biopragmatics / bioontologies

🏷️ Unified access to biomedical ontologies
https://bioontologies.readthedocs.io
MIT License
8 stars 1 forks source link

API Improvements #8

Closed cthoyt closed 1 year ago

cthoyt commented 1 year ago

This PR has multiple useful additions including:

  1. Auto-merge of ontologies
  2. Loading local OBO Graph JSON
  3. Performance improvements when loading bioregistry converter (related to #7)
  4. Better normalization of properties and access to them
  5. Simpler interface for getting version after parsing

Blocked by

codecov-commenter commented 1 year ago

Codecov Report

Base: 38.04% // Head: 35.22% // Decreases project coverage by -2.81% :warning:

Coverage data is based on head (57bf12b) compared to base (ee28000). Patch coverage: 25.80% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #8 +/- ## ========================================== - Coverage 38.04% 35.22% -2.82% ========================================== Files 10 10 Lines 665 687 +22 Branches 127 132 +5 ========================================== - Hits 253 242 -11 - Misses 400 432 +32 - Partials 12 13 +1 ``` | [Impacted Files](https://codecov.io/gh/biopragmatics/bioontologies/pull/8?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biopragmatics) | Coverage Δ | | |---|---|---| | [src/bioontologies/robot.py](https://codecov.io/gh/biopragmatics/bioontologies/pull/8/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biopragmatics#diff-c3JjL2Jpb29udG9sb2dpZXMvcm9ib3QucHk=) | `41.21% <21.05%> (-3.40%)` | :arrow_down: | | [src/bioontologies/obograph.py](https://codecov.io/gh/biopragmatics/bioontologies/pull/8/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biopragmatics#diff-c3JjL2Jpb29udG9sb2dpZXMvb2JvZ3JhcGgucHk=) | `44.13% <27.27%> (-0.79%)` | :arrow_down: | | [src/bioontologies/\_\_init\_\_.py](https://codecov.io/gh/biopragmatics/bioontologies/pull/8/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biopragmatics#diff-c3JjL2Jpb29udG9sb2dpZXMvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [src/bioontologies/upgrade/\_\_init\_\_.py](https://codecov.io/gh/biopragmatics/bioontologies/pull/8/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biopragmatics#diff-c3JjL2Jpb29udG9sb2dpZXMvdXBncmFkZS9fX2luaXRfXy5weQ==) | `0.00% <0.00%> (-40.63%)` | :arrow_down: | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biopragmatics). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=biopragmatics)

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