Replace data backend and increase flexibility.

wfondrie commented 11 months ago

This PR migrate the data backend for Depthcharge from HDF5 to Apache Arrow-based formats, and updates the API in the process.

Overall this PR simplifies the code base and allows for more flexibility in data parsing and usage for advanced users. Please note that I'm still adding documentation, but the code itself is ready for review.

codecov[bot] commented 11 months ago

Codecov Report

Merging #39 (c2a4d48) into main (54f36bf) will increase coverage by 1.00%. The diff coverage is 94.94%.

@@            Coverage Diff             @@
##             main      #39      +/-   ##
==========================================
+ Coverage   91.48%   92.48%   +1.00%     
==========================================
  Files          19       22       +3     
  Lines         963      972       +9     
==========================================
+ Hits          881      899      +18     
+ Misses         82       73       -9

Files	Coverage Δ
depthcharge/__init__.py	`100.00% <100.00%> (ø)`
depthcharge/data/__init__.py	`100.00% <100.00%> (ø)`
depthcharge/data/fields.py	`100.00% <100.00%> (ø)`
depthcharge/primitives.py	`96.66% <100.00%> (-0.65%)`	:arrow_down:
depthcharge/tokenizers/peptides.py	`70.42% <100.00%> (+1.76%)`	:arrow_up:
depthcharge/transformers/spectra.py	`97.87% <100.00%> (+1.87%)`	:arrow_up:
depthcharge/utils.py	`100.00% <100.00%> (+27.27%)`	:arrow_up:
depthcharge/version.py	`100.00% <100.00%> (ø)`
depthcharge/data/arrow.py	`97.14% <97.14%> (ø)`
depthcharge/data/parsers.py	`97.22% <96.19%> (+0.25%)`	:arrow_up:
... and 2 more

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wfondrie commented 11 months ago

@jspaezp, on second thought, I'll update the docs in a separate PR. This one is large enough 😅

wfondrie / depthcharge

Replace data backend and increase flexibility. #39

Codecov Report