refactor: amplicon_covs.py

[raaijmag]

refactor: ViroConstrictor.workflow.scripts.amplicon_covs.py - completely re-wrote the script from scratch
refactor: ViroConstrictor.workflow.scripts.amplicon_arg_parser.py - moved argument parsing logic from amplicon_covs to a different file
refactor: ViroConstrictor.workflow.scripts.init.py - added to import the argument parser to amplicon_covs.py

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[florianzwagemaker]

So this might be a bit of a nitpick but we probably should change some of the function names and/or classnames in this file before we go to include it in the 1.6.0 release.

I think the structure of this file is already a big improvement when it comes to readability and maintainability in the long term, but using something like ReadDirection as a classname, combined with its description, might cause confusion in future maintenance as this class (and actually the entire script) is not actually dealing with the direction of reads, but the direction of primers.

[florianzwagemaker]

I very much approve of this rework, even without the adjustment in the comment above.
However, the splitting of the argument parsing and the actual logic sets a bit of a precedence that we should commit to in a broader sense than just this script.
If we go this way where argument parsing is gathered in separate files then in my opinion we should do this for all the relevant scripts. Potentially combined with a more centralized approach for shared functions across these scripts.

I'd therefore suggest not directly merging this into dev right now, but instead we go to a separate featurebranch where we work this out further for all the relevant scripts and test if this works in a stable manner for both conda and containerized execution. Once we have that worked out then we can include it in the release plan for v1.6.0 so this improvement can finally be included.