Metadata-Version: 2.1
Name: moped
Version: 1.12.15
Summary: Stoichiometric metabolic modelling
Home-page: https://gitlab.com/marvin.vanaalst/moped
License: GPL-3.0-or-later
Keywords: modelling,stoichiometric,metacyc,blast
Author: Marvin van Aalst
Author-email: marvin.vanaalst@gmail.com
Maintainer: Marvin van Aalst
Maintainer-email: marvin.vanaalst@gmail.com
Requires-Python: >=3.8,<3.11
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: OS Independent
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development
Requires-Dist: Meneco (>=2.0.2,<3.0.0)
Requires-Dist: PyYAML (>=6.0,<7.0)
Requires-Dist: cobra (>=0.25.0,<0.26.0)
Requires-Dist: cycparser (>=1.2.1,<2.0.0)
Requires-Dist: gitchangelog (>=3.0.4,<4.0.0)
Requires-Dist: modelbase (>=1.9.2,<2.0.0)
Requires-Dist: numpy (>=1.22.4,<2.0.0)
Requires-Dist: pandas (>=1.4.2,<2.0.0)
Requires-Dist: pipdeptree (>=2.2.1,<3.0.0)
Requires-Dist: python-libsbml (>=5.19.5,<6.0.0)
Requires-Dist: tqdm (>=4.46.0,<5.0.0)
Project-URL: Documentation, https://moped.readthedocs.io/en/latest/
Project-URL: Repository, https://gitlab.com/marvin.vanaalst/moped
Description-Content-Type: text/markdown

# moped

[![DOI](https://img.shields.io/badge/DOI-10.3390%2Fmetabo12040275-blue)](https://doi.org/10.3390/metabo12040275)
[![pipeline status](https://gitlab.com/qtb-hhu/moped/badges/main/pipeline.svg)](https://gitlab.com/qtb-hhu/moped/-/commits/main)
[![coverage report](https://gitlab.com/qtb-hhu/moped/badges/main/coverage.svg)](https://gitlab.com/qtb-hhu/moped/-/commits/main)
[![Documentation Status](https://readthedocs.org/projects/moped/badge/?version=latest)](https://moped.readthedocs.io/en/latest/?badge=latest)
[![PyPi](https://img.shields.io/pypi/v/moped)](https://pypi.org/project/moped/)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
[![Downloads](https://pepy.tech/badge/moped)](https://pepy.tech/project/moped)


## Installation

You can install moped using pip

`pip install moped`

However, you will still need to install NCBI Blast if you want to use the genome / proteome reconstruction methods

If you are using conda or mamba, you can install blast from bioconda:

`conda install -c bioconda blast==2.12.0`
`mamba install -c bioconda blast==2.12.0`

If you want to install BLAST yourself:
- download the latest blast version from [NCBI](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
- Extract the downloaded folder to a path of your liking
- Add blast to your path e.g. by adding the following line to your .bashrc
  - `export PATH="your_blast_directory/bin:$PATH"`


## Documentation

Check out our tutorial on [readthedocs](https://moped.readthedocs.io/en/latest/)


## Contributing

All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome.
If you want to contribute code to the project, please consider our [contribution guide](https://gitlab.com/qtb-hhu/moped/-/blob/main/CONTRIBUTING.md)

## License

moped is licensed under [GPL 3](https://gitlab.com/qtb-hhu/moped/-/blob/main/LICENSE)

## Issues and support

If you experience issues using the software please contact us through our [issues](https://gitlab.com/qtb-hhu/moped/issues) page.

