Closed melihyilmaz closed 1 year ago
@wfondrie Should I add a unit test for detokenize
or is failure due to something else?
The above previous errors were due to a failure to upload test coverage to CodeCov, which hopefully I've fixed now 🤞
Should I add a unit test for ...
The answer to this question is always yes 😉
Merging #22 (16b9098) into main (23683c0) will not change coverage. The diff coverage is
100.00%
.
@@ Coverage Diff @@
## main #22 +/- ##
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Coverage 87.00% 87.00%
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Files 19 19
Lines 854 854
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Hits 743 743
Misses 111 111
Impacted Files | Coverage Δ | |
---|---|---|
depthcharge/components/transformers.py | 98.16% <100.00%> (ø) |
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Is there a good reason to every return a string? It seems like we should just make it always return a list. It seems easy enough for the user to join the string if they desire. 🤔
I'd ok with the breaking change for now, since I think Casanovo is currently the only dependent. What do you think @melihyilmaz and @bittremieux?
I concur.
Makes sense we can only return a list, I added it as an option earlier to avoid breaking things down.
Added option for
detokenize
to return peptide sequence as a list of amino acids rather than only in the string format. This was needed in the context of Casanovo for cases where multiple N-terminal modifications are predicted back to back (e.g. -17.027+42.011) and the downstream regex logic fails to differentiate these PTMs. Refer to below discussion for more details: https://github.com/Noble-Lab/casanovo/pull/87#discussion_r1023220461