Merge branch 'main' into main

Author: szhorvat

.all-contributorsrc

@@ -630,6 +630,15 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "BeaMarton13",
+      "name": "Bea Márton",
+      "avatar_url": "https://avatars.githubusercontent.com/u/204701577?v=4",
+      "profile": "https://github.com/BeaMarton13",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7

.github/workflows/build.yml

@@ -5,49 +5,36 @@ on: [push, pull_request]
 env:
   CIBW_ENVIRONMENT_PASS_LINUX: PYTEST_TIMEOUT
   CIBW_TEST_COMMAND: "cd {project} && pip install --prefer-binary '.[test]' && python -m pytest -v tests"
-  CIBW_SKIP: "cp36-* cp37-* cp38-* pp37-* pp38-*"
+  CIBW_SKIP: "cp38-* pp38-*"
   PYTEST_TIMEOUT: 60
 
 jobs:
   build_wheel_linux:
-    name: Build wheels on Linux (${{ matrix.wheel_arch }})
+    name: Build wheels on Linux (x86_64)
     runs-on: ubuntu-22.04
-    strategy:
-      fail-fast: false
-      matrix:
-        wheel_arch: [x86_64, i686]
-
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
-        name: Install Python
-        with:
-          python-version: '3.9'
-
       - name: Build wheels (manylinux)
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_BEFORE_BUILD: "yum install -y flex bison libxml2-devel zlib-devel cairo-devel && pip install -U cmake pip setuptools wheel && python setup.py build_c_core"
-          CIBW_BUILD: "*-manylinux_${{ matrix.wheel_arch }}"
+          CIBW_BUILD: "*-manylinux_x86_64"
           CIBW_ENABLE: pypy
-          # Skip tests for Python 3.10 onwards because SciPy does not have
-          # 32-bit wheels for Linux.
-          CIBW_TEST_SKIP: "cp310-manylinux_i686 cp311-manylinux_i686 cp312-manylinux_i686 cp313-manylinux_i686"
 
       - name: Build wheels (musllinux)
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_BEFORE_BUILD: "apk add flex bison libxml2-dev zlib-dev cairo-dev && pip install -U cmake pip setuptools wheel && python setup.py build_c_core"
-          CIBW_BUILD: "*-musllinux_${{ matrix.wheel_arch }}"
+          CIBW_BUILD: "*-musllinux_x86_64"
           CIBW_TEST_COMMAND: "cd {project} && pip install --prefer-binary '.[test-musl]' && python -m pytest -v tests"
 
       - uses: actions/upload-artifact@v4
         with:
-          name: wheels-linux-${{ matrix.wheel_arch }}
+          name: wheels-linux-x86_64
           path: ./wheelhouse/*.whl
 
   build_wheel_linux_aarch64_manylinux:
@@ -60,7 +47,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels (manylinux)
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_BEFORE_BUILD: "yum install -y flex bison libxml2-devel zlib-devel cairo-devel && pip install -U cmake pip setuptools wheel && python setup.py build_c_core"
           CIBW_ARCHS_LINUX: aarch64
@@ -82,7 +69,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels (musllinux)
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_BEFORE_BUILD: "apk add flex bison libxml2-dev zlib-dev cairo-dev && pip install -U cmake pip setuptools wheel && python setup.py build_c_core"
           CIBW_ARCHS_LINUX: aarch64
@@ -99,7 +86,7 @@ jobs:
     runs-on: macos-latest
     env:
       LLVM_VERSION: "14.0.5"
-      MACOSX_DEPLOYMENT_TARGET: "10.9"
+      MACOSX_DEPLOYMENT_TARGET: "10.15"
     strategy:
       matrix:
         include:
@@ -129,15 +116,9 @@ jobs:
           path: ~/local
           key: deps-cache-v2-${{ runner.os }}-${{ matrix.cmake_arch }}-llvm${{ env.LLVM_VERSION }}
 
-      - uses: actions/setup-python@v5
-        name: Install Python
-        with:
-          python-version: '3.9'
-
       - name: Install OS dependencies
         if: steps.cache-c-core.outputs.cache-hit != 'true' || steps.cache-c-deps.outputs.cache-hit != 'true' # Only needed when building the C core or libomp
-        run:
-          brew install ninja autoconf automake libtool
+        run: brew install ninja autoconf automake libtool
 
       - name: Install OpenMP library
         if: steps.cache-c-deps.outputs.cache-hit != 'true'
@@ -151,7 +132,7 @@ jobs:
           cmake --install .
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_ARCHS_MACOS: "${{ matrix.wheel_arch }}"
           CIBW_BEFORE_BUILD: "pip install -U setuptools && python setup.py build_c_core"
@@ -177,16 +158,15 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.12.1'
+          python-version: "3.12.1"
 
       - name: Install OS dependencies
-        run:
-          sudo apt install ninja-build cmake flex bison
+        run: sudo apt install ninja-build cmake flex bison
 
       - uses: mymindstorm/setup-emsdk@v14
         with:
-          version: '3.1.58'
-          actions-cache-folder: 'emsdk-cache'
+          version: "3.1.58"
+          actions-cache-folder: "emsdk-cache"
 
       - name: Build wheel
         run: |
@@ -208,28 +188,32 @@ jobs:
 
   build_wheel_win:
     name: Build wheels on Windows (${{ matrix.cmake_arch }})
-    runs-on: windows-2019
     strategy:
       matrix:
         include:
           - cmake_arch: Win32
             wheel_arch: win32
             vcpkg_arch: x86
+            os: windows-2022
+            test_extra: test
           - cmake_arch: x64
             wheel_arch: win_amd64
             vcpkg_arch: x64
+            os: windows-2022
+            test_extra: test
+          - cmake_arch: ARM64
+            wheel_arch: win_arm64
+            vcpkg_arch: arm64
+            os: windows-11-arm
+            test_extra: test-win-arm64
+    runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
-        name: Install Python
-        with:
-          python-version: '3.9'
-
       - name: Cache installed C core
         id: cache-c-core
         uses: actions/cache@v4
@@ -250,18 +234,18 @@ jobs:
       - name: Install VCPKG libraries
         run: |
           %VCPKG_INSTALLATION_ROOT%\vcpkg.exe integrate install
-          %VCPKG_INSTALLATION_ROOT%\vcpkg.exe install libxml2:${{ matrix.vcpkg_arch }}-windows-static-md
+          %VCPKG_INSTALLATION_ROOT%\vcpkg.exe install liblzma:${{ matrix.vcpkg_arch }}-windows-static-md libxml2:${{ matrix.vcpkg_arch }}-windows-static-md
         shell: cmd
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v3.0.1
         env:
           CIBW_BEFORE_BUILD: "pip install -U setuptools && python setup.py build_c_core"
           CIBW_BUILD: "*-${{ matrix.wheel_arch }}"
           CIBW_ENABLE: pypy
-          CIBW_TEST_COMMAND: "cd /d {project} && pip install --prefer-binary \".[test]\" && python -m pytest tests"
+          CIBW_TEST_COMMAND: 'cd /d {project} && pip install --prefer-binary ".[${{ matrix.test_extra }}]" && python -m pytest tests'
           # Skip tests for Python 3.10 onwards because SciPy does not have
-          # 32-bit wheels for Linux.
+          # 32-bit wheels for Windows any more
           CIBW_TEST_SKIP: "cp310-win32 cp311-win32 cp312-win32 cp313-win32"
           IGRAPH_CMAKE_EXTRA_ARGS: -DCMAKE_BUILD_TYPE=RelWithDebInfo -DVCPKG_TARGET_TRIPLET=${{ matrix.vcpkg_arch }}-windows-static-md -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -A ${{ matrix.cmake_arch }}
           IGRAPH_EXTRA_LIBRARY_PATH: C:/vcpkg/installed/${{ matrix.vcpkg_arch }}-windows-static-md/lib/
@@ -293,13 +277,12 @@ jobs:
 
       - name: Install OS dependencies
         if: steps.cache-c-core.outputs.cache-hit != 'true' # Only needed when building the C core
-        run:
-          sudo apt install ninja-build cmake flex bison
+        run: sudo apt install ninja-build cmake flex bison
 
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.9'
+          python-version: "3.9"
 
       - name: Build sdist
         run: |
@@ -341,30 +324,21 @@ jobs:
 
       - name: Install OS dependencies
         if: steps.cache-c-core.outputs.cache-hit != 'true' # Only needed when building the C core
-        run:
-          sudo apt install ninja-build cmake flex bison
+        run: sudo apt install ninja-build cmake flex bison
 
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.12'
-
-      - name: Install test dependencies
-        run: |
-          pip install --prefer-binary pytest pytest-timeout setuptools
-
-      - name: Build C core
-        env:
-          IGRAPH_USE_SANITIZERS: 1
-        run: |
-          python setup.py build_c_core
+          python-version: "3.12"
 
       - name: Build and install Python extension
         env:
           IGRAPH_USE_SANITIZERS: 1
         run: |
-          # NOTE: install calls "build" first
-          python setup.py install
+          # We cannot install the test dependency group because many test dependencies cause
+          # false positives in the sanitizer
+          pip install --prefer-binary networkx pytest pytest-timeout
+          pip install -e .
 
       # Only pytest, and nothing else should be run in this section due to the presence of LD_PRELOAD.
       # The ASan/UBSan library versions need to be updated when switching to a newer Ubuntu/GCC.

CHANGELOG.md

@@ -1,12 +1,14 @@
 # igraph Python interface changelog
 
-## [main]
+## [0.11.9] - 2025-06-11
 
 ### Changed
 
 - Dropped support for Python 3.8 as it has now reached its end of life.
 
-- The C core of igraph was updated to version 0.10.15.
+- The C core of igraph was updated to version 0.10.16.
+
+- Added `Graph.simple_cycles()` to find simple cycles in the graph.
 
 ## [0.11.8] - 2024-10-25
 
@@ -43,30 +45,30 @@
 
 ### Added
 
- - Added `Graph.Hypercube()` for creating n-dimensional hypercube graphs.
+- Added `Graph.Hypercube()` for creating n-dimensional hypercube graphs.
 
- - Added `Graph.Chung_Lu()` for sampling from the Chung-Lu model as well as
+- Added `Graph.Chung_Lu()` for sampling from the Chung-Lu model as well as
    several related models.
 
- - Added `Graph.is_complete()` to test if there is a connection between all
+- Added `Graph.is_complete()` to test if there is a connection between all
    distinct pairs of vertices.
 
- - Added `Graph.is_clique()` to test if a set of vertices forms a clique.
+- Added `Graph.is_clique()` to test if a set of vertices forms a clique.
 
- - Added `Graph.is_independent_vertex_set()` to test if some vertices form an
+- Added `Graph.is_independent_vertex_set()` to test if some vertices form an
    independent set.
 
- - Added `Graph.mean_degree()` for a convenient way to compute the average
+- Added `Graph.mean_degree()` for a convenient way to compute the average
    degree of a graph.
 
 ### Changed
 
- - The C core of igraph was updated to version 0.10.13.
+- The C core of igraph was updated to version 0.10.13.
 
- - `Graph.rewire()` now attempts to perform edge swaps 10 times the number of
+- `Graph.rewire()` now attempts to perform edge swaps 10 times the number of
    edges by default.
 
- - Error messages issued when an attribute is not found now mention the name
+- Error messages issued when an attribute is not found now mention the name
    and type of that attribute.
 
 ## [0.11.5] - 2024-05-07
@@ -87,18 +89,18 @@
 
 - Deprecated `PyCObject` API calls in the C code were replaced by calls to
   `PyCapsule`, thanks to @DavidRConnell in
-  https://github.com/igraph/python-igraph/pull/763
+  <https://github.com/igraph/python-igraph/pull/763>
 
 - `get_shortest_path()` documentation was clarified by @JDPowell648 in
-  https://github.com/igraph/python-igraph/pull/764
+  <https://github.com/igraph/python-igraph/pull/764>
 
 - It is now possible to link to an existing igraph C core on MSYS2, thanks to
-  @Kreijstal in https://github.com/igraph/python-igraph/pull/770
+  @Kreijstal in <https://github.com/igraph/python-igraph/pull/770>
 
 ### Fixed
 
 - Bugfix in the NetworkX graph conversion code by @rmmaf in
-  https://github.com/igraph/python-igraph/pull/767
+  <https://github.com/igraph/python-igraph/pull/767>
 
 ## [0.11.4]
 
@@ -719,11 +721,11 @@
 ## [0.8.3]
 
 This is the last released version of `python-igraph` without a changelog file.
-Please refer to the commit logs at https://github.com/igraph/python-igraph for
+Please refer to the commit logs at <https://github.com/igraph/python-igraph> for
 a list of changes affecting versions up to 0.8.3. Notable changes after 0.8.3
 are documented above.
 
-[main]: https://github.com/igraph/python-igraph/compare/0.11.8...main
+[0.11.9]: https://github.com/igraph/python-igraph/compare/0.11.8...0.11.9
 [0.11.8]: https://github.com/igraph/python-igraph/compare/0.11.7...0.11.8
 [0.11.7]: https://github.com/igraph/python-igraph/compare/0.11.6...0.11.7
 [0.11.6]: https://github.com/igraph/python-igraph/compare/0.11.5...0.11.6

CONTRIBUTORS.md

@@ -95,6 +95,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/m1-s"><img src="https://avatars.githubusercontent.com/u/94642227?v=4?s=100" width="100px;" alt="Michael Schneider"/><br /><sub><b>Michael Schneider</b></sub></a><br /><a href="https://github.com/igraph/python-igraph/commits?author=m1-s" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="http://thomaskrijnen.com/"><img src="https://avatars.githubusercontent.com/u/1096535?v=4?s=100" width="100px;" alt="Thomas Krijnen"/><br /><sub><b>Thomas Krijnen</b></sub></a><br /><a href="https://github.com/igraph/python-igraph/commits?author=aothms" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/GenieTim"><img src="https://avatars.githubusercontent.com/u/8596965?v=4?s=100" width="100px;" alt="Tim Bernhard"/><br /><sub><b>Tim Bernhard</b></sub></a><br /><a href="https://github.com/igraph/python-igraph/commits?author=GenieTim" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/BeaMarton13"><img src="https://avatars.githubusercontent.com/u/204701577?v=4?s=100" width="100px;" alt="Bea Márton"/><br /><sub><b>Bea Márton</b></sub></a><br /><a href="https://github.com/igraph/python-igraph/commits?author=BeaMarton13" title="Code">💻</a></td>
     </tr>
   </tbody>
 </table>

MANIFEST.in

@@ -8,6 +8,10 @@ include scripts/*.sh
 include scripts/*.py
 include tests/*.py
 
+include CHANGELOG.md
+include CONTRIBUTORS.md
+include CITATION.cff
+
 graft vendor/source/igraph
 
 graft doc

doc/examples_sphinx-gallery/cluster_contraction.py

@@ -12,7 +12,7 @@
 
 # %%
 # We begin by load the graph from file. The file containing this network can be
-# downloaded `here <http://www-personal.umich.edu/~mejn/netdata/>`_.
+# downloaded `here <https://www-personal.umich.edu/~mejn/netdata/>`_.
 g = ig.load("./lesmis/lesmis.gml")
 
 # %%