    parent_node: str = None
 
     @property
     def stored_items(self) -> List:
@@ -271,7 +273,7 @@ def _create_and_add_transform(
         units: str,
         vector: QVector3D,
         depends_on: Transformation,
-        values: Union[Dataset, Group],
+        values: Union[Dataset, Group, StreamModule],
         target_pos: int = -1,
     ) -> Transformation:
         if name is None:

nexus_constructor/model/module.py

@@ -57,7 +57,8 @@ class StreamModules(Enum):
 
 @attr.s
 class FileWriterModule(ABC):
-    attributes = attr.ib(type=Attributes, factory=Attributes, init=False)
+    name: str = None
+    parent_node: str = None    attributes = attr.ib(type=Attributes, factory=Attributes, init=False)
     writer_module = attr.ib(type=str, init=False)
     parent_node = attr.ib(type="Group")