Refactor parse.py and ParseSettings.py

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 parse.py and ParseSettings.py #270

Closed wolski closed 2 months ago

wolski commented 3 months ago

Merge the ParseSettings and ParseInputs into one class since the variables in ParseSettings are used in ParseInputs
Move package variables into the class which is using them.
refactor the ParseSettings into ParseSettings and ParseSettingsWithModification.

Move the functionality into proteobench/io/dda_quant_data

wolski commented 2 months ago

closing because partially adressed in PR #272