Methods are documented. Some variable names and function names should still be updated but the method and parameter descriptions are there (almost everywhere). I added some short descriptions in the package development file too.
This PR also has some updated tests, and added tests for the workflow module (and visualisations to confirm functionality in the dev-viz directory). Also updated all the workflow parsing methods so they are using JSON now.
OBS: have not updated the QC pipeline for long, so that is quite outdated. Will do that the next PR.
Methods are documented. Some variable names and function names should still be updated but the method and parameter descriptions are there (almost everywhere). I added some short descriptions in the package development file too.
This PR also has some updated tests, and added tests for the workflow module (and visualisations to confirm functionality in the dev-viz directory). Also updated all the workflow parsing methods so they are using JSON now.
OBS: have not updated the QC pipeline for long, so that is quite outdated. Will do that the next PR.