🐛 fix networkx conda deps

cdlib/algorithms/internal/GDMP2_nx.py

@@ -117,7 +117,12 @@ def GDMP2(graph, min_threshold=0.75):
         x1 = adj_matrix[:, x]
         for y in range(x, col):
             y1 = adj_matrix[:, y]
-            M[x][y] = 1 - scipy.spatial.distance.cosine(x1, y1)
+            try:
+                M[x][y] = 1 - scipy.spatial.distance.cosine(x1, y1)
+            except ValueError:
+                x1 = np.ndarray(x1.flatten())[0]
+                y1 = np.ndarray(y1.flatten())[0]
+                M[x][y] = 1 - scipy.spatial.distance.cosine(x1, y1)
 
     tuples = []
     # On basis of zero graph

cdlib/algorithms/internal/SiblinarityAntichain.py

@@ -48,9 +48,14 @@ def __init__(self, node_id_dict, similarity_matrix, Lambda, with_replacement):
         self.similarity_matrix = similarity_matrix
         self.node_id_dict = node_id_dict
         self.strength = similarity_matrix.sum(axis=0)
-        self.strength = {
-            n: self.strength[node_id_dict[n]] for n in node_id_dict.keys()
-        }  # sum over rows?
+        try:
+            self.strength = {
+                n: self.strength[node_id_dict[n]] for n in node_id_dict.keys()
+            }  # sum over rows?
+        except IndexError:
+            self.strength = {
+                n: self.strength[0, node_id_dict[n]] for n in node_id_dict.keys()
+            }
         self.total_weight = similarity_matrix.sum()  # /2
         self.Lambda = Lambda
         self.with_replacement = with_replacement

conda/meta.yaml

@@ -13,11 +13,9 @@ requirements:
     - python==3.9
     - angel_cd
     - bimlpa
-  #  - chinese_whispers
     - demon
     - dynetx
     - eva_lcd
-  #  - karateclub
     - leidenalg
     - markov_clustering
     - matplotlib
@@ -28,7 +26,6 @@ requirements:
     - pip
     - pooch
     - pulp
-  #  - pyclustering
     - python-igraph
     - python-levenshtein
     - python-louvain
@@ -37,15 +34,13 @@ requirements:
     - seaborn
     - thresholdclustering
     - tqdm
-  #  - wurlitzer
     - setuptools
   build:
     - python
     - setuptools
   run:
     - angel_cd
     - bimlpa
-  #  - chinese_whispers
     - demon
     - dynetx
     - eva_lcd
@@ -57,7 +52,6 @@ requirements:
     - pandas
     - pooch
     - pulp
- #   - pyclustering
     - python-igraph
     - python-levenshtein
     - python-louvain

docs/conf.py

@@ -126,18 +126,18 @@ def __getattr__(cls, name):
 master_doc = "index"
 
 # General information about the project.
-project = u"CDlib"
-copyright = u"2019, Giulio Rossetti"
-author = u"Giulio Rossetti"
+project = "CDlib"
+copyright = "2019, Giulio Rossetti"
+author = "Giulio Rossetti"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u"0.2.6"
+version = "0.2.6"
 # The full version, including alpha/beta/rc tags.
-release = u"0.2.6"
+release = "0.2.6"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -200,10 +200,10 @@ def __getattr__(cls, name):
 
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
-html_title = u"CDlib - Community Discovery library"
+html_title = "CDlib - Community Discovery library"
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-html_short_title = u"CDlib"
+html_short_title = "CDlib"
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -302,7 +302,7 @@ def __getattr__(cls, name):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "CDlib.tex", u"CDlib Documentation", u"Giulio Rossetti", "manual")
+    (master_doc, "CDlib.tex", "CDlib Documentation", "Giulio Rossetti", "manual")
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -330,7 +330,7 @@ def __getattr__(cls, name):
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "CDlib", u"CDlib Documentation", [author], 1)]
+man_pages = [(master_doc, "CDlib", "CDlib Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -345,7 +345,7 @@ def __getattr__(cls, name):
     (
         master_doc,
         "CDlib",
-        u"CDlib Documentation",
+        "CDlib Documentation",
         author,
         "CDlib",
         "Community Discovery Library",

environment.yml

@@ -1,12 +1,11 @@
 name: cdlib
 dependencies:
 - python=3.9
-#- graph-tool # ==2.44
 - numpy
 - matplotlib
 - scikit-learn
 - tqdm
-- networkx
+- networkx>=3.0
 - demon
 - python-louvain
 - nf1
@@ -17,11 +16,9 @@ dependencies:
 - eva_lcd
 - bimlpa
 - markov_clustering
-# - chinese_whispers
 - python-igraph
 - angel_cd
 - pooch
 - dynetx
 - thresholdclustering
-#- pyclustering
 - python-Levenshtein

requirements.txt

@@ -1,11 +1,11 @@
 numpy
 future
 matplotlib
-scikit-learn
+scikit - learn
 tqdm
-networkx>=3.0
+networkx >= 3.0
 demon
-python-louvain>=0.16
+python - louvain >= 0.16
 nf1
 scipy
 pulp
@@ -15,12 +15,12 @@ eva_lcd
 bimlpa
 markov_clustering
 # chinese_whispers
-python-igraph>=0.10
-angel-cd
+python - igraph >= 0.10
+angel - cd
 pooch
 dynetx
 thresholdclustering
 pyclustering
 cython
-python-Levenshtein
-bayanpy
+python - Levenshtein
+bayanpy