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biopragmatics / bioregistry

📮 An integrative registry of biological databases, ontologies, and nomenclatures.
https://bioregistry.io
MIT License
107 stars 47 forks source link

Reorganize repository structure #1103

Closed cthoyt closed 2 months ago

cthoyt commented 2 months ago

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 #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.

codecov[bot] commented 2 months ago

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.

:exclamation: 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 :warning:
src/bioregistry/external/go/__init__.py 56.00% 11 Missing :warning:
src/bioregistry/external/biolink/__init__.py 54.54% 10 Missing :warning:
src/bioregistry/cli.py 0.00% 8 Missing :warning:
src/bioregistry/external/obofoundry/__init__.py 63.63% 8 Missing :warning:
src/bioregistry/external/prefixcommons/__init__.py 84.21% 3 Missing :warning:
src/bioregistry/external/align.py 0.00% 2 Missing :warning:
src/bioregistry/external/alignment_utils.py 33.33% 2 Missing :warning:
src/bioregistry/external/cellosaurus/__init__.py 86.66% 2 Missing :warning:
src/bioregistry/external/cheminf/__init__.py 83.33% 2 Missing :warning:
... and 21 more
Additional details and impacted files ```diff @@ 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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