Closed wfondrie closed 1 year ago
Merging #34 (38cee4e) into main (2bfd7f1) will increase coverage by
5.82%
. The diff coverage is91.06%
.
@@ Coverage Diff @@
## main #34 +/- ##
==========================================
+ Coverage 85.67% 91.50% +5.82%
==========================================
Files 15 19 +4
Lines 705 965 +260
==========================================
+ Hits 604 883 +279
+ Misses 101 82 -19
Impacted Files | Coverage Δ | |
---|---|---|
depthcharge/tokenizers/peptides.py | 68.65% <68.65%> (ø) |
|
depthcharge/tokenizers/tokenizer.py | 91.83% <91.83%> (ø) |
|
depthcharge/data/spectrum_datasets.py | 93.12% <93.12%> (ø) |
|
depthcharge/transformers/peptides.py | 94.54% <94.54%> (ø) |
|
depthcharge/transformers/spectra.py | 96.00% <96.00%> (ø) |
|
depthcharge/primitives.py | 97.31% <97.31%> (ø) |
|
depthcharge/__init__.py | 100.00% <100.00%> (ø) |
|
depthcharge/constants.py | 100.00% <100.00%> (ø) |
|
depthcharge/data/__init__.py | 100.00% <100.00%> (ø) |
|
depthcharge/data/parsers.py | 96.96% <100.00%> (+1.69%) |
:arrow_up: |
... and 8 more |
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Yikes - peptide tokenization is much too slow right now to be useful. It takes about 36 ms on my Mac per peptide, which doesn't scale to thousands. 🤔
I'm going to go ahead and merge this. Please still leave a review and I'll fix problems in another PR!
This PR makes sweeping changes across depthcharge, implementing some lessons learned using it with Casanovo and such. These include:
spectrum_utils
andpyteomics
.Tight integration with
spectrum_utils
💪There may be things that I've missed, but this is a big PR that I'm excited about!
Still TODO: