Fix #224 uid counter initialisation

tests/classes/test_hypergraph.py

@@ -1,3 +1,5 @@
+from itertools import count
+
 import pytest
 
 import xgi
@@ -265,6 +267,10 @@ def test_add_edges_from_format1():
     assert list(H.edges) == [e[1] for e in edges]
     assert H.edges.members(dtype=dict) == {e[1]: e[0] for e in edges}
 
+    # check counter
+    H.add_edge([1, 9, 2])
+    assert H.edges.members(101) == {1, 9, 2}
+
 
 def test_add_edges_from_format2():
     edges = [
@@ -278,6 +284,9 @@ def test_add_edges_from_format2():
     assert H.edges.members() == [e[0] for e in edges]
     for idx, e in enumerate(H.edges):
         assert H.edges[e] == edges[idx][1]
+    # check counter
+    H.add_edge([1, 9, 2])
+    assert H.edges.members(3) == {1, 9, 2}
 
 
 def test_add_edges_from_format3():
@@ -292,14 +301,20 @@ def test_add_edges_from_format3():
     assert H.edges.members() == [e[0] for e in edges]
     for idx, e in enumerate(H.edges):
         assert H.edges[e] == edges[idx][2]
+    # check counter
+    H.add_edge([1, 9, 2])
+    assert H.edges.members(0) == {1, 9, 2}
 
 
 def test_add_edges_from_dict():
-    edges = {"one": [0, 1], "two": [1, 2], "three": [2, 3, 4]}
+    edges = {"one": [0, 1], "two": [1, 2], 2: [2, 3, 4]}
     H = xgi.Hypergraph()
     H.add_edges_from(edges)
-    assert list(H.edges) == ["one", "two", "three"]
+    assert list(H.edges) == ["one", "two", 2]
     assert H.edges.members() == [set(edges[e]) for e in edges]
+    # check counter
+    H.add_edge([1, 9, 2])
+    assert H.edges.members(3) == {1, 9, 2}
 
 
 def test_add_edges_from_attr_precedence():
@@ -377,6 +392,14 @@ def test_copy(edgelist1):
     assert list(copy.edges.members()) == list(H.edges.members())
     assert H._hypergraph == copy._hypergraph
 
+    H1 = xgi.Hypergraph()
+    H1.add_edge((1, 2), id="x")
+    copy2 = H1.copy()  # does not throw error because of str id
+    assert list(copy2.nodes) == list(H1.nodes)
+    assert list(copy2.edges) == list(H1.edges)
+    assert list(copy2.edges.members()) == list(H1.edges.members())
+    assert H1._hypergraph == copy2._hypergraph
+
 
 def test_copy_issue128():
     # see https://github.com/ComplexGroupInteractions/xgi/issues/128

xgi/classes/hypergraph.py

@@ -606,6 +606,23 @@ def add_edges_from(self, ebunch_to_add, **attr):
                         self._node_attr[n] = self._node_attr_dict_factory()
                     self._node[n].add(uid)
                 self._edge_attr[uid] = self._hyperedge_attr_dict_factory()
+
+            # If we don't set the start of self._edge_uid correctly, it will start at 0,
+            # which will overwrite any existing edges when calling add_edge().  First, we
+            # use the somewhat convoluted float(e).is_integer() instead of using
+            # isinstance(e, int) because there exist integer-like numeric types (such as
+            # np.int32) which fail the isinstance() check.
+            edges_with_int_id = [
+                int(e)
+                for e in self.edges
+                if (not isinstance(e, str)) and float(e).is_integer()
+            ]
+
+            # Then, we set the start at one plus the maximum edge ID that is an integer,
+            # because count() only yields integer IDs.
+            start = max(edges_with_int_id) + 1 if edges_with_int_id else 0
+            self._edge_uid = count(start=start)
+
             return
 
         # in formats 1-4 we only know that ebunch_to_add is an iterable, so we iterate
@@ -668,6 +685,24 @@ def add_edges_from(self, ebunch_to_add, **attr):
             try:
                 e = next(new_edges)
             except StopIteration:
+
+                if format2 or format4:
+                    # If we don't set the start of self._edge_uid correctly, it will start at 0,
+                    # which will overwrite any existing edges when calling add_edge().  First, we
+                    # use the somewhat convoluted float(e).is_integer() instead of using
+                    # isinstance(e, int) because there exist integer-like numeric types (such as
+                    # np.int32) which fail the isinstance() check.
+                    edges_with_int_id = [
+                        int(e)
+                        for e in self.edges
+                        if (not isinstance(e, str)) and float(e).is_integer()
+                    ]
+
+                    # Then, we set the start at one plus the maximum edge ID that is an integer,
+                    # because count() only yields integer IDs.
+                    start = max(edges_with_int_id) + 1 if edges_with_int_id else 0
+                    self._edge_uid = count(start=start)
+
                 break
 
     def add_weighted_edges_from(self, ebunch, weight="weight", **attr):
@@ -989,7 +1024,11 @@ def copy(self):
         # use the somewhat convoluted float(e).is_integer() instead of using
         # isinstance(e, int) because there exist integer-like numeric types (such as
         # np.int32) which fail the isinstance() check.
-        edges_with_int_id = [int(e) for e in self.edges if float(e).is_integer()]
+        edges_with_int_id = [
+            int(e)
+            for e in self.edges
+            if (not isinstance(e, str)) and float(e).is_integer()
+        ]
 
         # Then, we set the start at one plus the maximum edge ID that is an integer,
         # because count() only yields integer IDs.

xgi/classes/simplicialcomplex.py

@@ -386,6 +386,22 @@ def add_simplices_from(self, ebunch_to_add, max_order=None, **attr):
                 faces = self._subfaces(members)
                 self.add_simplices_from(faces)
 
+            # If we don't set the start of self._edge_uid correctly, it will start at 0,
+            # which will overwrite any existing edges when calling add_edge().  First, we
+            # use the somewhat convoluted float(e).is_integer() instead of using
+            # isinstance(e, int) because there exist integer-like numeric types (such as
+            # np.int32) which fail the isinstance() check.
+            edges_with_int_id = [
+                int(e)
+                for e in self.edges
+                if (not isinstance(e, str)) and float(e).is_integer()
+            ]
+
+            # Then, we set the start at one plus the maximum edge ID that is an integer,
+            # because count() only yields integer IDs.
+            start = max(edges_with_int_id) + 1 if edges_with_int_id else 0
+            self._edge_uid = count(start=start)
+
             return
 
         # in formats 1-4 we only know that ebunch_to_add is an iterable, so we iterate
@@ -478,6 +494,24 @@ def add_simplices_from(self, ebunch_to_add, max_order=None, **attr):
             try:
                 e = next(new_edges)
             except StopIteration:
+
+                if format2 or format4:
+                    # If we don't set the start of self._edge_uid correctly, it will start at 0,
+                    # which will overwrite any existing edges when calling add_edge().  First, we
+                    # use the somewhat convoluted float(e).is_integer() instead of using
+                    # isinstance(e, int) because there exist integer-like numeric types (such as
+                    # np.int32) which fail the isinstance() check.
+                    edges_with_int_id = [
+                        int(e)
+                        for e in self.edges
+                        if (not isinstance(e, str)) and float(e).is_integer()
+                    ]
+
+                    # Then, we set the start at one plus the maximum edge ID that is an integer,
+                    # because count() only yields integer IDs.
+                    start = max(edges_with_int_id) + 1 if edges_with_int_id else 0
+                    self._edge_uid = count(start=start)
+
                 break
 
     def close(self):

xgi/convert.py

@@ -7,12 +7,8 @@
 from numpy import matrix, ndarray
 from scipy.sparse import coo_matrix, csc_matrix, csr_matrix, lil_matrix
 
-from .classes import (
-    Hypergraph,
-    SimplicialComplex,
-    maximal_simplices,
-    set_edge_attributes,
-)
+from .classes import (Hypergraph, SimplicialComplex, maximal_simplices,
+                      set_edge_attributes)
 from .exception import XGIError
 from .generators import empty_hypergraph, empty_simplicial_complex
 from .linalg import adjacency_matrix, incidence_matrix

xgi/dynamics/synchronization.py

@@ -3,8 +3,8 @@
 import numpy as np
 
 import xgi
-from ..exception import XGIError
 
+from ..exception import XGIError
 
 __all__ = [
     "compute_kuramoto_order_parameter",

xgi/utils/utilities.py

@@ -38,7 +38,9 @@ def dual_dict(edge_dict):
     return dict(node_dict)
 
 
-def powerset(iterable, include_empty=False, include_full=False, include_singletons=True):
+def powerset(
+    iterable, include_empty=False, include_full=False, include_singletons=True
+):
     """Returns all possible subsets of the elements in iterable, with options
     to include the empty set and the set containing all elements.
 
@@ -60,7 +62,7 @@ def powerset(iterable, include_empty=False, include_full=False, include_singleto
     Notes
     -----
     include_empty overrides include_singletons if True: singletons will always
-    be included if the empty set is. 
+    be included if the empty set is.
 
     Examples
     --------
@@ -72,7 +74,7 @@ def powerset(iterable, include_empty=False, include_full=False, include_singleto
     """
 
     start = 1 if include_singletons else 2
-    start = 0 if include_empty else start # overrides include_singletons if True
+    start = 0 if include_empty else start  # overrides include_singletons if True
     end = 1 if include_full else 0
 
     s = list(iterable)