MetaNetX

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.
• 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
2. flake8
   • pycodestyle
   • pyflakes
   • mccabe
   • pydocstyle
   • bugbear
3. The NumPy docstring standard
4. 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