Minor fixes (#164)

xgi-org · Sep 8, 2022 · 70c4bb3 · 70c4bb3
1 parent 20ce1b8
commit 70c4bb3
Show file tree

Hide file tree

Showing 37 changed files with 40 additions and 134 deletions.
diff --git a/docs/source/api/classes.rst b/docs/source/api/classes.rst
@@ -11,4 +11,4 @@ classes package
    ~xgi.classes.simplicialcomplex
    ~xgi.classes.reportviews
    ~xgi.classes.hypergraphviews
-   ~xgi.classes.function
+   ~xgi.classes.function
diff --git a/docs/source/api/classes/xgi.classes.function.rst b/docs/source/api/classes/xgi.classes.function.rst
@@ -7,6 +7,7 @@
 
    .. rubric:: Functions
 
+   .. autofunction:: convert_labels_to_integers
    .. autofunction:: create_empty_copy
    .. autofunction:: degree_counts
    .. autofunction:: degree_histogram
@@ -22,4 +23,4 @@
    .. autofunction:: max_edge_order
    .. autofunction:: set_edge_attributes
    .. autofunction:: set_node_attributes
-   .. autofunction:: unique_edge_sizes
+   .. autofunction:: unique_edge_sizes
diff --git a/docs/source/api/classes/xgi.classes.hypergraph.Hypergraph.rst b/docs/source/api/classes/xgi.classes.hypergraph.Hypergraph.rst
@@ -37,12 +37,12 @@
       ~Hypergraph.remove_node_from_edge
       ~Hypergraph.clear
       ~Hypergraph.clear_edges
-
+      ~Hypergraph.cleanup
 
    .. rubric:: Methods that return other hypergraphs
 
    .. autosummary::
       :nosignatures:
 
       ~Hypergraph.copy
-      ~Hypergraph.dual
+      ~Hypergraph.dual
diff --git a/docs/source/api/classes/xgi.classes.hypergraph.IDDict.rst b/docs/source/api/classes/xgi.classes.hypergraph.IDDict.rst
@@ -7,12 +7,8 @@
    :show-inheritance:
    :members:
 
-
-
 
-
    .. rubric:: Methods
 
    .. autosummary::
-      :nosignatures:
-
+      :nosignatures:
diff --git a/docs/source/api/classes/xgi.classes.hypergraph.rst b/docs/source/api/classes/xgi.classes.hypergraph.rst
@@ -13,13 +13,4 @@
 
         Hypergraph
 
-        IDDict
-
-
-
-
-
-
-
-
-
+        IDDict
diff --git a/docs/source/api/classes/xgi.classes.hypergraphviews.rst b/docs/source/api/classes/xgi.classes.hypergraphviews.rst
@@ -7,4 +7,4 @@
 
    .. rubric:: Functions
 
-   .. autofunction:: subhypergraph
+   .. autofunction:: subhypergraph
diff --git a/docs/source/api/classes/xgi.classes.reportviews.EdgeView.rst b/docs/source/api/classes/xgi.classes.reportviews.EdgeView.rst
@@ -26,4 +26,4 @@ xgi.classes.reportviews.EdgeView
       ~IDView.duplicates
       ~IDView.lookup
       ~IDView.filterby
-      ~IDView.filterby_attr
+      ~IDView.filterby_attr
diff --git a/docs/source/api/classes/xgi.classes.reportviews.IDView.rst b/docs/source/api/classes/xgi.classes.reportviews.IDView.rst
@@ -8,9 +8,6 @@ xgi.classes.reportviews.IDView
    :members:
 
 
-
-
-
    .. rubric:: Methods
 
    .. autosummary::

diff --git a/docs/source/api/classes/xgi.classes.reportviews.NodeView.rst b/docs/source/api/classes/xgi.classes.reportviews.NodeView.rst
@@ -26,4 +26,4 @@ xgi.classes.reportviews.NodeView
       ~IDView.duplicates
       ~IDView.lookup
       ~IDView.filterby
-      ~IDView.filterby_attr
+      ~IDView.filterby_attr
diff --git a/docs/source/api/classes/xgi.classes.reportviews.rst b/docs/source/api/classes/xgi.classes.reportviews.rst
@@ -13,4 +13,4 @@
 
         IDView
         NodeView
-        EdgeView
+        EdgeView
diff --git a/docs/source/api/classes/xgi.classes.simplicialcomplex.SimplicialComplex.rst b/docs/source/api/classes/xgi.classes.simplicialcomplex.SimplicialComplex.rst
@@ -18,7 +18,6 @@
       ~SimplicialComplex.num_nodes
 
 
-
    .. rubric:: Methods
 
    .. autosummary::
@@ -45,4 +44,4 @@
       ~SimplicialComplex.remove_edge
       ~SimplicialComplex.remove_edges_from
       ~SimplicialComplex.remove_simplex_id
-      ~SimplicialComplex.remove_simplex_ids_from
+      ~SimplicialComplex.remove_simplex_ids_from
diff --git a/docs/source/api/classes/xgi.classes.simplicialcomplex.rst b/docs/source/api/classes/xgi.classes.simplicialcomplex.rst
@@ -11,13 +11,4 @@
       :toctree: .
       :nosignatures:
 
-        SimplicialComplex
-
-
-
-
-
-
-
-
-
+        SimplicialComplex
diff --git a/docs/source/api/classes/xgi.linalg.matrix.rst b/docs/source/api/classes/xgi.linalg.matrix.rst
@@ -13,11 +13,4 @@
    .. autofunction:: incidence_matrix
    .. autofunction:: intersection_profile
    .. autofunction:: laplacian
-   .. autofunction:: multiorder_laplacian
-
-
-
-
-
-
-
+   .. autofunction:: multiorder_laplacian
diff --git a/docs/source/api/classes/xgi.utils.utilities.rst b/docs/source/api/classes/xgi.utils.utilities.rst
@@ -14,4 +14,4 @@
 
    .. rubric:: Functions
 
-   .. autofunction:: dual_dict
+   .. autofunction:: dual_dict
diff --git a/docs/source/api/generators.rst b/docs/source/api/generators.rst
@@ -9,4 +9,4 @@ generators package
 
    ~xgi.generators.classic
    ~xgi.generators.nonuniform
-   ~xgi.generators.uniform
+   ~xgi.generators.uniform
diff --git a/docs/source/api/generators/xgi.generators.classic.rst b/docs/source/api/generators/xgi.generators.classic.rst
@@ -10,11 +10,4 @@
    .. autofunction:: empty_hypergraph
    .. autofunction:: flag_complex
    .. autofunction:: star_clique
-   .. autofunction:: sunflower
-
-
-
-
-
-
-
+   .. autofunction:: sunflower
diff --git a/docs/source/api/generators/xgi.generators.nonuniform.rst b/docs/source/api/generators/xgi.generators.nonuniform.rst
@@ -12,11 +12,4 @@ xgi.generators.nonuniform
    .. autofunction:: random_flag_complex
    .. autofunction:: random_flag_complex_d2
    .. autofunction:: random_hypergraph
-   .. autofunction:: random_simplicial_complex
-
-
-
-
-
-
-
+   .. autofunction:: random_simplicial_complex
diff --git a/docs/source/api/generators/xgi.generators.uniform.rst b/docs/source/api/generators/xgi.generators.uniform.rst
@@ -7,11 +7,4 @@ xgi.generators.uniform
 
    .. rubric:: Functions
 
-   .. autofunction:: uniform_hypergraph_configuration_model
-
-
-
-
-
-
-
+   .. autofunction:: uniform_hypergraph_configuration_model
diff --git a/docs/source/api/linalg.rst b/docs/source/api/linalg.rst
@@ -7,4 +7,4 @@ linalg package
 .. autosummary::
    :toctree: classes
 
-   ~xgi.linalg.matrix
+   ~xgi.linalg.matrix
diff --git a/docs/source/api/readwrite.rst b/docs/source/api/readwrite.rst
@@ -11,4 +11,4 @@ readwrite package
    ~xgi.readwrite.edgelist
    ~xgi.readwrite.incidence
    ~xgi.readwrite.json
-   ~xgi.readwrite.xgi_data
+   ~xgi.readwrite.xgi_data
diff --git a/docs/source/api/readwrite/xgi.readwrite.bipartite.rst b/docs/source/api/readwrite/xgi.readwrite.bipartite.rst
@@ -10,11 +10,4 @@ xgi.readwrite.bipartite
    .. autofunction:: generate_bipartite_edgelist
    .. autofunction:: parse_bipartite_edgelist
    .. autofunction:: read_bipartite_edgelist
-   .. autofunction:: write_bipartite_edgelist
-
-
-
-
-
-
-
+   .. autofunction:: write_bipartite_edgelist
diff --git a/docs/source/api/readwrite/xgi.readwrite.edgelist.rst b/docs/source/api/readwrite/xgi.readwrite.edgelist.rst
@@ -10,11 +10,4 @@ xgi.readwrite.edgelist
    .. autofunction:: generate_edgelist
    .. autofunction:: parse_edgelist
    .. autofunction:: read_edgelist
-   .. autofunction:: write_edgelist
-
-
-
-
-
-
-
+   .. autofunction:: write_edgelist
diff --git a/docs/source/api/readwrite/xgi.readwrite.incidence.rst b/docs/source/api/readwrite/xgi.readwrite.incidence.rst
@@ -8,11 +8,4 @@ xgi.readwrite.incidence
    .. rubric:: Functions
 
    .. autofunction:: read_incidence_matrix
-   .. autofunction:: write_incidence_matrix
-
-
-
-
-
-
-
+   .. autofunction:: write_incidence_matrix
diff --git a/docs/source/api/readwrite/xgi.readwrite.json.rst b/docs/source/api/readwrite/xgi.readwrite.json.rst
@@ -8,11 +8,4 @@ xgi.readwrite.json
    .. rubric:: Functions
 
    .. autofunction:: read_json
-   .. autofunction:: write_json
-
-
-
-
-
-
-
+   .. autofunction:: write_json
diff --git a/docs/source/api/readwrite/xgi.readwrite.xgi_data.rst b/docs/source/api/readwrite/xgi.readwrite.xgi_data.rst
@@ -7,4 +7,4 @@ xgi.readwrite.xgi_data
 
    .. rubric:: Functions
 
-   .. autofunction:: load_xgi_data
+   .. autofunction:: load_xgi_data
diff --git a/docs/source/api/stats.rst b/docs/source/api/stats.rst
@@ -43,4 +43,4 @@ stats package
 
    ~xgi.stats.StatDispatcher
    ~xgi.stats.EdgeStatDispatcher
-   ~xgi.stats.NodeStatDispatcher
+   ~xgi.stats.NodeStatDispatcher
diff --git a/docs/source/api/stats/xgi.stats.EdgeStat.rst b/docs/source/api/stats/xgi.stats.EdgeStat.rst
@@ -31,4 +31,4 @@
       ~EdgeStat.min
       ~EdgeStat.std
       ~EdgeStat.var
-      ~EdgeStat.moment
+      ~EdgeStat.moment
diff --git a/docs/source/api/stats/xgi.stats.EdgeStatDispatcher.rst b/docs/source/api/stats/xgi.stats.EdgeStatDispatcher.rst
@@ -8,10 +8,7 @@
    :members:
 
 
-
-
-
    .. rubric:: Methods
 
    .. autosummary::
-      :nosignatures:
+      :nosignatures:
diff --git a/docs/source/api/stats/xgi.stats.MultiNodeStat.rst b/docs/source/api/stats/xgi.stats.MultiNodeStat.rst
@@ -24,4 +24,4 @@
       ~MultiNodeStat.asdict
       ~MultiNodeStat.aslist
       ~MultiNodeStat.asnumpy
-      ~MultiNodeStat.aspandas
+      ~MultiNodeStat.aspandas
diff --git a/docs/source/api/stats/xgi.stats.NodeStat.rst b/docs/source/api/stats/xgi.stats.NodeStat.rst
@@ -8,7 +8,6 @@
    :members:
    :inherited-members:
 
-
    .. rubric:: Attributes
 
    .. autosummary::
@@ -31,4 +30,4 @@
       ~NodeStat.min
       ~NodeStat.std
       ~NodeStat.var
-      ~NodeStat.moment
+      ~NodeStat.moment
diff --git a/docs/source/api/stats/xgi.stats.NodeStatDispatcher.rst b/docs/source/api/stats/xgi.stats.NodeStatDispatcher.rst
@@ -7,12 +7,8 @@
    :show-inheritance:
    :members:
 
-
-
 
-
    .. rubric:: Methods
 
    .. autosummary::
-      :nosignatures:
-
+      :nosignatures:
diff --git a/docs/source/api/stats/xgi.stats.StatDispatcher.rst b/docs/source/api/stats/xgi.stats.StatDispatcher.rst
@@ -8,12 +8,9 @@
    :members:
 
 
-
-
-
    .. rubric:: Methods
 
    .. autosummary::
       :nosignatures:
 
-      ~StatDispatcher.multi
+      ~StatDispatcher.multi
diff --git a/docs/source/api/utils.rst b/docs/source/api/utils.rst
@@ -7,4 +7,4 @@ utils package
 .. autosummary::
    :toctree: classes
 
-   ~xgi.utils.utilities
+   ~xgi.utils.utilities
diff --git a/xgi/classes/hypergraph.py b/xgi/classes/hypergraph.py
@@ -1002,10 +1002,8 @@ def cleanup(
                 nn = temp.nodes
                 ee = temp.edges
 
-                self.remove_nodes_from(list(self._node))
+                self.clear()
                 self.add_nodes_from((n, deepcopy(attr)) for n, attr in nn.items())
-
-                self.remove_edges_from(list(self._edge))
                 self.add_edges_from(
                     (e, id, deepcopy(temp.edges[id]))
                     for id, e in ee.members(dtype=dict).items()

diff --git a/xgi/classes/reportviews.py b/xgi/classes/reportviews.py
@@ -412,9 +412,7 @@ def duplicates(self):
         for idx, members in self._id_dict.items():
             hashes[frozenset(members)].append(idx)
         for _, edges in hashes.items():
-            if len(edges) == 1:
-                continue
-            else:
+            if len(edges) > 1:
                 dups.extend(sorted(edges)[1:])
         return self.__class__.from_view(self, bunch=dups)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,4 +7,4 @@

		.. rubric:: Functions

		.. autofunction:: subhypergraph
		.. autofunction:: subhypergraph
Original file line number	Diff line number	Diff line change
Expand Up		@@ -8,9 +8,6 @@ xgi.classes.reportviews.IDView
		:members:





		.. rubric:: Methods

		.. autosummary::
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -14,4 +14,4 @@

		.. rubric:: Functions

		.. autofunction:: dual_dict
		.. autofunction:: dual_dict
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,11 +7,4 @@ xgi.generators.uniform

		.. rubric:: Functions

		.. autofunction:: uniform_hypergraph_configuration_model







		.. autofunction:: uniform_hypergraph_configuration_model
Original file line number	Diff line number	Diff line change
Expand Up		@@ -7,4 +7,4 @@ xgi.readwrite.xgi_data

		.. rubric:: Functions

		.. autofunction:: load_xgi_data
		.. autofunction:: load_xgi_data