methcomp: method comparison for clinical chemistry

<div> <img src="https://raw.githubusercontent.com/wptmdoorn/methcomp/master/doc/_static/example_1.png" height="180"> <img src="https://raw.githubusercontent.com/wptmdoorn/methcomp/master/doc/_static/example_2.png" height="180"> <img src="https://raw.githubusercontent.com/wptmdoorn/methcomp/master/doc/_static/example_3.png" height="180"> <img src="https://raw.githubusercontent.com/wptmdoorn/methcomp/master/doc/_static/example_4.png" height="180"> </div> <br>

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Methcomp is a Python visualization library based and built on matplotlib. It provides a high-level interface for method comparison for clinical chemistry methods, amongst others.

Documentation

Online documentation is currently only available by clicking on here. Illustrative examples using the methcomp library can be found in examples/ directory and in the blog post here.

Dependencies

Methcomp supports Python 2 and 3. Installation requires numpy, scipy, pandas, and matplotlib.****

Installation

The latest stable release (and older versions) can be installed from PyPI:

pip install methcomp

Otherwise, you may instead want to use the development version from directly through Github:

pip install git+https://github.com/wptmdoorn/methcomp

Development

Testing

To test the code, run make pytest in the source directory. This will run the tests in the tests/ directory.

Pre-commit

This project supprts Pre-commit, to install it run

pip install pre-commit
pre-commit install

at the top level of this repo. After this git commit should run the chain of commands listed in .pre-commit-config.yaml. To force running the chain to run use

pre-commit run --all-files

A number of basic checks are executed by pre-commit, syntax checks for toml and yaml files, trimming of trailing whitespaces and ensuring newline at end of file, checking for merge conflict strings, warning about python debug statements, and fixing the python encoding pragmas at top of files. Pre-commit also runs Mypy as a static type checker, isort to sort imports, black to format code, and flake8 as a linter.