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Add pandas tools #416

Merged
merged 27 commits into from Jul 30, 2022
Merged

Add pandas tools #416

merged 27 commits into from Jul 30, 2022

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cthoyt
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@cthoyt cthoyt commented Jun 10, 2022

This pull request adds tools for processing data inside pandas DataFrames. It has functions for operations like:

  1. normalizing prefixes and CURIEs
  2. converting between LUIDs, CURIEs, and IRIs
  3. validating prefixes, LUIDs, and CURIEs

Notebook demo: https://nbviewer.org/github/biopragmatics/bioregistry/blob/pandas-tools/notebooks/Preparing%20the%20GO%20Annotation%20Database%20for%20Integration.ipynb

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codecov-commenter commented Jun 10, 2022

Codecov Report

Merging #416 (62f7132) into main (b06e58c) will increase coverage by 0.53%.
The diff coverage is 49.71%.

@@            Coverage Diff             @@
##             main     #416      +/-   ##
==========================================
+ Coverage   38.05%   38.58%   +0.53%     
==========================================
  Files         104      105       +1     
  Lines        5637     5803     +166     
  Branches     1134     1173      +39     
==========================================
+ Hits         2145     2239      +94     
- Misses       3359     3418      +59     
- Partials      133      146      +13     
Impacted Files Coverage Δ
src/bioregistry/__init__.py 100.00% <ø> (ø)
src/bioregistry/pandas.py 41.72% <41.72%> (ø)
src/bioregistry/resolve_identifier.py 77.08% <71.42%> (-2.92%) ⬇️
src/bioregistry/resource_manager.py 78.03% <83.33%> (+3.45%) ⬆️
src/bioregistry/schema/struct.py 82.10% <100.00%> (+0.28%) ⬆️

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@cthoyt cthoyt marked this pull request as ready for review July 29, 2022 23:55
@cthoyt cthoyt enabled auto-merge (squash) July 30, 2022 00:07
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2 participants