[RELEASE] cucim v24.10 #788
Merged
Conversation
This file contains 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
Forward-merge branch-24.08 into branch-24.10
…ration (#757) The following section of the dependencies.yaml was being ignored: ``` develop: common: - output_types: [conda, requirements, pyproject] packages: - pre-commit - black - ruff - isort ``` I noticed this because changing any values here and then running `rapids-dependency-file-generator` did not cause any corresponding change in the `pyproject.toml`. The root cause is the files section was defining `py_develop` twice (lines 64 and 72). The first time pointed to the desired `develop:` section shown above, but the second, duplicate one pointed to the `docs:` section instead. I renamed the second file target to `py_docs` to avoid ignoring the developer dependencies section. I tested locally by making changes to the develop: section to verify that they would now show up in the `pyproject.toml`. Ideally we could have `rapids-dependency-file-generator` raise an error or print a warning if duplicate names like this were found. Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - Ray Douglass (https://github.com/raydouglass) - https://github.com/jakirkham URL: #757
Forward-merge branch-24.08 into branch-24.10
Addresses an issue caught by [the style check]( https://github.com/rapidsai/cucim/actions/runs/10294105182/job/28491583850?pr=753#step:6:58 ). Namely a minor spelling issue Authors: - https://github.com/jakirkham Approvers: - Gigon Bae (https://github.com/gigony) - Gregory Lee (https://github.com/grlee77) URL: #759
This PR updates pre-commit hooks to the latest versions that are supported without causing style check errors. Authors: - Kyle Edwards (https://github.com/KyleFromNVIDIA) Approvers: - James Lamb (https://github.com/jameslamb) URL: #760
Remove the `pytest-lazy-fixture` plugin and use the replacement `pytest-lazy-fixtures` package instead. Address #755 Authors: - Gigon Bae (https://github.com/gigony) Approvers: - https://github.com/jakirkham URL: #756
…scalars (#764) This change avoids an issue with an internal `numpy.can_cast` call in CuPy's kernel fusion code when using NumPy 2.0. With this change all cuCIM tests passed using NumPy 2.0.1 and the CuPy 13.3dev branch. Fixes #742 Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - https://github.com/jakirkham - Gigon Bae (https://github.com/gigony) URL: #764
Contributes to rapidsai/build-planning#88 Finishes the work of dropping Python 3.9 support. This project stopped building / testing against Python 3.9 as of rapidsai/shared-workflows#235. This PR updates configuration and docs to reflect that. ## Notes for Reviewers ### How I tested this Checked that there were no remaining uses like this: ```shell git grep -E '3\.9' git grep '39' git grep 'py39' ``` And similar for variations on Python 3.8 (to catch things that were missed the last time this was done). Authors: - James Lamb (https://github.com/jameslamb) Approvers: - Gregory Lee (https://github.com/grlee77) - https://github.com/jakirkham - Bradley Dice (https://github.com/bdice) - Jake Awe (https://github.com/AyodeAwe) URL: #766
Fixes #768 Authors: - Gregory Lee (https://github.com/grlee77) - https://github.com/jakirkham Approvers: - https://github.com/jakirkham URL: #769
This PR removes the NumPy<2 pin which is expected to work for RAPIDS projects once CuPy 13.3.0 is released (CuPy 13.2.0 had some issues preventing the use with NumPy 2). Authors: - Sebastian Berg (https://github.com/seberg) - https://github.com/jakirkham Approvers: - James Lamb (https://github.com/jameslamb) - Gregory Lee (https://github.com/grlee77) - https://github.com/jakirkham URL: #762
This PR updates rapidsai/pre-commit-hooks to the version 0.4.0. Authors: - Kyle Edwards (https://github.com/KyleFromNVIDIA) Approvers: - James Lamb (https://github.com/jameslamb) URL: #772
We currently bundle some custom 2D convolution kernels not present in CuPy. We have additional testing of these internel kernels, but I found that on the Windows platform a subset of these tests currently fail. This MR disables auto-selection of these kernels on the Windows platform (will always fall back to CuPy's `cupyx.scipy.ndimage` kernels in this case). The test cases that are currently known to fail are skipped for now on Windows. Longer term it would be good to resolve the issues with the kernels, restore the test cases and enable use of these kernels on Windows. Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - https://github.com/jakirkham URL: #770
Contributes to rapidsai/build-planning#40 This PR adds support for Python 3.12. ## Notes for Reviewers This is part of ongoing work to add Python 3.12 support across RAPIDS. It temporarily introduces a build/test matrix including Python 3.12, from rapidsai/shared-workflows#213. A follow-up PR will revert back to pointing at the `branch-24.10` branch of `shared-workflows` once all RAPIDS repos have added Python 3.12 support. ### This will fail until all dependencies have been updates to Python 3.12 CI here is expected to fail until all of this project's upstream dependencies support Python 3.12. This can be merged whenever all CI jobs are passing. Authors: - James Lamb (https://github.com/jameslamb) Approvers: - Bradley Dice (https://github.com/bdice) URL: #773
Recently RAPIDS added wheel tests on Rocky Linux 8. This requires a change to support installing dependencies with `yum` on Rocky Linux 8. Authors: - Bradley Dice (https://github.com/bdice) Approvers: - James Lamb (https://github.com/jameslamb) URL: #774
While adding support for Python 3.12 in #773, we found a problem where `GPUtil` does not support Python 3.12 (#775). This PR removes the dependency on `GPUtil` and replaces it with `cupy`, which is already a dependency. Closes #775. Closes #776. Authors: - Bradley Dice (https://github.com/bdice) Approvers: - James Lamb (https://github.com/jameslamb) - Gregory Lee (https://github.com/grlee77) - Gigon Bae (https://github.com/gigony) URL: #777
…rmance of blob detectors and `corner_peaks`) (#782) It seems that we can get a large speedup in calls to `peak_local_max` when the default `min_distance=1` is specified. A bottleneck in that function can be the call to `ensure_spacing` which falls back to the CPU, but we don't need to call that function at all unless `min_distance>1` (no coordinates can be excluded if min_distance=1, so it is pointless to call it). I proposed the same changes upstream in scikit-image/scikit-image#7548. See additional comments and measurements made there. There should be no change in behavior with this MR, it is purely a performance improvement. Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - Gigon Bae (https://github.com/gigony) URL: #782
CuPy 13.3 removed dependence on jitify (see: cupy/cupy#8473) Make the same change in our vendored code (but only if CuPy >= 13.3). Authors: - Gregory Lee (https://github.com/grlee77) Approvers: - https://github.com/jakirkham URL: #781
Libraries such as jbig, libwebp-base, and zlib are not used for the functionality of cuCIM. These codec libraries are linked to libtiff only when available at build time. This patch explicitly disables external codecs and removes unnecessary dependencies from the `dependencies.yaml`. With this patch, I can confirm that they are not requested at all. ``` -- Support for external codecs: -- ZLIB support: OFF (requested) (availability) -- Pixar log-format algorithm: OFF (requested) FALSE (availability) -- JPEG support: OFF (requested) TRUE (availability) -- Old JPEG support: OFF (requested) TRUE (availability) -- JPEG 8/12 bit dual mode: OFF (requested) FALSE (availability) -- ISO JBIG support: OFF (requested) FALSE (availability) -- LZMA2 support: OFF (requested) (availability) -- ZSTD support: OFF (requested) (availability) -- WEBP support: OFF (requested) FALSE (availability) ``` Authors: - Gigon Bae (https://github.com/gigony) Approvers: - James Lamb (https://github.com/jameslamb) - https://github.com/jakirkham URL: #785
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #788 +/- ##
==========================================
+ Coverage 93.49% 93.56% +0.07%
==========================================
Files 129 129
Lines 10039 10044 +5
==========================================
+ Hits 9386 9398 +12
+ Misses 653 646 -7 ☔ View full report in Codecov by Sentry. |
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.
❄️ Code freeze for
branch-24.10and v24.10 releaseWhat does this mean?
Only critical/hotfix level issues should be merged into
branch-24.10until release (merging of this PR).What is the purpose of this PR?
branch-24.10intomainfor the release