srkpa/drug_drug_interactions

side_effects

Predict DDI and their side effects

Development, testing, and deployment tools

This section documents our process for running continuous integration (CI) tests and all the steps required during development.

Testing

We use nose for all our tests. To run the test, please use:

pytest -v tests/

Continuous Integration

You should test your code. A rudimentary configuration file for bitbucket-pipelines.yml is provided, but do not feel compelled to use it. It is just to help you get started

Conda Environment:

Please always provide a conda environnment, as the specific package versions you are using are important for your results to be reproductible. A simple test environment file with base dependencies is provided (env.yml). Channels are not specified here and therefore respect global Conda configuration

Additional Scripts:

• scripts
  • create_conda_env.py: Helper program for spinning up new conda environments based on a starter file with Python Version and Env. Name command-line options

Checklist for updates

• Make sure there is an/are issue(s) opened for your specific update
• Create the PR, referencing the issue
• Debug the PR as needed until tests pass
• Tag the final, debugged version
  • git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags
• Get the PR merged in

Versioneer Auto-version

Versioneer will automatically infer what version is installed by looking at the git tags and how many commits ahead this version is. The format follows PEP 440 and has the regular expression of:

\d+.\d+.\d+(?\+\d+-[a-z0-9]+)

If the version of this commit is the same as a git tag, the installed version is the same as the tag, e.g. side_effects-0.1.2, otherwise it will be appended with +X where X is the number of commits ahead from the last tag, and then -YYYYYY where the Y's are replaced with the git commit hash.

Copyright

Copyright (c) 2019, InVivo AI