grakelx 0.1.12__tar.gz

grakelx-0.1.12/LICENSE

@@ -0,0 +1,32 @@
+New BSD License
+
+Copyright (c) 2018- The grakel developers.
+All rights reserved.
+
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  a. Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+  b. Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+  c. Neither the name of the Scikit-learn Developers  nor the names of
+     its contributors may be used to endorse or promote products
+     derived from this software without specific prior written
+     permission. 
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+

grakelx-0.1.12/MANIFEST.in

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+include README.md
+include LICENSE
+
+include grakelx/kernels/_c_functions/*.pxd
+include grakelx/kernels/_c_functions/*.pyx
+recursive-include grakelx/kernels/_c_functions/include *
+recursive-include grakelx/kernels/_c_functions/src *
+
+recursive-include grakelx/kernels/_isomorphism/bliss-0.50 *
+include grakelx/kernels/_isomorphism/__init__.py
+include grakelx/kernels/_isomorphism/bliss.pyx
+include grakelx/kernels/_isomorphism/intpyblissmodule_2.cc
+include grakelx/kernels/_isomorphism/intpyblissmodule_3.cc
+include grakelx/kernels/_isomorphism/bliss.cpp
+prune grakelx/kernels/_isomorphism/__pycache__
+global-exclude *.so
+global-exclude __pycache__
+
+recursive-include tests/data/Cuneiform *
+recursive-include tests/data/MUTAG *
+
+include doc/*.rst
+include doc/conf.py
+include doc/Makefile
+include doc/make.bat
+recursive-include doc/documentation *
+recursive-include doc/benchmarks *
+recursive-include doc/_static *
+recursive-include doc/_templates *
+recursive-include doc/kernels *
+recursive-include doc/sphinxext *
+recursive-include examples *

grakelx-0.1.12/PKG-INFO

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+Metadata-Version: 2.4
+Name: grakelx
+Version: 0.1.12
+Summary: A scikit-learn compatible library for graph kernels
+Author-email: Ioannis Siglidis <y.siglidis@gmail.com>, Shaheen Acheche <neoshaheen@gmail.com>
+License: BSD-3-Clause
+Project-URL: Documentation, https://ysig.github.io/GraKeL/
+Project-URL: Homepage, https://github.com/SneachChea/GraKelX
+Project-URL: Repository, https://github.com/SneachChea/GraKelX
+Project-URL: Source Code, https://github.com/SneachChea/GraKelX
+Project-URL: Issue Tracker, https://github.com/SneachChea/GraKelX/issues
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Requires-Python: <4.0,>=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23.0
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: scipy>=1.8.0
+Requires-Dist: six>=1.11.0
+Requires-Dist: future>=0.16.0
+Requires-Dist: joblib
+Provides-Extra: lovasz
+Requires-Dist: cvxopt>=1.2.0; extra == "lovasz"
+Provides-Extra: io
+Requires-Dist: networkx<4,>=3; extra == "io"
+Requires-Dist: pandas; extra == "io"
+Provides-Extra: torch
+Requires-Dist: torch; extra == "torch"
+Requires-Dist: torch-geometric; extra == "torch"
+Provides-Extra: examples
+Requires-Dist: nltk; extra == "examples"
+Requires-Dist: networkx<4,>=3; extra == "examples"
+Provides-Extra: tutorials
+Requires-Dist: matplotlib; extra == "tutorials"
+Requires-Dist: nltk; extra == "tutorials"
+Requires-Dist: networkx<4,>=3; extra == "tutorials"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: sphinx-gallery; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
+Dynamic: license-file
+
+<p align="center">
+  <img width="50%" src="https://raw.githubusercontent.com/ysig/GraKeL/0.1a7/doc/_figures/logo.svg?sanitize=true" />
+</p>
+
+--------------------------------------------------------------------------------
+
+> [!NOTE]
+> **grakelx** is an independent fork of [GraKeL](https://github.com/ysig/GraKeL) by Siglidis, Nikolentzos, Limnios, Giatsidis, Skianis, and Vazirgiannis,
+> originally published in JMLR 2020. This fork continues maintenance and development under the **BSD 3-clause** license.
+> See [LICENSE](LICENSE) and the [Acknowledgements](#acknowledgements) section below.
+
+[![Pypi Versions](https://img.shields.io/pypi/pyversions/grakel.svg)](https://pypi.org/pypi/grakelx/)
+
+**[Upstream Documentation](https://ysig.github.io/GraKeL/)** | **[Paper](http://jmlr.org/papers/volume21/18-370/18-370.pdf)**
+
+*grakelx* is a library that provides implementations of several well-established graph kernels. The library unifies these kernels into a common framework. Furthermore, it provides implementations of some frameworks that work on top of graph kernels. Specifically, grakelx contains 16 kernels and 3 frameworks. The library is compatible with the [scikit-learn](http://scikit-learn.org/) pipeline allowing easy and fast integration inside machine learning algorithms.
+
+--------------------------------------------------------------------------------
+
+In detail, the following kernels and frameworks are currently implemented:
+
+* **[Vertex histogram kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.VertexHistogram.html)**
+* **[Edge histogram kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.EdgeHistogram.html)**
+* **[Shortest path kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.ShortestPath.html)** from Borgwardt and Kriegel: [Shortest-path kernels on graphs](https://www.dbs.ifi.lmu.de/~borgward/papers/BorKri05.pdf) (ICDM 2005)
+* **[Graphlet kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.GraphletSampling.html)** from Shervashidze *et al.*: [Efficient graphlet kernels for large graph comparison](http://proceedings.mlr.press/v5/shervashidze09a/shervashidze09a.pdf) (AISTATS 2009)
+* **[Random walk kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.RandomWalk.html)** from Vishwanathan *et al.*: [Graph Kernels](http://www.jmlr.org/papers/volume11/vishwanathan10a/vishwanathan10a.pdf) (JMLR 11(Apr))
+* **[Neighborhood hash graph kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.NeighborhoodHash.html)** from Hido and Kashima: [A Linear-time Graph Kernel](https://ieeexplore.ieee.org/abstract/document/5360243) (ICDM 2009)
+* **[Weisfeiler-Lehman framework](https://ysig.github.io/GraKeL/latest/generated/grakel.WeisfeilerLehman.html)** from Shervashidze *et al.*: [Weisfeiler-Lehman Graph Kernels](http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf) (JMLR 12(Sep))
+* **[Neighborhood subgraph pairwise distance kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.NeighborhoodSubgraphPairwiseDistance.html)** from Costa and De Grave: [Fast Neighborhood Subgraph Pairwise Distance Kernel](https://pdfs.semanticscholar.org/7a10/f6a406b664d1159e7c4fefbdd6ac275aee53.pdf) (ICML 2010)
+* **[Lovasz-theta kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.LovaszTheta.html)** from Johansson *et al.*: [Global graph kernels using geometric embeddings](http://proceedings.mlr.press/v32/johansson14.pdf) (ICML 2014)
+* **[SVM-theta kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.SvmTheta.html)** from Johansson *et al.*: [Global graph kernels using geometric embeddings](http://proceedings.mlr.press/v32/johansson14.pdf) (ICML 2014)
+* **[Ordered decompositional DAG kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.OddSth.html)** from Da San Martino *et al.*: [A Tree-Based Kernel for Graphs](https://pdfs.semanticscholar.org/69ee/18dd7a214d4d656b5b95742212f050dabeac.pdf) (SDM 2012)
+* **[GraphHopper kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.GraphHopper.html)** from Feragen *et al.*: [Scalable kernels for graphs with continuous attributes](https://papers.nips.cc/paper/5155-scalable-kernels-for-graphs-with-continuous-attributes.pdf) (NIPS 2013)
+* **[Propagation kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.Propagation.html)** from Neumann *et al.*: [Propagation kernels: efficient graph kernels from propagated information](https://link.springer.com/content/pdf/10.1007/s10994-015-5517-9.pdf) (Machine Learning 102(2))
+* **[Pyramid match kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.PyramidMatch.html)** from Nikolentzos *et al.*: [Matching Node Embeddings for Graph Similarity](https://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/view/14494/14426) (AAAI 2017)
+* **[Subgraph matching kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.SubgraphMatching.html)** from Kriege and Mutzel: [Subgraph Matching Kernels for Attributed Graphs](https://arxiv.org/ftp/arxiv/papers/1206/1206.6483.pdf) (ICML 2012)
+* **[Multiscale Laplacian kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.MultiscaleLaplacian.html)** from Kondor and Pan: [The Multiscale Laplacian Graph Kernel](https://papers.nips.cc/paper/6135-the-multiscale-laplacian-graph-kernel.pdf) (NIPS 2016)
+* **[Core framework](https://ysig.github.io/GraKeL/latest/generated/grakel.CoreFramework.html)** from Nikolentzos *et al.*: [A Degeneracy Framework for Graph Similarity](https://www.ijcai.org/proceedings/2018/0360.pdf) (IJCAI 2018)
+* **[Weisfeiler-Lehman optimal assignment kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.WeisfeilerLehmanOptimalAssignment.html)** from Kriege *et al.*: [On Valid Optimal Assignment Kernels and Applications to Graph Classification](http://papers.nips.cc/paper/6166-on-valid-optimal-assignment-kernels-and-applications-to-graph-classification.pdf) (NIPS 2016)
+
+--------------------------------------------------------------------------------
+
+To learn how to install and use grakelx, and to find out more about the implemented kernels and frameworks, please read our [documentation](https://ysig.github.io/GraKeL/). To learn about the functionality of the library and about example applications, check out our [examples](https://github.com/SneachChea/GraKelX/tree/master/examples) in the `examples/` directory.
+
+In case you find a bug, please open an [issue](https://github.com/SneachChea/GraKelX/issues). To propose a new kernel, you can open a [feature request](https://github.com/SneachChea/GraKelX/issues).
+
+## Installation
+
+grakelx requires the following packages to be installed:
+
+* Python (>=3.10)
+* NumPy (>=1.23.0)
+* SciPy (>=1.8.0)
+* Cython (>=0.29.36)
+* cvxopt (>=1.2.0) [optional]
+* future (>=0.16.0)
+
+To install the package, run:
+
+```sh
+pip install grakelx
+```
+
+For local development with uv:
+
+```sh
+uv sync --group test
+uv run python setup.py build_ext --inplace
+uv run pre-commit install
+```
+
+## Running tests
+
+To test the package, execute:
+
+```sh
+uv run pytest
+```
+
+## Running examples
+
+```
+cd examples
+python shortest_path.py
+```
+
+## Cite
+
+If you use grakelx in a scientific publication, please cite the original GraKeL paper (<http://jmlr.org/papers/volume21/18-370/18-370.pdf>):
+
+```bibtex
+@article{JMLR:v21:18-370,
+  author  = {Giannis Siglidis and Giannis Nikolentzos and Stratis Limnios and Christos Giatsidis and Konstantinos Skianis and Michalis Vazirgiannis},
+  title   = {GraKeL: A Graph Kernel Library in Python},
+  journal = {Journal of Machine Learning Research},
+  year    = {2020},
+  volume  = {21},
+  number  = {54},
+  pages   = {1-5}
+}
+```
+
+## License
+
+grakelx is distributed under the **BSD 3-clause** license (same as the original GraKeL). The library makes use of the C++ source code of [BLISS](http://www.tcs.hut.fi/Software/bliss) (a tool for computing automorphism groups and canonical labelings of graphs) which is **LGPL** licensed. Furthermore, the [cvxopt](https://cvxopt.org/) package (a software package for convex optimization) which is an optional dependency of grakelx is **GPL** licensed.
+
+## Acknowledgements
+
+We would like to thank [@eddiebergman](https://github.com/eddiebergman) for modernizing the original GraKeL CI and extending Python support.
+
+This project is a fork of [GraKeL](https://github.com/ysig/GraKeL) by Giannis Siglidis, Giannis Nikolentzos, Stratis Limnios, Christos Giatsidis, Konstantinos Skianis, and Michalis Vazirgiannis, originally published in JMLR 2020 ([paper](http://jmlr.org/papers/volume21/18-370/18-370.pdf)). The original copyright holders are the GraKeL developers. All modifications and additions in this fork are released under the same **BSD 3-clause** license.

grakelx-0.1.12/README.md

@@ -0,0 +1,111 @@
+<p align="center">
+  <img width="50%" src="https://raw.githubusercontent.com/ysig/GraKeL/0.1a7/doc/_figures/logo.svg?sanitize=true" />
+</p>
+
+--------------------------------------------------------------------------------
+
+> [!NOTE]
+> **grakelx** is an independent fork of [GraKeL](https://github.com/ysig/GraKeL) by Siglidis, Nikolentzos, Limnios, Giatsidis, Skianis, and Vazirgiannis,
+> originally published in JMLR 2020. This fork continues maintenance and development under the **BSD 3-clause** license.
+> See [LICENSE](LICENSE) and the [Acknowledgements](#acknowledgements) section below.
+
+[![Pypi Versions](https://img.shields.io/pypi/pyversions/grakel.svg)](https://pypi.org/pypi/grakelx/)
+
+**[Upstream Documentation](https://ysig.github.io/GraKeL/)** | **[Paper](http://jmlr.org/papers/volume21/18-370/18-370.pdf)**
+
+*grakelx* is a library that provides implementations of several well-established graph kernels. The library unifies these kernels into a common framework. Furthermore, it provides implementations of some frameworks that work on top of graph kernels. Specifically, grakelx contains 16 kernels and 3 frameworks. The library is compatible with the [scikit-learn](http://scikit-learn.org/) pipeline allowing easy and fast integration inside machine learning algorithms.
+
+--------------------------------------------------------------------------------
+
+In detail, the following kernels and frameworks are currently implemented:
+
+* **[Vertex histogram kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.VertexHistogram.html)**
+* **[Edge histogram kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.EdgeHistogram.html)**
+* **[Shortest path kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.ShortestPath.html)** from Borgwardt and Kriegel: [Shortest-path kernels on graphs](https://www.dbs.ifi.lmu.de/~borgward/papers/BorKri05.pdf) (ICDM 2005)
+* **[Graphlet kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.GraphletSampling.html)** from Shervashidze *et al.*: [Efficient graphlet kernels for large graph comparison](http://proceedings.mlr.press/v5/shervashidze09a/shervashidze09a.pdf) (AISTATS 2009)
+* **[Random walk kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.RandomWalk.html)** from Vishwanathan *et al.*: [Graph Kernels](http://www.jmlr.org/papers/volume11/vishwanathan10a/vishwanathan10a.pdf) (JMLR 11(Apr))
+* **[Neighborhood hash graph kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.NeighborhoodHash.html)** from Hido and Kashima: [A Linear-time Graph Kernel](https://ieeexplore.ieee.org/abstract/document/5360243) (ICDM 2009)
+* **[Weisfeiler-Lehman framework](https://ysig.github.io/GraKeL/latest/generated/grakel.WeisfeilerLehman.html)** from Shervashidze *et al.*: [Weisfeiler-Lehman Graph Kernels](http://www.jmlr.org/papers/volume12/shervashidze11a/shervashidze11a.pdf) (JMLR 12(Sep))
+* **[Neighborhood subgraph pairwise distance kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.NeighborhoodSubgraphPairwiseDistance.html)** from Costa and De Grave: [Fast Neighborhood Subgraph Pairwise Distance Kernel](https://pdfs.semanticscholar.org/7a10/f6a406b664d1159e7c4fefbdd6ac275aee53.pdf) (ICML 2010)
+* **[Lovasz-theta kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.LovaszTheta.html)** from Johansson *et al.*: [Global graph kernels using geometric embeddings](http://proceedings.mlr.press/v32/johansson14.pdf) (ICML 2014)
+* **[SVM-theta kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.SvmTheta.html)** from Johansson *et al.*: [Global graph kernels using geometric embeddings](http://proceedings.mlr.press/v32/johansson14.pdf) (ICML 2014)
+* **[Ordered decompositional DAG kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.OddSth.html)** from Da San Martino *et al.*: [A Tree-Based Kernel for Graphs](https://pdfs.semanticscholar.org/69ee/18dd7a214d4d656b5b95742212f050dabeac.pdf) (SDM 2012)
+* **[GraphHopper kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.GraphHopper.html)** from Feragen *et al.*: [Scalable kernels for graphs with continuous attributes](https://papers.nips.cc/paper/5155-scalable-kernels-for-graphs-with-continuous-attributes.pdf) (NIPS 2013)
+* **[Propagation kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.Propagation.html)** from Neumann *et al.*: [Propagation kernels: efficient graph kernels from propagated information](https://link.springer.com/content/pdf/10.1007/s10994-015-5517-9.pdf) (Machine Learning 102(2))
+* **[Pyramid match kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.PyramidMatch.html)** from Nikolentzos *et al.*: [Matching Node Embeddings for Graph Similarity](https://www.aaai.org/ocs/index.php/AAAI/AAAI17/paper/view/14494/14426) (AAAI 2017)
+* **[Subgraph matching kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.SubgraphMatching.html)** from Kriege and Mutzel: [Subgraph Matching Kernels for Attributed Graphs](https://arxiv.org/ftp/arxiv/papers/1206/1206.6483.pdf) (ICML 2012)
+* **[Multiscale Laplacian kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.MultiscaleLaplacian.html)** from Kondor and Pan: [The Multiscale Laplacian Graph Kernel](https://papers.nips.cc/paper/6135-the-multiscale-laplacian-graph-kernel.pdf) (NIPS 2016)
+* **[Core framework](https://ysig.github.io/GraKeL/latest/generated/grakel.CoreFramework.html)** from Nikolentzos *et al.*: [A Degeneracy Framework for Graph Similarity](https://www.ijcai.org/proceedings/2018/0360.pdf) (IJCAI 2018)
+* **[Weisfeiler-Lehman optimal assignment kernel](https://ysig.github.io/GraKeL/latest/generated/grakel.WeisfeilerLehmanOptimalAssignment.html)** from Kriege *et al.*: [On Valid Optimal Assignment Kernels and Applications to Graph Classification](http://papers.nips.cc/paper/6166-on-valid-optimal-assignment-kernels-and-applications-to-graph-classification.pdf) (NIPS 2016)
+
+--------------------------------------------------------------------------------
+
+To learn how to install and use grakelx, and to find out more about the implemented kernels and frameworks, please read our [documentation](https://ysig.github.io/GraKeL/). To learn about the functionality of the library and about example applications, check out our [examples](https://github.com/SneachChea/GraKelX/tree/master/examples) in the `examples/` directory.
+
+In case you find a bug, please open an [issue](https://github.com/SneachChea/GraKelX/issues). To propose a new kernel, you can open a [feature request](https://github.com/SneachChea/GraKelX/issues).
+
+## Installation
+
+grakelx requires the following packages to be installed:
+
+* Python (>=3.10)
+* NumPy (>=1.23.0)
+* SciPy (>=1.8.0)
+* Cython (>=0.29.36)
+* cvxopt (>=1.2.0) [optional]
+* future (>=0.16.0)
+
+To install the package, run:
+
+```sh
+pip install grakelx
+```
+
+For local development with uv:
+
+```sh
+uv sync --group test
+uv run python setup.py build_ext --inplace
+uv run pre-commit install
+```
+
+## Running tests
+
+To test the package, execute:
+
+```sh
+uv run pytest
+```
+
+## Running examples
+
+```
+cd examples
+python shortest_path.py
+```
+
+## Cite
+
+If you use grakelx in a scientific publication, please cite the original GraKeL paper (<http://jmlr.org/papers/volume21/18-370/18-370.pdf>):
+
+```bibtex
+@article{JMLR:v21:18-370,
+  author  = {Giannis Siglidis and Giannis Nikolentzos and Stratis Limnios and Christos Giatsidis and Konstantinos Skianis and Michalis Vazirgiannis},
+  title   = {GraKeL: A Graph Kernel Library in Python},
+  journal = {Journal of Machine Learning Research},
+  year    = {2020},
+  volume  = {21},
+  number  = {54},
+  pages   = {1-5}
+}
+```
+
+## License
+
+grakelx is distributed under the **BSD 3-clause** license (same as the original GraKeL). The library makes use of the C++ source code of [BLISS](http://www.tcs.hut.fi/Software/bliss) (a tool for computing automorphism groups and canonical labelings of graphs) which is **LGPL** licensed. Furthermore, the [cvxopt](https://cvxopt.org/) package (a software package for convex optimization) which is an optional dependency of grakelx is **GPL** licensed.
+
+## Acknowledgements
+
+We would like to thank [@eddiebergman](https://github.com/eddiebergman) for modernizing the original GraKeL CI and extending Python support.
+
+This project is a fork of [GraKeL](https://github.com/ysig/GraKeL) by Giannis Siglidis, Giannis Nikolentzos, Stratis Limnios, Christos Giatsidis, Konstantinos Skianis, and Michalis Vazirgiannis, originally published in JMLR 2020 ([paper](http://jmlr.org/papers/volume21/18-370/18-370.pdf)). The original copyright holders are the GraKeL developers. All modifications and additions in this fork are released under the same **BSD 3-clause** license.

grakelx-0.1.12/doc/.special.rst

@@ -0,0 +1,42 @@
+.. Color profiles for Sphinx.
+.. Has to be used with hacks.css (bitbucket.org/lbesson/web-sphinx/src/master/.static/hacks.css)
+.. role:: black
+.. role:: gray
+.. role:: grey
+.. role:: silver
+.. role:: white
+.. role:: maroon
+.. role:: red
+.. role:: magenta
+.. role:: fuchsia
+.. role:: pink
+.. role:: orange
+.. role:: yellow
+.. role:: lime
+.. role:: green
+.. role:: olive
+.. role:: teal
+.. role:: cyan
+.. role:: aqua
+.. role:: blue
+.. role:: navy
+.. role:: purple
+
+.. role:: under
+.. role:: over
+.. role:: blink
+.. role:: line
+.. role:: strike
+
+.. role:: it
+.. role:: ob
+
+.. role:: small
+.. role:: large
+
+.. role:: center
+.. role:: left
+.. role:: right
+
+
+.. (c) Lilian Besson, 2011-2016, https://bitbucket.org/lbesson/web-sphinx/

grakelx-0.1.12/doc/Makefile

@@ -0,0 +1,184 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> 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 "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@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)/*
+	-rm -rf auto_examples/
+	-rm -rf generated/*
+	-rm -rf modules/generated/*
+
+html:
+	# These two lines make the build a bit more lengthy, and the
+	# the embedding of images more robust
+	rm -rf $(BUILDDIR)/html/_images
+	#rm -rf _build/doctrees/
+	$(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/project-template.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/project-template.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/project-template"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/project-template"
+	@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."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@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."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+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."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."