scikit-network 0.30.0__cp310-cp310-win_amd64.whl → 0.32.1__cp310-cp310-win_amd64.whl

sknetwork/topology/weisfeiler_lehman_core.pyx

@@ -1,7 +1,5 @@
 # distutils: language = c++
 # cython: language_level=3
-# cython: linetrace=True
-# distutils: define_macros=CYTHON_TRACE_NOGIL=1
 """
 Created on July 1, 2020
 @author: Pierre Pebereau <pierre.pebereau@telecom-paris.fr>

sknetwork/utils/__init__.py

@@ -1,37 +1,7 @@
 """utils module"""
+from sknetwork.data import Bunch
 from sknetwork.utils.check import is_symmetric
 from sknetwork.utils.format import *
 from sknetwork.utils.membership import get_membership, from_membership
 from sknetwork.utils.neighbors import get_neighbors, get_degrees, get_weights
-from sknetwork.utils.simplex import projection_simplex, projection_simplex_array, projection_simplex_csr
 from sknetwork.utils.tfidf import get_tfidf
-
-
-class Bunch(dict):
-    """Container object for datasets.
-    Dictionary-like object that exposes its keys as attributes.
-
-    This code is taken from scikit-learn.
-    >>> bunch = Bunch(a=1, b=2)
-    >>> bunch['a']
-    1
-    >>> bunch.a
-    1
-    >>> bunch.b = 3
-    >>> bunch['b']
-    3
-    >>> bunch.c = 4
-    >>> bunch['c']
-    4
-    """
-    def __init__(self, **kwargs):
-        super().__init__(kwargs)
-
-    def __setattr__(self, key, value):
-        self[key] = value
-
-    def __getattr__(self, key):
-        try:
-            return self[key]
-        except KeyError:
-            raise AttributeError(key)

sknetwork/utils/check.py

@@ -121,7 +121,7 @@ def make_weights(distribution: str, adjacency: sparse.csr_matrix) -> np.ndarray:
 
 
 def check_format(input_matrix: Union[sparse.csr_matrix, sparse.csc_matrix, sparse.coo_matrix, sparse.lil_matrix,
-                                     np.ndarray]) -> sparse.csr_matrix:
+                                     np.ndarray], allow_empty: bool = False) -> sparse.csr_matrix:
     """Check whether the matrix is a NumPy array or a Scipy sparse matrix and return
     the corresponding Scipy CSR matrix.
     """
@@ -129,7 +129,7 @@ def check_format(input_matrix: Union[sparse.csr_matrix, sparse.csc_matrix, spars
     if type(input_matrix) not in formats:
         raise TypeError('The input matrix must be in Scipy sparse format or Numpy ndarray format.')
     input_matrix = sparse.csr_matrix(input_matrix)
-    if input_matrix.nnz == 0:
+    if not allow_empty and input_matrix.nnz == 0:
         raise ValueError('The input matrix is empty.')
     return input_matrix
 

sknetwork/utils/format.py

@@ -30,7 +30,7 @@ def directed2undirected(adjacency: Union[sparse.csr_matrix, SparseLR],
 
     or
 
-    :math:`\\max(A,A^T)`
+    :math:`\\max(A,A^T) > 0` (binary)
 
     If the initial adjacency matrix :math:`A` is binary, bidirectional edges have weight 2
     (first method, default) or 1 (second method).
@@ -134,7 +134,7 @@ def bipartite2undirected(biadjacency: Union[sparse.csr_matrix, SparseLR]) -> Uni
 
 
 def get_adjacency(input_matrix: Union[sparse.csr_matrix, np.ndarray], allow_directed: bool = True,
-                  force_bipartite: bool = False, force_directed: bool = False)\
+                  force_bipartite: bool = False, force_directed: bool = False, allow_empty: bool = False)\
         -> Tuple[sparse.csr_matrix, bool]:
     """Check the input matrix and return a proper adjacency matrix.
     Parameters
@@ -150,8 +150,10 @@ def get_adjacency(input_matrix: Union[sparse.csr_matrix, np.ndarray], allow_dire
     force_directed :
         If ``True`` return :math:`A  = \\begin{bmatrix} 0 & B \\\\ 0 & 0 \\end{bmatrix}`.
         Otherwise (default), return :math:`A  = \\begin{bmatrix} 0 & B \\\\ B^T & 0 \\end{bmatrix}`.
+    allow_empty :
+        If ``True``, allow the input matrix to be empty.
     """
-    input_matrix = check_format(input_matrix)
+    input_matrix = check_format(input_matrix, allow_empty=allow_empty)
     bipartite = False
     if force_bipartite or not is_square(input_matrix) or not (allow_directed or is_symmetric(input_matrix)):
         bipartite = True

sknetwork/utils/membership.py

@@ -20,9 +20,9 @@ def get_membership(labels: np.ndarray, dtype=bool, n_labels: Optional[int] = Non
     Parameters
     ----------
     labels :
-        Label of each node.
+        Label of each node (integers).
     dtype :
-        Type of the entries. Boolean by default.
+        Type of the output. Boolean by default.
     n_labels : int
         Number of labels.
 

sknetwork/utils/tests/test_check.py

@@ -4,7 +4,7 @@
 import unittest
 
 from sknetwork.data import cyclic_digraph
-from sknetwork.data.test_graphs import test_graph_disconnect
+from sknetwork.data.test_graphs import test_disconnected_graph
 from sknetwork.utils.check import *
 from sknetwork.utils.format import check_csr_or_slr
 
@@ -26,7 +26,7 @@ class TestChecks(unittest.TestCase):
 
     def test_check_connected(self):
         with self.assertRaises(ValueError):
-            check_connected(test_graph_disconnect())
+            check_connected(test_disconnected_graph())
 
     def test_check_symmetry(self):
         with self.assertRaises(ValueError):
@@ -153,7 +153,7 @@ class TestChecks(unittest.TestCase):
         adjacency = cyclic_digraph(3)
         with self.assertRaises(ValueError):
             check_scaling(-1, adjacency, regularize=True)
-        adjacency = test_graph_disconnect()
+        adjacency = test_disconnected_graph()
         with self.assertRaises(ValueError):
             check_scaling(-1, adjacency, regularize=False)
 

sknetwork/utils/tests/test_format.py

@@ -58,4 +58,6 @@ class TestFormats(unittest.TestCase):
 
     def test_check(self):
         with self.assertRaises(ValueError):
-            check_format(sparse.csr_matrix((3, 4)))
+            check_format(sparse.csr_matrix((3, 4)), allow_empty=False)
+        adjacency = check_format(np.array([[0, 2], [2, 3]]))
+        self.assertTrue(adjacency.shape == (2, 2))

sknetwork/utils/values.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Created on Apr, 2019
+Created in April 2019
 @author: Nathan de Lara <nathan.delara@polytechnique.org>
 """
 import warnings

sknetwork/visualization/__init__.py

@@ -1,4 +1,4 @@
 """Visualization module."""
 
-from sknetwork.visualization.dendrograms import svg_dendrogram
-from sknetwork.visualization.graphs import svg_graph, svg_bigraph
+from sknetwork.visualization.dendrograms import visualize_dendrogram, svg_dendrogram
+from sknetwork.visualization.graphs import visualize_graph, visualize_bigraph, svg_graph, svg_bigraph

sknetwork/visualization/dendrograms.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Created on April 2020
+Created in April 2020
 @author: Thomas Bonald <bonald@enst.fr>
 """
 from typing import Iterable, Optional
@@ -158,12 +158,12 @@ def svg_dendrogram_left(dendrogram, names, width, height, margin, margin_text, s
     return svg
 
 
-def svg_dendrogram(dendrogram: np.ndarray, names: Optional[np.ndarray] = None, rotate: bool = False, width: float = 400,
-                   height: float = 300, margin: float = 10, margin_text: float = 5, scale: float = 1,
-                   line_width: float = 2, n_clusters: int = 2, color: str = 'black', colors: Optional[Iterable] = None,
-                   font_size: int = 12, reorder: bool = False, rotate_names: bool = True,
-                   filename: Optional[str] = None):
-    """Return SVG image of a dendrogram.
+def visualize_dendrogram(dendrogram: np.ndarray, names: Optional[np.ndarray] = None, rotate: bool = False,
+                         width: float = 400, height: float = 300, margin: float = 10, margin_text: float = 5,
+                         scale: float = 1, line_width: float = 2, n_clusters: int = 2, color: str = 'black',
+                         colors: Optional[Iterable] = None, font_size: int = 12, reorder: bool = False,
+                         rotate_names: bool = True, filename: Optional[str] = None):
+    """Return the image of a dendrogram in SVG format.
 
     Parameters
     ----------
@@ -227,3 +227,51 @@ def svg_dendrogram(dendrogram: np.ndarray, names: Optional[np.ndarray] = None, r
             f.write(svg)
 
     return svg
+
+
+def svg_dendrogram(dendrogram: np.ndarray, names: Optional[np.ndarray] = None, rotate: bool = False, width: float = 400,
+                   height: float = 300, margin: float = 10, margin_text: float = 5, scale: float = 1,
+                   line_width: float = 2, n_clusters: int = 2, color: str = 'black', colors: Optional[Iterable] = None,
+                   font_size: int = 12, reorder: bool = False, rotate_names: bool = True,
+                   filename: Optional[str] = None):
+    """Return the image of a dendrogram in SVG format.
+
+    Alias for visualize_dendrogram.
+
+    Parameters
+    ----------
+    dendrogram :
+        Dendrogram to display.
+    names :
+        Names of leaves.
+    rotate :
+        If ``True``, rotate the tree so that the root is on the left.
+    width :
+        Width of the image (margins excluded).
+    height :
+        Height of the image (margins excluded).
+    margin :
+        Margin.
+    margin_text :
+        Margin between leaves and their names, if any.
+    scale :
+        Scaling factor.
+    line_width :
+        Line width.
+    n_clusters :
+        Number of coloured clusters to display.
+    color :
+        Default SVG color for the dendrogram.
+    colors :
+        SVG colors of the clusters of the dendrogram (optional).
+    font_size :
+        Font size.
+    reorder :
+        If ``True``, reorder leaves so that left subtree has more leaves than right subtree.
+    rotate_names :
+        If ``True``, rotate names of leaves (only valid if **rotate** is ``False``).
+    filename :
+        Filename for saving image (optional).
+    """
+    return visualize_dendrogram(dendrogram, names, rotate, width, height, margin, margin_text, scale, line_width,
+                                n_clusters, color, colors, font_size, reorder, rotate_names, filename)