grakel-dev 0.1a5

# GraKeL: A library for graph kernels

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**grakel** is a library compatible with the project of [scikit-learn](http://scikit-learn.org/)

Installing grakel
=================

The grakel library requires:

* Python [>=2.7, >= 3.5]
* NumPy [>= 1.8.2]
* SciPy [>= 0.13.3]
* Cython [>= 0.27.3]
* cvxopt [>= 1.2.0] [optional: lovasz]
* future [>=0.16.0] (for python 2.7)

For installing dependencies the procedure is the well known:
```shell
(sudo) pip install extension>=extension_version
```
depending on if `pip` has superuser privilages.

To install the *development-version* of the module execute:
```shell
$ (sudo) pip install grakel-dev
```

Usage
=====
To learn how to use the GraKeL api **as a user**, please read the [documentation][doc] on sections *Introduction* and *A longer introduction*
(in case your are full of curiosity).

Testing
=======
In order for the following to work you first need to build the package cython extension
locally by executing:
```shell
$ python setup.py build_ext -i
```

To test the package, execute:
```shell
$ nosetests
```

for executing unit_tests or use a testing-interface for testing the `kernel` module:
```shell
$ python grakel/tests/test_kernels.py --help
usage: test_kernels.py [-h] [--verbose] [--problematic] [--slow]
[--ignore_warnings] [--dataset DATASET] [--normalize]
[--develop | --all | --main]

A test file for all kernels

optional arguments:
-h, --help show this help message and exit
--verbose print kernels with their outputs on stdout
--problematic allow execution of problematic test cases in development
--slow allow execution of slow test cases in development
--ignore_warnings ignore warnings produced by kernel executions
--dataset DATASET chose the datset you want the tests to be executed
--normalize normalize the kernel output
--develop execute only tests connected with current development
--all execute all tests
--main execute the main tests [default]

```

for testing `graph_kernels`:
```shell
$ python grakel/tests/test_graph_kernel.py --help
usage: test_graph_kernels.py [-h] [--verbose] [--problematic] [--slow]
[--normalize] [--ignore_warnings]
[--dataset DATASET] [--develop | --all | --main]

A test file for all kernels

optional arguments:
-h, --help show this help message and exit
--verbose print kernels with their outputs on stdout
--problematic allow execution of problematic test cases in development
--slow allow execution of slow test cases in development
--normalize normalize the kernel output
--ignore_warnings ignore warnings produced by kernel executions
--dataset DATASET chose the datset you want the tests to be executed
--develop execute only tests connected with current development
--all execute all tests
--main execute the main tests [default]

```

and for testing the `Graph` class:
```shell
$ python grakel/tests/test_graph.py --help
usage: test_graph.py [-h] [--verbose] [--ignore_warnings]

A test file for all `Graph` type objects

optional arguments:
-h, --help show this help message and exit
--verbose verbose outputs on stdout
--ignore_warnings ignore warnings produced by kernel executions
```
You can also execute the kernel test locally through a *test-main-function* as
```shell
$ python -m grakel.tests
```

Contributing
============
For learning how to integrate your own kernel, please read section *Write your own kernel* inside
the package [documentation][doc].
For contributing to the GraKeL project, please read section *contributing* inside the package [documentation][doc].

[doc]: https://ysig.github.io/GraKeL/dev/

Citation
========
If you use GraKeL in a scientific publication, please cite our paper:
```
@article{siglidis2018grakel,
title={GraKeL: A Graph Kernel Library in Python},
author={Siglidis, Giannis and Nikolentzos, Giannis and Limnios, Stratis and Giatsidis, Christos and Skianis, Konstantinos and Vazirgiannis, Michalis},
journal={arXiv preprint arXiv:1806.02193},
year={2018}
}
```