https://github.com/dd-decaf/metanetx

https://github.com/dd-decaf/metanetx

Last synced: 6 days ago
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• Host: GitHub
• URL: https://github.com/dd-decaf/metanetx
• Owner: DD-DeCaF
• License: apache-2.0
• Created: 2019-06-06T12:28:59.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2020-05-29T16:11:46.000Z (over 4 years ago)
• Last Synced: 2024-11-09T14:25:51.288Z (2 months ago)
• Language: Python
• Size: 125 MB
• Stars: 0
• Watchers: 6
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# MetaNetX

[![Build Status](https://travis-ci.org/DD-DeCaF/metanetx.svg?branch=master)](https://travis-ci.org/DD-DeCaF/metanetx)

[![Codecov](https://codecov.io/gh/DD-DeCaF/metanetx/branch/master/graph/badge.svg)](https://codecov.io/gh/DD-DeCaF/metanetx/branch/master)

## Development

Run `make setup` first when initializing the project for the first time. Type

`make` to see all commands.

### Source files

The MetaNetX source files are stored in `data/`.

Reaction names are not part of MetaNetX, but collected manually by running

`./scripts/generate_reaction_names.py`. Note that the script takes several hours

to complete. Names are retrieved from cross referenced databases (currently

BiGG, kegg, ModelSEED and EC numbers are checked).

### Environment

Specify environment variables in a `.env` file. See `docker-compose.yml` for the

possible variables and their default values.

* Set `ENVIRONMENT` to either

  * `development`,

  * `testing`, or

  * `production`.

* `SECRET_KEY` Flask secret key. Will be randomly generated in development and testing environments.

* `SENTRY_DSN` DSN for reporting exceptions to

  [Sentry](https://docs.sentry.io/clients/python/integrations/flask/).

* `ALLOWED_ORIGINS`: Comma-seperated list of CORS allowed origins.

### Code style

In order of priority, code must adhere to the rules of the following tools:

1. [black](https://github.com/ambv/black)

2. [flake8](http://flake8.pycqa.org/en/latest/)

    * pycodestyle

    * pyflakes

    * mccabe

    * [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html)

    * [bugbear](https://github.com/PyCQA/flake8-bugbear)

3. The [NumPy docstring standard](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard)

4. [isort](https://github.com/timothycrosley/isort)

### Updating Python dependencies

To compile a new requirements file and then re-build the service with the new requirements, run:

    make pip-compile build