Code review: overview

[sillitoe]

It would be great to have some level of code review for this project.

The first step would be to provide a general overview:

• is the general strategy sound?
• could any of the tasks be simplified / removed?
• are we happy with the existing frameworks (eg Flask, Luigi, SQLAlchemy)

[sillitoe]

For info: @sreenathnair has suggested a couple of changes in the development branch.

• Flask -> FastAPI
• PostgreSQL -> MongoDB

[sillitoe]

This work has been completed (before and during BioHackathon2021).

Overview:

• Flask -> FastAPI (API only, lose local web pages)
• PostgreSQL -> MongoDB (easier to work with JSON documents)
• Luigi -> Snakemake (simpler to work with)
• Quality score -> drop for the moment (TODO)

Git flow:

• old default branch master archived to master-deprecated
• new default branch is main
• all changes get merged to development
• changes can be merged from development to main at any point