Define __all__ across all subpackage __init__.py files

tests/core/test_hypergraph.py

@@ -547,7 +547,7 @@ def test_random_edge_shuffle(edgelist4):
     assert len(H._edge[1]) == len(S._edge[1])
 
     # verify dual of edge dict is nodes dict
-    assert xgi.utilities.dual_dict(H._edge) == H._node
+    assert xgi.dual_dict(H._edge) == H._node
 
     # hypergraph with more than two edges
     S = xgi.Hypergraph(edgelist4)
@@ -568,7 +568,7 @@ def test_random_edge_shuffle(edgelist4):
         assert len(H._edge[edge_id]) == len(S._edge[edge_id])
 
     # verify dual of edge dict is nodes dict
-    assert xgi.utilities.dual_dict(H._edge) == H._node
+    assert xgi.dual_dict(H._edge) == H._node
 
     # random hypergraph
     S = xgi.random_hypergraph(50, [0.1, 0.01, 0.001], seed=1)
@@ -588,7 +588,7 @@ def test_random_edge_shuffle(edgelist4):
         assert len(H._node[node_id]) == len(S._node[node_id])
 
     # verify dual of edge dict is nodes dict
-    assert xgi.utilities.dual_dict(H._edge) == H._node
+    assert xgi.dual_dict(H._edge) == H._node
 
 
 def test_duplicate_edges(edgelist1):

xgi/__init__.py

@@ -25,3 +25,17 @@
 
 
 __version__ = "0.10"
+
+__all__ = (
+    core.__all__
+    + algorithms.__all__
+    + communities.__all__
+    + convert.__all__
+    + drawing.__all__
+    + dynamics.__all__
+    + generators.__all__
+    + linalg.__all__
+    + readwrite.__all__
+    + stats.__all__
+    + utils.__all__
+)

xgi/algorithms/__init__.py

@@ -14,3 +14,42 @@
 from .properties import *
 from .shortest_path import *
 from .simpliciality import *
+
+__all__ = [
+    "dynamical_assortativity",
+    "degree_assortativity",
+    "clique_eigenvector_centrality",
+    "h_eigenvector_centrality",
+    "z_eigenvector_centrality",
+    "node_edge_centrality",
+    "line_vector_centrality",
+    "katz_centrality",
+    "uniform_h_eigenvector_centrality",
+    "clustering_coefficient",
+    "local_clustering_coefficient",
+    "two_node_clustering_coefficient",
+    "is_connected",
+    "connected_components",
+    "largest_connected_component",
+    "number_connected_components",
+    "node_connected_component",
+    "largest_connected_hypergraph",
+    "equal",
+    "num_edges_order",
+    "max_edge_order",
+    "is_uniform",
+    "is_possible_order",
+    "edge_neighborhood",
+    "degree_counts",
+    "degree_histogram",
+    "unique_edge_sizes",
+    "density",
+    "incidence_density",
+    "single_source_shortest_path_length",
+    "shortest_path_length",
+    "edit_simpliciality",
+    "simplicial_edit_distance",
+    "face_edit_simpliciality",
+    "mean_face_edit_distance",
+    "simplicial_fraction",
+]

xgi/communities/__init__.py

@@ -1,2 +1,4 @@
 from . import spectral
 from .spectral import *
+
+__all__ = ["spectral_clustering"]

xgi/convert/__init__.py

@@ -24,3 +24,33 @@
 from .line_graph import *
 from .pandas import *
 from .simplex import *
+
+__all__ = [
+    "from_bipartite_edgelist",
+    "to_bipartite_edgelist",
+    "from_bipartite_graph",
+    "to_bipartite_graph",
+    "to_encapsulation_dag",
+    "empirical_subsets_filter",
+    "to_graph",
+    "to_hif_dict",
+    "from_hif_dict",
+    "to_hypergraph",
+    "to_dihypergraph",
+    "to_simplicial_complex",
+    "cut_to_order",
+    "from_hyperedge_dict",
+    "to_hyperedge_dict",
+    "from_hyperedge_list",
+    "to_hyperedge_list",
+    "to_hypergraph_dict",
+    "from_hypergraph_dict",
+    "from_incidence_matrix",
+    "to_incidence_matrix",
+    "to_line_graph",
+    "from_bipartite_pandas_dataframe",
+    "to_bipartite_pandas_dataframe",
+    "from_simplex_dict",
+    "from_max_simplices",
+    "k_skeleton",
+]

xgi/core/__init__.py

@@ -2,3 +2,5 @@
 from .dihypergraph import DiHypergraph
 from .globalviews import subhypergraph
 from .simplicialcomplex import SimplicialComplex
+
+__all__ = ["Hypergraph", "DiHypergraph", "SimplicialComplex", "subhypergraph"]

xgi/drawing/__init__.py

@@ -1,2 +1,25 @@
 from .layout import *
 from .draw import *
+
+__all__ = [
+    "random_layout",
+    "pairwise_spring_layout",
+    "barycenter_spring_layout",
+    "weighted_barycenter_spring_layout",
+    "pca_transform",
+    "circular_layout",
+    "spiral_layout",
+    "barycenter_kamada_kawai_layout",
+    "bipartite_spring_layout",
+    "edge_positions_from_barycenters",
+    "draw",
+    "draw_nodes",
+    "draw_hyperedges",
+    "draw_simplices",
+    "draw_node_labels",
+    "draw_hyperedge_labels",
+    "draw_multilayer",
+    "draw_bipartite",
+    "draw_undirected_dyads",
+    "draw_directed_dyads",
+]

xgi/dynamics/__init__.py

@@ -1,2 +1,9 @@
 from . import synchronization
 from .synchronization import *
+
+__all__ = [
+    "simulate_kuramoto",
+    "simulate_simplicial_kuramoto",
+    "compute_kuramoto_order_parameter",
+    "compute_simplicial_order_parameter",
+]

xgi/generators/__init__.py

@@ -14,3 +14,31 @@
 from .simple import *
 from .simplicial_complexes import *
 from .uniform import *
+
+__all__ = [
+    "empty_hypergraph",
+    "empty_simplicial_complex",
+    "empty_dihypergraph",
+    "trivial_hypergraph",
+    "complete_hypergraph",
+    "star_clique",
+    "sunflower",
+    "complement",
+    "ring_lattice",
+    "watts_strogatz_hypergraph",
+    "random_hypergraph",
+    "fast_random_hypergraph",
+    "chung_lu_hypergraph",
+    "dcsbm_hypergraph",
+    "node_swap",
+    "shuffle_hyperedges",
+    "flag_complex",
+    "flag_complex_d2",
+    "random_flag_complex",
+    "random_flag_complex_d2",
+    "random_simplicial_complex",
+    "uniform_hypergraph_configuration_model",
+    "uniform_erdos_renyi_hypergraph",
+    "uniform_HSBM",
+    "uniform_HPPM",
+]

xgi/linalg/__init__.py

@@ -2,3 +2,17 @@
 from .hodge_matrix import *
 from .hypergraph_matrix import *
 from .laplacian_matrix import *
+
+__all__ = [
+    "boundary_matrix",
+    "hodge_laplacian",
+    "adjacency_matrix",
+    "incidence_matrix",
+    "intersection_profile",
+    "clique_motif_matrix",
+    "degree_matrix",
+    "adjacency_tensor",
+    "laplacian",
+    "multiorder_laplacian",
+    "normalized_hypergraph_laplacian",
+]

xgi/readwrite/__init__.py

@@ -6,3 +6,23 @@
 from .incidence import *
 from .json import *
 from .xgi_data import *
+
+__all__ = [
+    "load_bigg_data",
+    "read_bipartite_edgelist",
+    "write_bipartite_edgelist",
+    "parse_bipartite_edgelist",
+    "read_edgelist",
+    "write_edgelist",
+    "parse_edgelist",
+    "read_hif",
+    "write_hif",
+    "read_hif_collection",
+    "write_hif_collection",
+    "read_incidence_matrix",
+    "write_incidence_matrix",
+    "read_json",
+    "write_json",
+    "load_xgi_data",
+    "download_xgi_data",
+]

xgi/stats/__init__.py

@@ -113,8 +113,9 @@ def name(self):
         ('degree', 'degree(order=3)')
         >>> H.nodes.multi([da, d3]).asdict(transpose=True).keys()
         dict_keys(['degree', 'degree(order=3)'])
-        >>> H.nodes.multi([da, d3]).aspandas().columns
-        Index(['degree', 'degree(order=3)'], dtype='object')
+        >>> cols = H.nodes.multi([da, d3]).aspandas().columns
+        >>> list(cols)
+        ['degree', 'degree(order=3)']
 
         """
         name = f"{self.func.__name__}"

xgi/utils/__init__.py

@@ -2,3 +2,24 @@
 from .tensor import *
 from .trie import *
 from .utilities import *
+
+__all__ = [
+    "IDDict",
+    "Trie",
+    "binomial_sequence",
+    "convert_labels_to_integers",
+    "crest_r",
+    "dual_dict",
+    "find_triangles",
+    "geometric",
+    "get_network_type",
+    "hist",
+    "pairwise_incidence",
+    "powerset",
+    "request_json_from_url",
+    "request_json_from_url_cached",
+    "subfaces",
+    "ttsv1",
+    "ttsv2",
+    "update_uid_counter",
+]