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====================================================
memote - the genome-scale metabolic model test suite
MEMOTE - the genome-scale metabolic model test suite
====================================================

.. image:: https://img.shields.io/pypi/v/memote.svg
:target: https://pypi.python.org/pypi/memote
:target: https://pypi.org/project/memote/
:alt: Current PyPI Version

.. image:: https://img.shields.io/travis/opencobra/memote.svg
:target: https://travis-ci.org/opencobra/memote
.. image:: https://img.shields.io/pypi/pyversions/memote.svg
:target: https://pypi.org/project/memote/
:alt: Supported Python Versions

.. 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://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://readthedocs.org/projects/memote/badge/?version=latest
:target: https://memote.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. 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: Coverage
: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
:target: https://gitter.im/opencobra/memote
:alt: Gitter

.. summary-start
Expand All @@ -35,7 +50,7 @@ model building community:
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:
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
Expand All @@ -61,27 +76,19 @@ at via GitHub pages for your repository.
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
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:
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
This is the preferred method to install `MEMOTE`, as it will always install the
most recent stable release.

.. who-start
Expand Down Expand Up @@ -131,16 +138,16 @@ 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:
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
:target: http://novonordiskfonden.dk/en

.. image:: https://innovationsfonden.dk/sites/all/themes/novigo/logo.png
:target: https://innovationsfonden.dk/da
:target: https://innovationsfonden.dk/da

.. image:: http://dd-decaf.eu/images/decaf-logo-md.svg
:target: http://dd-decaf.eu/
:target: http://dd-decaf.eu/

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`:
Expand Down

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