Metadata-Version: 2.1
Name: fbc-curation
Version: 0.1.6
Summary: FBC reference files for SBML model curation.
Home-page: https://github.com/matthiaskoenig/fbc_curation
Author: Matthias Koenig
Author-email: konigmatt@googlemail.com
Maintainer: Matthias Koenig
Maintainer-email: konigmatt@googlemail.com
License: LGPL-3.0
Download-URL: https://pypi.org/project/fbc-curation
Project-URL: Source Code, https://github.com/matthiaskoenig/fbc_curation
Project-URL: Documentation, https://github.com/matthiaskoenig/fbc_curation
Project-URL: Bug Tracker, https://github.com/matthiaskoenig/fbc_curation/issues
Description: fbc_curation
        =============
        
        .. image:: https://github.com/matthiaskoenig/sbmlsim/workflows/CI-CD/badge.svg
           :target: https://github.com/matthiaskoenig/fbc_curation/workflows/CI-CD
           :alt: GitHub Actions CI/CD Status
        
        .. image:: https://img.shields.io/pypi/v/fbc-curation.svg
           :target: https://pypi.org/project/fbc_curation/
           :alt: Current PyPI Version
        
        .. image:: https://img.shields.io/pypi/pyversions/fbc-curation.svg
           :target: https://pypi.org/project/fbc_curation/
           :alt: Supported Python Versions
        
        .. image:: https://img.shields.io/pypi/l/fbc-curation.svg
           :target: http://opensource.org/licenses/LGPL-3.0
           :alt: GNU Lesser General Public License 3
        
        .. image:: https://readthedocs.org/projects/fbc_curation/badge/?version=latest
           :target: https://fbc-curation.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
        .. image:: https://codecov.io/gh/matthiaskoenig/fbc_curation/branch/develop/graph/badge.svg
           :target: https://codecov.io/gh/matthiaskoenig/fbc_curation
           :alt: Codecov
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3708271.svg
           :target: https://doi.org/10.5281/zenodo.3708271
           :alt: Zenodo DOI
        
        .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
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        ``fbc_curation``: Reproducibility of constraint-based models
        available from 
        `https://github.com/matthiaskoenig/fbc_curation <https://github.com/matthiaskoenig/fbc_curation>`_.
        
        This repository creates standardized reference files for a given FBC model based on cobrapy and glpk. These files can be used in the model curation process for validating the model behavior. The format of the standardized reference files is described below. 
        Currently two separate implementations of the reference files are included in the package:
        
        * ``cobrapy`` based on COBRApy (Constraint-Based Reconstruction and Analysis in Python) available from `https://github.com/opencobra/cobrapy <https://github.com/opencobra/cobrapy>`_
        * ``cameo`` based on Cameo (Cameo—Computer Aided Metabolic Engineering and Optimization) available from `https://github.com/biosustain/cameo <https://github.com/biosustain/cameo>`_
        
        
        ``fbc_curation`` is a python package which can be included in python applications. In addition a command line tool is provided which allows easy usage outside of python.
        
        The documentation is available on `https://fbc-curation.readthedocs.io <https://fbc-curation.readthedocs.io>`__.
        If you have any questions or issues please `open an issue <https://github.com/matthiaskoenig/fbc_curation/issues>`__.
        
        
        Documentation
        ==============
        .. image:: https://readthedocs.org/projects/fbc_curation/badge/?version=latest
           :target: https://fbc-curation.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
        The documentation is available on `https://fbc-curation.readthedocs.io <https://fbc-curation.readthedocs.io>`__.
        
        
        How to cite
        ===========
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3708271.svg
           :target: https://doi.org/10.5281/zenodo.3597770
           :alt: Zenodo DOI
        
        Installation
        ============
        ``fbc_curation`` is available from `pypi <https://pypi.python.org/pypi/fbc-curation>`__ and
        can be installed via::
        
            pip install fbc-curation
        
        
        Develop version
        ---------------
        The latest develop version can be installed via::
        
            pip install git+https://github.com/matthiaskoenig/fbc-curation.git@develop
        
        Or via cloning the repository and installing via::
        
            git clone https://github.com/matthiaskoenig/fbc_curation.git
            cd fbc_curation
            pip install -e .
        
        To install for development use::
        
            pip install -e .[development]
            
        Testing
        --------
        To run the tests clone the repository::
        
            git clone https://github.com/matthiaskoenig/fbc_curation.git
            cd fbc_curation
            pip install -e .
            pytest
        
        
        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 ``fbc_curation`` 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 is supported by the Federal Ministry of Education and Research (BMBF, Germany)
        within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054).
        
        
        © 2020 Matthias König
        
Keywords: modeling,reproducibility,SBML,fbc
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: development
