Merge remote-tracking branch 'origin/master'

Author: saibalmars

.github/workflows/build.yml

@@ -18,43 +18,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-latest, macOS-latest]
         include:
           - os: ubuntu-latest
-            path: ~/.cache/pip
           - os: macos-latest
-            path: ~/Library/Caches/pip
 
     steps:
-    - uses: actions/cache@v2
-      with:
-        path: ${{ matrix.path }}
-        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-${{ matrix.python-version }}-
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Setup macOS dependencies
-      if: startsWith(runner.os, 'macOS')
-      run: |
-        brew install libomp
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        python -m pip install cython
-        python -m pip install numpy
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        $CONDA/bin/conda install -c conda-forge --file requirements.txt flake8 pytest
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        $CONDA/bin/pytest

GraphRicciCurvature/OllivierRicci.py

@@ -19,11 +19,11 @@
 
 
 import heapq
-import importlib
 import math
 import multiprocessing as mp
 import time
 from functools import lru_cache
+from importlib import util
 
 import networkit as nk
 import networkx as nx
@@ -690,7 +690,7 @@ def __init__(self, G: nx.Graph, weight="weight", alpha=0.5, method="OTDSinkhornM
         self.lengths = {}  # all pair shortest path dictionary
         self.densities = {}  # density distribution dictionary
 
-        assert importlib.util.find_spec("ot"), \
+        assert util.find_spec("ot"), \
             "Package POT: Python Optimal Transport is required for Sinkhorn distance."
 
         if not nx.get_edge_attributes(self.G, weight):

GraphRicciCurvature/util.py

@@ -1,5 +1,5 @@
 import logging
-import community as community_louvain
+import community.community_louvain as community_louvain
 import networkx as nx
 import numpy as np
 from functools import partial, partialmethod

my_surgery.py

@@ -1,8 +1,8 @@
+from importlib import util
+
+import community as community_louvain
 import networkx as nx
 import numpy as np
-import importlib
-import community as community_louvain
-import matplotlib.pyplot as plt
 
 
 def ARI(G, clustering, clustering_label="club"):
@@ -24,10 +24,10 @@ def ARI(G, clustering, clustering_label="club"):
         Adjust Rand Index for predicted community.
     """
 
-    if importlib.util.find_spec("sklearn") is not None:
+    if util.find_spec("sklearn") is not None:
         from sklearn import preprocessing, metrics
     else:
-        print("scikit-learn not installed...")
+        print("scikit-learn not installed, skipped...")
         return -1
 
     complex_list = nx.get_node_attributes(G, clustering_label)
@@ -107,6 +107,12 @@ def check_accuracy(G_origin, weight="weight", clustering_label="value", plot_cut
         To plot the good guessed cut or not.
 
     """
+    if util.find_spec("matplotlib") is not None:
+        import matplotlib.pyplot as plt
+    else:
+        print("matplotlib not installed, skipped to show the cut graph...")
+        return -1
+
     G = G_origin.copy()
     modularity, ari = [], []
     maxw = max(nx.get_edge_attributes(G, weight).values())