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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1103 +/- ##
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- Coverage 72.05% 72.05% -0.01%
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Files 92 92
Lines 3246 3249 +3
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+ Hits 2339 2341 +2
- Misses 907 908 +1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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| ("ENSEMBL:ENSG00000157764", "identifiers.org/ensembl/ENSG00000157764"), | ||
| ("OMIM:613647", "identifiers.org/mim/613647"), | ||
| ("UBERON:0000001", "purl.obolibrary.org/obo/UBERON_0000001"), | ||
| ("WormBase:WBGene00000001", "identifiers.org/wb/WBGene00000001"), |
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At some point, some curie expansions started giving http or https where before they were giving the opposite - I'm not sure what resulted in this difference.
These changes just give the test a little more wiggle room while asserting that the important content of the URI itself is correct
| """Abstract interface for grounding text to entities""" | ||
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| def ground_entity(self, text: str) -> Entity: | ||
| def ground_entity(self, text: str) -> List[Entity]: |
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Doesn't affect runtime, but is a useful fix for IDE linters/type checkers
| nlp = None | ||
| grounding_implementation = None | ||
| nlp: Optional[spacy.language.Language] = None | ||
| grounding_implementation: Optional[GroundingInterface] = None |
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Same thing here - just helps type checking
| semsimian() | ||
| spacyner() | ||
| # oak() | ||
| yield |
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the on_event("startup") listener was deprecated by FastAPI
glass-ships
requested review from
kevinschaper and
ptgolden
and removed request for
kevinschaper
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Thanks thats great, thanks for being so fast and responsive. |
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not sure why the frontend lint test is failing here but it at least is unrelated to changes made in this PR |
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Yes this looks very good now! Thank you @glass-ships :) |
2 participants
Updates pyproject.toml, documentation, makefile, and github actions to use
uvinstead ofpoetry.Dependency resolution is much faster since uv is written in Rust, and all poetry functionality we currently use is also available in uv. For instance, in a fresh environment, uv installs monarch-py and all its dependencies in less than 1 minutes, where poetry has historically taken as long as an hour depending on a variety of circumstances.
One minor thing to note is that, similar to the poetry configuration,
versionin the pyproject.toml is set to 0.0.0, getting automatically set by the github action to be whatever the latest tag number is.There does exist an equivalent uv-dynamic-versioning and a git issue with uv to track implementation of being able to set
dynamic = ["version"]in the pyproject.toml.However, this is just a nice to have, and shouldn't affect any workflow or git actions.
The locally installed version will just show up as 0.0.0, which also currently happens with poetry.