Fix broken "See Also" links

xgi/algorithms/properties.py

@@ -152,7 +152,7 @@ def edge_neighborhood(H, n, include_self=False):
 
     See Also
     --------
-    neighbors
+    ~xgi.core.views.IDView.neighbors
 
     Examples
     --------

xgi/convert/bipartite_edges.py

@@ -21,7 +21,7 @@ def from_bipartite_edgelist(edges):
 
     See Also
     --------
-    to_hyperedge_list
+    ~xgi.convert.edgelist.from_hyperedge_list
     """
     if len(edges[0]) == 3:  # directed
         H = DiHypergraph()
@@ -55,7 +55,7 @@ def to_bipartite_edgelist(H):
 
     See Also
     --------
-    from_hyperedge_list
+    ~xgi.convert.edgelist.to_hyperedge_list
     """
     if isinstance(H, DiHypergraph):
         edgelist = []

xgi/convert/higher_order_network.py

@@ -58,7 +58,7 @@ def to_hypergraph(data, create_using=None):
 
     See Also
     --------
-    from_max_simplices : Constructs a hypergraph from the maximal simplices of a simplicial complex.
+    ~xgi.utils.utilities.from_max_simplices : Constructs a hypergraph from the maximal simplices of a simplicial complex.
 
     """
     if data is None:

xgi/convert/hyperedges.py

@@ -30,7 +30,8 @@ def from_hyperedge_dict(d, create_using=None):
     See Also
     --------
     to_hyperedge_dict
-
+    from_hyperedge_list
+    to_hyperedge_list
     """
     H = empty_hypergraph(create_using)
     H.add_edges_from((members, uid) for uid, members in d.items())
@@ -54,6 +55,8 @@ def to_hyperedge_dict(H):
     See Also
     --------
     from_hyperedge_dict
+    to_hyperedge_list
+    from_hyperedge_list
     """
     return H.edges.members(dtype=dict)
 
@@ -76,6 +79,8 @@ def from_hyperedge_list(d, create_using=None, max_order=None):
     See Also
     --------
     to_hyperedge_list
+    from_hyperedge_dict
+    to_hyperedge_dict
     """
     H = empty_hypergraph(create_using)
     if isinstance(H, SimplicialComplex):
@@ -101,5 +106,7 @@ def to_hyperedge_list(H):
     See Also
     --------
     from_hyperedge_list
+    to_hyperedge_dict
+    from_hyperedge_dict
     """
     return H.edges.members()

xgi/convert/hypergraph_dict.py

@@ -28,6 +28,11 @@ def to_hypergraph_dict(H):
         If node IDs will be collapsed when casting to a string.
     XGIError
         If edge Ids will be collapsed when casting to a string.
+
+    See Also
+    --------
+    ~xgi.readwrite.json.read_json
+    ~xgi.readwrite.json.write_json
     """
     data = {}
     data["type"] = get_network_type(H)
@@ -94,7 +99,8 @@ def from_hypergraph_dict(data, nodetype=None, edgetype=None, max_order=None):
 
     See Also
     --------
-    read_json
+    ~xgi.readwrite.json.read_json
+    ~xgi.readwrite.json.write_json
 
     """
     H = empty_hypergraph()

xgi/convert/incidence.py

@@ -37,7 +37,7 @@ def from_incidence_matrix(d, create_using=None, nodelabels=None, edgelabels=None
 
     See Also
     --------
-    incidence_matrix
+    ~xgi.linalg.hypergraph_matrix.incidence_matrix
     to_incidence_matrix
     """
     I = coo_array(d)
@@ -92,7 +92,7 @@ def to_incidence_matrix(H, sparse=True, index=False):
 
     See Also
     --------
-    incidence_matrix
+    ~xgi.linalg.hypergraph_matrix.incidence_matrix
     from_incidence_matrix
     """
     return incidence_matrix(H, sparse=sparse, index=index)

xgi/core/dihypergraph.py

@@ -52,6 +52,10 @@ class DiHypergraph:
     **attr : dict, optional, default: None
         Attributes to add to the hypergraph as key, value pairs.
 
+    See Also
+    --------
+    ~xgi.core.hypergraph.Hypergraph
+    
     Notes
     -----
     Unique IDs are assigned to each node and edge internally and are used to refer to
@@ -145,10 +149,10 @@ def __init__(self, incoming_data=None, **attr):
         self._edge_attr = self._edge_attr_dict_factory()
 
         self._nodeview = DiNodeView(self)
-        """A :class:`~xgi.core.direportviews.DiNodeView` of the directed hypergraph."""
+        """A :class:`~xgi.core.views.DiNodeView` of the directed hypergraph."""
 
         self._edgeview = DiEdgeView(self)
-        """An :class:`~xgi.core.direportviews.DiEdgeView` of the directed hypergraph."""
+        """An :class:`~xgi.core.views.DiEdgeView` of the directed hypergraph."""
 
         if incoming_data is not None:
             # This import needs to happen when this function is called, not when it is
@@ -1043,7 +1047,7 @@ def freeze(self):
 
         See Also
         --------
-        frozen : Method that raises an error when a user tries to modify the hypergraph
+        ~xgi.exception.frozen : Method that raises an error when a user tries to modify the hypergraph
         is_frozen : Check whether a dihypergraph is frozen
 
         Examples

xgi/core/hypergraph.py

@@ -44,6 +44,11 @@ class Hypergraph:
         Attributes to add to the hypergraph as key, value pairs.
         By default, None.
 
+    See Also
+    --------
+    ~xgi.core.simplicialcomplex.SimplicialComplex
+    ~xgi.core.dihypergraph.DiHypergraph
+
     Notes
     -----
     Unique IDs are assigned to each node and edge internally and are used to refer to
@@ -128,10 +133,10 @@ def __init__(self, incoming_data=None, **attr):
         self._edge_attr = self._edge_attr_dict_factory()
 
         self._nodeview = NodeView(self)
-        """A :class:`~xgi.core.reportviews.NodeView` of the hypergraph."""
+        """A :class:`~xgi.core.views.NodeView` of the hypergraph."""
 
         self._edgeview = EdgeView(self)
-        """An :class:`~xgi.core.reportviews.EdgeView` of the hypergraph."""
+        """An :class:`~xgi.core.views.EdgeView` of the hypergraph."""
 
         if incoming_data is not None:
             # This import needs to happen when this function is called, not when it is
@@ -1490,7 +1495,7 @@ def freeze(self):
 
         See Also
         --------
-        frozen : Method that raises an error when a user tries to modify the hypergraph
+        ~xgi.exception.frozen : Method that raises an error when a user tries to modify the hypergraph
         is_frozen : Check whether a hypergraph is frozen
 
         Examples

xgi/core/views.py

@@ -362,7 +362,7 @@ def neighbors(self, id, s=1):
 
         See Also
         --------
-        ~xgi.core.function.edge_neighborhood
+        ~xgi.algorithms.properties.edge_neighborhood
 
         Examples
         --------

xgi/generators/uniform.py

@@ -289,7 +289,7 @@ def uniform_erdos_renyi_hypergraph(n, m, p, p_type="degree", seed=None):
 
     See Also
     --------
-    random_hypergraph
+    ~xgi.generators.random.random_hypergraph
     """
     if seed is not None:
         np.random.seed(seed)

xgi/stats/diedgestats.py

@@ -3,7 +3,7 @@
 This module is part of the stats package, and it defines edge-level statistics.  That
 is, each function defined in this module is assumed to define an edge-quantity mapping.
 Each callable defined here is accessible via a `Network` object, or a
-:class:`~xgi.core.reportviews.DiEdgeView` object.  For more details, see the `tutorial
+:class:`~xgi.core.views.DiEdgeView` object.  For more details, see the `tutorial
 <https://xgi.readthedocs.io/en/stable/api/tutorials/focus_6.html>`_.
 
 Examples

xgi/stats/dinodestats.py

@@ -3,7 +3,7 @@
 This module is part of the stats package, and it defines node-level statistics.  That
 is, each function defined in this module is assumed to define a node-quantity mapping.
 Each callable defined here is accessible via a `Network` object, or a
-:class:`~xgi.core.reportviews.NodeView` object.  For more details, see the `tutorial
+:class:`~xgi.core.views.NodeView` object.  For more details, see the `tutorial
 <https://xgi.readthedocs.io/en/stable/api/tutorials/focus_6.html>`_.
 
 Examples

xgi/stats/edgestats.py

@@ -3,7 +3,7 @@
 This module is part of the stats package, and it defines edge-level statistics.  That
 is, each function defined in this module is assumed to define an edge-quantity mapping.
 Each callable defined here is accessible via a `Network` object, or a
-:class:`~xgi.core.reportviews.EdgeView` object.  For more details, see the `tutorial
+:class:`~xgi.core.views.EdgeView` object.  For more details, see the `tutorial
 <https://xgi.readthedocs.io/en/stable/api/tutorials/focus_6.html>`_.
 
 Examples

xgi/stats/nodestats.py

@@ -3,7 +3,7 @@
 This module is part of the stats package, and it defines node-level statistics.  That
 is, each function defined in this module is assumed to define a node-quantity mapping.
 Each callable defined here is accessible via a `Network` object, or a
-:class:`~xgi.core.reportviews.NodeView` object.  For more details, see the `tutorial
+:class:`~xgi.core.views.NodeView` object.  For more details, see the `tutorial
 <https://xgi.readthedocs.io/en/stable/api/tutorials/focus_6.html>`_.
 
 Examples

xgi/utils/utilities.py

@@ -453,9 +453,9 @@ def hist(vals, bins=10, bin_edges=False, density=False, log_binning=False):
 
     Parameters
     ----------
-    vals : Numpy array
+    vals : numpy.ndarray
         The array of values
-    bins : int, list, or Numpy array
+    bins : int, list, or numpy.ndarray
         The number of bins or the bin edges.
         By default, 10.
     bin_edges : bool
@@ -470,7 +470,7 @@ def hist(vals, bins=10, bin_edges=False, density=False, log_binning=False):
 
     Returns
     -------
-    Pandas DataFrame
+    ~pandas.DataFrame
         A two-column table with "bin_center" and "value" columns,
         where "value" is a count or a probability. If `bin_edges`
         is True, outputs two additional columns, `bin_lo` and `bin_hi`,