fix: minor tweaks to make Pyright accept _Graph type annotations

Author: ntamas

src/codegen/internal_functions.py.in

@@ -27,7 +27,7 @@ from .wrappers import (
     _Vector,
     _VectorBool,
     _VectorInt,
-    _VectorIntList
+    _VectorIntList,
 )
 
 # fmt: off

src/igraph_ctypes/_internal/functions.py

@@ -27,7 +27,7 @@
     _Vector,
     _VectorBool,
     _VectorInt,
-    _VectorIntList
+    _VectorIntList,
 )
 
 # fmt: off
@@ -845,17 +845,18 @@ def erdos_renyi_game_gnp(n: int, p: float, directed: bool = False, loops: bool =
     return graph
 
 
-def erdos_renyi_game_gnm(n: int, m: int, directed: bool = False, loops: bool = False) -> _Graph:
+def erdos_renyi_game_gnm(n: int, m: int, directed: bool = False, loops: bool = False, multiple: bool = False) -> _Graph:
     """Type-annotated wrapper for ``igraph_erdos_renyi_game_gnm``."""
     # Prepare input arguments
     c_graph = _Graph()
     c_n = n
     c_m = m
     c_directed = any_to_igraph_bool_t(directed)
     c_loops = any_to_igraph_bool_t(loops)
+    c_multiple = any_to_igraph_bool_t(multiple)
 
     # Call wrapped function
-    igraph_erdos_renyi_game_gnm(c_graph, c_n, c_m, c_directed, c_loops)
+    igraph_erdos_renyi_game_gnm(c_graph, c_n, c_m, c_directed, c_loops, c_multiple)
 
     # Prepare output arguments
     graph = c_graph.mark_initialized()
@@ -3475,8 +3476,8 @@ def create_bipartite(types: Iterable[Any], edges: Iterable[int], directed: bool
     return graph
 
 
-def incidence(incidence: MatrixLike, directed: bool = False, mode: NeighborMode = NeighborMode.ALL, multiple: bool = False) -> Tuple[_Graph, BoolArray]:
-    """Type-annotated wrapper for ``igraph_incidence``."""
+def biadjacency(incidence: MatrixLike, directed: bool = False, mode: NeighborMode = NeighborMode.ALL, multiple: bool = False) -> Tuple[_Graph, BoolArray]:
+    """Type-annotated wrapper for ``igraph_biadjacency``."""
     # Prepare input arguments
     c_graph = _Graph()
     c_types = _VectorBool.create(0)
@@ -3486,7 +3487,7 @@ def incidence(incidence: MatrixLike, directed: bool = False, mode: NeighborMode
     c_multiple = any_to_igraph_bool_t(multiple)
 
     # Call wrapped function
-    igraph_incidence(c_graph, c_types, c_incidence, c_directed, c_mode, c_multiple)
+    igraph_biadjacency(c_graph, c_types, c_incidence, c_directed, c_mode, c_multiple)
 
     # Prepare output arguments
     graph = c_graph.mark_initialized()
@@ -3496,8 +3497,8 @@ def incidence(incidence: MatrixLike, directed: bool = False, mode: NeighborMode
     return graph, types
 
 
-def get_incidence(graph: _Graph, types: Optional[Iterable[Any]] = None) -> Tuple[RealArray, IntArray, IntArray]:
-    """Type-annotated wrapper for ``igraph_get_incidence``."""
+def get_biadjacency(graph: _Graph, types: Optional[Iterable[Any]] = None) -> Tuple[RealArray, IntArray, IntArray]:
+    """Type-annotated wrapper for ``igraph_get_biadjacency``."""
     # Prepare input arguments
     c_graph = graph
     c_types = iterable_to_igraph_vector_bool_t_view(types) if types is not None else None
@@ -3506,7 +3507,7 @@ def get_incidence(graph: _Graph, types: Optional[Iterable[Any]] = None) -> Tuple
     c_col_ids = _VectorInt.create(0)
 
     # Call wrapped function
-    igraph_get_incidence(c_graph, c_types, c_res, c_row_ids, c_col_ids)
+    igraph_get_biadjacency(c_graph, c_types, c_res, c_row_ids, c_col_ids)
 
     # Prepare output arguments
     res = igraph_matrix_t_to_numpy_array(c_res)
@@ -4216,17 +4217,18 @@ def bibcoupling(graph: _Graph, vids: VertexSelector = "all") -> RealArray:
     return res
 
 
-def similarity_dice(graph: _Graph, vids: VertexSelector = "all", mode: NeighborMode = NeighborMode.ALL, loops: bool = False) -> RealArray:
+def similarity_dice(graph: _Graph, vit_from: VertexSelector = "all", vit_to: VertexSelector = "all", mode: NeighborMode = NeighborMode.ALL, loops: bool = False) -> RealArray:
     """Type-annotated wrapper for ``igraph_similarity_dice``."""
     # Prepare input arguments
     c_graph = graph
     c_res = _Matrix.create(0)
-    c_vids = vertex_selector_to_igraph_vs_t(vids, graph)
+    c_vit_from = vertex_selector_to_igraph_vs_t(vit_from, graph)
+    c_vit_to = vertex_selector_to_igraph_vs_t(vit_to, graph)
     c_mode = c_int(mode)
     c_loops = any_to_igraph_bool_t(loops)
 
     # Call wrapped function
-    igraph_similarity_dice(c_graph, c_res, c_vids.unwrap(), c_mode, c_loops)
+    igraph_similarity_dice(c_graph, c_res, c_vit_from.unwrap(), c_vit_to.unwrap(), c_mode, c_loops)
 
     # Prepare output arguments
     res = igraph_matrix_t_to_numpy_array(c_res)
@@ -4291,17 +4293,18 @@ def similarity_inverse_log_weighted(graph: _Graph, vids: VertexSelector = "all",
     return res
 
 
-def similarity_jaccard(graph: _Graph, vids: VertexSelector = "all", mode: NeighborMode = NeighborMode.ALL, loops: bool = False) -> RealArray:
+def similarity_jaccard(graph: _Graph, vit_from: VertexSelector = "all", vit_to: VertexSelector = "all", mode: NeighborMode = NeighborMode.ALL, loops: bool = False) -> RealArray:
     """Type-annotated wrapper for ``igraph_similarity_jaccard``."""
     # Prepare input arguments
     c_graph = graph
     c_res = _Matrix.create(0)
-    c_vids = vertex_selector_to_igraph_vs_t(vids, graph)
+    c_vit_from = vertex_selector_to_igraph_vs_t(vit_from, graph)
+    c_vit_to = vertex_selector_to_igraph_vs_t(vit_to, graph)
     c_mode = c_int(mode)
     c_loops = any_to_igraph_bool_t(loops)
 
     # Call wrapped function
-    igraph_similarity_jaccard(c_graph, c_res, c_vids.unwrap(), c_mode, c_loops)
+    igraph_similarity_jaccard(c_graph, c_res, c_vit_from.unwrap(), c_vit_to.unwrap(), c_mode, c_loops)
 
     # Prepare output arguments
     res = igraph_matrix_t_to_numpy_array(c_res)
@@ -4786,8 +4789,6 @@ def graphlets_project(graph: _Graph, cliques: Iterable[Iterable[VertexLike]], Mu
 
 # igraph_hrg_game: no Python type known for type: HRG
 
-# igraph_hrg_dendrogram: no Python type known for type: HRG
-
 # igraph_hrg_consensus: no Python type known for type: HRG
 
 # igraph_hrg_predict: no Python type known for type: HRG
@@ -4798,6 +4799,8 @@ def graphlets_project(graph: _Graph, cliques: Iterable[Iterable[VertexLike]], Mu
 
 # igraph_hrg_size: no Python type known for type: HRG
 
+# igraph_from_hrg_dendrogram: no Python type known for type: HRG
+
 # igraph_get_adjacency: no Python type known for type: GETADJACENCY
 
 # igraph_get_adjacency_sparse: no Python type known for type: SPARSEMAT

src/igraph_ctypes/_internal/lib.py

@@ -622,7 +622,7 @@ def _load_igraph_c_library():
 
 igraph_erdos_renyi_game_gnm = _lib.igraph_erdos_renyi_game_gnm
 igraph_erdos_renyi_game_gnm.restype = handle_igraph_error_t
-igraph_erdos_renyi_game_gnm.argtypes = [POINTER(igraph_t), igraph_integer_t, igraph_integer_t, igraph_bool_t, igraph_bool_t]
+igraph_erdos_renyi_game_gnm.argtypes = [POINTER(igraph_t), igraph_integer_t, igraph_integer_t, igraph_bool_t, igraph_bool_t, igraph_bool_t]
 
 igraph_degree_sequence_game = _lib.igraph_degree_sequence_game
 igraph_degree_sequence_game.restype = handle_igraph_error_t
@@ -1212,13 +1212,13 @@ def _load_igraph_c_library():
 igraph_create_bipartite.restype = handle_igraph_error_t
 igraph_create_bipartite.argtypes = [POINTER(igraph_t), POINTER(igraph_vector_bool_t), POINTER(igraph_vector_int_t), igraph_bool_t]
 
-igraph_incidence = _lib.igraph_incidence
-igraph_incidence.restype = handle_igraph_error_t
-igraph_incidence.argtypes = [POINTER(igraph_t), POINTER(igraph_vector_bool_t), POINTER(igraph_matrix_t), igraph_bool_t, igraph_neimode_t, igraph_bool_t]
+igraph_biadjacency = _lib.igraph_biadjacency
+igraph_biadjacency.restype = handle_igraph_error_t
+igraph_biadjacency.argtypes = [POINTER(igraph_t), POINTER(igraph_vector_bool_t), POINTER(igraph_matrix_t), igraph_bool_t, igraph_neimode_t, igraph_bool_t]
 
-igraph_get_incidence = _lib.igraph_get_incidence
-igraph_get_incidence.restype = handle_igraph_error_t
-igraph_get_incidence.argtypes = [POINTER(igraph_t), POINTER(igraph_vector_bool_t), POINTER(igraph_matrix_t), POINTER(igraph_vector_int_t), POINTER(igraph_vector_int_t)]
+igraph_get_biadjacency = _lib.igraph_get_biadjacency
+igraph_get_biadjacency.restype = handle_igraph_error_t
+igraph_get_biadjacency.argtypes = [POINTER(igraph_t), POINTER(igraph_vector_bool_t), POINTER(igraph_matrix_t), POINTER(igraph_vector_int_t), POINTER(igraph_vector_int_t)]
 
 igraph_is_bipartite = _lib.igraph_is_bipartite
 igraph_is_bipartite.restype = handle_igraph_error_t
@@ -1450,7 +1450,7 @@ def _load_igraph_c_library():
 
 igraph_similarity_dice = _lib.igraph_similarity_dice
 igraph_similarity_dice.restype = handle_igraph_error_t
-igraph_similarity_dice.argtypes = [POINTER(igraph_t), POINTER(igraph_matrix_t), igraph_vs_t, igraph_neimode_t, igraph_bool_t]
+igraph_similarity_dice.argtypes = [POINTER(igraph_t), POINTER(igraph_matrix_t), igraph_vs_t, igraph_vs_t, igraph_neimode_t, igraph_bool_t]
 
 igraph_similarity_dice_es = _lib.igraph_similarity_dice_es
 igraph_similarity_dice_es.restype = handle_igraph_error_t
@@ -1466,7 +1466,7 @@ def _load_igraph_c_library():
 
 igraph_similarity_jaccard = _lib.igraph_similarity_jaccard
 igraph_similarity_jaccard.restype = handle_igraph_error_t
-igraph_similarity_jaccard.argtypes = [POINTER(igraph_t), POINTER(igraph_matrix_t), igraph_vs_t, igraph_neimode_t, igraph_bool_t]
+igraph_similarity_jaccard.argtypes = [POINTER(igraph_t), POINTER(igraph_matrix_t), igraph_vs_t, igraph_vs_t, igraph_neimode_t, igraph_bool_t]
 
 igraph_similarity_jaccard_es = _lib.igraph_similarity_jaccard_es
 igraph_similarity_jaccard_es.restype = handle_igraph_error_t
@@ -1580,10 +1580,6 @@ def _load_igraph_c_library():
 igraph_hrg_game.restype = handle_igraph_error_t
 igraph_hrg_game.argtypes = [POINTER(igraph_t), POINTER(igraph_hrg_t)]
 
-igraph_hrg_dendrogram = _lib.igraph_hrg_dendrogram
-igraph_hrg_dendrogram.restype = handle_igraph_error_t
-igraph_hrg_dendrogram.argtypes = [POINTER(igraph_t), POINTER(igraph_hrg_t)]
-
 igraph_hrg_consensus = _lib.igraph_hrg_consensus
 igraph_hrg_consensus.restype = handle_igraph_error_t
 igraph_hrg_consensus.argtypes = [POINTER(igraph_t), POINTER(igraph_vector_int_t), POINTER(igraph_vector_t), POINTER(igraph_hrg_t), igraph_bool_t, igraph_integer_t]
@@ -1604,6 +1600,10 @@ def _load_igraph_c_library():
 igraph_hrg_size.restype = igraph_integer_t
 igraph_hrg_size.argtypes = [POINTER(igraph_hrg_t)]
 
+igraph_from_hrg_dendrogram = _lib.igraph_from_hrg_dendrogram
+igraph_from_hrg_dendrogram.restype = handle_igraph_error_t
+igraph_from_hrg_dendrogram.argtypes = [POINTER(igraph_t), POINTER(igraph_hrg_t), POINTER(igraph_vector_t)]
+
 igraph_get_adjacency = _lib.igraph_get_adjacency
 igraph_get_adjacency.restype = handle_igraph_error_t
 igraph_get_adjacency.argtypes = [POINTER(igraph_t), POINTER(igraph_matrix_t), igraph_get_adjacency_t, POINTER(igraph_vector_t), igraph_loops_t]

src/igraph_ctypes/_internal/utils.py

@@ -1,7 +1,12 @@
 from ctypes import c_char_p
+from typing import Union
 
+__all__ = ("bytes_to_str",)
 
-def bytes_to_str(value: bytes, encoding: str = "utf-8", errors: str = "replace") -> str:
+
+def bytes_to_str(
+    value: Union[bytes, c_char_p], encoding: str = "utf-8", errors: str = "replace"
+) -> str:
     """Converts a C string represented as a Python bytes object or as a
     ctypes ``c_char_p`` object into a Python string, using the given encoding
     and error handling.

src/igraph_ctypes/_internal/wrappers.py

@@ -168,7 +168,8 @@ def __init__(self, instance: Optional[T] = None):
                 initialized = False
             elif not isinstance(instance, cls_outer):
                 raise TypeError(
-                    f"{name} must wrap an object of type {cls_outer!r}, got {type(instance)!r}"
+                    f"{name} must wrap an object of type {cls_outer!r}, "
+                    f"got {type(instance)!r}"
                 )
             else:
                 initialized = True
@@ -178,7 +179,11 @@ def __init__(self, instance: Optional[T] = None):
     return BoxedClass
 
 
-_Graph = create_boxed("_Graph", igraph_t, destructor=igraph_destroy)
+# This trickery is needed to ensure that Pyright does to trip up on _Graph annotations
+class _Graph(create_boxed("_Graph", igraph_t, destructor=igraph_destroy)):
+    pass
+
+
 _Matrix = create_boxed(
     "_Matrix",
     igraph_matrix_t,