A framework to rerun text mining tools on the latest publications
Project description
=========
PubRunner
=========
|pypi| |build-status| |coverage| |docs| |license|
.. |pypi| image:: https://img.shields.io/pypi/v/pubrunner.svg
:target: https://pypi.python.org/pypi/pubrunner
:alt: PyPI Release
.. |build-status| image:: https://travis-ci.org/jakelever/pubrunner.svg?branch=master
:target: https://travis-ci.org/jakelever/pubrunner
:alt: Travis CI status
.. |coverage| image:: https://coveralls.io/repos/github/jakelever/pubrunner/badge.svg?branch=master
:target: https://coveralls.io/github/jakelever/pubrunner?branch=master
:alt: Coverage status
.. |docs| image:: https://readthedocs.org/projects/pubrunner/badge/?version=stable
:target: http://pubrunner.readthedocs.io/en/stable/
:alt: Documentation status
.. |license| image:: https://img.shields.io/badge/License-MIT-blue.svg
:target: https://opensource.org/licenses/MIT
:alt: MIT license
PubRunner is a framework to keep text mining tools running on the latest publications.
Installation
------------
PubRunner uses Python3 and can be installed via `pip`_ from `PyPI`_::
$ pip install pubrunner
Usage
-----
To run Pubrunner, you just need to provide it with a path to a biomedical text mining tool (e.g. a Github repo or a local directory). The flag --test tells Pubrunner to execute the test set. Omitting that gets Pubrunner to run the tool on the full corpus (which for Ab3P is PubMed).::
$ pubrunner --test https://github.com/jakelever/Ab3P
Is PubRunner for me?
--------------------
Are you a biomedical text mining tool developer? Then likely yes. PubRunner makes it easy to run a text mining tool across PubMed and keep it working!
Examples
--------
Check out the `examples directory`_ to see a small number of projects that use PubRunner on Pubmed.
Documentation
--------
Documentation including a tutorial can be found at the `readthedocs`_ page.
Contributing
------------
Contributions are very welcome.
License
-------
Distributed under the terms of the `MIT`_ license, "pubrunner" is free and open source software
Issues
------
If you encounter any problems, please `file an issue`_ along with a detailed description.
.. _`readthedocs`: http://pubrunner.readthedocs.io/en/stable/
.. _`MIT`: http://opensource.org/licenses/MIT
.. _`file an issue`: https://github.com/jakelever/pubrunner/issues
.. _`pip`: https://pypi.python.org/pypi/pip/
.. _`PyPI`: https://pypi.python.org/pypi
.. _`examples directory`: https://github.com/jakelever/pubrunner/tree/master/examples
PubRunner
=========
|pypi| |build-status| |coverage| |docs| |license|
.. |pypi| image:: https://img.shields.io/pypi/v/pubrunner.svg
:target: https://pypi.python.org/pypi/pubrunner
:alt: PyPI Release
.. |build-status| image:: https://travis-ci.org/jakelever/pubrunner.svg?branch=master
:target: https://travis-ci.org/jakelever/pubrunner
:alt: Travis CI status
.. |coverage| image:: https://coveralls.io/repos/github/jakelever/pubrunner/badge.svg?branch=master
:target: https://coveralls.io/github/jakelever/pubrunner?branch=master
:alt: Coverage status
.. |docs| image:: https://readthedocs.org/projects/pubrunner/badge/?version=stable
:target: http://pubrunner.readthedocs.io/en/stable/
:alt: Documentation status
.. |license| image:: https://img.shields.io/badge/License-MIT-blue.svg
:target: https://opensource.org/licenses/MIT
:alt: MIT license
PubRunner is a framework to keep text mining tools running on the latest publications.
Installation
------------
PubRunner uses Python3 and can be installed via `pip`_ from `PyPI`_::
$ pip install pubrunner
Usage
-----
To run Pubrunner, you just need to provide it with a path to a biomedical text mining tool (e.g. a Github repo or a local directory). The flag --test tells Pubrunner to execute the test set. Omitting that gets Pubrunner to run the tool on the full corpus (which for Ab3P is PubMed).::
$ pubrunner --test https://github.com/jakelever/Ab3P
Is PubRunner for me?
--------------------
Are you a biomedical text mining tool developer? Then likely yes. PubRunner makes it easy to run a text mining tool across PubMed and keep it working!
Examples
--------
Check out the `examples directory`_ to see a small number of projects that use PubRunner on Pubmed.
Documentation
--------
Documentation including a tutorial can be found at the `readthedocs`_ page.
Contributing
------------
Contributions are very welcome.
License
-------
Distributed under the terms of the `MIT`_ license, "pubrunner" is free and open source software
Issues
------
If you encounter any problems, please `file an issue`_ along with a detailed description.
.. _`readthedocs`: http://pubrunner.readthedocs.io/en/stable/
.. _`MIT`: http://opensource.org/licenses/MIT
.. _`file an issue`: https://github.com/jakelever/pubrunner/issues
.. _`pip`: https://pypi.python.org/pypi/pip/
.. _`PyPI`: https://pypi.python.org/pypi
.. _`examples directory`: https://github.com/jakelever/pubrunner/tree/master/examples
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