.. image:: https://github.com/matthiaskoenig/pkpdbib/raw/develop/docs/images/favicon/pkpdbib-100x100-300dpi.png
:align: left
:alt: pkpdbib logo
pkpdbib: python utilities for metadata and COMBINE archives
==============================================================
|icon1| |icon2| |icon3| |icon4| |icon5| |icon6| |icon7|
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:alt: GitHub Actions CI/CD Status
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:target: https://pypi.org/project/pkpdbib/
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.. |icon4| image:: https://img.shields.io/pypi/l/pkpdbib.svg
:target: http://opensource.org/licenses/LGPL-3.0
:alt: GNU Lesser General Public License 3
.. |icon5| image:: https://zenodo.org/badge/10.5281/zenodo.11076700.svg
:target: https://doi.org/10.5281/zenodo.11076700
:alt: Zenodo DOI
.. |icon6| image:: https://img.shields.io/badge/code%20style-black-000000.svg
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pkpdbib is a collection of python utilities for working with
pharmacokinetics/pharmacodynamics (PK/PD) literature with source code available from
`https://github.com/matthiaskoenig/pkpdbib <https://github.com/matthiaskoenig/pkpdbib>`__.
If you have any questions or issues please `open an issue <https://github.com/matthiaskoenig/pkpdbib/issues>`__.
How to cite
===========
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.11076700.svg
:target: https://doi.org/10.5281/zenodo.11076700
:alt: Zenodo DOI
Contributing
============
Contributions are always welcome!
License
=======
* Source Code: `LGPLv3 <http://opensource.org/licenses/LGPL-3.0>`__
* Documentation: `CC BY-SA 4.0 <http://creativecommons.org/licenses/by-sa/4.0/>`__
The pkpdbib source is released under both the GPL and LGPL licenses version 2 or
later. You may choose which license you choose to use the software under.
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License or the GNU Lesser General Public
License as published by the Free Software Foundation, either version 2 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.
Funding
=======
Matthias König (MK) was supported by the Federal Ministry of Education and Research
(BMBF, Germany) within the research network Systems Medicine of the Liver
(**LiSyM**, grant number 031L0054). MK is supported by the Federal Ministry of
Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and
by the German Research Foundation (DFG) within the Research Unit Program FOR 5151
QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection
- A Systems Medicine Approach) by grant number 436883643 and by grant number
465194077 (Priority Programme SPP 2311, Subproject SimLivA).
Installation
============
`pkpdbib` is available from `pypi <https://pypi.python.org/pypi/pkpdbib>`__ and
can be installed via::
pip install pkpdbib
Develop version
---------------
The latest develop version can be installed via::
pip install git+https://github.com/matthiaskoenig/pkpdbib.git@develop
Or via cloning the repository and installing via::
git clone https://github.com/matthiaskoenig/pkpdbib.git
cd pkpdbib
pip install -e .
To install for development use::
pip install -e .[development]
Documentation
=============
Retrieve PDFs via Sci-hub
- Open the zotero library, select items without PDF attachment, right click -> Export items -> CSV -> <substance>.csv
Run script from `src/pkdb_literature/scihub.tools`::
scihub_pdfs -z <substance>.csv
© 2021-2024 Matthias König
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