Metadata-Version: 1.2
Name: memote
Version: 0.11.1
Summary: the genome-scale metabolic model test suite
Home-page: https://github.com/opencobra/memote
Author: Moritz E. Beber
Author-email: morbeb@biosustain.dtu.dk
License: Apache Software License Version 2.0
Download-URL: https://pypi.org/pypi/memote/
Description: ====================================================
        memote - the genome-scale metabolic model test suite
        ====================================================
        
        .. image:: https://img.shields.io/pypi/v/memote.svg
                :target: https://pypi.python.org/pypi/memote
        
        .. image:: https://img.shields.io/travis/opencobra/memote.svg
                :target: https://travis-ci.org/opencobra/memote
        
        .. image:: https://ci.appveyor.com/api/projects/status/github/opencobra/memote?branch=develop&svg=true
                :target: https://ci.appveyor.com/project/cobrapy39491/memote/branch/develop
        
        .. image:: https://readthedocs.org/projects/memote/badge/?version=latest
                :target: https://memote.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        .. image:: https://codecov.io/gh/opencobra/memote/branch/master/graph/badge.svg
                :target: https://codecov.io/gh/opencobra/memote
                :alt: Coverage
        
        .. image:: https://badges.gitter.im/opencobra/memote.svg
                :target: https://gitter.im/opencobra/memote
                :alt: Gitter
        
        .. summary-start
        
        Our goal in promoting this tool is to achieve two major shifts in the metabolic
        model building community:
        
        1. Models should be version-controlled such that changes can be tracked and if
           necessary reverted. Ideally, they should be available through a public
           repository such as GitHub that will allow other researchers to inspect,
           share, and contribute to the model.
        2. Models should, for the benefit of the community and for research gain, live
           up to certain standards and minimal functionality.
        
        The `memote` tool therefore performs four subfunctions:
        
        1. Create a skeleton git repository for the model.
        2. Run the current model through a `test suite that represents the community
           standard`_.
        3. Generate an informative report which details the results of the test suite in
           a visually appealing manner.
        4. (Re-)compute test statistics for an existing version controlled history of
           a metabolic model.
        
        And in order to make this process as easy as possible the generated repository
        can easily be integrated with continuous integration testing providers such as
        Travis CI, which means that anytime you push a model change to GitHub, the test
        suite will be run automatically and a report will be available for you to look
        at via GitHub pages for your repository.
        
        .. _test suite that represents the community    standard: 
          https://github.com/opencobra/memote/wiki/Test-Catalog
        
        .. summary-end
        
        * Documentation: https://memote.readthedocs.io/.
        
        Installation
        ============
        
        **Please Note**: With its
        `retirement on the horizon <https://pythonclock.org>`_ we decided to stop
        testing against Python 2.7,
        and `like many others <https://python3statement.org>`_, want to focus entirely
        on Python 3.
        Hence, we cannot guarantee that `memote` will still function as expected
        on older versions of Python.
        
        Before installing `memote`, make sure that you have correctly installed the
        latest version of `git <https://git-scm.com/>`_.
        
        Moreover, we highly recommend creating a Python virtualenv for your model
        testing purposes.
        
        To install `memote`, run this command in your terminal:
        
        .. code-block:: console
        
            $ pip install memote
        
        This is the preferred method to install `memote`, as it will always install the
        most recent stable release.
        
        .. who-start
        
        Contact
        =======
        
        For comments and questions get in touch via
        
        * our `gitter chatroom <https://gitter.im/opencobra/memote>`_
        * or open a `GitHub issue <https://github.com/opencobra/memote/issues/new>`_.
        
        Are you excited about this project? Consider `contributing
        <https://memote.readthedocs.io/en/latest/contributing.html>`_ by adding novel
        tests, reporting or fixing bugs, and generally help us make this a better
        software for everyone.
        
        Copyright
        =========
        
        * Copyright (c) 2017, Novo Nordisk Foundation Center for Biosustainability,
          Technical University of Denmark.
        * Free software: `Apache Software License 2.0 <LICENSE>`_
        
        .. who-end
        
        Credits
        =======
        
        This package was created with Cookiecutter_ and the
        `audreyr/cookiecutter-pypackage`_ project template.
        
        `Memote` relies on click_ for the command line interface, pytest_ for unit
        and model tests, gitpython_ for interacting with git repositories, 
        pandas_ for tabular datastructures and data input, jinja2_ for interacting 
        with HTML templates, cobrapy_ for analysing genome-scale metabolic 
        models, python_libsbml_ for reading and writing Systems Biology Markup 
        Language (SBML_), ruamel_ for handling YAML generation, travispy_ and 
        travis-encrypt_ for interacting with Travis CI, pygithub_ for access to the 
        Github API, sympy_ for matrix calculations, sqlalchemy_ for managing 
        ``history`` results, numpydoc_ for beautifully formatted doc strings using 
        sphinx_, pylru_ for caching, goodtables_ for validation of tabular data, 
        depinfo_ for pretty printing our dependencies, six_ and future_ for backward 
        and forward compatibility.
        
        The Memote Report App user interface is built with `Angular 5`_, 
        `Angular Flex-Layout`_, and `Angular Material`_. We rely on Taucharts_ for plotting 
        results.
        
        The initial development of `memote` has received funding from:
        
        .. image:: https://upload.wikimedia.org/wikipedia/commons/d/d5/Novo_nordisk_foundation_Logo.png
                :target: http://novonordiskfonden.dk/en
        
        .. image:: https://innovationsfonden.dk/sites/all/themes/novigo/logo.png
                :target: https://innovationsfonden.dk/da
        
        .. image:: http://dd-decaf.eu/images/decaf-logo-md.svg
                :target: http://dd-decaf.eu/
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: 
          https://github.com/audreyr/cookiecutter-pypackage
        .. _click: http://click.pocoo.org/5/
        .. _pytest: https://docs.pytest.org/en/latest/
        .. _gitpython: https://github.com/gitpython-developers/GitPython
        .. _pandas: https://pypi.org/project/pandas/
        .. _jinja2: http://jinja.pocoo.org/
        .. _cobrapy: https://github.com/opencobra/cobrapy
        .. _python_libsbml: https://pypi.org/project/python-libsbml/
        .. _SBML: http://sbml.org/Main_Page
        .. _ruamel: https://pypi.org/project/ruamel.yaml/
        .. _travispy: https://pypi.org/project/TravisPy/
        .. _travis-encrypt: https://pypi.org/project/travis-encrypt/
        .. _pygithub: https://github.com/PyGithub/PyGithub
        .. _sympy: http://www.sympy.org/en/index.html
        .. _sqlalchemy: http://www.sqlalchemy.org/
        .. _numpydoc: https://github.com/numpy/numpydoc
        .. _sphinx: http://www.sphinx-doc.org/en/stable/
        .. _pylru: https://pypi.org/project/pylru/
        .. _goodtables: https://github.com/frictionlessdata/goodtables-py
        .. _depinfo: https://pypi.org/project/depinfo/
        .. _six: https://pypi.org/project/six/
        .. _future: https://pypi.org/project/future/
        .. _Angular 5: https://angular.io/
        .. _Angular Flex-Layout: https://github.com/angular/flex-layout
        .. _Angular Material: https://material.angular.io/
        .. _Taucharts: https://taucharts.com/
        
Keywords: memote,metabolic,constrained-based,model,COBRA,test suite,quality control,quality assurance
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: !=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7
