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leidenalg-0.10.2/ 0000775 0000000 0000000 00000000000 14553441322 0013521 5 ustar 00root root 0000000 0000000 leidenalg-0.10.2/.gitattributes 0000664 0000000 0000000 00000000051 14553441322 0016410 0 ustar 00root root 0000000 0000000 * text=auto
src/_version.py export-subst
leidenalg-0.10.2/.github/ 0000775 0000000 0000000 00000000000 14553441322 0015061 5 ustar 00root root 0000000 0000000 leidenalg-0.10.2/.github/dependabot.yml 0000664 0000000 0000000 00000000166 14553441322 0017714 0 ustar 00root root 0000000 0000000 version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "weekly"
leidenalg-0.10.2/.github/workflows/ 0000775 0000000 0000000 00000000000 14553441322 0017116 5 ustar 00root root 0000000 0000000 leidenalg-0.10.2/.github/workflows/build.yml 0000664 0000000 0000000 00000022032 14553441322 0020737 0 ustar 00root root 0000000 0000000 name: Build and test, upload to PyPI on release
on:
push:
branches:
- master
- '*'
tags:
- '*'
pull_request:
branches:
- master
env:
CIBW_TEST_REQUIRES: ddt
CIBW_TEST_COMMAND: "cd {project} && python -m unittest -v"
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_SKIP: "cp36-*"
MACOSX_DEPLOYMENT_TARGET: "10.9"
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]
steps:
- uses: actions/checkout@v4
with:
submodules: true
fetch-depth: 0
- uses: actions/setup-python@v5
name: Install Python
with:
python-version: '3.8'
- name: Build wheels (manylinux)
uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_BEFORE_BUILD: "yum install -y flex bison &&
pip install cmake wheel &&
{package}/scripts/build_igraph.sh &&
{package}/scripts/build_libleidenalg.sh "
CIBW_ARCHS_LINUX: ${{ matrix.wheel_arch }}
CIBW_BUILD: "*-manylinux_${{ matrix.wheel_arch }}"
CIBW_ENVIRONMENT: >
CFLAGS='-I/project/build-deps/install/include/ -L/project/build-deps/install/lib64/ -L/project/build-deps/install/lib/'
LD_LIBRARY_PATH='/project/build-deps/install/lib64/:/project/build-deps/install/lib/'
- name: Build wheels (musllinux)
uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_BEFORE_BUILD: "apk add flex bison zlib-dev &&
pip install cmake wheel &&
{package}/scripts/build_igraph.sh &&
{package}/scripts/build_libleidenalg.sh"
CIBW_BUILD: "*-musllinux_${{ matrix.wheel_arch }}"
CIBW_TEST_EXTRAS: "test-musl"
CIBW_ENVIRONMENT: >
CFLAGS='-I/project/build-deps/install/include/ -L/project/build-deps/install/lib64/ -L/project/build-deps/install/lib/'
LD_LIBRARY_PATH='/project/build-deps/install/lib64/:/project/build-deps/install/lib/'
- uses: actions/upload-artifact@v4
with:
name: wheels-linux-${{ matrix.wheel_arch }}
path: ./wheelhouse/*.whl
build_wheel_linux_aarch64:
name: Build wheels on Linux (aarch64)
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v4
with:
submodules: true
fetch-depth: 0
- name: Set up QEMU
id: qemu
uses: docker/setup-qemu-action@v3
- name: Build wheels (manylinux)
uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_BEFORE_BUILD: "yum install -y flex bison zlib-devel &&
pip install cmake wheel &&
{package}/scripts/build_igraph.sh &&
{package}/scripts/build_libleidenalg.sh"
CIBW_ARCHS_LINUX: aarch64
CIBW_BUILD: "*-manylinux_aarch64"
CIBW_ENVIRONMENT: >
CFLAGS='-I/project/build-deps/install/include/ -L/project/build-deps/install/lib64/ -L/project/build-deps/install/lib/'
LD_LIBRARY_PATH='/project/build-deps/install/lib64/:/project/build-deps/install/lib/'
- uses: actions/upload-artifact@v4
with:
name: wheels-linux-aarch64
path: ./wheelhouse/*.whl
build_wheel_macos:
name: Build wheels on macOS (${{ matrix.wheel_arch }})
runs-on: macos-latest
env:
LLVM_VERSION: "14.0.5"
strategy:
matrix:
include:
- cmake_arch: x86_64
wheel_arch: x86_64
- cmake_arch: arm64
extra_cmake_args: -DF2C_EXTERNAL_ARITH_HEADER=../../../etc/arith_apple_m1.h -DIEEE754_DOUBLE_ENDIANNESS_MATCHES=ON
wheel_arch: arm64
steps:
- uses: actions/checkout@v4
with:
submodules: true
fetch-depth: 0
- name: Cache installed C core
id: cache-c-core
uses: actions/cache@v3
with:
path: build-deps
key: C-core-cache-${{ runner.os }}-${{ matrix.cmake_arch }}-llvm${{ env.LLVM_VERSION }}-${{ hashFiles('scripts/build_igraph.sh') }}-${{ hashFiles('scripts/build_libleidenalg.sh') }}
- uses: actions/setup-python@v5
name: Install Python
with:
python-version: '3.8'
- name: Install OS dependencies
if: steps.cache-c-core.outputs.cache-hit != 'true' || steps.cache-c-deps.outputs.cache-hit != 'true' # Only needed when building the C core
run:
brew install ninja cmake
- name: Build wheels
uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_ARCHS_MACOS: "${{ matrix.wheel_arch }}"
CIBW_BEFORE_BUILD: "{package}/scripts/build_igraph.sh &&
{package}/scripts/build_libleidenalg.sh"
CIBW_ENVIRONMENT: >
CFLAGS='-Wno-unused-command-line-argument -I/Users/runner/work/leidenalg/leidenalg/build-deps/install/include/ -L/Users/runner/work/leidenalg/leidenalg/build-deps/install/lib64/ -L/Users/runner/work/leidenalg/leidenalg/build-deps/install/lib/'
REPAIR_LIBRARY_PATH="${DYLD_LIBRARY_PATH}:/Users/runner/work/leidenalg/leidenalg/build-deps/install/lib64/:/Users/runner/work/leidenalg/leidenalg/build-deps/install/lib/"
EXTRA_CMAKE_ARGS="-DCMAKE_OSX_ARCHITECTURES=${{ matrix.cmake_arch }} ${{ matrix.extra_cmake_args }}"
CIBW_REPAIR_WHEEL_COMMAND: >
DYLD_LIBRARY_PATH=$REPAIR_LIBRARY_PATH delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}
- uses: actions/upload-artifact@v4
with:
name: wheels-macos-${{ matrix.wheel_arch }}
path: ./wheelhouse/*.whl
build_wheel_win:
name: Build wheels on Windows (${{ matrix.cmake_arch }})
runs-on: windows-2022
strategy:
fail-fast: false
matrix:
include:
- cmake_arch: Win32
wheel_arch: win32
- cmake_arch: x64
wheel_arch: win_amd64
steps:
- uses: actions/checkout@v4
with:
submodules: true
fetch-depth: 0
- uses: actions/setup-python@v5
name: Install Python
with:
python-version: '3.8'
- name: Cache installed C core
id: cache-c-core
uses: actions/cache@v3
with:
path: build-deps
key: C-core-cache-${{ runner.os }}-${{ matrix.cmake_arch }}-llvm${{ env.LLVM_VERSION }}-${{ hashFiles('scripts/build_igraph.sh') }}-${{ hashFiles('scripts/build_libleidenalg.sh') }}
- name: Install build dependencies
if: steps.cache-c-core.outputs.cache-hit != 'true' # Only needed when building the C core
run: choco install winflexbison3 cmake ninja
- name: Build wheels
uses: pypa/cibuildwheel@v2.16.2
env:
CIBW_BEFORE_BUILD: "{package}/scripts/build_igraph.bat &&
{package}/scripts/build_libleidenalg.bat &&
pip install delvewheel"
CIBW_BUILD: "*-${{ matrix.wheel_arch }}"
CIBW_TEST_COMMAND: "cd /d {project} && python -m unittest -v"
CIBW_SKIP: "cp36-* pp*"
CIBW_ENVIRONMENT: >
LIB="D:/a/leidenalg/leidenalg/build-deps/install/lib;$LIB"
INCLUDE="D:/a/leidenalg/leidenalg/build-deps/install/include/;$INCLUDE"
PATH="D:/a/leidenalg/leidenalg/build-deps/install/bin;$PATH"
EXTRA_CMAKE_ARGS="-A ${{ matrix.cmake_arch }}"
CIBW_REPAIR_WHEEL_COMMAND: "delvewheel repair -w {dest_dir} {wheel}"
- uses: actions/upload-artifact@v4
with:
name: wheels-win-${{ matrix.wheel_arch }}
path: ./wheelhouse/*.whl
build_sdist:
name: Build sdist
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
submodules: true
fetch-depth: 0
- uses: actions/setup-python@v5
name: Install Python
with:
python-version: '3.8'
- name: Install pypa/build
run: pip3 install build
- name: Build sdist
run: |
python3 -m build --sdist
- uses: actions/upload-artifact@v4
with:
name: wheels-sdist
path: dist/*.tar.gz
upload_pypi:
needs: [build_wheel_linux, build_wheel_linux_aarch64, build_wheel_macos, build_wheel_win, build_sdist]
runs-on: ubuntu-latest
# upload to PyPI on every push from the master branch
if: github.event_name == 'push' &&
startsWith(github.ref, 'refs/tags')
steps:
- uses: actions/download-artifact@v4
with:
pattern: wheels-*
merge-multiple: true
path: dist
# Upload tagged versions to production PyPI
- name: Publish distribution 📦 to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
password: ${{ secrets.PYPI_API_TOKEN }} leidenalg-0.10.2/.gitignore 0000664 0000000 0000000 00000000741 14553441322 0015513 0 ustar 00root root 0000000 0000000 MANIFEST
build/
dist/
lib/
nbproject/
leidenalg.egg-info/
wlib/
bin/
obj/
Makefile
*.log
**/*.o
**/*.so
**/*.pyc
files.txt
files_py3.txt
callgrind*
main.cpp
leiden-dists.zip
leidenalg.cbp
leidenalg.depend
leidenalg.layout
leiden.log
igraphcore/
**/*.swp
valgrind-python.supp
test/
test_install.sh
massif*
.vscode/
*.code-workspace
PACKAGE.txt
vendor/source/igraph
vendor/source/install
vendor/install
src/leidenalg/version.py
pip-wheel-metadata
.eggs/
doc/source/_build
build-deps
leidenalg-0.10.2/.gitmodules 0000664 0000000 0000000 00000000000 14553441322 0015664 0 ustar 00root root 0000000 0000000 leidenalg-0.10.2/.readthedocs.yml 0000664 0000000 0000000 00000001166 14553441322 0016613 0 ustar 00root root 0000000 0000000 # .readthedocs.yml
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
# Required
version: 2
conda:
environment: build-doc.yml
# Optionally build your docs in additional formats such as PDF and ePub
formats: all
# Optionally set the version of Python and requirements required to build your docs
build:
os: ubuntu-22.04
tools:
python: "mambaforge-4.10"
python:
install:
- method: pip
path: .
submodules:
include: all
recursive: true
# Build documentation in the doc/source directory with Sphinx
sphinx:
configuration: doc/source/conf.py leidenalg-0.10.2/CHANGELOG 0000664 0000000 0000000 00000005402 14553441322 0014734 0 ustar 00root root 0000000 0000000 0.10.2
- Also allow python-igraph >= 0.11
- Upgrade C core to 0.10.8 for binary wheels
0.10.1
- Switched to pyproject.toml based build
- Making use of Limited API
- Make available aarch64 wheels
0.10.0
- Changed default refinement to consider a random neighbouring community.
- Changed C++ core into external library at https://github.com/vtraag/libleidenalg.
0.9.1
- Allow node sizes to be float (PR #115)
- Added correct_self_loops argument to CPMVertexPartition
0.9.0
- Update C core to 0.10.1
0.8.10
- Fixed installation from source package (issue #101)
0.8.9
- Fixed bug with renaming of python-igraph to igraph (issue #93)
- Removed irrelevant node_sizes argument for RBConfigurationVertexPartition and ModularityVertexPartition
- Improved documentation
0.8.8
- Corrected relabeling bug (PR #82)
- Improved error handling, avoiding some crashses (issue #81)
0.8.7
- Improved numerical stability
0.8.6
- Removed accidentally left DEBUG statement
0.8.5
- Corrected iterating over nodes (PR #70).
- Fixed segfault with move_nodes_constrained (issue #68)
- Fixed problem with initial_membership (issue #66)
0.8.4
- Update C core to 0.9.1
- Fixed caching problem (issue #62)
- Fixed missing node_sizes for modularity (issue #60)
0.8.3
- Fixed missing parameter in find_partition_multiplex by @TomKellyGenetics (PR #50)
0.8.2
- New option to constrain community size by @orenbenkiki (PR #46)
- Great performance improvement by @ragibson (PR #40)
- Minor improvements and clarifications
0.8.1
- Fixed performance problem (issue #35)
- Improved documentation
0.8.0
- New option to keep some nodes "fixed" by @iosonofabio (PR #8, #9)
- Corrected bipartite clustering
- Corrected some documentation
- Several minor bugfixes
0.6.1
- Minor corrections to documentation
- Added doctest to examples in documentation
- Removed trailing semicolons throughout code
- Corrected some errors in CPMVertexPartition.Bipartite
0.6.0
- Major API changes, now exposing actual classes and optimisation routine.
- Improved algorithm, now runs faster and finds better solutions.
- Improved error handling, doing more type checking.
- Improved documentation throughout, now done using Sphinx and available from
readthedocs.org.
- Now includes testing module, available through python setup.py test.
0.5.3
- Fixed bug concerning weights (were rounded to integers).
- Improved documentation.
- Included an HOWTO on extending the current package.
- Fixed some minor bugs.
0.5.2
- Ensured that random neighbour selection works in O(1) rather than O(k), with
k the average number of neighbours.
- Optimized the calculation of weight from/to community.
- Included some missing references.
0.5.1
Corrected some mistakes which prevented it from being properly used on PyPi.
No serious changes were made.
0.5
Initial release
leidenalg-0.10.2/LICENSE 0000664 0000000 0000000 00000104505 14553441322 0014533 0 ustar 00root root 0000000 0000000 GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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.
leidenalg-0.10.2/MANIFEST 0000664 0000000 0000000 00000001427 14553441322 0014656 0 ustar 00root root 0000000 0000000 # file GENERATED by distutils, do NOT edit
LICENSE
README.md
setup.py
include/CPMVertexPartition.h
include/GraphHelper.h
include/LinearResolutionParameterVertexPartition.h
include/ModularityVertexPartition.h
include/MutableVertexPartition.h
include/Optimiser.h
include/RBConfigurationVertexPartition.h
include/RBERVertexPartition.h
include/SignificanceVertexPartition.h
include/SurpriseVertexPartition.h
include/pynterface.h
src/CPMVertexPartition.cpp
src/GraphHelper.cpp
src/LinearResolutionParameterVertexPartition.cpp
src/ModularityVertexPartition.cpp
src/MutableVertexPartition.cpp
src/Optimiser.cpp
src/RBConfigurationVertexPartition.cpp
src/RBERVertexPartition.cpp
src/SignificanceVertexPartition.cpp
src/SurpriseVertexPartition.cpp
src/__init__.py
src/functions.py
src/pynterface.cpp
leidenalg-0.10.2/MANIFEST.in 0000664 0000000 0000000 00000000334 14553441322 0015257 0 ustar 00root root 0000000 0000000 include LICENSE
include CHANGELOG
include README.rst
include pyproject.toml
include include/
include MANIFEST.in
include tests/*.py
exclude .git*
exclude *.yml
exclude release*
prune .github
graft vendor/source/igraph
leidenalg-0.10.2/README.rst 0000664 0000000 0000000 00000021562 14553441322 0015216 0 ustar 00root root 0000000 0000000 leidenalg
==============
This package implements the Leiden algorithm in ``C++`` and exposes it to
``python``. It relies on ``(python-)igraph`` for it to function. Besides the
relative flexibility of the implementation, it also scales well, and can be run
on graphs of millions of nodes (as long as they can fit in memory). The core
function is ``find_partition`` which finds the optimal partition using the
Leiden algorithm [1]_, which is an extension of the Louvain algorithm [2]_ for a
number of different methods. The methods currently implemented are (1)
modularity [3]_, (2) Reichardt and Bornholdt's model using the configuration
null model and the Erdös-Rényi null model [4]_, (3) the Constant Potts model
(CPM) [5]_, (4) Significance [6]_, and finally (5) Surprise [7]_. In addition,
it supports multiplex partition optimisation allowing community detection on for
example negative links [8]_ or multiple time slices [9]_. There is the
possibility of only partially optimising a partition, so that some community
assignments remain fixed [10]_. It also provides some support for community
detection on bipartite graphs. See the `documentation
`_ for more information.
.. image:: https://readthedocs.org/projects/leidenalg/badge
:target: http://leidenalg.readthedocs.io/en/latest/
:alt: Leiden documentation status
.. image:: https://github.com/vtraag/leidenalg/actions/workflows/build.yml/badge.svg?branch=master
:target: https://github.com/vtraag/leidenalg/actions/workflows/build.yml
:alt: Leiden build status (GitHub Actions)
.. image:: https://zenodo.org/badge/146722095.svg
:target: https://zenodo.org/badge/latestdoi/146722095
:alt: DOI
.. image:: https://anaconda.org/conda-forge/leidenalg/badges/version.svg
:target: https://anaconda.org/conda-forge/leidenalg
:alt: Anaconda (conda-forge)
Installation
------------
In short: ``pip install leidenalg``. All major platforms are supported on
Python>=3.6, earlier versions of Python are no longer supported. Alternatively,
you can install from Anaconda (channel ``conda-forge``).
For Unix like systems it is possible to install from source. For Windows this is
more complicated, and you are recommended to use the binary wheels. This Python
interface depends on the C++ package ``libleidenalg`` which in turn depends on
``igraph``. You will need to build these packages yourself before you are able
to build this Python interface.
Make sure you have all necessary tools for compilation. In Ubuntu this can be
installed using ``sudo apt-get install build-essential autoconf automake flex
bison``, please refer to the documentation for your specific system. Make sure
that not only ``gcc`` is installed, but also ``g++``, as the ``leidenalg``
package is programmed in ``C++``. Note that there are build scripts included in
the ``scripts/`` directory. These are also used to build the binary wheels.
1. Compile (and install) the C core of ``igraph`` (version >= 0.10). You can use
the file ``build_igraph.sh`` (on Unix-like systems) or ``build_igraph.bat``
(on Windows) in the ``scripts/`` directory to do this. For more details, see
https://igraph.org/c/doc/igraph-Installation.html.
2. Compile (and install) the C core of ``libleidenalg`` (version >= 0.10). You
can use the file ``build_libleidenalg.sh`` (on Unix-like systems) or
``build_libleidenalg.bat`` (on Windows) in the ``scripts/`` directory to do
this. For more details, see https://github.com/vtraag/libleidenalg.
3. Build the Python interface using ``python setup.py build`` and ``python
setup.py install``, or use ``pip install .``
You can check if all went well by running a variety of tests using ``python -m
unittest``.
Troubleshooting
---------------
In case of any problems, best to start over with a clean environment. Make sure
you remove the ``igraph`` and ``leidenalg`` package completely. Then, do a
complete reinstall starting from ``pip install leidenalg``. In case you
installed from source, and built the C libraries of ``igraph`` and
``libleidenalg`` yourself, remove them completely and rebuild and reinstall
them.
Usage
-----
This is the Python interface for the C++ package ``libleidenalg``. There are no
plans at the moment for developing an R interface to the package. However, there
have been various efforts to port the package to R. These typically do not offer
all available functionality or have some other limitations, but nonetheless may
be very useful. The available ports are:
- https://github.com/cole-trapnell-lab/leidenbase
- https://github.com/TomKellyGenetics/leiden
- https://github.com/kharchenkolab/leidenAlg
Please refer to the documentation for more details
on function calls and parameters.
This implementation is made for flexibility, but ``igraph`` nowadays also
includes an implementation of the Leiden algorithm internally. That
implementation is less flexible: the implementation only works on undirected
graphs, and only CPM and modularity are supported. It is likely to be
substantially faster though.
Just to get you started, below the essential parts.
To start, make sure to import the packages:
>>> import leidenalg
>>> import igraph as ig
We'll create a random graph for testing purposes:
>>> G = ig.Graph.Erdos_Renyi(100, 0.1);
For simply finding a partition use:
>>> part = leidenalg.find_partition(G, leidenalg.ModularityVertexPartition);
Contribute
----------
Source code: https://github.com/vtraag/leidenalg
Issue tracking: https://github.com/vtraag/leidenalg/issues
See the documentation on `Implementation` for more details on how to
contribute new methods.
References
----------
Please cite the references appropriately in case they are used.
.. [1] Traag, V.A., Waltman. L., Van Eck, N.-J. (2018). From Louvain to
Leiden: guaranteeing well-connected communities. Scientific reports, 9(1), 5233.
`10.1038/s41598-019-41695-z `_
.. [2] Blondel, V. D., Guillaume, J.-L., Lambiotte, R., & Lefebvre, E. (2008).
Fast unfolding of communities in large networks. Journal of Statistical
Mechanics: Theory and Experiment, 10008(10), 6.
`10.1088/1742-5468/2008/10/P10008 `_
.. [3] Newman, M. E. J., & Girvan, M. (2004). Finding and evaluating community
structure in networks. Physical Review E, 69(2), 026113.
`10.1103/PhysRevE.69.026113 `_
.. [4] Reichardt, J., & Bornholdt, S. (2006). Statistical mechanics of
community detection. Physical Review E, 74(1), 016110.
`10.1103/PhysRevE.74.016110 `_
.. [5] Traag, V. A., Van Dooren, P., & Nesterov, Y. (2011). Narrow scope for
resolution-limit-free community detection. Physical Review E, 84(1),
016114. `10.1103/PhysRevE.84.016114
`_
.. [6] Traag, V. A., Krings, G., & Van Dooren, P. (2013). Significant scales in
community structure. Scientific Reports, 3, 2930. `10.1038/srep02930
`_
.. [7] Traag, V. A., Aldecoa, R., & Delvenne, J.-C. (2015). Detecting
communities using asymptotical surprise. Physical Review E, 92(2),
022816. `10.1103/PhysRevE.92.022816
`_
.. [8] Traag, V. A., & Bruggeman, J. (2009). Community detection in networks
with positive and negative links. Physical Review E, 80(3), 036115.
`10.1103/PhysRevE.80.036115
`_
.. [9] Mucha, P. J., Richardson, T., Macon, K., Porter, M. A., & Onnela, J.-P.
(2010). Community structure in time-dependent, multiscale, and multiplex
networks. Science, 328(5980), 876–8. `10.1126/science.1184819
`_
.. [10] Zanini, F., Berghuis, B. A., Jones, R. C., Robilant, B. N. di,
Nong, R. Y., Norton, J., Clarke, Michael F., Quake, S. R. (2019).
northstar: leveraging cell atlases to identify healthy and neoplastic
cells in transcriptomes from human tumors. BioRxiv, 820928.
`10.1101/820928 `_
Licence
-------
Copyright (C) 2020 V.A. Traag
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with
this program. If not, see http://www.gnu.org/licenses/.
leidenalg-0.10.2/build-doc.yml 0000664 0000000 0000000 00000000332 14553441322 0016104 0 ustar 00root root 0000000 0000000 name: build-doc
channels:
- conda-forge
dependencies:
- python
- igraph>=0.10,<0.11
- libleidenalg>=0.11,<0.12
- python-igraph>=0.10,<0.11
- ddt
- sphinx
- sphinx_rtd_theme
- flex
- bison
- cmake
leidenalg-0.10.2/doc/ 0000775 0000000 0000000 00000000000 14553441322 0014266 5 ustar 00root root 0000000 0000000 leidenalg-0.10.2/doc/source/ 0000775 0000000 0000000 00000000000 14553441322 0015566 5 ustar 00root root 0000000 0000000 leidenalg-0.10.2/doc/source/advanced.rst 0000664 0000000 0000000 00000026263 14553441322 0020076 0 ustar 00root root 0000000 0000000 Advanced
========
The basic interface explained in the :ref:`Introduction` should provide you
enough to start detecting communities. However, perhaps you want to improve the
partitions further or want to do some more advanced analysis. In this section,
we will explain this in more detail.
Optimiser
---------
Although the package provides simple access to the function
:func:`~leidenalg.find_partition`, there is actually an underlying
:class:`~leidenalg.Optimiser` class that is doing the actual work. We can also
explicitly construct an :class:`~leidenalg.Optimiser` object:
>>> optimiser = la.Optimiser()
The function :func:`~leidenalg.find_partition` then does nothing else then
calling :func:`~leidenalg.Optimiser.optimise_partition` on the provided
partition.
.. testsetup::
G = ig.Graph.Erdos_Renyi(100, p=5./100)
partition = la.CPMVertexPartition(G)
>>> diff = optimiser.optimise_partition(partition)
:func:`~leidenalg.Optimiser.optimise_partition` simply tries to improve any
provided partition. We can thus try to repeatedly call
:func:`~leidenalg.Optimiser.optimise_partition` to keep on improving the current
partition:
>>> G = ig.Graph.Erdos_Renyi(100, p=5./100)
>>> partition = la.ModularityVertexPartition(G)
>>> diff = 1
>>> while diff > 0:
... diff = optimiser.optimise_partition(partition)
Even if a call to :func:`~leidenalg.Optimiser.optimise_partition` did not improve
the current partition, it is still possible that a next call will improve the
partition. Of course, if the current partition is already optimal, this will
never happen, but it is not possible to decide whether a partition is optimal.
This functionality of repeating multiple iterations is actually already
built-in. You can simply call
>>> diff = optimiser.optimise_partition(partition, n_iterations=10)
If ``n_iterations < 0`` the optimiser continues iterating until it encounters
an iterations that did not improve the partition.
The :func:`~leidenalg.Optimiser.optimise_partition` itself is built on two other
basic algorithms: :func:`~leidenalg.Optimiser.move_nodes` and
:func:`~leidenalg.Optimiser.merge_nodes`. You can also call these functions
yourself. For example:
>>> diff = optimiser.move_nodes(partition)
or
>>> diff = optimiser.merge_nodes(partition)
The simpler Louvain algorithm aggregates the partition and repeats the
:func:`~leidenalg.Optimiser.move_nodes` on the aggregated partition. We can easily
emulate that:
>>> partition = la.ModularityVertexPartition(G)
>>> while optimiser.move_nodes(partition) > 0:
... partition = partition.aggregate_partition()
This summarises the whole Louvain algorithm in just three lines of code.
Although this finds the final aggregate partition, it leaves unclear the actual
partition on the level of the individual nodes. In order to do that, we need to
update the membership based on the aggregate partition, for which we use the
function
:func:`~leidenalg.VertexPartition.MutableVertexPartition.from_coarse_partition`.
>>> partition = la.ModularityVertexPartition(G)
>>> partition_agg = partition.aggregate_partition()
>>> while optimiser.move_nodes(partition_agg) > 0:
... partition.from_coarse_partition(partition_agg)
... partition_agg = partition_agg.aggregate_partition()
Now ``partition_agg`` contains the aggregate partition and ``partition``
contains the actual partition of the original graph ``G``. Of course,
``partition_agg.quality() == partition.quality()`` (save some rounding).
Instead of :func:`~leidenalg.Optimiser.move_nodes`, you could also use
:func:`~leidenalg.Optimiser.merge_nodes`. These functions depend on choosing
particular alternative communities: the documentation of the functions provides
more detail.
One possibility is that rather than aggregating the partition based on the
current partition, you can first refine the partition and then aggregate it.
This is what is done in the Leiden algorithm, and can be done using the functions
:func:`~leidenalg.Optimiser.move_nodes_constrained` and
:func:`~leidenalg.Optimiser.merge_nodes_constrained`. Implementing this, you
end up with the following high-level implementation of the Leiden algorithm:
>>> # Set initial partition
>>> partition = la.ModularityVertexPartition(G)
>>> refined_partition = la.ModularityVertexPartition(G)
>>> partition_agg = refined_partition.aggregate_partition()
>>>
>>> while optimiser.move_nodes(partition_agg):
...
... # Get individual membership for partition
... partition.from_coarse_partition(partition_agg, refined_partition.membership)
...
... # Refine partition
... refined_partition = la.ModularityVertexPartition(G)
... optimiser.merge_nodes_constrained(refined_partition, partition)
...
... # Define aggregate partition on refined partition
... partition_agg = refined_partition.aggregate_partition()
...
... # But use membership of actual partition
... aggregate_membership = [None] * len(refined_partition)
... for i in range(G.vcount()):
... aggregate_membership[refined_partition.membership[i]] = partition.membership[i]
... partition_agg.set_membership(aggregate_membership)
These functions in turn rely on two key functions of the partition:
:func:`~leidenalg.VertexPartition.MutableVertexPartition.diff_move` and
:func:`~leidenalg.VertexPartition.MutableVertexPartition.move_node`. The first
calculates the difference when moving a node, and the latter actually moves the
node, and updates all necessary internal administration. The
:func:`~leidenalg.Optimiser.move_nodes` then does something as follows
>>> for v in G.vs:
... best_comm = max(range(len(partition)),
... key=lambda c: partition.diff_move(v.index, c))
... partition.move_node(v.index, best_comm)
The actual implementation is more complicated, but this gives the general idea.
This package builds on a previous implementation of the Louvain algorithm in
`louvain-igraph `_. To illustrate
the difference between ``louvain-igraph`` and ``leidenalg``, we ran both
algorithms for 10 iterations on a `Youtube network
`_ of more than 1 million
nodes and almost 3 million edges.
.. image:: figures/speed.png
The results are quite clear: Leiden is able to achieve a higher modularity in
less time. It also points out that it is usually a good idea to run Leiden for
at least two iterations; this is also the default setting.
Note that even if the Leiden algorithm did not find any improvement in this
iteration, it is always possible that it will find some improvement in the next
iteration.
Resolution profile
------------------
Some methods accept so-called resolution parameters, such as
:class:`~leidenalg.CPMVertexPartition` or
:class:`~leidenalg.RBConfigurationVertexPartition`. Although some methods may seem
to have some 'natural' resolution, in reality this is often quite arbitrary.
However, the methods implemented here (which depend in a linear way on
resolution parameters) allow for an effective scanning of a full range for the
resolution parameter. In particular, these methods somehow can be formulated as
:math:`Q = E - \gamma N` where :math:`E` and :math:`N` are some other
quantities. In the case for :class:`~leidenalg.CPMVertexPartition` for example,
:math:`E = \sum_c m_c` is the number of internal edges and :math:`N = \sum_c
\binom{n_c}{2}` is the sum of the internal possible edges. The essential
insight for these formulations [1]_ is that if there is an optimal partition
for both :math:`\gamma_1` and :math:`\gamma_2` then the partition is also
optimal for all :math:`\gamma_1 \leq \gamma \leq \gamma_2`.
Such a resolution profile can be constructed using the
:class:`~leidenalg.Optimiser` object.
>>> G = ig.Graph.Famous('Zachary')
>>> optimiser = la.Optimiser()
>>> profile = optimiser.resolution_profile(G, la.CPMVertexPartition,
... resolution_range=(0,1))
Plotting the resolution parameter versus the total number of internal edges we
thus obtain something as follows:
.. image:: figures/resolution_profile.png
Now ``profile`` contains a list of partitions of the specified type
(:class:`~leidenalg.CPMVertexPartition` in this case) for
resolution parameters at which there was a change. In particular,
``profile[i]`` should be better until ``profile[i+1]``, or stated otherwise for
any resolution parameter between ``profile[i].resolution_parameter`` and
``profile[i+1].resolution_parameter`` the partition at position ``i`` should be
better. Of course, there will be some variations because
:func:`~leidenalg.Optimiser.optimise_partition` will find partitions of varying
quality. The change points can then also vary for different runs.
This function repeatedly calls :func:`~leidenalg.Optimiser.optimise_partition`
and can therefore require a lot of time. Especially for resolution parameters
right around a change point there may be many possible partitions, thus
requiring a lot of runs.
Fixed nodes
-----------
For some purposes, it might be beneficial to only update part of a partition.
For example, perhaps we previously already ran the Leiden algorithm on some
dataset, and did some analysis on the resulting partition. If we then gather new
data, and in particular new nodes, it might be useful to keep the previous
community assignments fixed, while only updating the community assignments for
the new nodes. This can be done using the ``is_membership_fixed`` argument of
:func:`~leidenalg.Optimiser.find_partition`, see [2]_ for some details.
For example, suppose we previously detected ``partition`` for graph ``G``, which
was extended to graph ``G2``. Assuming that the previously exiting nodes are
identical, we could create a new partition by doing
>>> new_membership = list(range(G2.vcount()))
... new_membership[:G.vcount()] = partition.membership
We can then only update the community assignments for the new nodes as follows
>>> new_partition = la.CPMVertexPartition(G2, new_membership,
... resolution_parameter=partition.resolution_parameter)
... is_membership_fixed = [i < G.vcount() for i in range(G2.vcount())]
>>> diff = optimiser.optimise_partition(new_partition, is_membership_fixed=is_membership_fixed)
In this example we used :class:`~leidenalg.CPMVertexPartition`. but any other
``VertexPartition`` would work as well.
Maximum community size
----------------------
In some cases, you may want to restrict the community sizes. It is possible to indicate this
by setting the :attr:`~leidenalg.Optimiser.max_comm_size` parameter so that this constraint is
taken into account during optimisation. In addition, it is possible to pass this parameter
directly when using :func:`~leidenalg.find_partition`. For example
>>> partition = la.find_partition(G, la.ModularityVertexPartition, max_comm_size=10)
References
----------
.. [1] Traag, V. A., Krings, G., & Van Dooren, P. (2013). Significant scales in
community structure. Scientific Reports, 3, 2930. `10.1038/srep02930
`_
.. [2] Zanini, F., Berghuis, B. A., Jones, R. C., Robilant, B. N. di,
Nong, R. Y., Norton, J., Clarke, Michael F., Quake, S. R. (2019).
northstar: leveraging cell atlases to identify healthy and neoplastic
cells in transcriptomes from human tumors. BioRxiv, 820928.
`10.1101/820928 `_
leidenalg-0.10.2/doc/source/conf.py 0000664 0000000 0000000 00000024534 14553441322 0017075 0 ustar 00root root 0000000 0000000 # -*- coding: utf-8 -*-
#
# leidenalg documentation build configuration file, created by
# sphinx-quickstart on Fri Oct 21 11:26:44 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
#import sys
#
#sys.path.insert(0, os.path.abspath('.'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.doctest',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.napoleon',
'sphinx.ext.autosectionlabel'
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['.templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The encoding of source files.
#
# source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'leidenalg'
copyright = u'2016, V.A. Traag'
author = u'V.A. Traag'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
from pkg_resources import get_distribution
# The full version, including alpha/beta/rc tags.
release = get_distribution('leidenalg').version
del get_distribution
# The short X.Y version.
version = '.'.join(release.split('.')[:2])
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#
# today = ''
#
# Else, today_fmt is used as the format for a strftime call.
#
# today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = []
# The reST default role (used for this markup: `text`) to use for all
# documents.
#
# default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#
# add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#
# add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
#html_theme = 'classic'
# on_rtd is whether we are on readthedocs.org, this line of code grabbed from docs.readthedocs.org
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
if not on_rtd: # only import and set the theme if we're building docs locally
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
# otherwise, readthedocs.org uses their theme by default, so no need to specify it
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
# html_theme_path = []
# The name for this set of Sphinx documents.
# " v documentation" by default.
#
# html_title = u'leidenalg v0.7.0'
# A shorter title for the navigation bar. Default is the same as html_title.
#
# html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
# html_logo = None
# The name of an image file (relative to this directory) to use as a favicon of
# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
# html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['.static']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#
# html_extra_path = []
# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
# html_last_updated_fmt = None
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#
# html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#
# html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#
# html_additional_pages = {}
# If false, no module index is generated.
#
# html_domain_indices = True
# If false, no index is generated.
#
# html_use_index = True
# If true, the index is split into individual pages for each letter.
#
# html_split_index = False
# If true, links to the reST sources are added to the pages.
#
# html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
# html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#
# html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#
# html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None
# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
#
# html_search_language = 'en'
# A dictionary with options for the search language support, empty by default.
# 'ja' uses this config value.
# 'zh' user can custom change `jieba` dictionary path.
#
# html_search_options = {'type': 'default'}
# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#
# html_search_scorer = 'scorer.js'
# Output file base name for HTML help builder.
htmlhelp_basename = 'leidendoc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'leidenalg.tex', u'leidenalg Documentation',
u'V.A. Traag', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
# latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#
# latex_use_parts = False
# If true, show page references after internal links.
#
# latex_show_pagerefs = False
# If true, show URL addresses after external links.
#
# latex_show_urls = False
# Documents to append as an appendix to all manuals.
#
# latex_appendices = []
# It false, will not define \strong, \code, itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True
# If false, no module index is generated.
#
# latex_domain_indices = True
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'leidenalg', u'leidenalg Documentation',
[author], 1)
]
# If true, show URL addresses after external links.
#
# man_show_urls = False
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'leidenalg', u'leidenalg Documentation',
author, 'leidenalg', 'One line description of project.',
'Miscellaneous'),
]
autoclass_content = 'both'
# Documents to append as an appendix to all manuals.
#
# texinfo_appendices = []
# If false, no module index is generated.
#
# texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False
doctest_global_setup = """
import igraph as ig
import leidenalg as la
"""
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