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MetaNetX

Build Status Codecov

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
  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