Pull request #112: Hotfix/HYP-354 hypergraph.collapse methods have ba…

…d documentation and deprecation warnings aren t

Merge in HYP/hypernetx from hotfix/HYP-354-hypergraph.collapse_-methods-have-bad-documentation-and-deprecation-warnings-aren-t to master

* commit '677895b0677ade095fac8824a3ccbe6f8766ab76':
  bump: version 2.0.4 → 2.0.5
  HYP-354 Fix docstrings and display deprecation warnings

.cz.toml

@@ -1,6 +1,6 @@
 [tool.commitizen]
 name = "cz_conventional_commits"
-version = "2.0.4"
+version = "2.0.5"
 version_files = [
     "setup.py",
     "docs/source/conf.py",

docs/source/conf.py

@@ -19,7 +19,7 @@
 import os
 
 
-__version__ = "2.0.4"
+__version__ = "2.0.5"
 
 
 # If extensions (or modules to document with autodoc) are in another directory,

hypernetx/__init__.py

@@ -11,4 +11,4 @@
 from hypernetx.utils import *
 from hypernetx.utils.toys import *
 
-__version__ = "2.0.4"
+__version__ = "2.0.5"

hypernetx/classes/entity.py

@@ -542,7 +542,6 @@ def elements_by_level(self, level1, level2):
         return self.elements_by_column(col1, col2)
 
     def elements_by_column(self, col1, col2):
-
         """System of sets representation of two columns (levels) of the underlying data table
 
         Each item in col1 defines a set containing all the col2 items
@@ -572,7 +571,9 @@ def elements_by_column(self, col1, col2):
             self._state_dict["elements"] = defaultdict(dict)
         if col2 not in self._state_dict["elements"][col1]:
             level = self.index(col1)
-            elements = self._dataframe.groupby(col1)[col2].unique().to_dict()
+            elements = (
+                self._dataframe.groupby(col1, observed=False)[col2].unique().to_dict()
+            )
             self._state_dict["elements"][col1][col2] = {
                 item: AttrList(entity=self, key=(level, item), initlist=elem)
                 for item, elem in elements.items()
@@ -1378,13 +1379,14 @@ def _properties_from_dataframe(self, props: pd.DataFrame) -> None:
                 pass  # data already parsed, no literal eval needed
             else:
                 warnings.warn("parsed property dict column from string literal")
-
         if props.index.nlevels == 1:
             props = props.reindex(self.properties.index, level=1)
 
         # combine with existing properties
         # non-null values in new props override existing value
+        warnings.simplefilter(action="ignore", category=RuntimeWarning)
         properties = props.combine_first(self.properties)
+        warnings.simplefilter(action="default", category=RuntimeWarning)
         # update misc. column to combine existing and new misc. property dicts
         # new props override existing value for overlapping misc. property dict keys
         properties[self._misc_props_col] = self.properties[

hypernetx/classes/entityset.py

@@ -531,7 +531,7 @@ def collapse_identical_elements(
         # group by level 0 (set), aggregate level 1 (set elements) as frozenset
         collapse = (
             self._dataframe[self._data_cols]
-            .groupby(self._data_cols[0], as_index=False)
+            .groupby(self._data_cols[0], as_index=False, observed=False)
             .agg(frozenset)
         )
 

hypernetx/classes/hypergraph.py

@@ -2,8 +2,10 @@
 # All rights reserved.
 from __future__ import annotations
 
-import pickle
 import warnings
+
+warnings.filterwarnings("default", category=DeprecationWarning)
+
 from copy import deepcopy
 from collections import defaultdict
 from collections.abc import Sequence, Iterable
@@ -326,7 +328,6 @@ def __init__(
         ### cell properties
 
         if setsystem is None:  #### Empty Case
-
             self._edges = EntitySet({})
             self._nodes = EntitySet({})
             self._state_dict = {}
@@ -1336,7 +1337,7 @@ def collapse_nodes(
         return_equivalence_classes=False,
         use_reps=None,
         return_counts=None,
-    ):
+    ) -> Hypergraph:
         """
         Constructs a new hypergraph gotten by identifying nodes contained by
         the same edges
@@ -1349,15 +1350,15 @@ def collapse_nodes(
             Returns a dictionary of node equivalence classes keyed by frozen
             sets of edges
 
-        use_reps : boolean, optional, default = False - Deprecated, this no
-            longer works and will be removed. Choose a single element from the
+        use_reps : boolean, optional, default = None
+            [DEPRECATED; WILL BE REMOVED IN NEXT RELEASE] Choose a single element from the
             collapsed nodes as uid for the new node, otherwise uses a frozen
-            set of the uids of nodes in the equivalence class
-
-        return_counts: boolean, - Deprecated, this no longer works and will be
-            removed if use_reps is True the new nodes have uids given by a
+            set of the uids of nodes in the equivalence class. If use_reps is True the new nodes have uids given by a
             tuple of the rep and the count
 
+        return_counts: boolean, optional, default = None
+            [DEPRECATED; WILL BE REMOVED IN NEXT RELEASE]
+
         Returns
         -------
         new hypergraph : Hypergraph
@@ -1373,16 +1374,10 @@ def collapse_nodes(
         Example
         -------
 
-            >>> h = Hypergraph(EntitySet('example',elements=[Entity('E1', /
-                                        ['a','b']),Entity('E2',['a','b'])]))
-            >>> h.incidence_dict
-            {'E1': {'a', 'b'}, 'E2': {'a', 'b'}}
+            >>> data = {'E1': ('a', 'b'), 'E2': ('a', 'b')}))
+            >>> h = Hypergraph(data)
             >>> h.collapse_nodes().incidence_dict
-            {'E1': {frozenset({'a', 'b'})}, 'E2': {frozenset({'a', 'b'})}}
-            ### Fix this
-            >>> h.collapse_nodes(use_reps=True).incidence_dict
-            {'E1': {('a', 2)}, 'E2': {('a', 2)}}
-
+            {'E1': ['a: 2'], 'E2': ['a: 2']}
         """
         if use_reps is not None or return_counts is not None:
             msg = """
@@ -1416,25 +1411,25 @@ def collapse_nodes_and_edges(
 
         name: str, optional, default = None
 
-        use_reps: boolean, optional, default = False
-            Choose a single element from the collapsed elements as a
-            representative
-
-        return_counts: boolean, optional, default = True
-            if use_reps is True the new elements are keyed by a tuple of the
-            rep and the count
-
         return_equivalence_classes: boolean, optional, default = False
             Returns a dictionary of edge equivalence classes keyed by frozen
             sets of nodes
 
+        use_reps: boolean, optional, default = None
+            [DEPRECATED; WILL BE REMOVED IN NEXT RELEASE] Choose a single element from the collapsed elements as a
+            representative. If use_reps is True, the new elements are keyed by a tuple of the
+            rep and the count.
+
+        return_counts: boolean, optional, default = None
+            [DEPRECATED; WILL BE REMOVED IN NEXT RELEASE]
+
         Returns
         -------
         new hypergraph : Hypergraph
 
         Notes
         -----
-        Collapses the Nodes and Edges EntitySets. Two nodes(edges) are
+        Collapses the Nodes and Edges of EntitySets. Two nodes(edges) are
         duplicates if their respective memberships(elements) are the same.
         Using this as an equivalence relation, the uids of the nodes(edges)
         are partitioned into equivalence classes. A single member of the
@@ -1444,12 +1439,12 @@ def collapse_nodes_and_edges(
         Example
         -------
 
-            >>> h = Hypergraph(EntitySet('example',elements=[Entity('E1', /
-                                           ['a','b']),Entity('E2',['a','b'])]))
+            >>> data = {'E1': ('a', 'b'), 'E2': ('a', 'b')}
+            >>> h = Hypergraph(data)
             >>> h.incidence_dict
-            {'E1': {'a', 'b'}, 'E2': {'a', 'b'}}
-            >>> h.collapse_nodes_and_edges().incidence_dict   ### Fix this
-            {('E1', 2): {('a', 2)}}
+            {'E1': ['a', 'b'], 'E2': ['a', 'b']}
+            >>> h.collapse_nodes_and_edges().incidence_dict
+            {'E1: 2': ['a: 2']}
 
         """
         if use_reps is not None or return_counts is not None:

setup.py

@@ -1,5 +1,5 @@
 from setuptools import setup
 
-__version__ = "2.0.4"
+__version__ = "2.0.5"
 
 setup(version=__version__)