Refactor module - Githubissues

Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.

https://proteobench.readthedocs.io

Apache License 2.0

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Refactor module #272

Closed wolski closed 3 months ago

wolski commented 3 months ago

This is a Draft, and I am happy to discuss it here or on Slack or Zoom.

To have less duplicated code in this pull request:

I removed duplicated toml files
I removed the peptideform module
I moved the code for parsing to io/parsing I want to go through the parse code later this week to remove duplicated code before I can start to work on issue #270

Additionally

I moved the Datapoint to proteobench/utils/, see issue #269, which might not be it's final location.
I moved the plotting function to /utils/plotting/ see issue #269

I am teaching until Friday, but will try to move forward with the refactoring on Friday.

wolski commented 3 months ago

Still to do:

move code for benchmark scores out of the module
move generate_intermediate from module to benchmarkscores?

I have a bit more time this week.

wolski commented 3 months ago

moved

Module.generate_datapoint to quant_datapoint
Module.get_metrics to quant_datapoint
Module.convert_replicate_to_raw, generate_intermediate, compute_group_stats, compute_epsilon moved to score/quant/quantscore.py"

Still to do:

quant_datapoint and parse_settings_ion must not be accessed directly from StreamlitUI -> provide access through the module.

enryH commented 3 months ago

So far it looks good. I review again once it's not a draft anymore:)

wolski commented 3 months ago

Can you review, please, specifically whether I did not break functionality not covered by the unit tests? This is not final since work on #268 has not even started—but it can start in a new branch.

RobbinBouwmeester commented 3 months ago

Couple of points:

@wolski parse_settings_ion has to be accessed through the webinterface as we need to know what to fill the dropdown menu. This is not available anywhere else since you moved it there.
Everything in /proteobench/io/ needs to be moved to a subfolder like "DDA_quant/" otherwise it is very confusing what these scripts refer to
Everything in /proteobench/io_parsesettings/ needs to be moved to a subfolder like "DDA_quant/" otherwise it is not clear what module these belong to, furthermore naming needs to change as both the ion and peptidoform could refer to exactly the same name.

wolski commented 3 months ago

@RobbinBouwmeester I did move PRECURSOR_NAME to module and LOCAL_DEVELOPMENT to GUI (had to so GUI is still working).