docs: Add docstrings for classes and methods in ontoenv.pyi file

Author: gtfierro

python/src/ontoenv.pyi

@@ -1,6 +1,19 @@
 from typing import Optional, List, Union
 
 class Config:
+    """
+    Configuration class for setting up the ontology environment.
+
+    Attributes:
+        search_directories: Optional list of directories to search for ontologies.
+        require_ontology_names: Flag to require ontology names.
+        strict: Flag for strict mode.
+        offline: Flag to operate in offline mode.
+        resolution_policy: Policy for resolving ontologies.
+        root: Root directory for the environment.
+        includes: Optional list of patterns to include.
+        excludes: Optional list of patterns to exclude.
+    """
     def __init__(
         self,
         search_directories: Optional[List[str]] = None,
@@ -11,45 +24,148 @@ class Config:
         root: str = ".",
         includes: Optional[List[str]] = None,
         excludes: Optional[List[str]] = None,
-    ) -> None: ...
+    ) -> None:
+        """
+        Initialize the Config object with the given parameters.
+        """
+        ...
 
 class OntoEnv:
+    """
+    Ontology Environment class for managing ontologies.
+
+    Attributes:
+        config: Optional configuration object.
+        path: Path to the ontology environment.
+        recreate: Flag to recreate the environment.
+        read_only: Flag to set the environment as read-only.
+    """
     def __init__(
         self,
         config: Optional[Config] = None,
         path: Optional[Union[str, Path]] = ".",
         recreate: bool = False,
         read_only: bool = False,
-    ) -> None: ...
+    ) -> None:
+        """
+        Initialize the OntoEnv object with the given parameters.
+        """
+        ...
+
+    def update(self) -> None:
+        """
+        Update the ontology environment by reloading all ontologies.
+        """
+        ...
+
+    def is_read_only(self) -> bool:
+        """
+        Check if the ontology environment is read-only.
+
+        Returns:
+            A boolean indicating if the environment is read-only.
+        """
+        ...
+
+    def __repr__(self) -> str:
+        """
+        Return a string representation of the OntoEnv object.
+        """
+        ...
 
-    def update(self) -> None: ...
+    def import_graph(self, destination_graph, uri: str) -> None:
+        """
+        Import a graph from the given URI into the destination graph.
 
-    def is_read_only(self) -> bool: ...
+        Args:
+            destination_graph: The graph to import into.
+            uri: The URI of the graph to import.
+        """
+        ...
 
-    def __repr__(self) -> str: ...
+    def list_closure(self, uri: str) -> List[str]:
+        """
+        List the ontologies in the imports closure of the given ontology.
 
-    def import_graph(self, destination_graph, uri: str) -> None: ...
+        Args:
+            uri: The URI of the ontology.
 
-    def list_closure(self, uri: str) -> List[str]: ...
+        Returns:
+            A list of ontology names in the closure.
+        """
+        ...
 
     def get_closure(
         self,
         uri: str,
         destination_graph: Optional = None,
         rewrite_sh_prefixes: bool = False,
         remove_owl_imports: bool = False,
-    ) -> None: ...
+    ) -> None:
+        """
+        Merge all graphs in the imports closure of the given ontology into a single graph.
+
+        Args:
+            uri: The URI of the ontology.
+            destination_graph: Optional graph to add the merged graph to.
+            rewrite_sh_prefixes: Flag to rewrite SH prefixes.
+            remove_owl_imports: Flag to remove OWL imports.
+        """
+        ...
+
+    def dump(self, includes: Optional[str] = None) -> None:
+        """
+        Print the contents of the OntoEnv.
+
+        Args:
+            includes: Optional string to filter the output.
+        """
+        ...
+
+    def import_dependencies(self, graph) -> None:
+        """
+        Import the dependencies of the given graph into the graph.
+
+        Args:
+            graph: The graph to import dependencies into.
+        """
+        ...
+
+    def add(self, location) -> None:
+        """
+        Add a new ontology to the OntoEnv.
 
-    def dump(self, includes: Optional[str] = None) -> None: ...
+        Args:
+            location: The location of the ontology to add.
+        """
+        ...
 
-    def import_dependencies(self, graph) -> None: ...
+    def refresh(self) -> None:
+        """
+        Refresh the OntoEnv by re-loading all remote graphs and loading any local graphs which have changed.
+        """
+        ...
 
-    def add(self, location) -> None: ...
+    def get_graph(self, uri: str) -> None:
+        """
+        Export the graph with the given URI to an rdflib.Graph.
 
-    def refresh(self) -> None: ...
+        Args:
+            uri: The URI of the graph to export.
+        """
+        ...
 
-    def get_graph(self, uri: str) -> None: ...
+    def get_ontology_names(self) -> List[str]:
+        """
+        Get the names of all ontologies in the OntoEnv.
 
-    def get_ontology_names(self) -> List[str]: ...
+        Returns:
+            A list of ontology names.
+        """
+        ...
 
-    def to_rdflib_dataset(self) -> None: ...
+    def to_rdflib_dataset(self) -> None:
+        """
+        Convert the OntoEnv to an rdflib.Dataset.
+        """
+        ...