PyOpenSci REVIEW - 59 some more minor changes #60
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Codecov ReportBase: 97.50% // Head: 97.50% // No change to project coverage 👍
Additional details and impacted files@@ Coverage Diff @@
## main #60 +/- ##
=======================================
Coverage 97.50% 97.50%
=======================================
Files 5 5
Lines 160 160
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Hits 156 156
Misses 4 4 Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
Batalex
reviewed
Jan 31, 2023
| meta_values = [ | ||
| [ | ||
| str(v).replace("nan", "") | ||
| for k, v in pgap.get_meta_info_for_HMM(hmm).items() | ||
| if k != "#ncbi_accession" | ||
| ] | ||
| for hmm in hmm_group.split("|") # row.hmm.split("|") | ||
| for hmm in row.hmm.split("|") |
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Addressing these issues from reviewer @Batalex in PyOpenSci
I have not profiled the code to see if there is a performance bottleneck there, but I would use itertuples instead of iterrows in addHMMmetaInfoToHits. itertuples is much faster if you need to iterate over data frames one row at a timeThis was changed in this PR
Here getting rid of
getattrMy personal recommendation is to define the text encoding whenever a text file descriptor is opened. Even if this is not feasible at the moment, this is a tiny step toward Windows compatibility, and it removes a little bit of uncertainty.The MG1655.gb file is stored in the tests folder, which is not included in the package. Therefore, when the package is installed using conda, it is not downloaded.There are a few discrepancies in types, some of them could be fixed by converting argparse.ArgumentParser instances to CommandArgs before using themHere using typing's union to indicate flexible type