Repository navigation
build(deps): upgrade to ultrack 0.8, clearing the last alert and the zarr cap - #313
Merged
Merged
Conversation
…zarr cap ultrack 0.8.0 resolves both problems we filed against 0.7.2: * royerlab/ultrack#283 -- the `pyarrow<20` cap is gone (now `pyarrow>=16.1.0`), so pyarrow moves 19.0.1 -> 25.0.1 and GHSA-rgxp-2hwp-jwgg no longer applies. That was the one alert #310 could not clear; biahub is now at zero open Dependabot alerts. * royerlab/ultrack#284 -- large_chunk_size casts its computed chunk sizes to plain ints instead of leaking np.int64, so zarr no longer needs capping below 3.3. Verified directly: on zarr 3.3.0 it returns (1, 3, 16, 16) as four Python ints and array_apply completes. Note the zarr side is fixed but unreleased -- zarr-developers/zarr-python#4257 is merged, yet PyPI is still on the unpatched 3.3.0. Dropping the cap is safe because the fix reaching us comes from ultrack's casting, not from zarr; ultrack was the only caller in our tree passing numpy integer chunk sizes. Also worth recording: pyarrow 25 ships cp314 wheels, so it is no longer what blocks Python 3.14. ultrack 0.8 declares `requires-python <3.14` instead, which is at least an explicit bound rather than a source build that fails on a missing Arrow C++ toolchain. 126 passed, 1 skipped -- including the track tests that zarr 3.3.0 broke under ultrack 0.7.2. Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Follow-up to #310. ultrack 0.8.0 fixes both issues we filed against 0.7.2, so the two workarounds that PR carried can come out.
The last alert is gone
royerlab/ultrack#283 — ultrack 0.8 declares
pyarrow>=16.1.0, dropping the<20cap. pyarrow moves 19.0.1 → 25.0.1, so GHSA-rgxp-2hwp-jwgg no longer applies.biahub is now at zero open Dependabot alerts. Verified by rematching the remaining open advisory against the resolved lockfile.
The zarr cap is gone
royerlab/ultrack#284 —
large_chunk_sizenow casts its computed chunk sizes to plain ints instead of leakingnp.int64, sozarr<3.3is no longer needed. zarr moves 3.2.1 → 3.3.0.Verified directly rather than assumed, because the zarr-side fix is merged but not released — zarr-developers/zarr-python#4257 landed, but PyPI is still on the unpatched 3.3.0. Against that exact version:
So dropping the cap is safe because the fix reaching us comes from ultrack's casting, not from zarr. ultrack was the only caller in our tree passing numpy integer chunk sizes (iohub writes
chunk_shapeinto OME-Zarr JSON and never goes through zarr's chunk-normalization path).Python 3.14
pyarrow 25 ships cp314 wheels, so it is no longer the 3.14 blocker that #310 noted. ultrack 0.8 declares
requires-python <3.14instead — still blocked, but by an explicit bound rather than an sdist build that fails on a missing Arrow C++ toolchain.Verification
pytest: 126 passed, 1 skipped — including the track tests that zarr 3.3.0 broke under ultrack 0.7.2ultrack,zarrandpyarrowchange in the lockfile🤖 Generated with Claude Code