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python3Packages.llvmlite: 0.45.0 -> 0.46.0; python3Packages.numba: 0.62.0 -> 0.63.1 #478299

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Merged
kirillrdy merged 2 commits into from
Jan 9, 2026
Merged

python3Packages.llvmlite: 0.45.0 -> 0.46.0; python3Packages.numba: 0.62.0 -> 0.63.1 #478299

kirillrdy merged 2 commits into from
Jan 9, 2026

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@fsagbuya fsagbuya commented Jan 9, 2026

Things done

  • Built on platform:
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • Tested, as applicable:
  • Ran nixpkgs-review on this PR. See nixpkgs-review usage.
  • Tested basic functionality of all binary files, usually in ./result/bin/.
  • Nixpkgs Release Notes
    • Package update: when the change is major or breaking.
  • NixOS Release Notes
    • Module addition: when adding a new NixOS module.
    • Module update: when the change is significant.
  • Fits CONTRIBUTING.md, pkgs/README.md, maintainers/README.md and other READMEs.

Add a 👍 reaction to pull requests you find important.

@fsagbuya fsagbuya added the backport release-25.11 Backport PR automatically label Jan 9, 2026
@nixpkgs-ci nixpkgs-ci bot added 10.rebuild-linux: 101-500 This PR causes between 101 and 500 packages to rebuild on Linux. 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 9.needs: reviewer This PR currently has no reviewers requested and needs attention. 6.topic: python Python is a high-level, general-purpose programming language. labels Jan 9, 2026
@fsagbuya fsagbuya requested a review from kirillrdy January 9, 2026 06:15
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kirillrdy commented Jan 9, 2026

you can now use python3Packages as attribute name in your commits, unless your change is for specific version of python

@fsagbuya
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fsagbuya commented Jan 9, 2026

you can now use python3Packages as attribute name in your commits, unless your change is for specific version of python

I'm confuse when to use one, before I have lint error when using python3Packages.

@nixpkgs-ci nixpkgs-ci bot removed the 9.needs: reviewer This PR currently has no reviewers requested and needs attention. label Jan 9, 2026
@fsagbuya fsagbuya force-pushed the update_llvmlite_numba branch from dfa847c to 524aedb Compare January 9, 2026 06:21
@fsagbuya fsagbuya changed the title python313Packages.llvmlite: 0.45.0 -> 0.46.0; python313Packages.numba: 0.62.0 -> 0.63.1 python3Packages.llvmlite: 0.45.0 -> 0.46.0; python3Packages.numba: 0.62.0 -> 0.63.1 Jan 9, 2026
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kirillrdy commented Jan 9, 2026

you can now use python3Packages as attribute name in your commits, unless your change is for specific version of python

I'm confuse when to use one, before I have lint error when using python3Packages.

you can see https://github.com/NixOS/nixpkgs/pulls?q=is%3Apr+is%3Aopen+python3Packages its pretty common these days

in the past bug in ofborg prevented builds for python3Packages, if you have linter you can disable that rule now

@fsagbuya
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fsagbuya commented Jan 9, 2026

you can now use python3Packages as attribute name in your commits, unless your change is for specific version of python

I'm confuse when to use one, before I have lint error when using python3Packages.

you can see https://github.com/NixOS/nixpkgs/pulls?q=is%3Apr+is%3Aopen+python3Packages its pretty common these days

in the past bug in ofborg prevented builds for python3Packages, if you have linter you can disable that rule now

Thanks. Updated.

kirillrdy
kirillrdy approved these changes Jan 9, 2026
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nixpkgs-review result

Generated using nixpkgs-review.

Command: nixpkgs-review pr 478299
Commit: 524aedb4d9cabf91a3840fd6826fdfe8cb1ce050

x86_64-linux

❌ 14 packages failed to build:
  • dbx
  • dbx.dist
  • python313Packages.clu
  • python313Packages.clu.dist
  • python313Packages.cnvkit
  • python313Packages.cnvkit.dist
  • python313Packages.dm-sonnet
  • python313Packages.dm-sonnet.dist
  • python313Packages.executorch
  • python313Packages.executorch.dist
  • python313Packages.tensorflow-datasets
  • python313Packages.tensorflow-datasets.dist
  • python313Packages.torchrl
  • python313Packages.torchrl.dist
✅ 223 packages built:
  • alpaca
  • backgroundremover
  • backgroundremover.dist
  • beets (beets-minimal, python313Packages.beets, python313Packages.beets-minimal)
  • beets.dist (beets-minimal.dist, python313Packages.beets-minimal.dist, python313Packages.beets.dist)
  • beets.doc (beets-minimal.doc, python313Packages.beets-minimal.doc, python313Packages.beets.doc)
  • beets.man (beets-minimal.man, python313Packages.beets-minimal.man, python313Packages.beets.man)
  • calibre
  • dolfinx
  • exo
  • exo.dist
  • home-assistant-component-tests.tami4
  • lacus
  • lacus.dist
  • minari (python313Packages.minari)
  • minari.dist (python313Packages.minari.dist)
  • mlflow-server
  • mlflow-server.dist
  • molbar (python313Packages.molbar)
  • molbar.dist (python313Packages.molbar.dist)
  • music-assistant
  • music-assistant.dist
  • newelle
  • openai-whisper (python313Packages.openai-whisper)
  • openai-whisper.dist (python313Packages.openai-whisper.dist)
  • pianotrans
  • pianotrans.dist
  • piper-tts
  • piper-tts.dist
  • pitivi
  • python313Packages.ale-py
  • python313Packages.ale-py.dist
  • python313Packages.anndata
  • python313Packages.anndata.dist
  • python313Packages.apricot-select
  • python313Packages.apricot-select.dist
  • python313Packages.array-api-compat
  • python313Packages.array-api-compat.dist
  • python313Packages.arviz
  • python313Packages.arviz.dist
  • python313Packages.awkward
  • python313Packages.awkward-pandas
  • python313Packages.awkward-pandas.dist
  • python313Packages.awkward.dist
  • python313Packages.ax-platform
  • python313Packages.ax-platform.dist
  • python313Packages.bambi
  • python313Packages.bambi.dist
  • python313Packages.beetcamp
  • python313Packages.beetcamp.dist
  • python313Packages.beets-alternatives
  • python313Packages.beets-alternatives.dist
  • python313Packages.beets-audible
  • python313Packages.beets-audible.dist
  • python313Packages.corner
  • python313Packages.corner.dist
  • python313Packages.correctionlib
  • python313Packages.correctionlib.dist
  • python313Packages.cppe
  • python313Packages.cppe.dist
  • python313Packages.dask-glm
  • python313Packages.dask-glm.dist
  • python313Packages.dask-ml
  • python313Packages.dask-ml.dist
  • python313Packages.datashader
  • python313Packages.datashader.dist
  • python313Packages.dscribe
  • python313Packages.dscribe.dist
  • python313Packages.fast-array-utils
  • python313Packages.fast-array-utils.dist
  • python313Packages.fenics-dolfinx
  • python313Packages.fenics-dolfinx.dist
  • python313Packages.fenics-ffcx
  • python313Packages.fenics-ffcx.dist
  • python313Packages.galois
  • python313Packages.galois.dist
  • python313Packages.gumath
  • python313Packages.gumath.dist
  • python313Packages.gymnasium
  • python313Packages.gymnasium.dist
  • python313Packages.kserve
  • python313Packages.kserve.dist
  • python313Packages.lacuscore
  • python313Packages.lacuscore.dist
  • python313Packages.lerobot
  • python313Packages.lerobot.dist
  • python313Packages.librosa
  • python313Packages.librosa.dist
  • python313Packages.llvmlite
  • python313Packages.llvmlite.dist
  • python313Packages.loompy
  • python313Packages.loompy.dist
  • python313Packages.markitdown
  • python313Packages.markitdown.dist
  • python313Packages.mlcroissant
  • python313Packages.mlcroissant.dist
  • python313Packages.mlflow
  • python313Packages.mlflow.dist
  • python313Packages.mmcv
  • python313Packages.mmcv.dist
  • python313Packages.mmengine
  • python313Packages.mmengine.dist
  • python313Packages.mplhep
  • python313Packages.mplhep.dist
  • python313Packages.numba
  • python313Packages.numba-scipy
  • python313Packages.numba-scipy.dist
  • python313Packages.numba.dist
  • python313Packages.numbaWithCuda
  • python313Packages.numbaWithCuda.dist
  • python313Packages.numbagg
  • python313Packages.numbagg.dist
  • python313Packages.numpy-groupies
  • python313Packages.numpy-groupies.dist
  • python313Packages.nutpie
  • python313Packages.nutpie.dist
  • python313Packages.pettingzoo
  • python313Packages.pettingzoo.dist
  • python313Packages.piano-transcription-inference
  • python313Packages.piano-transcription-inference.dist
  • python313Packages.plopp
  • python313Packages.plopp.dist
  • python313Packages.pomegranate
  • python313Packages.pomegranate.dist
  • python313Packages.pyannote-audio
  • python313Packages.pyannote-audio.dist
  • python313Packages.pygmo
  • python313Packages.pymatting
  • python313Packages.pymatting.dist
  • python313Packages.pymc
  • python313Packages.pymc.dist
  • python313Packages.pymoo
  • python313Packages.pymoo.dist
  • python313Packages.pynndescent
  • python313Packages.pynndescent.dist
  • python313Packages.pypasser
  • python313Packages.pypasser.dist
  • python313Packages.pyscf
  • python313Packages.pyscf.dist
  • python313Packages.pytensor
  • python313Packages.pytensor.dist
  • python313Packages.rembg
  • python313Packages.rembg.dist
  • python313Packages.resampy
  • python313Packages.resampy.dist
  • python313Packages.sagemaker-mlflow
  • python313Packages.sagemaker-mlflow.dist
  • python313Packages.scanpy
  • python313Packages.scanpy.dist
  • python313Packages.scikit-bio
  • python313Packages.scikit-bio.dist
  • python313Packages.scikit-tda
  • python313Packages.scikit-tda.dist
  • python313Packages.scipp
  • python313Packages.scipp.dist
  • python313Packages.shap
  • python313Packages.shap.dist
  • python313Packages.shimmy
  • python313Packages.shimmy.dist
  • python313Packages.simple-dftd3
  • python313Packages.simple-dftd3.dist
  • python313Packages.skrl
  • python313Packages.skrl.dist
  • python313Packages.sparse
  • python313Packages.sparse.dist
  • python313Packages.speechrecognition
  • python313Packages.speechrecognition.dist
  • python313Packages.stable-baselines3
  • python313Packages.stable-baselines3.dist
  • python313Packages.stumpy
  • python313Packages.stumpy.dist
  • python313Packages.stytra
  • python313Packages.stytra.dist
  • python313Packages.tami4edgeapi
  • python313Packages.tami4edgeapi.dist
  • python313Packages.tianshou
  • python313Packages.tianshou.dist
  • python313Packages.timezonefinder
  • python313Packages.timezonefinder.dist
  • python313Packages.tinygrad
  • python313Packages.tinygrad.dist
  • python313Packages.torch-audiomentations
  • python313Packages.torch-audiomentations.dist
  • python313Packages.torchcrepe
  • python313Packages.torchcrepe.dist
  • python313Packages.torchlibrosa
  • python313Packages.torchlibrosa.dist
  • python313Packages.torchtune
  • python313Packages.torchtune.dist
  • python313Packages.trackpy
  • python313Packages.trackpy.dist
  • python313Packages.tsfresh
  • python313Packages.tsfresh.dist
  • python313Packages.umap-learn
  • python313Packages.umap-learn.dist
  • python313Packages.uproot
  • python313Packages.uproot.dist
  • python313Packages.vllm
  • python313Packages.vllm.dist
  • python313Packages.vmas
  • python313Packages.vmas.dist
  • whisperx (python313Packages.whisperx)
  • whisperx.dist (python313Packages.whisperx.dist)
  • python313Packages.xarray-einstats
  • python313Packages.xarray-einstats.dist
  • python313Packages.xclim
  • python313Packages.xclim.dist
  • python313Packages.ydata-profiling
  • python313Packages.ydata-profiling.dist
  • rembg
  • rembg.dist
  • sasview
  • sasview.dist
  • supergee
  • tts
  • tts.dist
  • unbook
  • vllm
  • vllm.dist
  • whisper-ctranslate2
  • whisper-ctranslate2.dist
  • wyoming-piper
  • wyoming-piper.dist
Error logs: `x86_64-linux`
python313Packages.cnvkit 
See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
FAILED test/test_commands.py::CommandTests::test_segment_parallel - FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0!
You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy.
A typical example is when you are setting values in a column of a DataFrame, like:

df["col"][row_indexer] = value


Use df.loc[row_indexer, "col"] = values instead, to perform the assignment in a single step and ensure this keeps updating the original df.


See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy

FAILED test/test_r.py::RTests::test_cbs - FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0!

You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy.

A typical example is when you are setting values in a column of a DataFrame, like:


df["col"][row_indexer] = value


Use df.loc[row_indexer, "col"] = values instead, to perform the assignment in a single step and ensure this keeps updating the original df.


See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy

============ 4 failed, 64 passed, 2 deselected in 160.66s (0:02:40) ============

python313Packages.executorch 
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/xx-pad/xx-pad-p4-scalar-u16.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/xx-transposev/xx-transposev-1x1-scalar-memcpy.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2-k-over-64.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2minus-k-over-4.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2-k-over-2048.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2minus-k-over-8.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2minus-k-over-16.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2minus-k-over-32.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2minus-k-over-64.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/exp2minus-k-over-2048.c.o
[ 68%] Building C object backends/xnnpack/third-party/XNNPACK/CMakeFiles/xnnpack-microkernels-prod.dir/src/tables/vlog.c.o
[ 68%] Linking C static library libxnnpack-microkernels-prod.a
[ 68%] Built target xnnpack-microkernels-prod
[ 68%] Linking CXX static library libeigen_blas.a
[ 68%] Built target eigen_blas
make[1]: *** [CMakeFiles/Makefile2:1156: CMakeFiles/portable_lib.dir/rule] Error 2
make: *** [Makefile:221: portable_lib] Error 2
error: command '/nix/store/l49d16mmf8q7fjjpyb5fm9kk7shilhnn-python3.13-cmake-4.1.2/bin/cmake' failed with exit code 2

ERROR Backend subprocess exited when trying to invoke build_wheel

python313Packages.tensorflow-datasets 
ERROR tensorflow_datasets/rl_unplugged/rlu_rwrl/rlu_rwrl_test.py::RluRwrlTest::test_info - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/rl_unplugged/rlu_rwrl/rlu_rwrl_test.py::RluRwrlTest::test_registered - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/rl_unplugged/rlu_rwrl/rlu_rwrl_test.py::RluRwrlTest::test_session - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/rl_unplugged/rlu_rwrl/rlu_rwrl_test.py::RluRwrlTest::test_tags_are_valid - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/dataset_importer_builder_test.py::MockRDSDatasetTestRlds::test_baseclass - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/dataset_importer_builder_test.py::MockRDSDatasetTestRlds::test_info - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/dataset_importer_builder_test.py::MockRDSDatasetTestRlds::test_registered - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/dataset_importer_builder_test.py::MockRDSDatasetTestRlds::test_session - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/dataset_importer_builder_test.py::MockRDSDatasetTestRlds::test_tags_are_valid - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestRlds::test_baseclass - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestRlds::test_info - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestRlds::test_registered - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestRlds::test_session - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestRlds::test_tags_are_valid - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestSd::test_baseclass - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestSd::test_info - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestSd::test_registered - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestSd::test_session - ModuleNotFoundError: No module named 'importlib_resources'
ERROR tensorflow_datasets/robotics/mt_opt/mt_opt_test.py::MtOptTestSd::test_tags_are_valid - ModuleNotFoundError: No module named 'importlib_resources'
= 35 failed, 3195 passed, 570 skipped, 584 warnings, 128 errors in 372.34s (0:06:12) =
python313Packages.torchrl 
SKIPPED [1] test/test_trainer.py:725: torchsnapshot not found
SKIPPED [1] test/test_trainer.py:1021: torchsnapshot not found
SKIPPED [4] test/test_transforms.py:1567: Testing R3M on cuda only
SKIPPED [1] test/test_transforms.py:1634: Testing R3M on cuda only
SKIPPED [8] test/test_transforms.py:1670: Testing R3M on cuda only
SKIPPED [2] test/test_transforms.py:1719: Testing R3M on cuda only
SKIPPED [1] test/test_transforms.py:1771: no dm_control detected
SKIPPED [2] test/test_transforms.py:8938: Testing VIP on cuda only
SKIPPED [4] test/test_transforms.py:8974: Testing VIP on cuda only
SKIPPED [1] test/test_transforms.py:9071: Testing VIP on cuda only
SKIPPED [8] test/test_transforms.py:9161: Testing VIP on cuda only
SKIPPED [2] test/test_transforms.py:9208: Testing VIP on cuda only
SKIPPED [2] test/test_transforms.py:9392: VC1 should run on cuda
SKIPPED [2] test/test_transforms.py:9471: VC1 should run on cuda
SKIPPED [1] test/test_transforms.py:9792: Nested spawned multiprocessed is currently failing in python 3.11. See https://github.com/python/cpython/pull/108568 for info and fix.
SKIPPED [1] test/test_transforms.py:10176: Nested spawned multiprocessed is currently failing in python 3.11. See https://github.com/python/cpython/pull/108568 for info and fix.
SKIPPED [1] test/test_transforms.py:10831: no cuda device found
SKIPPED [1] test/test_transforms.py:11507: no dm_control detected
FAILED test/test_collector.py::TestCollectorGeneric::test_env_that_errors[MultiSyncDataCollector] - ValueError: process object is closed
= 1 failed, 20927 passed, 3055 skipped, 2450 deselected, 82700 warnings in 2011.37s (0:33:31) =

@kirillrdy kirillrdy added this pull request to the merge queue Jan 9, 2026
Merged via the queue into NixOS:master with commit 51a0d41 Jan 9, 2026
28 of 32 checks passed
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nixpkgs-ci bot commented Jan 9, 2026

Successfully created backport PR for release-25.11:

@nixpkgs-ci nixpkgs-ci bot mentioned this pull request Jan 9, 2026
Merged
@github-actions github-actions bot added the 8.has: port to stable This PR already has a backport to the stable release. label Jan 9, 2026
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6.topic: python Python is a high-level, general-purpose programming language. 8.has: port to stable This PR already has a backport to the stable release. 10.rebuild-darwin: 11-100 This PR causes between 11 and 100 packages to rebuild on Darwin. 10.rebuild-linux: 101-500 This PR causes between 101 and 500 packages to rebuild on Linux. backport release-25.11 Backport PR automatically

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