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diff --git a/.git_archival.json b/.git_archival.json new file mode 100644 index 000000000..9869b5923 --- /dev/null +++ b/.git_archival.json @@ -0,0 +1,7 @@ +{ + "hash-full": "$Format:%H$", + "hash-short": "$Format:%h$", + "timestamp": "$Format:%cI$", + "refs": "$Format:%D$", + "describe": "$Format:%(describe:tags=true,match=[0-9]*)$" +} diff --git a/.gitattributes b/.gitattributes index c7158f857..56669188e 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1 @@ -*.c linguist-language=Python +.git_archival.json export-subst diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml new file mode 100644 index 000000000..71e72eb9a --- /dev/null +++ b/.github/FUNDING.yml @@ -0,0 +1,2 @@ +github: igraph +open_collective: igraph diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index 31afa92c3..60eeaa013 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -19,4 +19,3 @@ Explain when and for what purpose the feature would be useful. **References** List any relevant references (papers or books describing relevant algorithms). - diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 000000000..5ace4600a --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,6 @@ +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "weekly" diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 000000000..686944ff0 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,5 @@ + + + + +- [ ] By submitting this pull request, I assign the copyright of my contribution to _The igraph development team_. diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 260e36efe..8af4dece1 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -1,152 +1,228 @@ -name: Build and test, upload to PyPI on release +# Name cannot contain commas because of setup-emsdk job +name: Build and test on: [push, pull_request] env: - CIBW_TEST_COMMAND: "cd {project} && python -m pytest tests" - CIBW_TEST_EXTRAS: "test" - CIBW_SKIP: "*musllinux*" - CIBW_MANYLINUX_X86_64_IMAGE: "manylinux2014" - CIBW_MANYLINUX_I686_IMAGE: "manylinux2014" - CIBW_MANYLINUX_PYPY_X86_64_IMAGE: "manylinux2014" - CIBW_MANYLINUX_PYPY_I686_IMAGE: "manylinux2014" + CIBW_ENVIRONMENT_PASS_LINUX: PYTEST_TIMEOUT + CIBW_TEST_COMMAND: "cd {project} && pip install --prefer-binary '.[test]' && python -m pytest -v tests" + CIBW_SKIP: "cp38-* pp38-*" + PYTEST_TIMEOUT: 60 jobs: build_wheel_linux: - name: Build wheels on Linux (${{ matrix.wheel_arch }}) - runs-on: ubuntu-20.04 - strategy: - fail-fast: false - matrix: - wheel_arch: [x86_64, i686] - + name: Build wheels on Linux (x86_64) + runs-on: ubuntu-22.04 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v5 with: submodules: true fetch-depth: 0 - - uses: actions/setup-python@v2 - name: Install Python - with: - python-version: '3.8' + - name: Build wheels (manylinux) + uses: pypa/cibuildwheel@v3.0.1 + env: + CIBW_BEFORE_BUILD: "yum install -y flex bison libxml2-devel zlib-devel cairo-devel && pip install -U cmake pip setuptools wheel && python setup.py build_c_core" + CIBW_BUILD: "*-manylinux_x86_64" + CIBW_ENABLE: pypy - - name: Build wheels - uses: joerick/cibuildwheel@v2.4.0 + - name: Build wheels (musllinux) + uses: pypa/cibuildwheel@v3.0.1 env: - CIBW_BEFORE_BUILD: "yum install -y flex bison libxml2-devel zlib-devel && pip install cmake && python setup.py build_c_core" - CIBW_BUILD: "*-manylinux_${{ matrix.wheel_arch }}" - # Skip tests for Python 3.10 because SciPy does not have a 32-bit - # wheel for Linux yet - CIBW_TEST_SKIP: "cp310-manylinux_i686" + 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_x86_64" + CIBW_TEST_COMMAND: "cd {project} && pip install --prefer-binary '.[test-musl]' && python -m pytest -v tests" - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: + name: wheels-linux-x86_64 path: ./wheelhouse/*.whl - build_wheel_linux_aarch64: - name: Build wheels on Linux (aarch64) - runs-on: ubuntu-20.04 - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') + build_wheel_linux_aarch64_manylinux: + name: Build wheels on Linux (aarch64/manylinux) + runs-on: ubuntu-22.04-arm steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v5 with: submodules: true fetch-depth: 0 - - name: Set up QEMU - id: qemu - uses: docker/setup-qemu-action@v1 - - - name: Build wheels - uses: joerick/cibuildwheel@v2.4.0 + - name: Build wheels (manylinux) + uses: pypa/cibuildwheel@v3.0.1 env: - CIBW_BEFORE_BUILD: "yum install -y flex bison libxml2-devel zlib-devel && pip install cmake && python setup.py build_c_core" + 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 CIBW_BUILD: "*-manylinux_aarch64" + CIBW_ENABLE: pypy - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: + name: wheels-linux-aarch64-manylinux + path: ./wheelhouse/*.whl + + build_wheel_linux_aarch64_musllinux: + name: Build wheels on Linux (aarch64/musllinux) + runs-on: ubuntu-22.04-arm + steps: + - uses: actions/checkout@v5 + with: + submodules: true + fetch-depth: 0 + + - name: Build wheels (musllinux) + 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 + CIBW_BUILD: "*-musllinux_aarch64" + 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-aarch64-musllinux path: ./wheelhouse/*.whl build_wheel_macos: name: Build wheels on macOS (${{ matrix.wheel_arch }}) - runs-on: macos-10.15 + runs-on: macos-latest + env: + LLVM_VERSION: "14.0.5" + MACOSX_DEPLOYMENT_TARGET: "10.15" strategy: matrix: include: - cmake_arch: x86_64 wheel_arch: x86_64 - cmake_arch: arm64 - cmake_extra_args: -DF2C_EXTERNAL_ARITH_HEADER=../../../etc/arith_apple_m1.h + cmake_extra_args: -DF2C_EXTERNAL_ARITH_HEADER=../../../etc/arith_apple_m1.h -DIEEE754_DOUBLE_ENDIANNESS_MATCHES=ON wheel_arch: arm64 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v5 with: submodules: true fetch-depth: 0 - name: Cache installed C core id: cache-c-core - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: vendor/install - key: C-core-cache-v2-${{ runner.os }}-${{ matrix.cmake_arch }}-${{ hashFiles('.git/modules/vendor/source/igraph/HEAD') }} + key: C-core-cache-${{ runner.os }}-${{ matrix.cmake_arch }}-llvm${{ env.LLVM_VERSION }}-${{ hashFiles('.git/modules/**/HEAD') }} - - uses: actions/setup-python@v2 - name: Install Python + - name: Cache C core dependencies + id: cache-c-deps + uses: actions/cache@v4 with: - python-version: '3.8' + path: ~/local + key: deps-cache-v2-${{ runner.os }}-${{ matrix.cmake_arch }}-llvm${{ env.LLVM_VERSION }} - name: Install OS dependencies - if: steps.cache-c-core.outputs.cache-hit != 'true' # Only needed when building the C core - run: - brew install ninja autoconf automake libtool cmake + if: steps.cache-c-core.outputs.cache-hit != 'true' || steps.cache-c-deps.outputs.cache-hit != 'true' # Only needed when building the C core or libomp + run: brew install ninja autoconf automake libtool + + - name: Install OpenMP library + if: steps.cache-c-deps.outputs.cache-hit != 'true' + run: | + wget https://github.com/llvm/llvm-project/releases/download/llvmorg-$LLVM_VERSION/openmp-$LLVM_VERSION.src.tar.xz + tar xf openmp-$LLVM_VERSION.src.tar.xz + cd openmp-$LLVM_VERSION.src + mkdir build && cd build + cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/local -DLIBOMP_ENABLE_SHARED=OFF -DCMAKE_OSX_ARCHITECTURES=${{ matrix.cmake_arch }} + cmake --build . + cmake --install . - name: Build wheels - uses: joerick/cibuildwheel@v2.4.0 + uses: pypa/cibuildwheel@v3.0.1 env: CIBW_ARCHS_MACOS: "${{ matrix.wheel_arch }}" - CIBW_BEFORE_BUILD: "python setup.py build_c_core" - IGRAPH_CMAKE_EXTRA_ARGS: -DCMAKE_OSX_ARCHITECTURES=${{ matrix.cmake_arch }} ${{ matrix.cmake_extra_args }} + CIBW_BEFORE_BUILD: "pip install -U setuptools && python setup.py build_c_core" + CIBW_ENABLE: pypy + CIBW_ENVIRONMENT: "LDFLAGS=-L$HOME/local/lib" + IGRAPH_CMAKE_EXTRA_ARGS: -DCMAKE_OSX_ARCHITECTURES=${{ matrix.cmake_arch }} ${{ matrix.cmake_extra_args }} -DCMAKE_PREFIX_PATH=$HOME/local - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: + name: wheels-macos-${{ matrix.wheel_arch }} path: ./wheelhouse/*.whl + build_wheel_wasm: + name: Build wheels for WebAssembly + runs-on: ubuntu-22.04 + + steps: + - uses: actions/checkout@v5 + with: + submodules: true + fetch-depth: 0 + + - uses: actions/setup-python@v5 + name: Install Python + with: + python-version: "3.12.1" + + - name: Install OS dependencies + run: sudo apt install ninja-build cmake flex bison + + - uses: mymindstorm/setup-emsdk@v14 + with: + version: "3.1.58" + actions-cache-folder: "emsdk-cache" + + - name: Build wheel + run: | + pip install pyodide-build==0.26.2 + python3 scripts/fix_pyodide_build.py + pyodide build + + - name: Setup upterm session + uses: lhotari/action-upterm@v1 + if: ${{ failure() }} + with: + limit-access-to-actor: true + wait-timeout-minutes: 5 + + - uses: actions/upload-artifact@v4 + with: + name: wheels-wasm + path: ./dist/*.whl + build_wheel_win: name: Build wheels on Windows (${{ 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: ${{ matrix.os }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v5 with: submodules: true fetch-depth: 0 - - uses: actions/setup-python@v2 - name: Install Python - with: - python-version: '3.8' - - name: Cache installed C core id: cache-c-core - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: vendor/install - key: C-core-build-v1-${{ runner.os }}-${{ matrix.cmake_arch }}-${{ hashFiles('.git/modules/vendor/source/igraph/HEAD') }} + key: C-core-cache-${{ runner.os }}-${{ matrix.cmake_arch }}-${{ hashFiles('.git/modules/**/HEAD') }} - name: Cache VCPKG - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: C:/vcpkg/installed/ key: vcpkg-${{ runner.os }}-${{ matrix.vcpkg_arch }} @@ -158,55 +234,55 @@ jobs: - name: Install VCPKG libraries run: | %VCPKG_INSTALLATION_ROOT%\vcpkg.exe integrate install - %VCPKG_INSTALLATION_ROOT%\vcpkg.exe install libxml2:${{ 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: joerick/cibuildwheel@v2.4.0 + uses: pypa/cibuildwheel@v3.0.1 env: - CIBW_BEFORE_BUILD: "python setup.py build_c_core" + CIBW_BEFORE_BUILD: "pip install -U setuptools && python setup.py build_c_core" CIBW_BUILD: "*-${{ matrix.wheel_arch }}" - # Skip tests for Python 3.10 because SciPy does not have a 32-bit - # wheel for Python 3.10 yet - CIBW_TEST_SKIP: "cp310-win32" - CIBW_TEST_COMMAND: "cd /d {project} && python -m pytest tests" + CIBW_ENABLE: pypy + CIBW_TEST_COMMAND: 'cd /d {project} && pip install --prefer-binary ".[${{ matrix.test_extra }}]" && python -m pytest tests' + # Skip tests for Python 3.10 onwards because SciPy does not have + # 32-bit wheels for 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/ IGRAPH_STATIC_EXTENSION: True - IGRAPH_EXTRA_LIBRARIES: libxml2,lzma,zlib,iconv,charset + IGRAPH_EXTRA_LIBRARIES: libxml2,lzma,zlib,iconv,charset,bcrypt IGRAPH_EXTRA_DYNAMIC_LIBRARIES: wsock32,ws2_32 - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: + name: wheels-win-${{ matrix.wheel_arch }} path: ./wheelhouse/*.whl build_sdist: name: Build sdist and test extra dependencies runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v5 with: submodules: true fetch-depth: 0 - name: Cache installed C core id: cache-c-core - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: | - vendor/build vendor/install - key: C-core-build-sdist-v1-${{ runner.os }}-${{ hashFiles('.git/modules/vendor/source/igraph/HEAD') }} + key: C-core-cache-${{ runner.os }}-${{ hashFiles('.git/modules/**/HEAD') }} - 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@v2 + - uses: actions/setup-python@v5 name: Install Python with: - python-version: '3.8' + python-version: "3.9" - name: Build sdist run: | @@ -216,72 +292,62 @@ jobs: - name: Test run: | - pip install numpy scipy pandas networkx pytest - python -m pytest tests + pip install --prefer-binary cairocffi numpy scipy pandas networkx pytest pytest-timeout + python -m pytest -v tests - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: + name: sdist path: dist/*.tar.gz # When updating 'runs-on', the ASan/UBSan library paths/versions must also be updated for LD_PRELOAD # for the "Test" step below. - # - # The C core is temporarily compiled with -DCMAKE_C_FLAGS="-DNDEBUG" because the Python test suite - # triggers a bug/assertion in RNG_INTEGER(): https://github.com/igraph/igraph/issues/2031 - # When this bug is fixed, remove NDEBUG and increment the cache version to v1. build_with_sanitizer: name: Build with sanitizers for debugging purposes - runs-on: ubuntu-20.04 + runs-on: ubuntu-latest env: - CC: "gcc -fsanitize=address -fsanitize=undefined" - CXX: "g++ -fsanitize=address -fsanitize=undefined" - CFLAGS: "-g -Og -fno-omit-frame-pointer -fdiagnostics-color" - CXXFLAGS: "-g -Og -fno-omit-frame-pointer -fdiagnostics-color" - IGRAPH_CMAKE_EXTRA_ARGS: -DUSE_SANITIZER="Address;Undefined" -DCMAKE_BUILD_TYPE=Debug -DFLEX_KEEP_LINE_NUMBERS=ON -DFORCE_COLORED_OUTPUT=ON -DCMAKE_C_FLAGS="-DNDEBUG" + IGRAPH_CMAKE_EXTRA_ARGS: -DFORCE_COLORED_OUTPUT=ON steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v5 with: submodules: true fetch-depth: 0 - + - name: Cache installed C core id: cache-c-core - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: | vendor/build vendor/install - key: C-core-build-sanitizer-v0-${{ runner.os }}-${{ hashFiles('.git/modules/vendor/source/igraph/HEAD') }} + key: C-core-build-sanitizer-v1-${{ runner.os }}-${{ hashFiles('.git/modules/vendor/source/igraph/HEAD') }} - 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@v2 + - uses: actions/setup-python@v5 name: Install Python with: - python-version: '3.10' - - - name: Build C core - 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 - - - name: Install test dependencies - run: | - pip install pytest numpy scipy pandas networkx + # 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. - # Leak detection is disabled because of many false (?) positives in Python itself. + # LD_PRELOAD needs to be specified in the "run" section to ensure that we + # do not pick up memory leaks in the wrapper shell (e.g., /bin/bash) - name: Test env: - LD_PRELOAD: "/lib/x86_64-linux-gnu/libasan.so.5:/lib/x86_64-linux-gnu/libubsan.so.1" - ASAN_OPTIONS: "detect_leaks=0" + ASAN_OPTIONS: "detect_stack_use_after_return=1" + LSAN_OPTIONS: "suppressions=etc/lsan-suppr.txt:print_suppressions=false" run: | - python -m pytest --capture=sys tests + sudo sysctl vm.mmap_rnd_bits=28 + LD_PRELOAD=/lib/x86_64-linux-gnu/libasan.so.8:/lib/x86_64-linux-gnu/libubsan.so.1 python -m pytest --capture=sys tests diff --git a/.gitignore b/.gitignore index ef7ad00fd..46689eff9 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,10 @@ vendor/install/ .DS_Store doc/source/gallery.rst +doc/source/tutorials +doc/linkcheck doc/api/ +doc/dash/ doc/html/ doc/jekyll_tools/vendor +doc/examples_sphinx-gallery/social_network.* diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 000000000..e67e6d125 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,15 @@ +fail_fast: true +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.6.0 + hooks: + - id: end-of-file-fixer + exclude: ^tests/drawing/plotly/baseline_images + - id: trailing-whitespace + + - repo: https://github.com/charliermarsh/ruff-pre-commit + rev: v0.3.5 + hooks: + - id: ruff + args: [--fix, --exit-non-zero-on-fix] + - id: ruff-format diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 000000000..7de01065a --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,48 @@ +# .readthedocs.yaml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +submodules: + include: + - vendor/source/igraph + recursive: true + +# Set the version of Python and other tools you might need +build: + os: ubuntu-22.04 + apt_packages: + - cmake + - flex + - bison + - libxml2-dev + - zlib1g-dev + + tools: + python: "3.11" + # You can also specify other tool versions: + # nodejs: "16" + # rust: "1.55" + # golang: "1.17" + + jobs: + pre_build: + - bash ./scripts/rtd_prebuild.sh + # One website complains about legacy SSL renegotiation (?), skip for now + #- python -m sphinx -b linkcheck doc/source/ _build/linkcheck + + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: doc/source/conf.py + +# If using Sphinx, optionally build your docs in additional formats such as PDF +# formats: +# - pdf + +# Optionally declare the Python requirements required to build your docs +python: + install: + - requirements: doc/source/requirements.txt diff --git a/CHANGELOG.md b/CHANGELOG.md index 4512056b0..3ccdc79e0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,374 @@ # igraph Python interface changelog -## [Development branch] +## [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 0.10.16. + +- Added `Graph.simple_cycles()` to find simple cycles in the graph. + +## [0.11.8] - 2024-10-25 + +### Fixed + +- Fixed documentation build on Read The Docs. No other changes compared to + 0.11.7. + +## [0.11.7] - 2024-10-24 + +### Added + +- Added `Graph.feedback_vertex_set()` to calculate a feedback vertex set of the + graph. + +- Added new methods to `Graph.feedback_arc_set()` that allows the user to + select the specific integer problem formulation used by the underlying + solver. + +### Changed + +- Ensured compatibility with Python 3.13. + +- The C core of igraph was updated to an interim commit (3dd336a) between + version 0.10.13 and version 0.10.15. Earlier versions of this changelog + mistakenly marked this revision as version 0.10.14. + +### Fixed + +- Fixed a potential memory leak in the `Graph.get_shortest_path_astar()` heuristic + function callback + +## [0.11.6] - 2024-07-08 + +### Added + +- Added `Graph.Hypercube()` for creating n-dimensional hypercube graphs. + +- 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 + distinct pairs of vertices. + +- 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 + independent set. + +- 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. + +- `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 + and type of that attribute. + +## [0.11.5] - 2024-05-07 + +### Added + +- Added a `prefixattr=...` keyword argument to `Graph.write_graphml()` that + allows the user to strip the `g_`, `v_` and `e_` prefixes from GraphML files + written by igraph. + +### Changed + +- `Graph.are_connected()` has now been renamed to `Graph.are_adjacent()`, + following up a similar change in the C core. The old name of the function + is deprecated but will be kept around until at least 0.12.0. + +- The C core of igraph was updated to version 0.10.12. + +- Deprecated `PyCObject` API calls in the C code were replaced by calls to + `PyCapsule`, thanks to @DavidRConnell in + + +- `get_shortest_path()` documentation was clarified by @JDPowell648 in + + +- It is now possible to link to an existing igraph C core on MSYS2, thanks to + @Kreijstal in + +### Fixed + +- Bugfix in the NetworkX graph conversion code by @rmmaf in + + +## [0.11.4] + +### Added + +- Added `Graph.Prufer()` to construct a graph from a Prüfer sequence. + +- Added `Graph.Bipartite_Degree_Sequence()` to construct a bipartite graph from + a bidegree sequence. + +- Added `Graph.is_biconnected()` to check if a graph is biconnected. + +### Fixed + +- Fixed import of `graph-tool` graphs for vertex properties where each property + has a vector value. + +- `Graph.Adjacency()` now accepts `Matrix` instances and other sequences as an + input, it is not limited to lists-of-lists-of-ints any more. + +## [0.11.3] - 2023-11-19 + +### Added + +- Added `Graph.__invalidate_cache()` for debugging and benchmarking purposes. + +### Changed + +- The C core of igraph was updated to version 0.10.8. + +### Fixed + +- Removed incorrectly added `loops=...` argument of `Graph.is_bigraphical()`. + +- Fixed a bug in the Matplotlib graph drawing backend that filled the interior of undirected curved edges. + +## [0.11.2] - 2023-10-12 + +### Fixed + +- Fixed plotting of null graphs with the Matplotlib backend. + +## [0.11.0] - 2023-10-12 + +### Added + +- `python-igraph` is now tested in Python 3.12. + +- Added `weights=...` keyword argument to `Graph.layout_kamada_kawai()`. + +### Changed + +- The `matplotlib` plotting infrastructure underwent major surgery and is now able to show consistent vertex and edge drawings at any level of zoom, including with animations, and for any aspect ratio. +- As a consequence of the restructuring at the previous point, vertex sizes are now specified in figure points and are not affected by axis limits or zoom. With the current conventions, `vertex_size=25` is a reasonable size for `igraph.plot`. +- As another consequence of the above, vertex labels now support offsets from the vertex center, in figure point units. +- As another consequence of the above, self loops are now looking better and their size can be controlled using the `edge_loop_size` argument in `igraph.plot`. +- As another consequence of the above, if using the `matplotlib` backend when plotting a graph, `igraph.plot` now does not return the `Axes` anymore. Instead, it returns a container artist called `GraphArtist`, which contains as children the elements of the graph plot: a `VertexCollection` for the vertices, and `EdgeCollection` for the edges, and so on. These objects can be used to modify the plot after the initial rendering, e.g. inside a Jupyter notebook, to fine tune the appearance of the plot. While documentation on specific graphic elements is still scant, more descriptive examples will follow in the future. + +### Fixed + +- Fixed drawing order of vertices in the Plotly backend (#691). + +### Removed + +- Dropped support for Python 3.7 as it has reached its end of life. + +## [0.10.8] - 2023-09-12 + +### Added + +- Added `is_bigraphical()` to test whether a pair of integer sequences can be the degree sequence of some bipartite graph. + +- Added `weights=...` keyword argument to `Graph.radius()` and `Graph.eccentricity()`. + +## [0.10.7] - 2023-09-04 + +### Added + +- `Graph.distances()`, `Graph.get_shortest_path()` and `Graph.get_shortest_paths()` now allow the user to select the algorithm to be used explicitly. + +### Changed + +- The C core of igraph was updated to version 0.10.7. + +- `Graph.distances()` now uses Dijkstra's algorithm when there are zero weights but no negative weights. Earlier versions switched to Bellman-Ford or Johnson in the presence of zero weights unnecessarily. + +### Fixed + +- Fixed a bug in `EdgeSeq.select(_incident=...)` for undirected graphs. + +- Fixed a memory leak in `Graph.distances()` when attempting to use Johnson's algorithm with `mode != "out"` + +## [0.10.6] - 2023-07-13 + +### Changed + +- The C core of igraph was updated to version 0.10.6. + +- `Graph.Incidence()` is now deprecated in favour of `Graph.Biadjacency()` as it constructs a bipartite graph from a _bipartite adjacency_ matrix. (The previous name was a mistake). Future versions might re-introduce `Graph.Incidence()` to construct a graph from its incidence matrix. + +- `Graph.get_incidence()` is now deprecated in favour of `Graph.get_biadjacency()` as it returns the _bipartite adjacency_ matrix of a graph and not its incidence matrix. (The previous name was a mistake). Future versions might re-introduce `Graph.get_incidence()` to return the incidence matrix of a graph. + +- Reverted the change in 0.10.5 that prevented adding vertices with integers as vertex names. Now we show a deprecation warning instead, and the addition of vertices with integer names will be prevented from version 0.11.0 only. + +### Fixed + +- Fixed a minor memory leak in `Graph.decompose()`. + +- The default vertex size of the Plotly backend was fixed so the vertices are + now visible by default without specifying an explicit size for them. + +## [0.10.5] - 2023-06-30 + +### Added + +- The `plot()` function now takes a `backend` keyword argument that can be used + to specify the plotting backend explicitly. + +- The `VertexClustering` object returned from `Graph.community_leiden()` now + contains an extra property named `quality` that stores the value of the + internal quality function optimized by the algorithm. + +- `Graph.Adjacency()` and `Graph.Weighted_Adjacency()` now supports + `loops="once"`, `loops="twice"` and `loops="ignore"` to control how loop + edges are handled in a more granular way. `loops=True` and `loops=False` + keep on working as in earlier versions. + +- Added `Graph.get_shortest_path()` as a convenience function for cases when + only one shortest path is needed between a given source and target vertices. + +- Added `Graph.get_shortest_path_astar()` to calculate the shortest path + between two vertices using the A-star algorithm and an appropriate + heuristic function. + +- Added `Graph.count_automorphisms()` to count the number of automorphisms + of a graph and `Graph.automorphism_group()` to calculate the generators of + the automorphism group of a graph. + +- The `VertexCover` constructor now allows referring to vertices by names + instead of IDs. + +### Fixed + +- `resolution` parameter is now correctly taken into account when calling + `Graph.modularity()` + +- `VertexClustering.giant()` now accepts the null graph. The giant component of + a null graph is the null graph according to our conventions. + +- `Graph.layout_reingold_tilford()` now accepts vertex names in the `roots=...` + keyword argument. + +- The plotting of curved directed edges with the Cairo backend is now fixed; + arrowheads were placed at the wrong position before this fix. + +### Changed + +- The C core of igraph was updated to version 0.10.5. + +### Removed + +- Removed defunct `Graph.community_leading_eigenvector_naive()` method. Not a + breaking change because it was already removed from the C core a long time + ago so the function in the Python interface did not do anything useful + either. + +## [0.10.4] - 2023-01-27 + +### Added + +- Added `Graph.vertex_coloring_greedy()` to calculate a greedy vertex coloring + for the graph. + +- Betweenness and edge betweenness scores can now be calculated for a subset of + the shortest paths originating from or terminating in a certain set of + vertices only. + +### Fixed + +- Fixed the drawing of `VertexDendrogram` instances, both in the Cairo and the + Matplotlib backends. +- The `cutoff` and `normalized` arguments of `Graph.closeness()` did not function correctly. + +## [0.10.3] - 2022-12-31 + +### Changed + +- The C core of igraph was updated to version 0.10.3. + +- UMAP layout now exposes the computation of the symmetrized edge weights via + `umap_compute_weights()`. The layout function, `Graph.layout_umap()`, can + now be called either on a directed graph with edge distances, or on an + undirected graph with edge weights, typically computed via + `umap_compute_weights()` or precomputed by the user. Moreover, the + `sampling_prob` argument was faulty and has been removed. See PR + [#613](https://github.com/igraph/python-igraph/pull/613) for details. + +- The `resolution_parameter` argument of `Graph.community_leiden()` was renamed + to `resolution` for sake of consistency. The old variant still works with a + deprecation warning, but will be removed in a future version. + +### Fixed + +- `Graph.Data_Frame()` now handles the `Int64` data type from `pandas`, thanks + to [@Adriankhl](https://github.com/Adriankhl). See PR + [#609](https://github.com/igraph/python-igraph/pull/609) for details. + +- `Graph.layout_lgl()` `root` argument is now optional (as it should have been). + +- The `VertexClustering` class now handles partial dendrograms correctly. + +## [0.10.2] - 2022-10-14 + +### Added + +- `python-igraph` is now tested in Python 3.11. + +- Added `Graph.modularity_matrix()` to calculate the modularity matrix of + a graph. + +- Added `Graph.get_k_shortest_paths()`, thanks to + [@sombreslames](https://github.com/user/sombreslames). See PR + [#577](https://github.com/igraph/python-igraph/pull/577) for details. + +- The `setup.py` script now also accepts environment variables instead of + command line arguments to configure several aspects of the build process + (i.e. whether a fully static extension is being built, or whether it is + allowed to use `pkg-config` to retrieve the compiler and linker flags for + an external `igraph` library instead of the vendored one). The environment + variables are named similarly to the command line arguments but in + uppercase, dashes replaced with underscores, and they are prefixed with + `IGRAPH_` (i.e. `--use-pkg-config` becomes `IGRAPH_USE_PKG_CONFIG`). + +### Changed + +- The C core of igraph was updated to version 0.10.2, fixing a range of bugs + originating from the C core. + +### Fixed + +- Fixed a crash in `Graph.decompose()` that was accidentally introduced in + 0.10.0 during the transition to `igraph_graph_list_t` in the C core. + +- `Clustering.sizes()` now works correctly even if the membership vector + contains `None` items. + +- `Graph.modularity()` and `Graph.community_multilevel()` now correctly expose + the `resolution` parameter. + +- Fixed a reference leak in `Graph.is_chordal()` that decreased the reference + count of Python's built-in `True` and `False` constants unnecessarily. + +- Unit tests updated to get rid of deprecation warnings in Python 3.11. + +## [0.10.1] - 2022-09-12 + +### Added + +- Added `Graph.minimum_cycle_basis()` and `Graph.fundamental_cycles()` + +- `Graph.average_path_length()` now supports edge weights. + +### Fixed + +- Restored missing exports from `igraph.__all__` that used to be in the main + `igraph` package before 0.10.0. + +## [0.10.0] - 2022-09-05 ### Added @@ -8,32 +376,87 @@ plotting backends, controlled by a configuration option. See PR [#425](https://github.com/igraph/python-igraph/pull/425) for more details. -- Added support for additional ways to construct a graph, such as from a +- Added support for additional ways to construct a graph, such as from a dictionary of dictionaries, and to export a graph object back to those data structures. See PR [#434](https://github.com/igraph/python-igraph/pull/434) for more details. +- `Graph.list_triangles()` lists all triangles in a graph. + +- `Graph.reverse_edges()` reverses some or all edges of a graph. + +- `Graph.Degree_Sequence()` now supports the `"no_multiple_uniform"` generation + method, which generates simple graphs, sampled uniformly, using rejection + sampling. + +- `Graph.Lattice()` now supports per-dimension periodicity control. + +- `Graph.get_adjacency()` now allows the user to specify whether loop edges + should be counted once or twice, or not at all. + +- `Graph.get_laplacian()` now supports left-, right- and symmetric normalization. + +- `Graph.modularity()` now supports setting the resolution with the + `resolution=...` parameter. + ### Changed +- The C core of igraph was updated to version 0.10.0. + +- We now publish `abi3` wheels on PyPI from CPython 3.9 onwards, making it + possible to use an already-built Python wheel with newer minor Python + releases (and also reducing the number of wheels we actually need to + publish). Releases for CPython 3.7 and 3.8 still use version-specific wheels + because the code of the C part of the extension contains conditional macros + for CPython 3.7 and 3.8. + - Changed default value of the `use_vids=...` argument of `Graph.DataFrame()` to `True`, thanks to [@fwitter](https://github.com/user/fwitter). +- `Graph.Degree_Sequence()` now accepts all sorts of sequences as inputs, not + only lists. + +### Fixed + +- The Matplotlib backend now allows `edge_color` and `edge_width` to be set + on an edge-by-edge basis. + ### Removed +- Dropped support for Python 3.6. + - Removed deprecated `UbiGraphDrawer`. - Removed deprecated `show()` method of `Plot` instances as well as the feature that automatically shows the plot when `plot()` is called with no target. +- Removed the `eids` keyword argument of `get_adjacency()`. + ### Deprecated - `Graph.clusters()` is now deprecated; use `Graph.connected_components()` or its already existing shorter alias, `Graph.components()`. -## [Unreleased] +- `Graph.shortest_paths()` is now deprecated; use `Graph.distances()` instead. + +## [0.9.11] + +### Added + +- We now publish `musllinux` wheels on PyPI. + +### Changed + +- Vendored igraph was updated to version 0.9.9. ### Fixed +- Graph union and intersection (by name) operators now verify that there are no + duplicate names within the individual graphs. + +- Fixed a memory leak in `Graph.union()` when edge maps were used; see + [#534](https://github.com/igraph/python-igraph/issues/534) for details. + - Fixed a bug in the Cairo and Matplotlib backends that prevented edges with labels from being drawn properly; see [#535](https://github.com/igraph/python-igraph/issues/535) for details. @@ -59,7 +482,7 @@ [#503](https://github.com/igraph/python-igraph/issues/503) for details. - Fixed potential memory leaks in `Graph.maximum_cardinality_search()`, - `Graph.get_all_simple_paths()`, `Graph.get_subisomorphisms_lad()`, + `Graph.get_all_simple_paths()`, `Graph.get_subisomorphisms_lad()`, `Graph.community_edge_betweenness()`, as well as the `union` and `intersection` operators. @@ -298,12 +721,29 @@ ## [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 for a list of changes affecting versions up to 0.8.3. Notable changes after 0.8.3 are documented above. -[Development branch]: https://github.com/igraph/python-igraph/compare/0.9.10..develop -[Unreleased]: https://github.com/igraph/python-igraph/compare/0.9.10..master +[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 +[0.11.5]: https://github.com/igraph/python-igraph/compare/0.11.4...0.11.5 +[0.11.4]: https://github.com/igraph/python-igraph/compare/0.11.3...0.11.4 +[0.11.3]: https://github.com/igraph/python-igraph/compare/0.11.2...0.11.3 +[0.11.2]: https://github.com/igraph/python-igraph/compare/0.11.0...0.11.2 +[0.11.0]: https://github.com/igraph/python-igraph/compare/0.10.8...0.11.0 +[0.10.8]: https://github.com/igraph/python-igraph/compare/0.10.7...0.10.8 +[0.10.7]: https://github.com/igraph/python-igraph/compare/0.10.6...0.10.7 +[0.10.6]: https://github.com/igraph/python-igraph/compare/0.10.5...0.10.6 +[0.10.5]: https://github.com/igraph/python-igraph/compare/0.10.4...0.10.5 +[0.10.4]: https://github.com/igraph/python-igraph/compare/0.10.3...0.10.4 +[0.10.3]: https://github.com/igraph/python-igraph/compare/0.10.2...0.10.3 +[0.10.2]: https://github.com/igraph/python-igraph/compare/0.10.1...0.10.2 +[0.10.1]: https://github.com/igraph/python-igraph/compare/0.10.0...0.10.1 +[0.10.0]: https://github.com/igraph/python-igraph/compare/0.9.11...0.10.0 +[0.9.11]: https://github.com/igraph/python-igraph/compare/0.9.10...0.9.11 [0.9.10]: https://github.com/igraph/python-igraph/compare/0.9.9...0.9.10 [0.9.9]: https://github.com/igraph/python-igraph/compare/0.9.8...0.9.9 [0.9.8]: https://github.com/igraph/python-igraph/compare/0.9.7...0.9.8 diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 000000000..e803bfa79 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,53 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: igraph +message: >- + If you use igraph, please cite it using the + metadata from this file. +type: software +authors: + - given-names: Gábor + family-names: Csárdi + orcid: 'https://orcid.org/0000-0001-7098-9676' + - given-names: Tamás + family-names: Nepusz + orcid: 'https://orcid.org/0000-0002-1451-338X' + - given-names: Szabolcs + family-names: Horvát + orcid: 'https://orcid.org/0000-0002-3100-523X' + - given-names: Vincent Antonio + family-names: Traag + orcid: 'https://orcid.org/0000-0003-3170-3879' + - given-names: Fabio + family-names: Zanini + orcid: 'https://orcid.org/0000-0001-7097-8539' + - given-names: Daniel + family-names: Noom +repository-code: 'https://github.com/igraph/python-igraph' +url: 'https://igraph.org' +abstract: >- + igraph is a C library for complex network analysis and + graph theory, with emphasis on efficiency, portability and + ease of use. +keywords: + - network analysis + - graph theory +license: GPL-2.0-or-later +version: 0.10.5 +date-released: '2023-07-01' +preferred-citation: + type: article + authors: + - given-names: Gábor + family-names: Csárdi + orcid: 'https://orcid.org/0000-0001-7098-9676' + - given-names: Tamás + family-names: Nepusz + orcid: 'https://orcid.org/0000-0002-1451-338X' + journal: "InterJournal, Complex Systems" + start: 1695 # First page number + title: "The igraph software package for complex network research" + year: 2006 + type: article diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md new file mode 100644 index 000000000..d22d5bd6f --- /dev/null +++ b/CONTRIBUTORS.md @@ -0,0 +1,111 @@ +## Contributors ✨ + +Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)): + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Tamás Nepusz
Tamás Nepusz

💻
Fabio Zanini
Fabio Zanini

💻
Kevin Zhu
Kevin Zhu

💻
Gábor Csárdi
Gábor Csárdi

💻
Szabolcs Horvát
Szabolcs Horvát

💻
Vincent Traag
Vincent Traag

💻
deeenes
deeenes

💻
Seungoh Han
Seungoh Han

💻
Artem V L
Artem V L

💻
Yesung(Isaac) Lee
Yesung(Isaac) Lee

💻
John Boy
John Boy

💻
Casper da Costa-Luis
Casper da Costa-Luis

💻
Alberto Alcolea
Alberto Alcolea

💻
Árpád Horváth
Árpád Horváth

💻
ebraminio
ebraminio

💻
Fabian Witter
Fabian Witter

💻
Jan Katins
Jan Katins

💻
Nick Eubank
Nick Eubank

💻
Peter Scott
Peter Scott

💻
Sriram-Pattabiraman
Sriram-Pattabiraman

💻
Sviatoslav
Sviatoslav

💻
Ah-Young Nho
Ah-Young Nho

💻
Frederik Harwath
Frederik Harwath

💻
Navid Dianati
Navid Dianati

💻
abe-winter
abe-winter

💻
Alejandro Rivero
Alejandro Rivero

💻
Ariki
Ariki

💻
Casper van Elteren
Casper van Elteren

💻
Charles Tapley Hoyt
Charles Tapley Hoyt

💻
Christoph Gohlke
Christoph Gohlke

💻
Christopher Falter
Christopher Falter

💻
FredInChina
FredInChina

💻
Friso van Vollenhoven
Friso van Vollenhoven

💻
Gabor Szarnyas
Gabor Szarnyas

💻
Gao Fangshu
Gao Fangshu

💻
Grzegorz Chilczuk
Grzegorz Chilczuk

💻
Gwyn Ciesla
Gwyn Ciesla

💻
Hong Xu
Hong Xu

💻
Jay Smith
Jay Smith

💻
MapleCCC
MapleCCC

💻
Marco Köpcke
Marco Köpcke

💻
Markus Elfring
Markus Elfring

💻
Martino Mensio
Martino Mensio

💻
Matas
Matas

💻
Mike Lissner
Mike Lissner

💻
Philipp A.
Philipp A.

💻
Puneetha Pai
Puneetha Pai

💻
S Murthy
S Murthy

💻
Scott Gigante
Scott Gigante

💻
Thierry Thomas
Thierry Thomas

💻
Willem van den Boom
Willem van den Boom

💻
Yisu Remy Wang
Yisu Remy Wang

💻
YY Ahn
YY Ahn

💻
kmankinen
kmankinen

💻
odidev
odidev

💻
sombreslames
sombreslames

💻
szcf-weiya
szcf-weiya

💻
tristanlatr
tristanlatr

💻
JDPowell648
JDPowell648

📖
k.h.lai
k.h.lai

💻
Anton Grübel
Anton Grübel

💻
flange-ipb
flange-ipb

💻
Paul m. p. Peny
Paul m. p. Peny

💻
David R. Connell
David R. Connell

💻
Rodrigo Monteiro de Moraes de Arruda Falcão
Rodrigo Monteiro de Moraes de Arruda Falcão

💻
Kreijstal
Kreijstal

💻
Michael Schneider
Michael Schneider

💻
Thomas Krijnen
Thomas Krijnen

💻
Tim Bernhard
Tim Bernhard

💻
Bea Márton
Bea Márton

💻
Sanat Kumar Gupta
Sanat Kumar Gupta

💻
+ + + + + + +This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! diff --git a/MANIFEST.in b/MANIFEST.in index 1a25d4486..39e2ee9fe 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,7 +1,21 @@ +prune docker +prune .git +prune .github + include src/_igraph/*.h include MANIFEST.in -include scripts/mkdoc.sh +include scripts/*.sh +include scripts/*.py include tests/*.py +include CHANGELOG.md +include CONTRIBUTORS.md +include CITATION.cff + graft vendor/source/igraph +graft doc +prune doc/html +prune doc/source/tutorials + +global-exclude .dockerignore .DS_Store .gitattributes .gitignore .gitmodules diff --git a/README.md b/README.md index 1f2643bfb..1f7162788 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ [![Build and test with tox](https://github.com/igraph/python-igraph/actions/workflows/build.yml/badge.svg)](https://github.com/igraph/python-igraph/actions/workflows/build.yml) -[![PyPI pyversions](https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8%20%7C%203.9%20%7C%203.10-blue)](https://pypi.python.org/pypi/igraph) +[![PyPI pyversions](https://img.shields.io/pypi/pyversions/igraph)](https://pypi.python.org/pypi/igraph) [![PyPI wheels](https://img.shields.io/pypi/wheel/igraph.svg)](https://pypi.python.org/pypi/igraph) +[![Documentation Status](https://readthedocs.org/projects/igraph/badge/?version=latest)](https://igraph.readthedocs.io/) -Python interface for the igraph library ---------------------------------------- +# Python interface for the igraph library igraph is a library for creating and manipulating graphs. It is intended to be as powerful (ie. fast) as possible to enable the @@ -13,9 +13,20 @@ analysis of large graphs. This repository contains the source code to the Python interface of igraph. -You can learn more about igraph [on our website](http://igraph.org/python/). +Since version 0.10.2, the documentation is hosted on +[readthedocs](https://igraph.readthedocs.io). Earlier versions are documented +on [our old website](https://igraph.org/python/versions/0.10.1/). -## Installation from PyPI +igraph is a collaborative work of many people from all around the world — +see the [list of contributors here](./CONTRIBUTORS.md). + +## Citation + +If you use igraph in your research, please cite + +> Csardi, G., & Nepusz, T. (2006). The igraph software package for complex network research. InterJournal, Complex Systems, 1695. + +# Installation We aim to provide wheels on PyPI for most of the stock Python versions; typically at least the three most recent minor releases from Python 3.x. @@ -28,7 +39,7 @@ pip install igraph See details in [Installing Python Modules](https://docs.python.org/3/installing/). -### Installation from source with pip on Debian / Ubuntu and derivatives +## Installation from source with pip on Debian / Ubuntu and derivatives If you need to compile igraph from source for some reason, you need to install some dependencies first: @@ -46,14 +57,15 @@ pip install igraph This should compile the C core of igraph as well as the Python extension automatically. -### Installation from source on Windows +## Installation from source on Windows It is now also possible to compile `igraph` from source under Windows for -Python 3.6 and later. Make sure that you have Microsoft Visual Studio 2015 or -later installed, and of course Python 3.6 or later. First extract the source to +Python 3.7 and later. Make sure that you have Microsoft Visual Studio 2015 or +later installed, and of course Python 3.7 or later. First extract the source to a suitable directory. If you launch the Developer command prompt and navigate to the directory where you extracted the source code, you should be able to build -and install igraph using `python setup.py install` +and install igraph using `pip install .`, assuming that you have `pip` +installed in your Python environment. You may need to set the architecture that you are building on explicitly by setting the environment variable @@ -62,8 +74,15 @@ set IGRAPH_CMAKE_EXTRA_ARGS=-A [arch] ``` where `[arch]` is either `Win32` for 32-bit builds or `x64` for 64-bit builds. +Also, when building in MSYS2, you need to set the `SETUPTOOLS_USE_DISTUTILS` +environment variable to `stdlib`; this is because MSYS2 uses a patched version +of `distutils` that conflicts with `setuptools >= 60.0`. -#### Enabling GraphML +> [!TIP] +> You need the following packages: +> `$MINGW_PACKAGE_PREFIX-python-pip $MINGW_PACKAGE_PREFIX-python-setuptools $MINGW_PACKAGE_PREFIX-cc $MINGW_PACKAGE_PREFIX-cmake` + +### Enabling GraphML By default, GraphML is disabled, because `libxml2` is not available on Windows in the standard installation. You can install `libxml2` on Windows using @@ -96,17 +115,17 @@ set IGRAPH_EXTRA_LIBRARIES=libxml2,lzma,zlib,iconv,charset set IGRAPH_EXTRA_DYNAMIC_LIBRARIES: wsock32,ws2_32 ``` -You can now build and install `igraph` again by simply running `python -setup.py build`. Please make sure to use a clean source tree, if you built -previously without GraphML, it will not update the build. +You can now build and install `igraph` again by simply running `pip install .`. +Please make sure to use a clean source tree, if you built previously without +GraphML, it will not update the build. -### Linking to an existing igraph installation +## Linking to an existing igraph installation The source code of the Python package includes the source code of the matching igraph version that the Python interface should compile against. However, if you want to link the Python interface to a custom installation of the C core -that has already been compiled and installed on your system, you can ask -`setup.py` to use the pre-compiled version. This option requires that your +that has already been compiled and installed on your system, you can ask our +build system to use the pre-compiled version. This option requires that your custom installation of igraph is discoverable with `pkg-config`. First, check whether `pkg-config` can tell you the required compiler and linker flags for igraph: @@ -117,19 +136,25 @@ pkg-config --cflags --libs igraph If `pkg-config` responds with a set of compiler and linker flags and not an error message, you are probably okay. You can then proceed with the -installation using pip: +installation using pip after setting the environment variable named +`IGRAPH_USE_PKG_CONFIG` to `1` to indicate that you want to use an +igraph instance discoverable with `pkg-config`: ```bash -pip install igraph --install-option="--use-pkg-config" +IGRAPH_USE_PKG_CONFIG=1 pip install igraph ``` Alternatively, if you have already downloaded and extracted the source code -of igraph, you can run `setup.py` directly: +of igraph, you can run `pip install` on the source tree directly: ```bash -python setup.py install --use-pkg-config +IGRAPH_USE_PKG_CONFIG=1 pip install . ``` +(Note that you need the `IGRAPH_USE_PKG_CONFIG=1` environment variable +for both invocations, otherwise the call to `pip install` would still +build the vendored C core instead of linking to an existing installation). + This option is primarily intended for package maintainers in Linux distributions so they can ensure that the packaged Python interface links to the packaged igraph library instead of bringing its own copy. @@ -137,8 +162,35 @@ the packaged igraph library instead of bringing its own copy. It is also useful on macOS if you want to link to the igraph library installed from Homebrew. -Due to the lack of support of `pkg-config` on Window, it is currently not -possible to build against an external library on Windows. +Due to the lack of support of `pkg-config` on MSVC, it is currently not +possible to build against an external library on MSVC. + +In case you are already using a MSYS2/[MinGW](https://www.mingw-w64.org/) and already have +[mingw-w64-igraph](https://packages.msys2.org/base/mingw-w64-igraph) installed, +simply type: +``` +IGRAPH_USE_PKG_CONFIG=1 SETUPTOOLS_USE_DISTUTILS=stdlib pip install igraph +``` +to build. + +**Warning:** the Python interface is guaranteed to work only with the same +version of the C core that is vendored inside the `vendor/source/igraph` +folder. While we try hard not to break API or ABI in the C core of igraph +between minor versions in the 0.x branch and we will keep on doing so for major +versions once 1.0 is released, there are certain functions in the C API that +are marked as _experimental_ (see the documentation of the C core for details), +and we reserve the right to break the APIs of those functions, even if they are +already exposed in a higher-level interface. This is because the easiest way to +test these functions in real-life research scenarios is to expose them in one +of the higher level interfaces. Therefore, if you unbundle the vendored source +code of igraph and link to an external version instead, we can make no +guarantees about stability unless you link to the exact same version as the +one we have vendored in this source tree. + +If you are curious about which version of the Python interface is compatible +with which version of the C core, you can look up the corresponding tag in +Github and check which revision of the C core the repository points to in +the `vendor/source/igraph` submodule. ## Compiling the development version @@ -151,8 +203,9 @@ pip install git+https://github.com/igraph/python-igraph This automatically fetches the development version from the repository, builds the package and installs it. By default, this will install the Python interface -from the `master` branch, which is used as the basis for the development of the -current release series. Unstable and breaking changes are being made in the `develop` branch. You can install this similarly by doing +from the `main` branch, which is used as the basis for the development of the +current release series. Unstable and breaking changes are being made in the +`develop` branch. You can install this similarly by doing ```bash pip install git+https://github.com/igraph/python-igraph@develop @@ -161,10 +214,9 @@ pip install git+https://github.com/igraph/python-igraph@develop In addition to `git`, the installation of the development version requires some additional dependencies, read further below for details. -For more information about installing directly from `git` using `pip` see +For more information about installing directly from `git` using `pip` see https://pip.pypa.io/en/stable/topics/vcs-support/#git. - Alternatively, you can clone this repository locally. This repository contains a matching version of the C core of `igraph` as a git submodule. In order to install the development version from source, you need to instruct git to check @@ -184,17 +236,20 @@ sudo apt install bison flex On macOS you can install these from Homebrew or MacPorts. On Windows you can install `winflexbison3` from Chocolatey. -Then, running the setup script should work if you have a C compiler and the -necessary build dependencies (see also the previous section): +Then you can install the package directly with `pip` (see also the previous section): ```bash -python setup.py build +pip install . ``` -You can install it using +If you would like to create a source distribution or a Python wheel instead of +installing the module directly in your Python environment, use a standard build +frontend like [build](https://pypa-build.readthedocs.io/en/stable/). If you +use [pipx](https://pypa.github.io/pipx/) to isolate command-line Python tools +in their own separate virtualenvs, you can simply run: ```bash -python setup.py install +pipx run build ``` ### Running unit tests @@ -206,7 +261,18 @@ with the built-in `unittest` module: python -m unittest ``` -## Contributing +Note that unit tests have additional dependencies like NumPy, PIL or +`matplotlib`. The unit test suite will try to do its best to skip tests +requiring external dependencies, but if you want to make sure that all the unit +tests are executed, either use `tox` (which will take care of installing the +test dependencies in a virtualenv), or install the module with the `test` +extras: + +```bash +pip install '.[test]' +``` + +# Contributing Contributions to `igraph` are welcome! @@ -216,34 +282,35 @@ that you would like to see included in the main tree, open a PR on this repo. To start developing `igraph`, follow the steps above about installing the development version. Make sure that you do so by cloning the repository locally so that you are able to make changes. -For easier development, you can install `igraph` in development mode so your changes in the Python source -code are picked up automatically by Python: +For easier development, you can install `igraph` in "editable" (i.e. +development) mode so your changes in the Python source code are picked up +automatically by Python: ```bash -python setup.py develop +pip install -e . ``` Changes that you make to the Python code do not need any extra action. However, if you adjust the source code of the C extension, you need to rebuild it by running -`python setup.py develop` again. Compilation of the C core of `igraph` is +`pip install -e .` again. Compilation of the C core of `igraph` is cached in ``vendor/build`` and ``vendor/install`` so subsequent builds are much faster than the first one as the C core does not need to be recompiled. -## Notes +# Notes -### Supported Python versions +## Supported Python versions We aim to keep up with the development cycle of Python and support all official Python versions that have not reached their end of life yet. Currently this -means that we support Python 3.6 to 3.9, inclusive. Please refer to [this -page](https://devguide.python.org/#branchstatus) for the status of Python +means that we support Python 3.9 to 3.13, inclusive. Please refer to [this +page](https://devguide.python.org/versions/) for the status of Python branches and let us know if you encounter problems with `igraph` on any of the non-EOL Python versions. Continuous integration tests are regularly executed on all non-EOL Python branches. -### PyPy +## PyPy This version of igraph is compatible with [PyPy](http://pypy.org/) and is regularly tested on [PyPy](http://pypy.org/) with ``tox``. However, the @@ -259,4 +326,3 @@ There are also some subtle differences between the CPython and PyPy versions: - ``GraphBase`` is hashable and iterable in PyPy but not in CPython. Since ``GraphBase`` is internal anyway, this is likely to stay this way. - diff --git a/doc/examples_sphinx-gallery/README.rst b/doc/examples_sphinx-gallery/README.rst new file mode 100644 index 000000000..6fe17a0c1 --- /dev/null +++ b/doc/examples_sphinx-gallery/README.rst @@ -0,0 +1,10 @@ +.. _gallery-of-examples: + +Gallery of Examples +=================== + +Gallery of examples for `python-igraph` illustrating graph generation, analysis, and plotting. + +Impatient? Check out the :ref:`tutorials-quickstart`. + +Too little detail? Read the :doc:`extended tutorial <../tutorial>`. diff --git a/doc/examples_sphinx-gallery/articulation_points.py b/doc/examples_sphinx-gallery/articulation_points.py new file mode 100644 index 000000000..6492f1f6f --- /dev/null +++ b/doc/examples_sphinx-gallery/articulation_points.py @@ -0,0 +1,39 @@ +""" +.. _tutorials-articulation-points: + +=================== +Articulation Points +=================== + +This example shows how to compute and visualize the `articulation points `_ in a graph using :meth:`igraph.GraphBase.articulation_points`. For an example on bridges instead, see :ref:`tutorials-bridges`. + +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# First, we construct a graph. This example shows usage of graph formulae: +g = ig.Graph.Formula( + "0-1-2-0, 3:4:5:6 - 3:4:5:6, 2-3-7-8", +) + +# %% +# Now we are aready to find the articulation points as a vertex sequence +articulation_points = g.vs[g.articulation_points()] + +# %% +# Finally, we can plot the graph +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + vertex_size=30, + vertex_color="lightblue", + vertex_label=range(g.vcount()), + vertex_frame_color=["red" if v in articulation_points else "black" for v in g.vs], + vertex_frame_width=[3 if v in articulation_points else 1 for v in g.vs], + edge_width=0.8, + edge_color="gray", +) +plt.show() diff --git a/doc/examples_sphinx-gallery/betweenness.py b/doc/examples_sphinx-gallery/betweenness.py new file mode 100644 index 000000000..7c52bdb08 --- /dev/null +++ b/doc/examples_sphinx-gallery/betweenness.py @@ -0,0 +1,91 @@ +""" +.. _tutorials-betweenness: + +======================= +Betweenness +======================= + +This example demonstrates how to visualize both vertex and edge betweenness with a custom defined color palette. We use the methods :meth:`igraph.GraphBase.betweenness` and :meth:`igraph.GraphBase.edge_betweenness` respectively, and demonstrate the effects on a standard `Krackhardt Kite `_ graph, as well as a `Watts-Strogatz `_ random graph. + +""" +import random +import matplotlib.pyplot as plt +from matplotlib.cm import ScalarMappable +from matplotlib.colors import LinearSegmentedColormap, Normalize +import igraph as ig + + +# %% +# We define a function that plots the graph on a Matplotlib axis, along with +# its vertex and edge betweenness values. The function also generates some +# color bars on the sides to see how they translate to each other. We use +# `Matplotlib's Normalize class `_ +# to ensure that our color bar ranges are correct, as well as *igraph*'s +# :meth:`igraph.utils.rescale` to rescale the betweennesses in the interval +# ``[0, 1]``. +def plot_betweenness(g, vertex_betweenness, edge_betweenness, ax, cax1, cax2): + """Plot vertex/edge betweenness, with colorbars + + Args: + g: the graph to plot. + ax: the Axes for the graph + cax1: the Axes for the vertex betweenness colorbar + cax2: the Axes for the edge betweenness colorbar + """ + + # Rescale betweenness to be between 0.0 and 1.0 + scaled_vertex_betweenness = ig.rescale(vertex_betweenness, clamp=True) + scaled_edge_betweenness = ig.rescale(edge_betweenness, clamp=True) + print(f"vertices: {min(vertex_betweenness)} - {max(vertex_betweenness)}") + print(f"edges: {min(edge_betweenness)} - {max(edge_betweenness)}") + + # Define mappings betweenness -> color + cmap1 = LinearSegmentedColormap.from_list("vertex_cmap", ["pink", "indigo"]) + cmap2 = LinearSegmentedColormap.from_list("edge_cmap", ["lightblue", "midnightblue"]) + + # Plot graph + g.vs["color"] = [cmap1(betweenness) for betweenness in scaled_vertex_betweenness] + g.vs["size"] = ig.rescale(vertex_betweenness, (10, 50)) + g.es["color"] = [cmap2(betweenness) for betweenness in scaled_edge_betweenness] + g.es["width"] = ig.rescale(edge_betweenness, (0.5, 1.0)) + ig.plot( + g, + target=ax, + layout="fruchterman_reingold", + vertex_frame_width=0.2, + ) + + # Color bars + norm1 = ScalarMappable(norm=Normalize(0, max(vertex_betweenness)), cmap=cmap1) + norm2 = ScalarMappable(norm=Normalize(0, max(edge_betweenness)), cmap=cmap2) + plt.colorbar(norm1, cax=cax1, orientation="horizontal", label="Vertex Betweenness") + plt.colorbar(norm2, cax=cax2, orientation="horizontal", label="Edge Betweenness") + + +# %% +# First, generate a graph, e.g. the Krackhardt Kite Graph: +random.seed(0) +g1 = ig.Graph.Famous("Krackhardt_Kite") + +# %% +# Then we can compute vertex and edge betweenness: +vertex_betweenness1 = g1.betweenness() +edge_betweenness1 = g1.edge_betweenness() + +# %% As a second example, we generate and analyze a Watts Strogatz graph: +g2 = ig.Graph.Watts_Strogatz(dim=1, size=150, nei=2, p=0.1) +vertex_betweenness2 = g2.betweenness() +edge_betweenness2 = g2.edge_betweenness() + +# %% +# Finally, we plot the two graphs, each with two colorbars for vertex/edge +# betweenness +fig, axs = plt.subplots( + 3, 2, + figsize=(7, 6), + gridspec_kw={"height_ratios": (20, 1, 1)}, +) +plot_betweenness(g1, vertex_betweenness1, edge_betweenness1, *axs[:, 0]) +plot_betweenness(g2, vertex_betweenness2, edge_betweenness2, *axs[:, 1]) +fig.tight_layout(h_pad=1) +plt.show() diff --git a/doc/source/tutorials/bipartite_matching/assets/bipartite_matching.py b/doc/examples_sphinx-gallery/bipartite_matching.py similarity index 53% rename from doc/source/tutorials/bipartite_matching/assets/bipartite_matching.py rename to doc/examples_sphinx-gallery/bipartite_matching.py index fdb400eae..1046e1322 100644 --- a/doc/source/tutorials/bipartite_matching/assets/bipartite_matching.py +++ b/doc/examples_sphinx-gallery/bipartite_matching.py @@ -1,16 +1,35 @@ +""" +.. _tutorials-bipartite-matching: + +========================== +Maximum Bipartite Matching +========================== + +This example demonstrates an efficient way to find and visualise a maximum biparite matching using :meth:`igraph.Graph.maximum_bipartite_matching`. +""" + import igraph as ig import matplotlib.pyplot as plt -# Assign nodes 0-4 to one side, and the nodes 5-8 to the other side +# %% +# First, we construct a bipartite graph, assigning: +# - nodes 0-4 to one side +# - nodes 5-8 to the other side g = ig.Graph.Bipartite( [0, 0, 0, 0, 0, 1, 1, 1, 1], - [(0, 5), (1, 6), (1, 7), (2, 5), (2, 8), (3, 6), (4, 5), (4, 6)] + [(0, 5), (1, 6), (1, 7), (2, 5), (2, 8), (3, 6), (4, 5), (4, 6)], ) + +# %% +# We can easily check that the graph is indeed bipartite: assert g.is_bipartite() +# %% +# Now can can compute the maximum bipartite matching: matching = g.maximum_bipartite_matching() -# Print pairings for each node on one side +# %% +# It's easy to print matching pairs of vertices matching_size = 0 print("Matching is:") for i in range(5): @@ -19,22 +38,17 @@ matching_size += 1 print("Size of maximum matching is:", matching_size) +# %% +# Finally, we can plot the bipartite graph, highlighting the edges connecting +# maximal matches by a red color: fig, ax = plt.subplots(figsize=(7, 3)) ig.plot( g, target=ax, layout=g.layout_bipartite(), - vertex_size=0.4, + vertex_size=30, vertex_label=range(g.vcount()), vertex_color="lightblue", edge_width=[3 if e.target == matching.match_of(e.source) else 1.0 for e in g.es], edge_color=["red" if e.target == matching.match_of(e.source) else "black" for e in g.es] ) - -# Matching is: -# 0 - 5 -# 1 - 7 -# 2 - 8 -# 3 - 6 -# 4 - None -# Size of maximum matching is: 4 diff --git a/doc/examples_sphinx-gallery/bipartite_matching_maxflow.py b/doc/examples_sphinx-gallery/bipartite_matching_maxflow.py new file mode 100644 index 000000000..eec39a81b --- /dev/null +++ b/doc/examples_sphinx-gallery/bipartite_matching_maxflow.py @@ -0,0 +1,68 @@ +""" +.. _tutorials-bipartite-matching-maxflow: + +========================================== +Maximum Bipartite Matching by Maximum Flow +========================================== + +This example presents how to visualise bipartite matching using maximum flow (see :meth:`igraph.Graph.maxflow`). + +.. note:: :meth:`igraph.Graph.maximum_bipartite_matching` is usually a better way to find the maximum bipartite matching. For a demonstration on how to use that method instead, check out :ref:`tutorials-bipartite-matching`. +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# We start by creating the bipartite directed graph. +g = ig.Graph( + 9, + [(0, 4), (0, 5), (1, 4), (1, 6), (1, 7), (2, 5), (2, 7), (2, 8), (3, 6), (3, 7)], + directed=True, +) + +# %% +# We assign: +# - nodes 0-3 to one side +# - nodes 4-8 to the other side +g.vs[range(4)]["type"] = True +g.vs[range(4, 9)]["type"] = False + +# %% +# Then we add a source (vertex 9) and a sink (vertex 10) +g.add_vertices(2) +g.add_edges([(9, 0), (9, 1), (9, 2), (9, 3)]) # connect source to one side +g.add_edges([(4, 10), (5, 10), (6, 10), (7, 10), (8, 10)]) # ... and sinks to the other + +flow = g.maxflow(9, 10) +print("Size of maximum matching (maxflow) is:", flow.value) + +# %% +# Let's compare the output against :meth:`igraph.Graph.maximum_bipartite_matching`: + +# delete the source and sink, which are unneeded for this function. +g2 = g.copy() +g2.delete_vertices([9, 10]) +matching = g2.maximum_bipartite_matching() +matching_size = sum(1 for i in range(4) if matching.is_matched(i)) +print("Size of maximum matching (maximum_bipartite_matching) is:", matching_size) + +# %% +# Last, we can display the original flow graph nicely with the matchings added. +# To achieve a pleasant visual effect, we set the positions of source and sink +# manually: +layout = g.layout_bipartite() +layout[9] = (2, -1) +layout[10] = (2, 2) + +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + layout=layout, + vertex_size=30, + vertex_label=range(g.vcount()), + vertex_color=["lightblue" if i < 9 else "orange" for i in range(11)], + edge_width=[1.0 + flow.flow[i] for i in range(g.ecount())], +) +plt.show() diff --git a/doc/examples_sphinx-gallery/bridges.py b/doc/examples_sphinx-gallery/bridges.py new file mode 100644 index 000000000..08dc47d48 --- /dev/null +++ b/doc/examples_sphinx-gallery/bridges.py @@ -0,0 +1,81 @@ +""" +.. _tutorials-bridges: + +======== +Bridges +======== + +This example shows how to compute and visualize the `bridges `_ in a graph using :meth:`igraph.GraphBase.bridges`. For an example on articulation points instead, see :ref:`tutorials-articulation-points`. +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# Let's start with a simple example. We begin by constructing a graph that +# includes a few bridges: +g = ig.Graph(14, [(0, 1), (1, 2), (2, 3), (0, 3), (0, 2), (1, 3), (3, 4), + (4, 5), (5, 6), (6, 4), (6, 7), (7, 8), (7, 9), (9, 10), (10 ,11), + (11 ,7), (7, 10), (8, 9), (8, 10), (5, 12), (12, 13)]) + +# %% +# Then we can use a function to actually find the bridges, i.e. the edges that +# connect different parts of the graph: +bridges = g.bridges() + +# %% +# We set a separate color for those edges, to emphasize then in a plot: +g.es["color"] = "gray" +g.es[bridges]["color"] = "red" +g.es["width"] = 0.8 +g.es[bridges]["width"] = 1.2 + +# %% +# Finally, we plot the graph using that emphasis: +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + vertex_size=30, + vertex_color="lightblue", + vertex_label=range(g.vcount()), +) +plt.show() + +# %% +# Advanced: Cutting Effect +# -------------------------- +# Bridges are edges that when removed, will separate the graph into more components then they started with. To emphasise the removal of edges from the graph, we can add small "x" effect to each of the bridges by using edge labels. + +# %% +# As before, we begin by constructing the graph: +g = ig.Graph(14, [(0, 1), (1, 2), (2, 3), (0, 3), (0, 2), (1, 3), (3, 4), + (4, 5), (5, 6), (6, 4), (6, 7), (7, 8), (7, 9), (9, 10), (10 ,11), + (11 ,7), (7, 10), (8, 9), (8, 10), (5, 12), (12, 13)]) + +# %% +# We then find and set the color for the bridges, but this time we also set a +# label for those edges: +bridges = g.bridges() +g.es["color"] = "gray" +g.es[bridges]["color"] = "red" +g.es["width"] = 0.8 +g.es[bridges]["width"] = 1.2 +g.es["label"] = "" +g.es[bridges]["label"] = "x" + +# %% +# Finally, we can plot the graph: +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + vertex_size=30, + vertex_color="lightblue", + vertex_label=range(g.vcount()), + edge_background="#FFF0", # transparent background color + edge_align_label=True, # make sure labels are aligned with the edge + edge_label=g.es["label"], + edge_label_color="red", +) +plt.show() diff --git a/doc/examples_sphinx-gallery/cluster_contraction.py b/doc/examples_sphinx-gallery/cluster_contraction.py new file mode 100644 index 000000000..fc02fc293 --- /dev/null +++ b/doc/examples_sphinx-gallery/cluster_contraction.py @@ -0,0 +1,146 @@ +""" +.. _tutorials-cluster-graph: + +=========================== +Generating Cluster Graphs +=========================== + +This example shows how to find the communities in a graph, then contract each community into a single node using :class:`igraph.clustering.VertexClustering`. For this tutorial, we'll use the *Donald Knuth's Les Miserables Network*, which shows the coapperances of characters in the novel *Les Miserables*. +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# We begin by load the graph from file. The file containing this network can be +# downloaded `here `_. +g = ig.load("./lesmis/lesmis.gml") + +# %% +# Now that we have a graph in memory, we can generate communities using +# :meth:`igraph.Graph.community_edge_betweenness` to separate out vertices into +# clusters. (For a more focused tutorial on just visualising communities, check +# out :ref:`tutorials-visualize-communities`). +communities = g.community_edge_betweenness() + +# %% +# For plots, it is convenient to convert the communities into a VertexClustering: +communities = communities.as_clustering() + +# %% +# We can also easily print out who belongs to each community: +for i, community in enumerate(communities): + print(f"Community {i}:") + for v in community: + print(f"\t{g.vs[v]['label']}") + +# %% +# Finally we can proceed to plotting the graph. In order to make each community +# stand out, we set "community colors" using an igraph palette: +num_communities = len(communities) +palette1 = ig.RainbowPalette(n=num_communities) +for i, community in enumerate(communities): + g.vs[community]["color"] = i + community_edges = g.es.select(_within=community) + community_edges["color"] = i + +# %% +# We can use a dirty hack to move the labels below the vertices ;-) +g.vs["label"] = ["\n\n" + label for label in g.vs["label"]] + +# %% +# Finally, we can plot the communities: +fig1, ax1 = plt.subplots() +ig.plot( + communities, + target=ax1, + mark_groups=True, + palette=palette1, + vertex_size=15, + edge_width=0.5, +) +fig1.set_size_inches(20, 20) + + +# %% +# Now let's try and contract the information down, using only a single vertex +# to represent each community. We start by defining x, y, and size attributes +# for each node in the original graph: +layout = g.layout_kamada_kawai() +g.vs["x"], g.vs["y"] = list(zip(*layout)) +g.vs["size"] = 15 +g.es["size"] = 15 + +# %% +# Then we can generate the cluster graph that compresses each community into a +# single, "composite" vertex using +# :meth:`igraph.VertexClustering.cluster_graph`: +cluster_graph = communities.cluster_graph( + combine_vertices={ + "x": "mean", + "y": "mean", + "color": "first", + "size": "sum", + }, + combine_edges={ + "size": "sum", + }, +) + +# %% +# .. note:: +# +# We took the mean of x and y values so that the nodes in the cluster +# graph are placed at the centroid of the original cluster. +# +# .. note:: +# +# ``mean``, ``first``, and ``sum`` are all built-in collapsing functions, +# along with ``prod``, ``median``, ``max``, ``min``, ``last``, ``random``. +# You can also define your own custom collapsing functions, which take in a +# list and return a single element representing the combined attribute +# value. For more details on igraph contraction, see +# :meth:`igraph.GraphBase.contract_vertices`. + + +# %% +# Finally, we can assign colors to the clusters and plot the cluster graph, +# including a legend to make things clear: +palette2 = ig.GradientPalette("gainsboro", "black") +g.es["color"] = [ + palette2.get(int(i)) + for i in ig.rescale(cluster_graph.es["size"], (0, 255), clamp=True) +] + +fig2, ax2 = plt.subplots() +ig.plot( + cluster_graph, + target=ax2, + palette=palette1, + # set a minimum size on vertex_size, otherwise vertices are too small + vertex_size=[max(20, size) for size in cluster_graph.vs["size"]], + edge_color=g.es["color"], + edge_width=0.8, +) + +# Add a legend +legend_handles = [] +for i in range(num_communities): + handle = ax2.scatter( + [], + [], + s=100, + facecolor=palette1.get(i), + edgecolor="k", + label=i, + ) + legend_handles.append(handle) + +ax2.legend( + handles=legend_handles, + title="Community:", + bbox_to_anchor=(0, 1.0), + bbox_transform=ax2.transAxes, +) + +fig2.set_size_inches(10, 10) diff --git a/doc/examples_sphinx-gallery/complement.py b/doc/examples_sphinx-gallery/complement.py new file mode 100644 index 000000000..b4f2f17a0 --- /dev/null +++ b/doc/examples_sphinx-gallery/complement.py @@ -0,0 +1,76 @@ +""" +.. _tutorials-complement: + +================ +Complement +================ + +This example shows how to generate the `complement graph `_ of a graph (sometimes known as the anti-graph) using :meth:`igraph.GraphBase.complementer`. +""" + +import igraph as ig +import matplotlib.pyplot as plt +import random + +# %% +# First, we generate a random graph +random.seed(0) +g1 = ig.Graph.Erdos_Renyi(n=10, p=0.5) + +# %% +# .. note:: +# We set the random seed to ensure the graph comes out exactly the same +# each time in the gallery. You don't need to do that if you're exploring +# really random graphs ;-) + +# %% +# Then we generate the complement graph: +g2 = g1.complementer(loops=False) + +# %% +# The union graph of the two is of course the full graph, i.e. a graph with +# edges connecting all vertices to all other vertices. Because we decided to +# ignore loops (aka self-edges) in the complementer, the full graph does not +# include loops either. +g_full = g1 | g2 + +# %% +# In case there was any doubt, the complement of the full graph is an +# empty graph, with the same vertices but no edges: +g_empty = g_full.complementer(loops=False) + +# %% +# To demonstrate these concepts more clearly, here's a layout of each of the +# four graphs we discussed (input, complement, union/full, complement of +# union/empty): +fig, axs = plt.subplots(2, 2) +ig.plot( + g1, + target=axs[0, 0], + layout="circle", + vertex_color="black", +) +axs[0, 0].set_title("Original graph") +ig.plot( + g2, + target=axs[0, 1], + layout="circle", + vertex_color="black", +) +axs[0, 1].set_title("Complement graph") + +ig.plot( + g_full, + target=axs[1, 0], + layout="circle", + vertex_color="black", +) +axs[1, 0].set_title("Union graph") +ig.plot( + g_empty, + target=axs[1, 1], + layout="circle", + vertex_color="black", +) +axs[1, 1].set_title("Complement of union graph") +plt.show() diff --git a/doc/examples_sphinx-gallery/configuration.py b/doc/examples_sphinx-gallery/configuration.py new file mode 100644 index 000000000..4e9c077eb --- /dev/null +++ b/doc/examples_sphinx-gallery/configuration.py @@ -0,0 +1,61 @@ +""" +.. _tutorials-configuration: + +====================== +Configuration Instance +====================== + +This example shows how to use igraph's :class:`configuration instance ` to set default igraph settings. This is useful for setting global settings so that they don't need to be explicitly stated at the beginning of every igraph project you work on. +""" + +import igraph as ig +import matplotlib.pyplot as plt +import random + +# %% +# First we define the default plotting backend, layout, and color palette. +ig.config["plotting.backend"] = "matplotlib" +ig.config["plotting.layout"] = "fruchterman_reingold" +ig.config["plotting.palette"] = "rainbow" + +# %% +# The updated configuration affects only the current session. Optionally, it +# can be saved using ``ig.config.save()``. By default, this function writes the +# configuration to ``~/.igraphrc`` on Linux and Max OS X systems, and in +# ``%USERPROFILE%\.igraphrc`` on Windows systems. + +# %% +# The configuration only needs to be saved to `.igraphrc` once, and it will +# be automatically used in all future sessions. Whenever you use igraph and +# this file exists, igraph will read its content and use those options as +# defaults. For example, let's create and plot a new graph to demonstrate: +random.seed(1) +g = ig.Graph.Barabasi(n=100, m=1) + +# %% +# We now calculate a color value between 0-200 for all nodes, for instance by +# computing the vertex betweenness: +betweenness = g.betweenness() +colors = [int(i * 200 / max(betweenness)) for i in betweenness] + +# %% +# Finally, we can plot the graph. You will notice that even though we did not +# create a dedicated figure and axes, matplotlib is now used by default: +ig.plot(g, vertex_color=colors, vertex_size=15, edge_width=0.3) +plt.show() + +# %% +# The full list of config settings can be found at +# :class:`igraph.Configuration`. +# +# .. note:: +# +# You can have multiple config files: specify each location via +# ``ig.config.save("./path/to/config/file")``. To load a specific config, +# import igraph and then call ``ig.config.load("./path/to/config/file")`` +# +# +# .. note:: +# +# To use a consistent style between individual plots (e.g. vertex sizes, +# colors, layout etc.) check out :ref:`tutorials-visual-style`. diff --git a/doc/examples_sphinx-gallery/connected_components.py b/doc/examples_sphinx-gallery/connected_components.py new file mode 100644 index 000000000..33c341fee --- /dev/null +++ b/doc/examples_sphinx-gallery/connected_components.py @@ -0,0 +1,45 @@ +""" +.. _tutorials-connected-components: + +===================== +Connected Components +===================== + +This example demonstrates how to visualise the connected components in a graph using :meth:`igraph.GraphBase.connected_components`. +""" + +import igraph as ig +import matplotlib.pyplot as plt +import random + +# %% +# First, we generate a randomized geometric graph with random vertex sizes. The +# seed is set to the example is reproducible in our manual: you don't really +# need it to understand the concepts. +random.seed(0) +g = ig.Graph.GRG(50, 0.15) + +# %% +# Now we can cluster the graph into weakly connected components, i.e. subgraphs +# that have no edges connecting them to one another: +components = g.connected_components(mode="weak") + +# %% +# Finally, we can visualize the distinct connected components of the graph: +fig, ax = plt.subplots() +ig.plot( + components, + target=ax, + palette=ig.RainbowPalette(), + vertex_size=7, + vertex_color=list(map(int, ig.rescale(components.membership, (0, 200), clamp=True))), + edge_width=0.7 +) +plt.show() + +# %% +# .. note:: +# +# We use the integers from 0 to 200 instead of 0 to 255 in our vertex +# colors, since 255 in the :class:`igraph.drawing.colors.RainbowPalette` +# corresponds to looping back to red. This gives us nicely distinct hues. diff --git a/doc/examples_sphinx-gallery/delaunay-triangulation.py b/doc/examples_sphinx-gallery/delaunay-triangulation.py new file mode 100644 index 000000000..3a25eebe1 --- /dev/null +++ b/doc/examples_sphinx-gallery/delaunay-triangulation.py @@ -0,0 +1,99 @@ +""" +.. _tutorials-delaunay-triangulation: + +====================== +Delaunay Triangulation +====================== + +This example demonstrates how to calculate the `Delaunay triangulation `_ of an input graph. We start by generating a set of points on a 2D grid using random ``numpy`` arrays and a graph with those vertex coordinates and no edges. + +""" + +import numpy as np +from scipy.spatial import Delaunay +import igraph as ig +import matplotlib.pyplot as plt + + +# %% +# We start by generating a random graph in the 2D unit cube, fixing the random +# seed to ensure reproducibility. +np.random.seed(0) +x, y = np.random.rand(2, 30) +g = ig.Graph(30) +g.vs["x"] = x +g.vs["y"] = y + +# %% +# Because we already set the `x` and `y` vertex attributes, we can use +# :meth:`igraph.Graph.layout_auto` to wrap them into a :class:`igraph.Layout` +# object. +layout = g.layout_auto() + +# %% +# Now we can calculate the delaunay triangulation using `scipy`'s :class:`scipy:scipy.spatial.Delaunay` class: +delaunay = Delaunay(layout.coords) + +# %% +# Given the triangulation, we can add the edges into the original graph: +for tri in delaunay.simplices: + g.add_edges([ + (tri[0], tri[1]), + (tri[1], tri[2]), + (tri[0], tri[2]), + ]) + +# %% +# Because adjacent triangles share an edge/side, the graph now contains some +# edges more than once. It's useful to simplify the graph to get rid of those +# multiedges, keeping each side only once: +g.simplify() + +# %% +# Finally, plotting the graph gives a good idea of what the triangulation looks +# like: +fig, ax = plt.subplots() +ig.plot( + g, + layout=layout, + target=ax, + vertex_size=4, + vertex_color="lightblue", + edge_width=0.8 +) +plt.show() + +# %% +# Alternative plotting style +# -------------------------- +# We can use :doc:`matplotlib ` to plot the faces of the +# triangles instead of the edges. First, we create a hue gradient for the +# triangle faces: +palette = ig.GradientPalette("midnightblue", "lightblue", 100) + +# %% +# Then we can "plot" the triangles using +# :class:`matplotlib:matplotlib.patches.Polygon` and the graph using +# :func:`igraph.plot() `: +fig, ax = plt.subplots() +for tri in delaunay.simplices: + # get the points of the triangle + tri_points = [delaunay.points[tri[i]] for i in range(3)] + + # calculate the vertical center of the triangle + center = (tri_points[0][1] + tri_points[1][1] + tri_points[2][1]) / 3 + + # draw triangle onto axes + poly = plt.Polygon(tri_points, color=palette.get(int(center * 100))) + ax.add_patch(poly) + +ig.plot( + g, + layout=layout, + target=ax, + vertex_size=0, + edge_width=0.2, + edge_color="white", +) +ax.set(xlim=(0, 1), ylim=(0, 1)) +plt.show() diff --git a/doc/examples_sphinx-gallery/erdos_renyi.py b/doc/examples_sphinx-gallery/erdos_renyi.py new file mode 100644 index 000000000..aeb808992 --- /dev/null +++ b/doc/examples_sphinx-gallery/erdos_renyi.py @@ -0,0 +1,59 @@ +""" +.. _tutorials-random: + +================= +Erdős-Rényi Graph +================= + +This example demonstrates how to generate `Erdős–Rényi graphs `_ using :meth:`igraph.GraphBase.Erdos_Renyi`. There are two variants of graphs: + +- ``Erdos_Renyi(n, p)`` will generate a graph from the so-called :math:`G(n,p)` model where each edge between any two pair of nodes has an independent probability ``p`` of existing. +- ``Erdos_Renyi(n, m)`` will pick a graph uniformly at random out of all graphs with ``n`` nodes and ``m`` edges. This is referred to as the :math:`G(n,m)` model. + +We generate two graphs of each, so we can confirm that our graph generator is truly random. +""" + +import igraph as ig +import matplotlib.pyplot as plt +import random + +# %% +# First, we set a random seed for reproducibility +random.seed(0) + +# %% +# Then, we generate two :math:`G(n,p)` Erdős–Rényi graphs with identical parameters: +g1 = ig.Graph.Erdos_Renyi(n=15, p=0.2, directed=False, loops=False) +g2 = ig.Graph.Erdos_Renyi(n=15, p=0.2, directed=False, loops=False) + +# %% +# For comparison, we also generate two :math:`G(n,m)` Erdős–Rényi graphs with a fixed number +# of edges: +g3 = ig.Graph.Erdos_Renyi(n=20, m=35, directed=False, loops=False) +g4 = ig.Graph.Erdos_Renyi(n=20, m=35, directed=False, loops=False) + +# %% +# We can print out summaries of each graph to verify their randomness +ig.summary(g1) +ig.summary(g2) +ig.summary(g3) +ig.summary(g4) + +# IGRAPH U--- 15 18 -- +# IGRAPH U--- 15 21 -- +# IGRAPH U--- 20 35 -- +# IGRAPH U--- 20 35 -- + +# %% +# Finally, we can plot the graphs to illustrate their structures and +# differences: +fig, axs = plt.subplots(2, 2) +# Probability +ig.plot(g1, target=axs[0, 0], layout="circle", vertex_color="lightblue") +ig.plot(g2, target=axs[0, 1], layout="circle", vertex_color="lightblue") +axs[0, 0].set_ylabel("Probability") +# N edges +ig.plot(g3, target=axs[1, 0], layout="circle", vertex_color="lightblue", vertex_size=15) +ig.plot(g4, target=axs[1, 1], layout="circle", vertex_color="lightblue", vertex_size=15) +axs[1, 0].set_ylabel("N. edges") +plt.show() diff --git a/doc/examples_sphinx-gallery/generate_dag.py b/doc/examples_sphinx-gallery/generate_dag.py new file mode 100644 index 000000000..1565a59ed --- /dev/null +++ b/doc/examples_sphinx-gallery/generate_dag.py @@ -0,0 +1,46 @@ +""" + +.. _tutorials-dag: + +====================== +Directed Acyclic Graph +====================== + +This example demonstrates how to create a random directed acyclic graph (DAG), which is useful in a number of contexts including for Git commit history. +""" + +import igraph as ig +import matplotlib.pyplot as plt +import random + + +# %% +# First, we set a random seed for reproducibility. +random.seed(0) + +# %% +# First, we generate a random undirected graph with a fixed number of edges, without loops. +g = ig.Graph.Erdos_Renyi(n=15, m=30, directed=False, loops=False) + +# %% +# Then we convert it to a DAG *in place*. This method samples DAGs with a given number of edges and vertices uniformly. +g.to_directed(mode="acyclic") + +# %% +# We can print out a summary of the DAG. +ig.summary(g) + + +# %% +# Finally, we can plot the graph using the Sugiyama layout from :meth:`igraph.Graph.layout_sugiyama`: +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + layout="sugiyama", + vertex_size=15, + vertex_color="grey", + edge_color="#222", + edge_width=1, +) +plt.show() diff --git a/doc/source/tutorials/isomorphism/assets/isomorphism.py b/doc/examples_sphinx-gallery/isomorphism.py similarity index 52% rename from doc/source/tutorials/isomorphism/assets/isomorphism.py rename to doc/examples_sphinx-gallery/isomorphism.py index b9544f62e..57c6034f4 100644 --- a/doc/source/tutorials/isomorphism/assets/isomorphism.py +++ b/doc/examples_sphinx-gallery/isomorphism.py @@ -1,12 +1,24 @@ +""" +.. _tutorials-isomorphism: + +=========== +Isomorphism +=========== + +This example shows how to check for `isomorphism `_ between small graphs using :meth:`igraph.GraphBase.isomorphic`. +""" + import igraph as ig import matplotlib.pyplot as plt -# Create Graphs +# %% +# First we generate three different graphs: g1 = ig.Graph([(0, 1), (0, 2), (0, 4), (1, 2), (1, 3), (2, 3), (2, 4), (3, 4)]) g2 = ig.Graph([(4, 2), (4, 3), (4, 0), (2, 3), (2, 1), (3, 1), (3, 0), (1, 0)]) g3 = ig.Graph([(4, 1), (4, 3), (4, 0), (2, 3), (2, 1), (3, 1), (3, 0), (1, 0)]) -# Check isomorphism +# %% +# To check whether they are isomorphic, we can use a simple method: print("Are the graphs g1 and g2 isomorphic?") print(g1.isomorphic(g2)) print("Are the graphs g1 and g3 isomorphic?") @@ -22,12 +34,18 @@ # Are the graphs g2 and g3 isomorphic? # False +# %% +# .. note:: +# `Graph isomorphism `_ is an equivalence +# relationship, i.e. if `g1 ~ g2` and `g2 ~ g3`, then automatically `g1 ~ g3`. Therefore, +# we could have skipped the last check. -# Plot graphs +# %% +# We can plot the graphs to get an idea about the problem: visual_style = { "vertex_color": "lightblue", "vertex_label": [0, 1, 2, 3, 4], - "vertex_size": 0.4, + "vertex_size": 25, } fig, axs = plt.subplots(1, 3) @@ -49,8 +67,20 @@ target=axs[2], **visual_style, ) -fig.text(0.38, 0.5, '$\simeq$' if g1.isomorphic(g2) else '$\\neq$', fontsize=15, ha='center', va='center') -fig.text(0.65, 0.5, '$\simeq$' if g2.isomorphic(g3) else '$\\neq$', fontsize=15, ha='center', va='center') - +fig.text( + 0.38, + 0.5, + "$\\simeq$" if g1.isomorphic(g2) else "$\\neq$", + fontsize=15, + ha="center", + va="center", +) +fig.text( + 0.65, + 0.5, + "$\\simeq$" if g2.isomorphic(g3) else "$\\neq$", + fontsize=15, + ha="center", + va="center", +) plt.show() - diff --git a/doc/examples_sphinx-gallery/lesmis/lesmis.gml b/doc/examples_sphinx-gallery/lesmis/lesmis.gml new file mode 100644 index 000000000..3c0751191 --- /dev/null +++ b/doc/examples_sphinx-gallery/lesmis/lesmis.gml @@ -0,0 +1,1913 @@ +Creator "Mark Newman on Fri Jul 21 12:44:53 2006" +graph +[ + node + [ + id 0 + label "Myriel" + ] + node + [ + id 1 + label "Napoleon" + ] + node + [ + id 2 + label "MlleBaptistine" + ] + node + [ + id 3 + label "MmeMagloire" + ] + node + [ + id 4 + label "CountessDeLo" + ] + node + [ + id 5 + label "Geborand" + ] + node + [ + id 6 + label "Champtercier" + ] + node + [ + id 7 + label "Cravatte" + ] + node + [ + id 8 + label "Count" + ] + node + [ + id 9 + label "OldMan" + ] + node + [ + id 10 + label "Labarre" + ] + node + [ + id 11 + label "Valjean" + ] + node + [ + id 12 + label "Marguerite" + ] + node + [ + id 13 + label "MmeDeR" + ] + node + [ + id 14 + label "Isabeau" + ] + node + [ + id 15 + label "Gervais" + ] + node + [ + id 16 + label "Tholomyes" + ] + node + [ + id 17 + label "Listolier" + ] + node + [ + id 18 + label "Fameuil" + ] + node + [ + id 19 + label "Blacheville" + ] + node + [ + id 20 + label 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000000000..8772c84b0 --- /dev/null +++ b/doc/examples_sphinx-gallery/lesmis/lesmis.txt @@ -0,0 +1,7 @@ +The file lesmis.gml contains the weighted network of coappearances of +characters in Victor Hugo's novel "Les Miserables". Nodes represent +characters as indicated by the labels and edges connect any pair of +characters that appear in the same chapter of the book. The values on the +edges are the number of such coappearances. The data on coappearances were +taken from D. E. Knuth, The Stanford GraphBase: A Platform for +Combinatorial Computing, Addison-Wesley, Reading, MA (1993). diff --git a/doc/examples_sphinx-gallery/maxflow.py b/doc/examples_sphinx-gallery/maxflow.py new file mode 100644 index 000000000..eb76684a4 --- /dev/null +++ b/doc/examples_sphinx-gallery/maxflow.py @@ -0,0 +1,41 @@ +""" +.. _tutorials-maxflow: + +============ +Maximum Flow +============ + +This example shows how to construct a max flow on a directed graph with edge capacities using :meth:`igraph.Graph.maxflow`. + +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# First, we generate a graph and assign a "capacity" to each edge: +g = ig.Graph(6, [(3, 2), (3, 4), (2, 1), (4, 1), (4, 5), (1, 0), (5, 0)], directed=True) +g.es["capacity"] = [7, 8, 1, 2, 3, 4, 5] + +# %% +# To find the max flow, we can simply run: +flow = g.maxflow(3, 0, capacity=g.es["capacity"]) + +print("Max flow:", flow.value) +print("Edge assignments:", flow.flow) + +# Output: +# Max flow: 6.0 +# Edge assignments [1.0, 5.0, 1.0, 2.0, 3.0, 3.0, 3.0] + +# %% +# Finally, we can plot the directed graph to look at the situation: +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + layout="circle", + vertex_label=range(g.vcount()), + vertex_color="lightblue", +) +plt.show() diff --git a/doc/examples_sphinx-gallery/minimum_spanning_trees.py b/doc/examples_sphinx-gallery/minimum_spanning_trees.py new file mode 100644 index 000000000..9177e976a --- /dev/null +++ b/doc/examples_sphinx-gallery/minimum_spanning_trees.py @@ -0,0 +1,53 @@ +""" +.. _tutorials-minimum-spanning-trees: + +====================== +Minimum Spanning Trees +====================== + +This example shows how to generate a `minimum spanning tree `_ from an input graph using :meth:`igraph.Graph.spanning_tree`. If you only need a regular spanning tree, check out :ref:`tutorials-spanning-trees`. + +""" + +import random +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# We start by generating a grid graph with random integer weights between 1 and +# 20: +random.seed(0) +g = ig.Graph.Lattice([5, 5], circular=False) +g.es["weight"] = [random.randint(1, 20) for _ in g.es] + +# %% +# We can then compute a minimum spanning tree using +# :meth:`igraph.Graph.spanning_tree`, making sure to pass in the randomly +# generated weights. +mst_edges = g.spanning_tree(weights=g.es["weight"], return_tree=False) + +# %% +# We can print out the minimum edge weight sum +print("Minimum edge weight sum:", sum(g.es[mst_edges]["weight"])) + +# Minimum edge weight sum: 136 + +# %% +# Finally, we can plot the graph, highlighting the edges that are part of the +# minimum spanning tree. +g.es["color"] = "lightgray" +g.es[mst_edges]["color"] = "midnightblue" +g.es["width"] = 1.0 +g.es[mst_edges]["width"] = 3.0 + +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + layout="grid", + vertex_color="lightblue", + edge_width=g.es["width"], + edge_label=g.es["weight"], + edge_background="white", +) +plt.show() diff --git a/doc/examples_sphinx-gallery/online_user_actions.py b/doc/examples_sphinx-gallery/online_user_actions.py new file mode 100644 index 000000000..47cc00ff5 --- /dev/null +++ b/doc/examples_sphinx-gallery/online_user_actions.py @@ -0,0 +1,105 @@ +""" +.. _tutorials-online-user-actions: + +=================== +Online user actions +=================== + +This example reproduces a typical data science situation in an internet company. We start from a pandas DataFrame with online user actions, for instance for an online text editor: the user can create a page, edit it, or delete it. We want to construct and visualize a graph of the users highlighting collaborations on the same page/project. +""" + +import igraph as ig +import numpy as np +import pandas as pd +import matplotlib.pyplot as plt + +# %% +# Let's start by preparing some toy data representing online users. Each row +# indicates a certain action taken by a user (e.g. click on a button within a +# website). Actual user data usually come with time stamp, but that's not +# essential for this example. +action_dataframe = pd.DataFrame( + [ + ["dsj3239asadsa3", "createPage", "greatProject"], + ["2r09ej221sk2k5", "editPage", "greatProject"], + ["dsj3239asadsa3", "editPage", "greatProject"], + ["789dsadafj32jj", "editPage", "greatProject"], + ["oi32ncwosap399", "editPage", "greatProject"], + ["4r4320dkqpdokk", "createPage", "miniProject"], + ["320eljl3lk3239", "editPage", "miniProject"], + ["dsj3239asadsa3", "editPage", "miniProject"], + ["3203ejew332323", "createPage", "private"], + ["3203ejew332323", "editPage", "private"], + ["40m11919332msa", "createPage", "private2"], + ["40m11919332msa", "editPage", "private2"], + ["dsj3239asadsa3", "createPage", "anotherGreatProject"], + ["2r09ej221sk2k5", "editPage", "anotherGreatProject"], + ], + columns=["userid", "action", "project"], +) + +# %% +# The goal of this example is to check when two users worked on the same page. +# We choose to use a weighted adjacency matrix for this, i.e. a table with rows +# and columns indexes by the users that has nonzero entries whenever folks +# collaborate. First, let's get the users and prepare an empty matrix: +users = action_dataframe["userid"].unique() +adjacency_matrix = pd.DataFrame( + np.zeros((len(users), len(users)), np.int32), + index=users, + columns=users, +) + +# %% +# Then, let's iterate over all projects one by one, and add all collaborations: +for _project, project_data in action_dataframe.groupby("project"): + project_users = project_data["userid"].values + for i1, user1 in enumerate(project_users): + for user2 in project_users[:i1]: + adjacency_matrix.at[user1, user2] += 1 + +# %% +# There are many ways to achieve the above matrix, so don't be surprised if you +# came up with another algorithm ;-) Now it's time to make the graph: +g = ig.Graph.Weighted_Adjacency(adjacency_matrix, mode="plus") + +# %% +# We can take a look at the graph via plotting functions. We can first make a +# layout: +layout = g.layout("circle") + +# %% +# Then we can prepare vertex sizes based on their closeness to other vertices +vertex_size = g.closeness() +vertex_size = [10 * v**2 if not np.isnan(v) else 10 for v in vertex_size] + +# %% +# Finally, we can plot the graph: +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + layout=layout, + vertex_label=g.vs["name"], + vertex_color="lightblue", + vertex_size=vertex_size, + edge_width=g.es["weight"], +) +plt.show() + +# %% +# Loops indicate "self-collaborations", which are not very meaningful. To +# filter out loops without losing the edge weights, we can use: +g = g.simplify(combine_edges="first") + +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + layout=layout, + vertex_label=g.vs["name"], + vertex_color="lightblue", + vertex_size=vertex_size, + edge_width=g.es["weight"], +) +plt.show() diff --git a/doc/examples_sphinx-gallery/personalized_pagerank.py b/doc/examples_sphinx-gallery/personalized_pagerank.py new file mode 100644 index 000000000..f7e2f9e2b --- /dev/null +++ b/doc/examples_sphinx-gallery/personalized_pagerank.py @@ -0,0 +1,98 @@ +""" +.. _tutorials-personalized_pagerank: + +=============================== +Personalized PageRank on a grid +=============================== + +This example demonstrates how to calculate and visualize personalized PageRank on a grid. We use the :meth:`igraph.Graph.personalized_pagerank` method, and demonstrate the effects on a grid graph. +""" + +# %% +# .. note:: +# +# The PageRank score of a vertex reflects the probability that a random walker will be at that vertex over the long run. At each step the walker has a 1 - damping chance to restart the walk and pick a starting vertex according to the probabilities defined in the reset vector. + +import igraph as ig +import matplotlib.cm as cm +import matplotlib.pyplot as plt +import numpy as np + +# %% +# We define a function that plots the graph on a Matplotlib axis, along with +# its personalized PageRank values. The function also generates a +# color bar on the side to see how the values change. +# We use `Matplotlib's Normalize class `_ +# to set the colors and ensure that our color bar range is correct. + + +def plot_pagerank(graph: ig.Graph, p_pagerank: list[float]): + """Plots personalized PageRank values on a grid graph with a colorbar. + + Parameters + ---------- + graph : ig.Graph + graph to plot + p_pagerank : list[float] + calculated personalized PageRank values + """ + # Create the axis for matplotlib + _, ax = plt.subplots(figsize=(8, 8)) + + # Create a matplotlib colormap + # coolwarm goes from blue (lowest value) to red (highest value) + cmap = cm.coolwarm + + # Normalize the PageRank values for colormap + normalized_pagerank = ig.rescale(p_pagerank) + + graph.vs["color"] = [cmap(pr) for pr in normalized_pagerank] + graph.vs["size"] = ig.rescale(p_pagerank, (20, 40)) + graph.es["color"] = "gray" + graph.es["width"] = 1.5 + + # Plot the graph + ig.plot(graph, target=ax, layout=graph.layout_grid()) + + # Add a colorbar + sm = cm.ScalarMappable( + norm=plt.Normalize(min(p_pagerank), max(p_pagerank)), cmap=cmap + ) + plt.colorbar(sm, ax=ax, label="Personalized PageRank") + + plt.title("Graph with Personalized PageRank") + plt.axis("equal") + plt.show() + + +# %% +# First, we generate a graph, e.g. a Lattice Graph, which basically is a ``dim x dim`` grid: +dim = 5 +grid_size = (dim, dim) # dim rows, dim columns +g = ig.Graph.Lattice(dim=grid_size, circular=False) + +# %% +# Then we initialize the ``reset_vector`` (it's length should be equal to the number of vertices in the graph): +reset_vector = np.zeros(g.vcount()) + +# %% +# Then we set the nodes to prioritize, for example nodes with indices ``0`` and ``18``: +reset_vector[0] = 1 +reset_vector[18] = 0.65 + +# %% +# Then we calculate the personalized PageRank: +personalized_page_rank = g.personalized_pagerank(damping=0.85, reset=reset_vector) + +# %% +# Finally, we plot the graph with the personalized PageRank values: +plot_pagerank(g, personalized_page_rank) + + +# %% +# Alternatively, we can play around with the ``damping`` parameter: +personalized_page_rank = g.personalized_pagerank(damping=0.45, reset=reset_vector) + +# %% +# Here we can see the same plot with the new damping parameter: +plot_pagerank(g, personalized_page_rank) diff --git a/doc/source/tutorials/quickstart/assets/quickstart.py b/doc/examples_sphinx-gallery/quickstart.py similarity index 52% rename from doc/source/tutorials/quickstart/assets/quickstart.py rename to doc/examples_sphinx-gallery/quickstart.py index 52edfab77..0735768e5 100644 --- a/doc/source/tutorials/quickstart/assets/quickstart.py +++ b/doc/examples_sphinx-gallery/quickstart.py @@ -1,14 +1,38 @@ +""" +.. _tutorials-quickstart: + +=========== +Quick Start +=========== +For the eager folks out there, this intro will give you a quick overview of the following operations: + +- Construct a graph +- Set attributes of nodes and edges +- Plot a graph using matplotlib +- Save the plot as an image +- Export and import a graph as a ``.gml`` file + +To find out more features that igraph has to offer, check out the :ref:`gallery`! + +""" + import igraph as ig import matplotlib.pyplot as plt -# Construct a graph with 3 vertices -n_vertices = 3 +# Construct a graph with 5 vertices +n_vertices = 5 edges = [(0, 1), (0, 2), (0, 3), (0, 4), (1, 2), (1, 3), (1, 4), (3, 4)] g = ig.Graph(n_vertices, edges) # Set attributes for the graph, nodes, and edges g["title"] = "Small Social Network" -g.vs["name"] = ["Daniel Morillas", "Kathy Archer", "Kyle Ding", "Joshua Walton", "Jana Hoyer"] +g.vs["name"] = [ + "Daniel Morillas", + "Kathy Archer", + "Kyle Ding", + "Joshua Walton", + "Jana Hoyer", +] g.vs["gender"] = ["M", "F", "F", "M", "F"] g.es["married"] = [False, False, False, False, False, False, False, True] @@ -18,27 +42,29 @@ # Plot in matplotlib # Note that attributes can be set globally (e.g. vertex_size), or set individually using arrays (e.g. vertex_color) -fig, ax = plt.subplots(figsize=(5,5)) +fig, ax = plt.subplots(figsize=(5, 5)) ig.plot( g, target=ax, - layout="circle", # print nodes in a circular layout - vertex_size=0.1, - vertex_color=["steelblue" if gender == "M" else "salmon" for gender in g.vs["gender"]], + layout="circle", # print nodes in a circular layout + vertex_size=30, + vertex_color=[ + "steelblue" if gender == "M" else "salmon" for gender in g.vs["gender"] + ], vertex_frame_width=4.0, vertex_frame_color="white", vertex_label=g.vs["name"], vertex_label_size=7.0, edge_width=[2 if married else 1 for married in g.es["married"]], - edge_color=["#7142cf" if married else "#AAA" for married in g.es["married"]] + edge_color=["#7142cf" if married else "#AAA" for married in g.es["married"]], ) plt.show() # Save the graph as an image file -fig.savefig('social_network.png') -fig.savefig('social_network.jpg') -fig.savefig('social_network.pdf') +fig.savefig("social_network.png") +fig.savefig("social_network.jpg") +fig.savefig("social_network.pdf") # Export and import a graph as a GML file. g.save("social_network.gml") diff --git a/doc/examples_sphinx-gallery/ring_animation.py b/doc/examples_sphinx-gallery/ring_animation.py new file mode 100644 index 000000000..33bd6a109 --- /dev/null +++ b/doc/examples_sphinx-gallery/ring_animation.py @@ -0,0 +1,92 @@ +""" +.. _tutorials-ring-animation: + +==================== +Ring Graph Animation +==================== + +This example demonstrates how to use :doc:`matplotlib:api/animation_api` in +order to animate a ring graph sequentially being revealed. + +""" + +import igraph as ig +import matplotlib.pyplot as plt +import matplotlib.animation as animation + +# sphinx_gallery_thumbnail_path = '_static/gallery_thumbnails/ring_animation.gif' + +# %% +# Create a ring graph, which we will then animate +g = ig.Graph.Ring(10, directed=True) + +# %% +# Compute a 2D ring layout that looks like an actual ring +layout = g.layout_circle() + + +# %% +# Prepare an update function. This "callback" function will be run at every +# frame and takes as a single argument the frame number. For simplicity, at +# each frame we compute a subgraph with only a fraction of the vertices and +# edges. As time passes, the graph becomes more and more complete until the +# whole ring is closed. +# +# .. note:: +# The beginning and end of the animation are a little tricky because only +# a vertex or edge is added, not both. Don't worry if you cannot understand +# all details immediately. +def _update_graph(frame): + # Remove plot elements from the previous frame + ax.clear() + + # Fix limits (unless you want a zoom-out effect) + ax.set_xlim(-1.5, 1.5) + ax.set_ylim(-1.5, 1.5) + + if frame < 10: + # Plot subgraph + gd = g.subgraph(range(frame)) + elif frame == 10: + # In the second-to-last frame, plot all vertices but skip the last + # edge, which will only be shown in the last frame + gd = g.copy() + gd.delete_edges(9) + else: + # Last frame + gd = g + + ig.plot(gd, target=ax, layout=layout[:frame], vertex_color="yellow") + + # Capture handles for blitting + if frame == 0: + nhandles = 0 + elif frame == 1: + nhandles = 1 + elif frame < 11: + # vertex, 2 for each edge + nhandles = 3 * frame + else: + # The final edge closing the circle + nhandles = 3 * (frame - 1) + 2 + + handles = ax.get_children()[:nhandles] + return handles + + +# %% +# Run the animation +fig, ax = plt.subplots() +ani = animation.FuncAnimation(fig, _update_graph, 12, interval=500, blit=True) +plt.ion() +plt.show() + +# %% +# .. note:: +# +# We use *igraph*'s :meth:`Graph.subgraph()` (see +# :meth:`igraph.GraphBase.induced_subgraph`) in order to obtain a section of +# the ring graph at a time for each frame. While sufficient for an easy +# example, this approach is not very efficient. Thinking of more efficient +# approaches, e.g. vertices with zero radius, is a useful exercise to learn +# the combination of igraph and matplotlib. diff --git a/doc/examples_sphinx-gallery/shortest_path_visualisation.py b/doc/examples_sphinx-gallery/shortest_path_visualisation.py new file mode 100644 index 000000000..fedad160a --- /dev/null +++ b/doc/examples_sphinx-gallery/shortest_path_visualisation.py @@ -0,0 +1,77 @@ +""" +.. _tutorials-shortest-paths: + +============== +Shortest Paths +============== + +This example demonstrates how to find the shortest distance between two vertices +of a weighted or an unweighted graph. +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# To find the shortest path or distance between two nodes, we can use :meth:`igraph.GraphBase.get_shortest_paths`. If we're only interested in counting the unweighted distance, then we can do the following: +g = ig.Graph(6, [(0, 1), (0, 2), (1, 3), (2, 3), (2, 4), (3, 5), (4, 5)]) +results = g.get_shortest_paths(1, to=4, output="vpath") + +# results = [[1, 0, 2, 4]] + +# %% +# We can print the result of the computation: +if len(results[0]) > 0: + # The distance is the number of vertices in the shortest path minus one. + print("Shortest distance is: ", len(results[0]) - 1) +else: + print("End node could not be reached!") + +# %% +# If the edges have weights, things are a little different. First, let's add +# weights to our graph edges: +g.es["weight"] = [2, 1, 5, 4, 7, 3, 2] + +# %% +# To get the shortest paths on a weighted graph, we pass the weights as an +# argument. For a change, we choose the output format as ``"epath"`` to +# receive the path as an edge list, which can be used to calculate the length +# of the path. +results = g.get_shortest_paths(0, to=5, weights=g.es["weight"], output="epath") + +# results = [[1, 3, 5]] + +if len(results[0]) > 0: + # Add up the weights across all edges on the shortest path + distance = 0 + for e in results[0]: + distance += g.es[e]["weight"] + print("Shortest weighted distance is: ", distance) +else: + print("End node could not be reached!") + +# %% +# .. note:: +# +# - :meth:`igraph.GraphBase.get_shortest_paths` returns a list of lists becuase the `to` argument can also accept a list of vertex IDs. In that case, the shortest path to all each vertex is found and stored in the results array. +# - If you're interested in finding *all* shortest paths, take a look at :meth:`igraph.GraphBase.get_all_shortest_paths`. + +# %% +# In case you are wondering how the visualization figure was done, here's the code: +g.es["width"] = 0.5 +g.es[results[0]]["width"] = 2.5 + +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + layout="circle", + vertex_color="steelblue", + vertex_label=range(g.vcount()), + edge_width=g.es["width"], + edge_label=g.es["weight"], + edge_color="#666", + edge_align_label=True, + edge_background="white", +) +plt.show() diff --git a/doc/examples_sphinx-gallery/simplify.py b/doc/examples_sphinx-gallery/simplify.py new file mode 100644 index 000000000..ed36b2da5 --- /dev/null +++ b/doc/examples_sphinx-gallery/simplify.py @@ -0,0 +1,90 @@ +""" +======== +Simplify +======== + +This example shows how to remove self loops and multiple edges using :meth:`igraph.GraphBase.simplify`. +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# We start with a graph that includes loops and multiedges: +g1 = ig.Graph( + [ + (0, 1), + (1, 2), + (2, 3), + (3, 4), + (4, 0), + (0, 0), + (1, 4), + (1, 4), + (0, 2), + (2, 4), + (2, 4), + (2, 4), + (3, 3), + ], +) + +# %% +# To simplify the graph, we must remember that the function operates in place, +# i.e. directly changes the graph that it is run on. So we need to first make a +# copy of our graph, and then simplify that copy to keep the original graph +# untouched: +g2 = g1.copy() +g2.simplify() + +# %% +# We can then proceed to plot both graphs to see the difference. First, let's +# choose a consistent visual style: +visual_style = { + "vertex_color": "lightblue", + "vertex_size": 20, + "vertex_label": [0, 1, 2, 3, 4], +} + +# %% +# And finally, let's plot them in twin axes, with rectangular frames around +# each plot: +fig, axs = plt.subplots(1, 2, sharex=True, sharey=True) +ig.plot( + g1, + layout="circle", + target=axs[0], + **visual_style, +) +ig.plot( + g2, + layout="circle", + target=axs[1], + **visual_style, +) +axs[0].set_title("Multigraph...") +axs[1].set_title("...simplified") +# Draw rectangles around axes +axs[0].add_patch( + plt.Rectangle( + (0, 0), + 1, + 1, + fc="none", + ec="k", + lw=4, + transform=axs[0].transAxes, + ) +) +axs[1].add_patch( + plt.Rectangle( + (0, 0), + 1, + 1, + fc="none", + ec="k", + lw=4, + transform=axs[1].transAxes, + ) +) +plt.show() diff --git a/doc/examples_sphinx-gallery/spanning_trees.py b/doc/examples_sphinx-gallery/spanning_trees.py new file mode 100644 index 000000000..cfca1135f --- /dev/null +++ b/doc/examples_sphinx-gallery/spanning_trees.py @@ -0,0 +1,57 @@ +""" +.. _tutorials-spanning-trees: + +============== +Spanning Trees +============== + +This example shows how to generate a spanning tree from an input graph using :meth:`igraph.Graph.spanning_tree`. For the related idea of finding a *minimum spanning tree*, see :ref:`tutorials-minimum-spanning-trees`. +""" + +import igraph as ig +import matplotlib.pyplot as plt +import random + +# %% +# First we create a two-dimensional, 6 by 6 lattice graph: +g = ig.Graph.Lattice([6, 6], circular=False) + +# %% +# We can compute the 2D layout of the graph: +layout = g.layout("grid") + +# %% +# To spice things up a little, we rearrange the vertex ids and compute a new +# layout. While not terribly useful in this context, it does make for a more +# interesting-looking spanning tree ;-) +random.seed(0) +permutation = list(range(g.vcount())) +random.shuffle(permutation) +g = g.permute_vertices(permutation) +new_layout = g.layout("grid") +for i in range(36): + new_layout[permutation[i]] = layout[i] +layout = new_layout + +# %% +# We can now generate a spanning tree: +spanning_tree = g.spanning_tree(weights=None, return_tree=False) + +# %% +# Finally, we can plot the graph with a highlight color for the spanning tree. +# We follow the usual recipe: first we set a few aesthetic options and then we +# leverage :func:`igraph.plot() ` and matplotlib for the +# heavy lifting: +g.es["color"] = "lightgray" +g.es[spanning_tree]["color"] = "midnightblue" +g.es["width"] = 0.5 +g.es[spanning_tree]["width"] = 3.0 + +fig, ax = plt.subplots() +ig.plot(g, target=ax, layout=layout, vertex_color="lightblue", edge_width=g.es["width"]) +plt.show() + +# %% +# .. note:: +# To invert the y axis such that the root of the tree is on top of the plot, +# you can call `ax.invert_yaxis()` before `plt.show()`. diff --git a/doc/examples_sphinx-gallery/stochastic_variability.py b/doc/examples_sphinx-gallery/stochastic_variability.py new file mode 100644 index 000000000..2afc01153 --- /dev/null +++ b/doc/examples_sphinx-gallery/stochastic_variability.py @@ -0,0 +1,171 @@ +""" +.. _tutorials-stochastic-variability: + +========================================================= +Stochastic Variability in Community Detection Algorithms +========================================================= + +This example demonstrates the use of stochastic community detection methods to check whether a network possesses a strong community structure, and whether the partitionings we obtain are meaningul. Many community detection algorithms are randomized, and return somewhat different results after each run, depending on the random seed that was set. When there is a robust community structure, we expect these results to be similar to each other. When the community structure is weak or non-existent, the results may be noisy and highly variable. We will employ several partion similarity measures to analyse the consistency of the results, including the normalized mutual information (NMI), the variation of information (VI), and the Rand index (RI). + +""" + +# %% +import igraph as ig +import matplotlib.pyplot as plt +import itertools +import random + +# %% +# .. note:: +# We set a random seed to ensure that the results look exactly the same in +# the gallery. You don't need to do this when exploring randomness. +random.seed(42) + +# %% +# We will use Zachary's karate club dataset [1]_, a classic example of a network +# with a strong community structure: +karate = ig.Graph.Famous("Zachary") + +# %% +# We will compare it to an an Erdős-Rényi :math:`G(n, m)` random network having +# the same number of vertices and edges. The parameters 'n' and 'm' refer to the +# vertex and edge count, respectively. Since this is a random network, it should +# have no community structure. +random_graph = ig.Graph.Erdos_Renyi(n=karate.vcount(), m=karate.ecount()) + +# %% +# First, let us plot the two networks for a visual comparison: + +# Create subplots +fig, axes = plt.subplots(1, 2, figsize=(12, 6), subplot_kw={"aspect": "equal"}) + +# Karate club network +ig.plot( + karate, + target=axes[0], + vertex_color="lightblue", + vertex_size=30, + vertex_label=range(karate.vcount()), + vertex_label_size=10, + edge_width=1, +) +axes[0].set_title("Karate club network") + +# Random network +ig.plot( + random_graph, + target=axes[1], + vertex_color="lightcoral", + vertex_size=30, + vertex_label=range(random_graph.vcount()), + vertex_label_size=10, + edge_width=1, +) +axes[1].set_title("Erdős-Rényi random network") + +plt.show() + + +# %% +# Function to compute similarity between partitions using various methods: +def compute_pairwise_similarity(partitions, method): + similarities = [] + + for p1, p2 in itertools.combinations(partitions, 2): + similarity = ig.compare_communities(p1, p2, method=method) + similarities.append(similarity) + + return similarities + + +# %% +# The Leiden method, accessible through :meth:`igraph.Graph.community_leiden()`, +# is a modularity maximization approach for community detection. Since exact +# modularity maximization is NP-hard, the algorithm employs a greedy heuristic +# that processes vertices in a random order. This randomness leads to +# variation in the detected communities across different runs, which is why +# results may differ each time the method is applied. The following function +# runs the Leiden algorithm multiple times: +def run_experiment(graph, iterations=100): + partitions = [ + graph.community_leiden(objective_function="modularity").membership + for _ in range(iterations) + ] + nmi_scores = compute_pairwise_similarity(partitions, method="nmi") + vi_scores = compute_pairwise_similarity(partitions, method="vi") + ri_scores = compute_pairwise_similarity(partitions, method="rand") + return nmi_scores, vi_scores, ri_scores + + +# %% +# Run the experiment on both networks: +nmi_karate, vi_karate, ri_karate = run_experiment(karate) +nmi_random, vi_random, ri_random = run_experiment(random_graph) + +# %% +# Finally, let us plot histograms of the pairwise similarities of the obtained +# partitionings to understand the result: +fig, axes = plt.subplots(2, 3, figsize=(12, 6)) +measures = [ + # Normalized Mutual Information (0-1, higher = more similar) + (nmi_karate, nmi_random, "NMI", 0, 1), + # Variation of Information (0+, lower = more similar) + (vi_karate, vi_random, "VI", 0, max(vi_karate + vi_random)), + # Rand Index (0-1, higher = more similar) + (ri_karate, ri_random, "RI", 0, 1), +] +colors = ["red", "blue", "green"] + +for i, (karate_scores, random_scores, measure, lower, upper) in enumerate(measures): + # Karate club histogram + axes[0][i].hist( + karate_scores, + bins=20, + range=(lower, upper), + density=True, # Probability density + alpha=0.7, + color=colors[i], + edgecolor="black", + ) + axes[0][i].set_title(f"{measure} - Karate club network") + axes[0][i].set_xlabel(f"{measure} score") + axes[0][i].set_ylabel("PDF") + + # Random network histogram + axes[1][i].hist( + random_scores, + bins=20, + range=(lower, upper), + density=True, + alpha=0.7, + color=colors[i], + edgecolor="black", + ) + axes[1][i].set_title(f"{measure} - Random network") + axes[1][i].set_xlabel(f"{measure} score") + axes[0][i].set_ylabel("PDF") + +plt.tight_layout() +plt.show() + +# %% +# We have compared the pairwise similarities using the NMI, VI, and RI measures +# between partitonings obtained for the karate club network (strong community +# structure) and a comparable random graph (which lacks communities). +# +# The Normalized Mutual Information (NMI) and Rand Index (RI) both quantify +# similarity, and take values from :math:`[0,1]`. Higher values indicate more +# similar partitionings, with a value of 1 attained when the partitionings are +# identical. +# +# The Variation of Information (VI) is a distance measure. It takes values from +# :math:`[0,\infty]`, with lower values indicating higher similarities. Identical +# partitionings have a distance of zero. +# +# For the karate club network, NMI and RI value are concentrated near 1, while +# VI is concentrated near 0, suggesting a robust community structure. In contrast +# the values obtained for the random network are much more spread out, showing +# inconsistent partitionings due to the lack of a clear community structure. + +# %% +# .. [1] W. Zachary: "An Information Flow Model for Conflict and Fission in Small Groups". Journal of Anthropological Research 33, no. 4 (1977): 452–73. https://www.jstor.org/stable/3629752 diff --git a/doc/examples_sphinx-gallery/topological_sort.py b/doc/examples_sphinx-gallery/topological_sort.py new file mode 100644 index 000000000..3c558f90b --- /dev/null +++ b/doc/examples_sphinx-gallery/topological_sort.py @@ -0,0 +1,60 @@ +""" +.. _tutorials-topological-sort: + +=================== +Topological sorting +=================== + +This example demonstrates how to get a topological sorting on a directed acyclic graph (DAG). A topological sorting of a directed graph is a linear ordering based on the precedence implied by the directed edges. It exists iff the graph doesn't have any cycle. In ``igraph``, we can use :meth:`igraph.GraphBase.topological_sorting` to get a topological ordering of the vertices. +""" + +import igraph as ig +import matplotlib.pyplot as plt + + +# %% +# First off, we generate a directed acyclic graph (DAG): +g = ig.Graph( + edges=[(0, 1), (0, 2), (1, 3), (2, 4), (4, 3), (3, 5), (4, 5)], + directed=True, +) + +# %% +# We can verify immediately that this is actually a DAG: +assert g.is_dag + +# %% +# A topological sorting can be computed quite easily by calling +# :meth:`igraph.GraphBase.topological_sorting`, which returns a list of vertex IDs. +# If the given graph is not DAG, the error will occur. +results = g.topological_sorting(mode="out") +print("Topological sort of g (out):", *results) + +# %% +# In fact, there are two modes of :meth:`igraph.GraphBase.topological_sorting`, +# ``'out'`` ``'in'``. ``'out'`` is the default and starts from a node with +# indegree equal to 0. Vice versa, ``'in'`` starts from a node with outdegree +# equal to 0. To call the other mode, we can simply use: +results = g.topological_sorting(mode="in") +print("Topological sort of g (in):", *results) + +# %% +# We can use :meth:`igraph.Vertex.indegree` to find the indegree of the node. +for i in range(g.vcount()): + print("degree of {}: {}".format(i, g.vs[i].indegree())) + +# % +# Finally, we can plot the graph to make the situation a little clearer. +# Just to change things up a bit, we use the matplotlib visualization mode +# inspired by `xkcd _: +with plt.xkcd(): + fig, ax = plt.subplots(figsize=(5, 5)) + ig.plot( + g, + target=ax, + layout="kk", + vertex_size=25, + edge_width=4, + vertex_label=range(g.vcount()), + vertex_color="white", + ) diff --git a/doc/examples_sphinx-gallery/visual_style.py b/doc/examples_sphinx-gallery/visual_style.py new file mode 100644 index 000000000..30c27d73b --- /dev/null +++ b/doc/examples_sphinx-gallery/visual_style.py @@ -0,0 +1,91 @@ +""" +.. _tutorials-visual-style: + +Visual styling +=========================== + +This example shows how to change the visual style of network plots. +""" + +import igraph as ig +import matplotlib.pyplot as plt +import random + +# %% +# To configure the visual style of a plot, we can create a dictionary with the +# various setting we want to customize: +visual_style = { + "edge_width": 0.3, + "vertex_size": 15, + "palette": "heat", + "layout": "fruchterman_reingold", +} + +# %% +# Let's see it in action! First, we generate four random graphs: +random.seed(1) +gs = [ig.Graph.Barabasi(n=30, m=1) for i in range(4)] + +# %% +# Then, we calculate a color colors between 0-255 for all nodes, e.g. using +# betweenness just as an example: +betweenness = [g.betweenness() for g in gs] +colors = [[int(i * 255 / max(btw)) for i in btw] for btw in betweenness] + +# %% +# Finally, we can plot the graphs using the same visual style for all graphs: +fig, axs = plt.subplots(2, 2) +axs = axs.ravel() +for g, color, ax in zip(gs, colors, axs): + ig.plot(g, target=ax, vertex_color=color, **visual_style) +plt.show() + + +# %% +# .. note:: +# If you would like to set global defaults, for example, always using the +# Matplotlib plotting backend, or using a particular color palette by +# default, you can use igraph's `configuration instance +# :class:`igraph.configuration.Configuration`. A quick example on how to use +# it can be found here: :ref:`tutorials-configuration`. + +# %% +# In the matplotlib backend, igraph creates a special container +# :class:`igraph.drawing.matplotlib.graph.GraphArtist` which is a matplotlib Artist +# and the first child of the target Axes. That object can be used to customize +# the plot appearance after the initial drawing, e.g.: +g = ig.Graph.Barabasi(n=30, m=1) +fig, ax = plt.subplots() +ig.plot(g, target=ax) +artist = ax.get_children()[0] +# Option 1: +artist.set(vertex_color="blue") +# Option 2: +artist.set_vertex_color("blue") +plt.show() + +# %% +# .. note:: +# The :meth:`igraph.drawing.matplotlib.graph.GraphArtist.set` method can +# be used to change multiple properties at once and is generally more +# efficient than multiple calls to specific ``artist.set_...`` methods. + +# %% +# In the matplotlib backend, you can also specify the size of self-loops, +# either as a number or a sequence of numbers, e.g.: +g = ig.Graph(n=5) +g.add_edge(2, 3) +g.add_edge(0, 0) +g.add_edge(1, 1) +fig, ax = plt.subplots() +ig.plot( + g, + target=ax, + vertex_size=20, + edge_loop_size=[ + 0, # ignored, the first edge is not a loop + 30, # loop for vertex 0 + 80, # loop for vertex 1 + ], +) +plt.show() diff --git a/doc/examples_sphinx-gallery/visualize_cliques.py b/doc/examples_sphinx-gallery/visualize_cliques.py new file mode 100644 index 000000000..c1ebd49d6 --- /dev/null +++ b/doc/examples_sphinx-gallery/visualize_cliques.py @@ -0,0 +1,69 @@ +""" +.. _tutorials-cliques: + +============ +Cliques +============ + +This example shows how to compute and visualize cliques of a graph using :meth:`igraph.GraphBase.cliques`. + +""" + +import igraph as ig +import matplotlib.pyplot as plt + +# %% +# First, let's create a graph, for instance the famous karate club graph: +g = ig.Graph.Famous("Zachary") + +# %% +# Computing cliques can be done as follows: +cliques = g.cliques(4, 4) + +# %% +# We can plot the result of the computation. To make things a little more +# interesting, we plot each clique highlighted in a separate axes: +fig, axs = plt.subplots(3, 4) +axs = axs.ravel() +for clique, ax in zip(cliques, axs): + ig.plot( + ig.VertexCover(g, [clique]), + mark_groups=True, + palette=ig.RainbowPalette(), + vertex_size=5, + edge_width=0.5, + target=ax, + ) +plt.axis("off") +plt.show() + + +# %% +# Advanced: improving plotting style +# ---------------------------------- +# If you want a little more style, you can color the vertices/edges within each +# clique to make them stand out: +fig, axs = plt.subplots(3, 4) +axs = axs.ravel() +for clique, ax in zip(cliques, axs): + # Color vertices yellow/red based on whether they are in this clique + g.vs["color"] = "yellow" + g.vs[clique]["color"] = "red" + + # Color edges black/red based on whether they are in this clique + clique_edges = g.es.select(_within=clique) + g.es["color"] = "black" + clique_edges["color"] = "red" + # also increase thickness of clique edges + g.es["width"] = 0.3 + clique_edges["width"] = 1 + + ig.plot( + ig.VertexCover(g, [clique]), + mark_groups=True, + palette=ig.RainbowPalette(), + vertex_size=5, + target=ax, + ) +plt.axis("off") +plt.show() diff --git a/doc/source/tutorials/visualize_communities/assets/visualize_communities.py b/doc/examples_sphinx-gallery/visualize_communities.py similarity index 50% rename from doc/source/tutorials/visualize_communities/assets/visualize_communities.py rename to doc/examples_sphinx-gallery/visualize_communities.py index 614bb612d..9ab696e8e 100644 --- a/doc/source/tutorials/visualize_communities/assets/visualize_communities.py +++ b/doc/examples_sphinx-gallery/visualize_communities.py @@ -1,14 +1,28 @@ +""" +.. _tutorials-visualize-communities: + +===================== +Communities +===================== + +This example shows how to visualize communities or clusters of a graph. +""" + import igraph as ig import matplotlib.pyplot as plt +# %% +# First, we generate a graph. We use a famous graph here for simplicity: g = ig.Graph.Famous("Zachary") -# Use edge betweenness to detect communities -# and covert into a VertexClustering +# %% +# Edge betweenness is a standard way to detect communities. We then covert into +# a :class:`igraph.VertexClustering` object for subsequent ease of use: communities = g.community_edge_betweenness() communities = communities.as_clustering() -# Color each vertex and edge based on its community membership +# %% +# Next, we color each vertex and edge based on its community membership: num_communities = len(communities) palette = ig.RainbowPalette(n=num_communities) for i, community in enumerate(communities): @@ -17,21 +31,25 @@ community_edges["color"] = i -# Plot with only vertex and edge coloring +# %% +# Last, we plot the graph. We use a fancy technique called proxy artists to +# make a legend. You can find more about that in matplotlib's +# :doc:`matplotlib:users/explain/axes/legend_guide`: fig, ax = plt.subplots() ig.plot( communities, palette=palette, edge_width=1, target=ax, - vertex_size=0.3, + vertex_size=20, ) # Create a custom color legend legend_handles = [] for i in range(num_communities): handle = ax.scatter( - [], [], + [], + [], s=100, facecolor=palette.get(i), edgecolor="k", @@ -40,9 +58,12 @@ legend_handles.append(handle) ax.legend( handles=legend_handles, - title='Community:', + title="Community:", bbox_to_anchor=(0, 1.0), bbox_transform=ax.transAxes, ) - plt.show() + +# %% +# For an example on how to generate the cluster graph from a vertex cluster, +# check out :ref:`tutorials-cluster-graph`. diff --git a/doc/jekyll_tools/Gemfile b/doc/jekyll_tools/Gemfile deleted file mode 100644 index 3e5e9cbd3..000000000 --- a/doc/jekyll_tools/Gemfile +++ /dev/null @@ -1,5 +0,0 @@ -source 'http://rubygems.org' - -gem 'jekyll-sitemap' -gem "webrick", "~> 1.7" -gem 'jekyll-redirect-from' diff --git a/doc/jekyll_tools/Gemfile.lock b/doc/jekyll_tools/Gemfile.lock deleted file mode 100644 index 710e3df51..000000000 --- a/doc/jekyll_tools/Gemfile.lock +++ /dev/null @@ -1,74 +0,0 @@ -GEM - remote: http://rubygems.org/ - specs: - addressable (2.8.0) - public_suffix (>= 2.0.2, < 5.0) - colorator (1.1.0) - concurrent-ruby (1.1.9) - em-websocket (0.5.3) - eventmachine (>= 0.12.9) - http_parser.rb (~> 0) - eventmachine (1.2.7) - ffi (1.15.4) - forwardable-extended (2.6.0) - http_parser.rb (0.8.0) - i18n (1.8.11) - concurrent-ruby (~> 1.0) - jekyll (4.2.1) - addressable (~> 2.4) - colorator (~> 1.0) - em-websocket (~> 0.5) - i18n (~> 1.0) - jekyll-sass-converter (~> 2.0) - jekyll-watch (~> 2.0) - kramdown (~> 2.3) - kramdown-parser-gfm (~> 1.0) - liquid (~> 4.0) - mercenary (~> 0.4.0) - pathutil (~> 0.9) - rouge (~> 3.0) - safe_yaml (~> 1.0) - terminal-table (~> 2.0) - jekyll-redirect-from (0.16.0) - jekyll (>= 3.3, < 5.0) - jekyll-sass-converter (2.1.0) - sassc (> 2.0.1, < 3.0) - jekyll-sitemap (1.4.0) - jekyll (>= 3.7, < 5.0) - jekyll-watch (2.2.1) - listen (~> 3.0) - kramdown (2.3.1) - rexml - kramdown-parser-gfm (1.1.0) - kramdown (~> 2.0) - liquid (4.0.3) - listen (3.7.0) - rb-fsevent (~> 0.10, >= 0.10.3) - rb-inotify (~> 0.9, >= 0.9.10) - mercenary (0.4.0) - pathutil (0.16.2) - forwardable-extended (~> 2.6) - public_suffix (4.0.6) - rb-fsevent (0.11.0) - rb-inotify (0.10.1) - ffi (~> 1.0) - rexml (3.2.5) - rouge (3.27.0) - safe_yaml (1.0.5) - sassc (2.4.0) - ffi (~> 1.9) - terminal-table (2.0.0) - unicode-display_width (~> 1.1, >= 1.1.1) - unicode-display_width (1.8.0) - webrick (1.7.0) - -PLATFORMS - x86_64-linux - -DEPENDENCIES - jekyll-redirect-from - jekyll-sitemap - webrick (~> 1.7) - -BUNDLED WITH - 2.2.26 diff --git a/doc/jekyll_tools/Makefile b/doc/jekyll_tools/Makefile deleted file mode 100644 index aa1a6dbf8..000000000 --- a/doc/jekyll_tools/Makefile +++ /dev/null @@ -1,130 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = build - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - -clean: - -rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." - -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - -singlehtml: - $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml - @echo - @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." - -pickle: - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -json: - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in $(BUILDDIR)/htmlhelp." - -qthelp: - $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp - @echo - @echo "Build finished; now you can run "qcollectiongenerator" with the" \ - ".qhcp project file in $(BUILDDIR)/qthelp, like this:" - @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/igraph.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/igraph.qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/igraph" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/igraph" - @echo "# devhelp" - -epub: - $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub - @echo - @echo "Build finished. The epub file is in $(BUILDDIR)/epub." - -latex: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo - @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." - @echo "Run \`make' in that directory to run these through (pdf)latex" \ - "(use \`make latexpdf' here to do that automatically)." - -latexpdf: - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex - @echo "Running LaTeX files through pdflatex..." - make -C $(BUILDDIR)/latex all-pdf - @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." - -text: - $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text - @echo - @echo "Build finished. The text files are in $(BUILDDIR)/text." - -man: - $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man - @echo - @echo "Build finished. The manual pages are in $(BUILDDIR)/man." - -changes: - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes - @echo - @echo "The overview file is in $(BUILDDIR)/changes." - -linkcheck: - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in $(BUILDDIR)/linkcheck/output.txt." - -doctest: - $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest - @echo "Testing of doctests in the sources finished, look at the " \ - "results in $(BUILDDIR)/doctest/output.txt." diff --git a/doc/jekyll_tools/_config.yml b/doc/jekyll_tools/_config.yml deleted file mode 100644 index b9a8a09d7..000000000 --- a/doc/jekyll_tools/_config.yml +++ /dev/null @@ -1,18 +0,0 @@ -name: igraph – the network analysis package -destination: jekyll_output -future: true -include: [ _static, _images ] -exclude: [ source, Gemfile, Gemfile.lock, build_old_sources.py ] -keep_files: [ ] -markdown: kramdown -kramdown: - input: GFM -url: "https://igraph.org/python" -plugins: - - jekyll-sitemap -defaults: - - - scope: - path: "" - values: - layout: "post" diff --git a/doc/jekyll_tools/_includes/defaults b/doc/jekyll_tools/_includes/defaults deleted file mode 100644 index 42baf8c90..000000000 --- a/doc/jekyll_tools/_includes/defaults +++ /dev/null @@ -1,16 +0,0 @@ -{% assign lang = "python" %} -{%- assign bodyclass = lang %} -{% assign title = page.title %} -{% assign mainheader = page.mainheader %} -{% assign lead = page.lead %} - -{% assign langname = 'python-igraph' %} -{% assign langversions = version | split: ", " %} -{% if title == nil %}{% assign title = 'python-igraph' %}{% endif %} -{% assign extramenu = '
  • Get started
  • ' %} -{% if mainheader == nil %} - {% assign mainheader = 'Get started with python-igraph' %} -{% endif %} -{% if lead == nil %} - {% assign lead = 'Install and start using igraph from Python' %} -{% endif %} diff --git a/doc/jekyll_tools/_layouts/default.html b/doc/jekyll_tools/_layouts/default.html deleted file mode 100644 index d74c2b8b1..000000000 --- a/doc/jekyll_tools/_layouts/default.html +++ /dev/null @@ -1,156 +0,0 @@ -{% include defaults %} - - - - - - - - - - - - - - {{ title }} - - - - - - - - - - - - - - - - - - - - {{ page.extrahead | default: layout.extrahead }} - - - -
    - - - {% if page.layout != "main" %} - -
    -
    -

    {{ page.mainheader | default: layout.mainheader }}

    -

    {{ page.lead | default: layout.lead }}

    -
    - -
    - - {% endif %} - - {{content}} - - - - -
    - - - - - - - - - -{% if page.animated_header or layout.animated_header %} - - -{% endif %} - - diff --git a/doc/jekyll_tools/_layouts/main.html b/doc/jekyll_tools/_layouts/main.html deleted file mode 100644 index 42c90e4f6..000000000 --- a/doc/jekyll_tools/_layouts/main.html +++ /dev/null @@ -1,75 +0,0 @@ ---- -layout: default -bodyclass: start-page -animated_header: true ---- - -
    -
    -

    igraph – - The network analysis package -

    -

    - igraph is a collection of network analysis tools with the - emphasis on efficiency, - portability and ease of use. igraph is - open source and free. igraph can be - programmed in R, Python, - Mathematica and C/C++. -

    -
    - igraph R package - python-igraph - IGraph/M - igraph C library -
    - -
    - -
    -
    -
    - -
    - -
    -
    - - - - {% for post in site.posts limit:10 %} - -
    -

    -   - {{ post.title }} -

    -
    -
    - - {{ post.content | extract_excerpt: post.url | redir_docs | smallheaders }} - -
    - - {% endfor %} - -

    All news →

    - -
    -
    -
    - -
    diff --git a/doc/jekyll_tools/_layouts/pydoctor.html b/doc/jekyll_tools/_layouts/pydoctor.html deleted file mode 100644 index e70459159..000000000 --- a/doc/jekyll_tools/_layouts/pydoctor.html +++ /dev/null @@ -1,18 +0,0 @@ ---- -layout: default -extrahead: -vmenu: true -doctype: api/ ---- - -
    -
    -
    -
    - - {{ content }} - -
    -
    -
    -
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border-left-width: 1px; - border-left-style: solid; -} - -#splitTables > table tr td:nth-child(1), .fieldTable tr td:nth-child(1) { - border-left: none; - width: 150px; -} - -#splitTables > table tr td:nth-child(2), .fieldTable tr td.fieldArg { - width: 200px; -} - -tr.package { - background-color: #fff3e0; -} - -tr.module { - background-color: #fff8e1; -} - -tr.class, tr.classvariable, tr.baseclassvariable { - background-color: #fffde7; -} - -tr.instancevariable, tr.baseinstancevariable, tr.variable, tr.attribute, tr.property { - background-color: #f3e5f5; -} - -tr.interface { - background-color: #fbe9e7; -} - -tr.method, tr.function, tr.basemethod, tr.baseclassmethod, tr.classmethod { - background-color: #f1f8e9; -} - -tr.private { - background-color: #f1f1f1; -} - -.fieldTable { - margin-top: 10px; -} - -.fieldName { - font-weight: bold; -} - - -#childList > div { - margin: 10px; - padding: 10px; - padding-bottom: 5px; -} - -.functionBody { - margin-left: 15px; -} - -.functionBody > #part { - font-style: italic; -} - -.functionBody > #part > a { - text-decoration: none; -} - -.functionBody .interfaceinfo { - font-style: italic; - margin-bottom: 3px; -} - -.functionBody > .undocumented { - - margin-top: 6px; - margin-bottom: 6px; -} - -/* -- Links to class/function/etc names are nested like this: - label - This applies to inline docstring content marked up as code, - for example L{foo} in epytext or `bar` in restructuredtext, - but also to links that are present in summary tables. -- 'functionHeader' is used for lines like `def func():` and `var =` -*/ -code, .pre, #childList > div .functionHeader, -#splitTables > table tr td:nth-child(2), .fieldTable tr td.fieldArg { - font-family: Menlo, Monaco, Consolas, "Courier New", monospace; -} -code, #childList > div .functionHeader, .fieldTable tr td.fieldArg { - font-size: 90%; - color: #222222; -} -code > a { - color:#c7254e; - background-color:#f9f2f4; -} -/* top navagation bar */ -.page-header > h1 { - margin-top: 0; -} -.page-header > h1 > code { - color: #971c3a; -} - -/* -This defines the code style, it's black on light gray. -It also overwrite the default values inherited from bootstrap min -*/ -code { - padding:2px 4px; - background-color: #f4f4f4; - border-radius:4px -} - - -a.functionSourceLink { - font-weight: normal; -} - - -#childList > div { - border-left-color: #03a9f4; - border-left-width: 1px; - border-left-style: solid; - background: #fafafa; -} - -.moduleDocstring { - margin: 20px; -} - -#partOf { - margin-top: -13px; - margin-bottom: 19px; -} - -.fromInitPy { - font-style: italic; -} - -pre { - padding-left: 0px; -} - -/* Private stuff */ - -body.private-hidden #splitTables .private, -body.private-hidden #childList .private, -body.private-hidden #summaryTree .private { - /* changed because we don't want to hide members that pydoctor considers - * private; currently igraph._igraph.GraphBase is private according to - * pydoctor because of the underscore */ - /* display: none; */ -} - -#showPrivate { - padding: 10px; -} - -#current-docs-container { - font-style: italic; - padding-top: 11px; -} - -/* Deprecation stuff */ - -.deprecationNotice { - margin: 10px; -} - -/* Syntax highlighting for source code */ - -.py-string { - color: #337ab7; -} -.py-comment { - color: #309078; - font-style: italic; -} -.py-keyword { - font-weight: bold; -} -.py-defname { - color: #a947b8; - font-weight: bold; -} -.py-builtin { - color: #fc7844; - font-weight: bold; -} - -/* Doctest */ - -pre.py-doctest { - padding: .5em; -} -.py-prompt, .py-more { - color: #a8a8a8; -} -.py-output { - color: #c7254e; -} - -/* Admonitions */ - -div.rst-admonition p.rst-admonition-title:after { - content: ":"; -} - -div.rst-admonition p.rst-admonition-title { - margin: 0; - padding: 0.1em 0 0.35em 0em; - font-weight: bold; -} - -div.rst-admonition p.rst-admonition-title { - color: #333333; -} - -div.rst-admonition { - padding: 8px; - margin-bottom: 20px; - background-color: #EEE; - border: 1px solid #CCC; - border-radius: 4px; -} - -div.warning, div.attention, div.danger, div.error, div.caution { - background-color: #ffcf9cb0; - border: 1px solid #ffbbaa; -} - -div.danger p.rst-admonition-title, div.error p.rst-admonition-title, div.caution p.rst-admonition-title { - color: #b94a48; -} - -div.tip p.rst-admonition-title, div.hint p.rst-admonition-title, div.important p.rst-admonition-title{ - color: #3a87ad; -} - -div.tip, div.hint, div.important { - background-color: #d9edf7; - border-color: #bce8f1; -} - - -/* igraph-specific customizations follow from here */ - -.pydoctor-navbar { - display: none; -} - -table.fieldTable tr td { - vertical-align: baseline; -} - -.moduleDocstring { - margin: 20px 0; -} - -.page-header h1 { - font-size: 24px; -} -.categoryHeader { - font-size: 18px !important; - padding: 0 0 0 8px; -} -#showPrivate { - display: none; -} -.undocumented { - font-style: normal !important; -} - - diff --git a/doc/jekyll_tools/css/syntax.css 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