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Reorganize repository structure #1103

Merged
merged 15 commits into from
Apr 18, 2024
Merged

Reorganize repository structure #1103

merged 15 commits into from
Apr 18, 2024

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cthoyt
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@cthoyt cthoyt commented Apr 18, 2024

This PR does the following:

  1. Consolidates the external registry getters (in bioregistry.external), the external registry alignment classes (in bioregistry.align the data artifacts (in bioregistry.data.external), and a few (3) configuration files (in bioregistry.data) into a single hierarchy in bioregistry.external.
  2. Moves the metaregistry curation sheets and the raw data from the repositories out of the src/ structure. They're now in the /exports/alignment/ and /exports/raw/ folders, respectively. The point of this is to reduce the size of the package that gets sent to PyPI, related to Bioregistry hit project size limit on PyPI #1100
  3. minor version bump to 0.11.X series

In theory, this shouldn't affect any downstream uses, since the bioregistry.align submodule isn't really for external users.

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codecov bot commented Apr 18, 2024

Codecov Report

Attention: Patch coverage is 75.63452% with 96 lines in your changes are missing coverage. Please review.

Project coverage is 43.97%. Comparing base (0b0f8b9) to head (02c12ee).
Report is 28 commits behind head on main.

❗ Current head 02c12ee differs from pull request most recent head c9d238b. Consider uploading reports for the commit c9d238b to get more accurate results

Files Patch % Lines
src/bioregistry/external/biocontext/__init__.py 52.50% 18 Missing and 1 partial ⚠️
src/bioregistry/external/go/__init__.py 56.00% 11 Missing ⚠️
src/bioregistry/external/biolink/__init__.py 54.54% 10 Missing ⚠️
src/bioregistry/cli.py 0.00% 8 Missing ⚠️
src/bioregistry/external/obofoundry/__init__.py 63.63% 8 Missing ⚠️
src/bioregistry/external/prefixcommons/__init__.py 84.21% 3 Missing ⚠️
src/bioregistry/external/align.py 0.00% 2 Missing ⚠️
src/bioregistry/external/alignment_utils.py 33.33% 2 Missing ⚠️
src/bioregistry/external/cellosaurus/__init__.py 86.66% 2 Missing ⚠️
src/bioregistry/external/cheminf/__init__.py 83.33% 2 Missing ⚠️
... and 21 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1103      +/-   ##
==========================================
+ Coverage   40.44%   43.97%   +3.53%     
==========================================
  Files         150      123      -27     
  Lines        8340     8163     -177     
  Branches     1637     1614      -23     
==========================================
+ Hits         3373     3590     +217     
+ Misses       4776     4381     -395     
- Partials      191      192       +1     

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@cthoyt cthoyt merged commit 02ae7c2 into main Apr 18, 2024
11 checks passed
@cthoyt cthoyt deleted the reorg-external-registries branch April 18, 2024 14:34
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