mwham requested to merge mwham_develop into master Feb 29, 2024

New additions

Updates dependencies - SQLAlchemy 2.0, Jinja 3, Pandas 2
Genomicc/Isaric NGS data with mappings
Clinical data dictionary
Column descriptions in clinical datasets
Phosp genotyping
Provides a CSV schema file per dataset, instead of everything in data_map.md

Tweaks and fixes

Fixes a connection hang in Database._drop_tables
Adds a test case for PBMC samples
WP5NGS: adds test cases for meta files and invalid data
New variable spec format
Removing old vcf logic
Fixes main export ignore list
Allowing for space-separated CSV files.
Simplifies export configs
Enables utils.read_file to select a specific Excel tab