Merge branch 'main' into josef-fix-incidence-to-adjacency

test/utils/test_structure.py

@@ -88,6 +88,18 @@ def test_neighborhood_list_to_neighborhood_dict(self):
         )
         assert out == d
 
+    def test_neighborhood_list_to_neighborhood_with_dict(self):
+        """Test that neighborhood_list_to_neighborhood_dict works correctly with specified node dictionary."""
+        node_dict = {1: "a", 2: "b", 3: "c"}
+        neigh_list = [(1, 2), (2, 1), (2, 3), (3, 2)]
+        neigh_dict = neighborhood_list_to_neighborhood_dict(
+            neigh_list, node_dict, node_dict
+        )
+        assert len(neigh_dict) == 3
+        assert neigh_dict["a"] == ["b"]
+        assert set(neigh_dict["b"]) == {"a", "c"}  # order irrelevant
+        assert neigh_dict["c"] == ["b"]
+
     def test_sparse_array_to_neighborhood_dict(self):
         """Test the sparse_array_to_neighborhood_dict function."""
         c = CellComplex()

toponetx/algorithms/spectrum.py

@@ -183,7 +183,7 @@ def laplacian_spectrum(matrix, weight="weight"):
     ----------
     matrix : scipy sparse matrix
 
-    weight : string or None, optional (default='weight')
+    weight : str or None, optional (default='weight')
        If None, then each cell has weight 1.
 
     Returns
@@ -203,17 +203,16 @@ def cell_complex_hodge_laplacian_spectrum(CX: CellComplex, rank: int, weight="we
     Parameters
     ----------
     matrix : scipy sparse matrix
-
-    weight : string or None, optional (default='weight')
+    weight : str or None, optional (default='weight')
         If None, then each cell has weight 1.
 
     Returns
     -------
     evals : NumPy array
         Eigenvalues.
 
-    Example
-    -------
+    Examples
+    --------
     >>> CX = CellComplex()
     >>> CX.add_cell([1,2,3,4],rank=2)
     >>> CX.add_cell([2,3,4,5],rank=2)
@@ -231,16 +230,15 @@ def simplicial_complex_hodge_laplacian_spectrum(
     Parameters
     ----------
     matrix : scipy sparse matrix
-
-    weight : string or None, optional (default='weight')
+    weight : str or None, optional (default='weight')
         If None, then each cell has weight 1.
 
     Returns
     -------
     evals : NumPy array
         Eigenvalues.
 
-    Example
+    Examples
     --------
     >>> SC=SimplicialComplex([[1,2,3],[2,3,5],[0,1]])
     >>> spectrum=simplicial_complex_hodge_laplacian_spectrum(SC,1)
@@ -254,7 +252,6 @@ def cell_complex_adjacency_spectrum(CX: CellComplex, rank):
     Parameters
     ----------
     matrix : scipy sparse matrix
-
     up : bool, default False
         whether to take the upper or lower adjacency
 
@@ -263,8 +260,8 @@ def cell_complex_adjacency_spectrum(CX: CellComplex, rank):
     evals : NumPy array
       Eigenvalues
 
-    Example
-    -------
+    Examples
+    --------
     >>> CX = CellComplex()
     >>> CX.add_cell([1,2,3,4],rank=2)
     >>> CX.add_cell([2,3,4,5],rank=2)
@@ -282,8 +279,7 @@ def simplicial_complex_adjacency_spectrum(
     Parameters
     ----------
     matrix : scipy sparse matrix
-
-    weight : string or None, optional (default='weight')
+    weight : str or None, optional (default='weight')
         If None, then each cell has weight 1.
 
     Returns
@@ -300,17 +296,16 @@ def combinatorial_complex_adjacency_spectrum(CC: CombinatorialComplex, r, k):
     Parameters
     ----------
     matrix : scipy sparse matrix
-
-    weight : string or None, optional (default='weight')
+    weight : str or None, default='weight'
         If None, then each cell has weight 1.
 
     Returns
     -------
     evals : NumPy array
         Eigenvalues
 
-    Example
-    -------
+    Examples
+    --------
     >>> CC = CombinatorialComplex(cells=[[1,2,3],[2,3], [0] ],ranks=[2,1,0] )
     >>> s = laplacian_spectrum( CC.adjacency_matrix( 0,2) )
     """

toponetx/classes/cell.py

@@ -1,10 +1,7 @@
 """Cell and CellView classes."""
 
-try:
-    from collections.abc import Iterable
-except ImportError:
-    from collections import Iterable
 from collections import Counter, deque
+from collections.abc import Iterable
 from itertools import zip_longest
 
 import numpy as np
@@ -13,7 +10,7 @@
 
 
 class Cell:
-    r"""Class representing a 2D cell.
+    """Class representing a 2D cell.
 
     A 2D cell is an elementary building block used to build a 2D cell complex, whether regular or non-regular.
 
@@ -96,7 +93,7 @@ def __init__(self, elements, name=None, regular=True, **attr):
         self.properties.update(attr)
 
     def __getitem__(self, item):
-        r"""Retrieve the value associated with the given key in the properties dictionary.
+        """Retrieve the value associated with the given key in the properties dictionary.
 
         Parameters
         ----------
@@ -118,7 +115,7 @@ def __getitem__(self, item):
             return self.properties[item]
 
     def __setitem__(self, key, item):
-        r"""Set the value associated with the given key in the properties dictionary.
+        """Set the value associated with the given key in the properties dictionary.
 
         Parameters
         ----------
@@ -135,7 +132,7 @@ def __setitem__(self, key, item):
 
     @property
     def is_regular(self):
-        r"""Check if a cell is regular.
+        """Check if a cell is regular.
 
         Return true is the Cell is a regular cell, and False otherwise
         """
@@ -151,7 +148,7 @@ def is_regular(self):
         return True
 
     def __len__(self):
-        r"""Get the number of elements in the cell.
+        """Get the number of elements in the cell.
 
         Returns
         -------
@@ -161,7 +158,7 @@ def __len__(self):
         return len(self._elements)
 
     def __iter__(self):
-        r"""Iterate over the elements in the cell.
+        """Iterate over the elements in the cell.
 
         Returns
         -------
@@ -171,7 +168,7 @@ def __iter__(self):
         return iter(self._elements)
 
     def sign(self, edge):
-        r"""Compute the sign of the edge with respect to the cell.
+        """Compute the sign of the edge with respect to the cell.
 
         This takes an edge as input and computes the sign of the edge with respect to the cell.
 
@@ -218,7 +215,7 @@ def __repr__(self):
 
     @property
     def boundary(self):
-        r"""Boundary.
+        """Boundary.
 
         A 2d cell is characterized by its boundary edges.
 
@@ -238,7 +235,7 @@ def reverse(self):
 
         Returns
         -------
-        _ : Cell
+        Cell
             New cell with the new reversed elements.
         """
         c = Cell(self._elements[::-1], name=self.name, regular=self._regular)
@@ -254,7 +251,7 @@ def is_homotopic_to(self, cell):
 
         Returns
         -------
-        _ : bool
+        bool
             Return True is self is homotopic to input cell and False otherwise.
         """
         return Cell._are_homotopic(self, cell) or Cell._are_homotopic(