A Python implementation of the NPC toolchain for import, quality-control, and preprocessing of metabolic profiling datasets.
- Version 1.0.1a
Source management is git-flow-like - no development in the master branch!
When merging into the develop branch, all new code must include unit-tests, and these tests should pass.
The nPYc Toolbox is built upon Python 3.6, and most dependencies can be satisfied by installing the Anaconda (v4.4.0 and above) distribution.
When merging from develop (or hotfix branches) into release, ensure:
- All references to the debugger are removed
- All paths are relative and platform agnostic
- All tests pass
Documentation is hosted on Read the Docs.
Documentation is generated via Sphinx Autodoc, documentation markup is in reStructuredText.
To build the documentation locally, cd into the docs directory and run:
make html
To clear the current documentation in order to rebuild after making changes, run:
make clean
Unit testing is managed via the unittest framework. Test coverage can be found on codecov.io.
To run all tests, cd into the Tests directory and run:
python -m unittest discover -v
Individual test modules can be run with:
python -m `test_filename` -v
When stored internally, and unless explicitly overriden, variables should conform to the units laid out in the Nomenclature of the documentation.