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aliquot-level-maf

Library to process aliquot-level MAF files.

This library requires Python 3.6+.

• aliquot-level-maf
  • Install pre-commit
    • Update secrets baseline for detect-secrets
  • Dependencies
    • Installing dependencies
    • Adding dependencies
  • Tests

Install pre-commit

This repository makes use of pre-commit for code formatting, linting and secrets detecting. In order to make use of it, you must run the following commands to install pre-commit.

pip install -r dev-requirements.txt
pre-commit install

Update secrets baseline for detect-secrets

We use detect-secrets to search for secrets being committed into the repo.

To update the .secrets.baseline file run

detect-secrets scan --update .secrets.baseline

.secrets.baseline contains all the string that were caught by detect-secrets but are not stored in plain text. Audit the baseline to view the secrets .

detect-secrets audit .secrets.baseline

Dependencies

Installing dependencies

pip install -r dev-requirements.txt

Adding dependencies

Adding development dependencies should go in dev-requirements.in. Then, execute:

pip-compile dev-requirements.in

to build the new dev-requirements.txt.

Tests

To run the tests, execute:

python -m pytest -lvv tests/

or, if you have tox installed, execute:

tox