.. image:: https://img.shields.io/pypi/v/memote.svg :target: https://pypi.org/project/memote/ :alt: Current PyPI Version
.. image:: https://img.shields.io/pypi/pyversions/memote.svg :target: https://pypi.org/project/memote/ :alt: Supported Python Versions
.. image:: https://img.shields.io/pypi/l/memote.svg :target: https://www.apache.org/licenses/LICENSE-2.0 :alt: Apache Software License Version 2.0
.. image:: https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg :target: .github/CODE_OF_CONDUCT.md :alt: Code of Conduct
.. image:: https://github.com/opencobra/memote/workflows/CI-CD/badge.svg :target: https://github.com/opencobra/memote/workflows/CI-CD :alt: GitHub Actions
.. image:: https://codecov.io/gh/opencobra/memote/branch/master/graph/badge.svg :target: https://codecov.io/gh/opencobra/memote :alt: Codecov
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/ambv/black :alt: Code Style Black
.. image:: https://readthedocs.org/projects/memote/badge/?version=latest :target: https://memote.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status
.. 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:
The MEMOTE tool therefore performs four subfunctions:
test suite that represents the community standard_.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
Before installing MEMOTE, please 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
For comments and questions get in touch via
gitter chatroom <https://gitter.im/opencobra/memote>_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.
Apache Software License 2.0 <LICENSE>_.. who-end
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/
FAQs
the genome-scale metabolic model test suite
We found that memote demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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