Merge branch 'develop'

.github/workflows/ci_checks.yml

@@ -16,9 +16,9 @@ jobs:
         python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -31,4 +31,4 @@ jobs:
       run: |
         py.test --doctest-modules --cov-report=xml --cov=sknetwork
     - name: Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4

.github/workflows/release.yml

@@ -13,13 +13,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.0
+        uses: pypa/cibuildwheel@v2.16.5
         env:
           CIBW_PLATFORM: auto
           CIBW_ARCHS: auto64
@@ -30,17 +30,18 @@ jobs:
           CIBW_BEFORE_BUILD_MACOS: "pip install -r requirements_dev.txt && pip install ."
           CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          path: ./wheelhouse/*.whl
+          path: wheelhouse
+          name: dist-${{ matrix.os }}-${{ matrix.python-version }}
 
   build_sdist:
       name: Build source distribution
       runs-on: ubuntu-latest
       steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
 
-        - uses: actions/setup-python@v3
+        - uses: actions/setup-python@v5
           name: Install Python
           with:
             python-version: '3.9'
@@ -51,20 +52,21 @@ jobs:
             python -m pip install -r requirements_dev.txt
             python setup.py sdist
 
-        - uses: actions/upload-artifact@v3
+        - uses: actions/upload-artifact@v4
           with:
             path: dist/*.tar.gz
 
   upload_pypi:
       needs: [ build_wheels, build_sdist ]
       runs-on: ubuntu-latest
       steps:
-          - uses: actions/download-artifact@v3
+          - uses: actions/download-artifact@v4
             with:
-              name: artifact
+              pattern: dist-*
+              merge-multiple: true
               path: dist
 
-          - uses: pypa/gh-action-pypi-publish@v1.4.2
+          - uses: pypa/gh-action-pypi-publish@v1.8.12
             with:
               user: __token__
               password: ${{ secrets.TWINE_PASSWORD }}

.github/workflows/wheels_build.yml

@@ -10,13 +10,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.0
+        uses: pypa/cibuildwheel@v2.16.5
         env:
           CIBW_PLATFORM: auto
           CIBW_ARCHS: auto64
@@ -27,17 +27,18 @@ jobs:
           CIBW_BEFORE_BUILD_MACOS: "pip install -r requirements_dev.txt && pip install ."
           CIBW_BUILD: cp38-* cp39-* cp310-* cp311-*
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          path: ./wheelhouse/*.whl
+          name: dist-${{ matrix.os }}-${{ matrix.python-version }}
+          path: wheelhouse
 
   build_sdist:
       name: Build source distribution
       runs-on: ubuntu-latest
       steps:
-          -   uses: actions/checkout@v3
+          -   uses: actions/checkout@v4
 
-          -   uses: actions/setup-python@v3
+          -   uses: actions/setup-python@v5
               name: Install Python
               with:
                   python-version: '3.9'
@@ -48,6 +49,6 @@ jobs:
                 python -m pip install -r requirements_dev.txt
                 python setup.py sdist
 
-          -   uses: actions/upload-artifact@v3
+          -   uses: actions/upload-artifact@v4
               with:
                   path: dist/*.tar.gz

AUTHORS.rst

@@ -39,3 +39,6 @@ Contributors
 * Flávio Juvenal
 * Wenzhuo Zhao
 * Henry Carscadden
+* Yiwen Peng
+* Ahmed Zaiou
+* Laurène David

HISTORY.rst

@@ -2,6 +2,16 @@
 History
 =======
 
+0.32.0 (2024-03-28)
+-------------------
+
+* Add Leiden clustering algorithm
+* Add k-center clustering algorithm
+* Add functions to detect and break cycles
+* Add damping factor in diffusion
+* Fix F1 scores
+* Remove hierarchical Louvain embedding
+* Get clustering coefficient for directed graphs
 
 0.31.0 (2023-05-22)
 -------------------

docs/reference/clustering.rst

@@ -49,6 +49,17 @@ When the graph is weighted, the degree of a node is replaced by its weight (sum
 
 .. autoclass:: sknetwork.clustering.Louvain
 
+Leiden
+------
+
+.. autoclass:: sknetwork.clustering.Leiden
+
+K-centers
+---------
+
+.. autoclass:: sknetwork.clustering.KCenters
+
+
 Propagation
 -----------
 .. autoclass:: sknetwork.clustering.PropagationClustering

docs/reference/embedding.rst

@@ -37,10 +37,6 @@ Louvain
 
 .. autoclass:: sknetwork.embedding.LouvainEmbedding
 
-Hierarchical Louvain
---------------------
-
-.. autoclass:: sknetwork.embedding.LouvainNE
 
 Force Atlas
 -----------

docs/reference/topology.rst

@@ -19,8 +19,14 @@ Structure
 
 .. autofunction:: sknetwork.topology.is_bipartite
 
+Cycles
+------
+
 .. autofunction:: sknetwork.topology.is_acyclic
 
+.. autofunction:: sknetwork.topology.get_cycles
+
+.. autofunction:: sknetwork.topology.break_cycles
 
 Core decomposition
 ------------------

docs/reference/visualization.rst

@@ -10,9 +10,9 @@ Graphs
 
 .. autofunction:: sknetwork.visualization.graphs.svg_graph
 
-.. autofunction:: sknetwork.visualization.graphs.svg_bigraph
+.. autofunction:: sknetwork.visualization.graphs.visualize_bigraph
 
 Dendrograms
 -----------
 
-.. autofunction:: sknetwork.visualization.dendrograms.svg_dendrogram
+.. autofunction:: sknetwork.visualization.dendrograms.visualize_dendrogram