Migrate to uv clean #447
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Migrate to uv clean #447
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- Replace Poetry with uv package manager - Update all GitHub workflows to use uv - Add uv.lock file and remove poetry.lock - Update pyproject.toml to use modern dependency groups - Remove obsolete tox.ini file
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #447 +/- ##
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+ Coverage 77.42% 77.45% +0.02%
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Files 52 52
Lines 4479 4479
Branches 1304 979 -325
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+ Hits 3468 3469 +1
Misses 783 783
+ Partials 228 227 -1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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… workflow This fixes ImportError for requests_cache module which is required by linkml-runtime tests.
…endencies This matches Poetry's '--all-extras' behavior which installs all optional dependencies needed for the linkml tests, instead of manually adding individual packages.
Instead of manually adding individual packages, use uv's dependency groups to properly install linkml-runtime with all its dev dependencies (docker, requests-cache, etc.) that are needed for linkml tests.
Docker is required by upstream linkml tests (imported in tests/conftest.py). With Poetry this worked due to implicit dependency resolution, but uv requires explicit declaration of dependencies.
The issue was that adding linkml-runtime to a dependency group doesn't automatically install linkml-runtime's dev dependencies. We need to explicitly add the packages that linkml tests require: docker and requests-cache.
Added debug step to see what's installed and added the remaining dependencies that linkml tests need: jsonpatch, testcontainers, and nbformat. This should resolve all the ImportError issues we've been seeing.
Instead of manually adding dependencies in the workflow, properly declare all dependencies needed for upstream linkml testing in linkml-runtime's dev dependency group: - docker (for container-based tests) - jsonpatch (for dict comparison utilities) - testcontainers (for PlantUML container tests) - nbformat & nbconvert (for notebook testing) - requests-cache (for caching test utilities) This makes the dependency management much cleaner and more maintainable.
The dependency group approach isn't working - uv isn't installing linkml-runtime's dev dependencies into linkml's environment. Fall back to explicitly installing every dependency that linkml tests need: docker, requests-cache, jsonpatch, testcontainers, nbformat, nbconvert. Sometimes you just have to be explicit with dependency management.
sierra-moxon
approved these changes
Aug 8, 2025
4 tasks
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This is a clean version of the uv intergration (not from my fork). This way we can make sure the weird things around "add docker when syncing uv" are only artifacts of a fork.