Docker Slim Image #8640

ericspod · 2025-11-23T00:17:49Z

Description

This is an attempt to create a slim Docker image which is smaller than the current one to avoid running out of space during testing. Various fixes have been included to account for test fails within the image. These appear to be all real issues that need to be addressed (eg. ONNX export) or fixes that should be integrated either way.

This excludes PyTorch 2.9 from the requirements for now to avoid legacy issues with ONNX, Torchscript, and other things. MONAI needs to be updated for PyTorch 2.9 support, specifically dropping the use of Torchscript in places as it's becoming obsolete in place of torch.export.

Some tests fail without enough shared memory, the command I'm using to run with is docker run -ti --rm --gpus '"device=0,1"' --shm-size=10gb -v $(pwd)/tests:/opt/monai/tests monai_slim /bin/bash to tests with GPUs 0 and 1.

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Signed-off-by: Eric Kerfoot <eric.kerfoot@gmail.com>

…n the slim Docker image, all of which appear to be real errors. Signed-off-by: Eric Kerfoot <eric.kerfoot@gmail.com>

for more information, see https://pre-commit.ci

…ply.github.com> I, Eric Kerfoot <17726042+ericspod@users.noreply.github.com>, hereby add my Signed-off-by to this commit: 566c2bc Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

I, Eric Kerfoot <eric.kerfoot@kcl.ac.uk>, hereby add my Signed-off-by to this commit: 510987d Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

coderabbitai · 2025-11-23T01:15:57Z

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Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

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ericspod · 2025-12-06T22:28:47Z

Nine tests in the image currently fail. The first 4 are related to auto3dseg and mention a value "image_stats" being missing from a config file, these tests pass when run in isolation however. The others relate to the GMM module and not being able to compile it since nvcc is missing from image, which is true since the CUDA toolkit is omitted for size reasons.

Output of the errors

======================================================================
ERROR: test_ensemble (tests.integration.test_auto3dseg_ensemble.TestEnsembleBuilder.test_ensemble)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/monai/monai/bundle/config_parser.py", line 158, in __getitem__
    look_up_option(k, config, print_all_options=False) if isinstance(config, dict) else config[int(k)]
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/utils/module.py", line 141, in look_up_option
    raise ValueError(f"Unsupported option '{opt_str}', " + supported_msg)
ValueError: Unsupported option 'image_stats', 

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/monai/tests/integration/test_auto3dseg_ensemble.py", line 155, in test_ensemble
    bundle_generator.generate(self.work_dir, num_fold=1)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 660, in generate
    gen_algo.export_to_disk(output_folder, name, fold=f_id)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 193, in export_to_disk
    self.fill_records = self.fill_template_config(self.data_stats_files, self.output_path, **kwargs)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp324gd5iq/workdir/algorithm_templates/dints/scripts/algo.py", line 79, in fill_template_config
  File "/opt/monai/monai/bundle/config_parser.py", line 161, in __getitem__
    raise KeyError(f"query key: {k}") from e
KeyError: 'query key: image_stats'

======================================================================
ERROR: test_get_history (tests.integration.test_auto3dseg_hpo.TestHPO.test_get_history)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/monai/monai/bundle/config_parser.py", line 158, in __getitem__
    look_up_option(k, config, print_all_options=False) if isinstance(config, dict) else config[int(k)]
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/utils/module.py", line 141, in look_up_option
    raise ValueError(f"Unsupported option '{opt_str}', " + supported_msg)
ValueError: Unsupported option 'image_stats', 

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/monai/tests/integration/test_auto3dseg_hpo.py", line 129, in setUp
    bundle_generator.generate(work_dir, num_fold=1)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 660, in generate
    gen_algo.export_to_disk(output_folder, name, fold=f_id)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 193, in export_to_disk
    self.fill_records = self.fill_template_config(self.data_stats_files, self.output_path, **kwargs)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp324gd5iq/workdir/algorithm_templates/dints/scripts/algo.py", line 79, in fill_template_config
  File "/opt/monai/monai/bundle/config_parser.py", line 161, in __getitem__
    raise KeyError(f"query key: {k}") from e
KeyError: 'query key: image_stats'

======================================================================
ERROR: test_run_algo (tests.integration.test_auto3dseg_hpo.TestHPO.test_run_algo)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/monai/monai/bundle/config_parser.py", line 158, in __getitem__
    look_up_option(k, config, print_all_options=False) if isinstance(config, dict) else config[int(k)]
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/utils/module.py", line 141, in look_up_option
    raise ValueError(f"Unsupported option '{opt_str}', " + supported_msg)
ValueError: Unsupported option 'image_stats', 

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/monai/tests/integration/test_auto3dseg_hpo.py", line 129, in setUp
    bundle_generator.generate(work_dir, num_fold=1)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 660, in generate
    gen_algo.export_to_disk(output_folder, name, fold=f_id)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 193, in export_to_disk
    self.fill_records = self.fill_template_config(self.data_stats_files, self.output_path, **kwargs)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp324gd5iq/workdir/algorithm_templates/dints/scripts/algo.py", line 79, in fill_template_config
  File "/opt/monai/monai/bundle/config_parser.py", line 161, in __getitem__
    raise KeyError(f"query key: {k}") from e
KeyError: 'query key: image_stats'

======================================================================
ERROR: test_run_optuna (tests.integration.test_auto3dseg_hpo.TestHPO.test_run_optuna)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/monai/monai/bundle/config_parser.py", line 158, in __getitem__
    look_up_option(k, config, print_all_options=False) if isinstance(config, dict) else config[int(k)]
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/utils/module.py", line 141, in look_up_option
    raise ValueError(f"Unsupported option '{opt_str}', " + supported_msg)
ValueError: Unsupported option 'image_stats', 

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/monai/tests/integration/test_auto3dseg_hpo.py", line 129, in setUp
    bundle_generator.generate(work_dir, num_fold=1)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 660, in generate
    gen_algo.export_to_disk(output_folder, name, fold=f_id)
  File "/opt/monai/monai/apps/auto3dseg/bundle_gen.py", line 193, in export_to_disk
    self.fill_records = self.fill_template_config(self.data_stats_files, self.output_path, **kwargs)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmp324gd5iq/workdir/algorithm_templates/dints/scripts/algo.py", line 79, in fill_template_config
  File "/opt/monai/monai/bundle/config_parser.py", line 161, in __getitem__
    raise KeyError(f"query key: {k}") from e
KeyError: 'query key: image_stats'

======================================================================
ERROR: test_cuda_0_2_batches_1_dimensions_1_channels_2_classes_2_mixtures (tests.networks.layers.test_gmm.GMMTestCase.test_cuda_0_2_batches_1_dimensions_1_channels_2_classes_2_mixtures)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2595, in _run_ninja_build
    subprocess.run(
  File "/usr/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 127.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/tests/networks/layers/test_gmm.py", line 287, in test_cuda
    gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/networks/layers/gmm.py", line 44, in __init__
    self.compiled_extension = load_module(
                              ^^^^^^^^^^^^
  File "/opt/monai/monai/_extensions/loader.py", line 89, in load_module
    module = load(
             ^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 1681, in load
    return _jit_compile(
           ^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2138, in _jit_compile
    _write_ninja_file_and_build_library(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2290, in _write_ninja_file_and_build_library
    _run_ninja_build(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2612, in _run_ninja_build
    raise RuntimeError(message) from e
RuntimeError: Error building extension 'gmm_1_2_1_Linux_3_11_2_28_12_8'

======================================================================
ERROR: test_cuda_1_1_batches_1_dimensions_5_channels_2_classes_1_mixtures (tests.networks.layers.test_gmm.GMMTestCase.test_cuda_1_1_batches_1_dimensions_5_channels_2_classes_1_mixtures)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2595, in _run_ninja_build
    subprocess.run(
  File "/usr/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 127.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/tests/networks/layers/test_gmm.py", line 287, in test_cuda
    gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/networks/layers/gmm.py", line 44, in __init__
    self.compiled_extension = load_module(
                              ^^^^^^^^^^^^
  File "/opt/monai/monai/_extensions/loader.py", line 89, in load_module
    module = load(
             ^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 1681, in load
    return _jit_compile(
           ^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2138, in _jit_compile
    _write_ninja_file_and_build_library(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2290, in _write_ninja_file_and_build_library
    _run_ninja_build(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2612, in _run_ninja_build
    raise RuntimeError(message) from e
RuntimeError: Error building extension 'gmm_5_2_1_Linux_3_11_2_28_12_8'

======================================================================
ERROR: test_cuda_2_1_batches_2_dimensions_2_channels_4_classes_4_mixtures (tests.networks.layers.test_gmm.GMMTestCase.test_cuda_2_1_batches_2_dimensions_2_channels_4_classes_4_mixtures)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2595, in _run_ninja_build
    subprocess.run(
  File "/usr/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 127.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/tests/networks/layers/test_gmm.py", line 287, in test_cuda
    gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/networks/layers/gmm.py", line 44, in __init__
    self.compiled_extension = load_module(
                              ^^^^^^^^^^^^
  File "/opt/monai/monai/_extensions/loader.py", line 89, in load_module
    module = load(
             ^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 1681, in load
    return _jit_compile(
           ^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2138, in _jit_compile
    _write_ninja_file_and_build_library(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2290, in _write_ninja_file_and_build_library
    _run_ninja_build(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2612, in _run_ninja_build
    raise RuntimeError(message) from e
RuntimeError: Error building extension 'gmm_2_4_1_Linux_3_11_2_28_12_8'

======================================================================
ERROR: test_cuda_3_1_batches_3_dimensions_1_channels_2_classes_1_mixtures (tests.networks.layers.test_gmm.GMMTestCase.test_cuda_3_1_batches_3_dimensions_1_channels_2_classes_1_mixtures)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2595, in _run_ninja_build
    subprocess.run(
  File "/usr/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 127.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/parameterized/parameterized.py", line 620, in standalone_func
    return func(*(a + p.args), **p.kwargs, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/tests/networks/layers/test_gmm.py", line 287, in test_cuda
    gmm = GaussianMixtureModel(features_tensor.size(1), mixture_count, class_count, verbose_build=True)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/monai/monai/networks/layers/gmm.py", line 44, in __init__
    self.compiled_extension = load_module(
                              ^^^^^^^^^^^^
  File "/opt/monai/monai/_extensions/loader.py", line 89, in load_module
    module = load(
             ^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 1681, in load
    return _jit_compile(
           ^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2138, in _jit_compile
    _write_ninja_file_and_build_library(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2290, in _write_ninja_file_and_build_library
    _run_ninja_build(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2612, in _run_ninja_build
    raise RuntimeError(message) from e
RuntimeError: Error building extension 'gmm_1_2_1_Linux_3_11_2_28_12_8_v1'

======================================================================
ERROR: test_load (tests.networks.layers.test_gmm.GMMTestCase.test_load)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2595, in _run_ninja_build
    subprocess.run(
  File "/usr/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['ninja', '-v']' returned non-zero exit status 127.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/monai/tests/networks/layers/test_gmm.py", line 310, in test_load
    load_module("gmm", {"CHANNEL_COUNT": 2, "MIXTURE_COUNT": 2, "MIXTURE_SIZE": 3}, verbose_build=True)
  File "/opt/monai/monai/_extensions/loader.py", line 89, in load_module
    module = load(
             ^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 1681, in load
    return _jit_compile(
           ^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2138, in _jit_compile
    _write_ninja_file_and_build_library(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2290, in _write_ninja_file_and_build_library
    _run_ninja_build(
  File "/usr/local/lib/python3.11/dist-packages/torch/utils/cpp_extension.py", line 2612, in _run_ninja_build
    raise RuntimeError(message) from e
RuntimeError: Error building extension 'gmm_2_2_3_Linux_3_11_2_28_12_8'

It's a simple matter of forcing the GMM module to build when building the image, this also fails if used as a RUN command: python -c 'from monai._extensions import load_module;load_module("gmm", {"CHANNEL_COUNT": 2, "MIXTURE_COUNT": 2, "MIXTURE_SIZE": 3}, verbose_build=True)'

ericspod and others added 13 commits July 16, 2025 18:03

Initial version of a slim Dockerfile

510987d

Updates to clean up build

983a833

Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Updates to produce slimmest Docker image possible

566c2bc

Update to dockerfile with a possibly working config

a07a861

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Update

47b3ce3

Signed-off-by: Eric Kerfoot <eric.kerfoot@gmail.com>

Merge remote-tracking branch 'origin/dev' into docker_slim

463bb91

Merge remote-tracking branch 'origin/dev' into docker_slim

23b7fb6

Updates to various components, tests, and configs to pass tests withi…

5e7283f

…n the slim Docker image, all of which appear to be real errors. Signed-off-by: Eric Kerfoot <eric.kerfoot@gmail.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

7942ab3

for more information, see https://pre-commit.ci

DCO Remediation Commit for Eric Kerfoot <17726042+ericspod@users.nore…

9887f81

…ply.github.com> I, Eric Kerfoot <17726042+ericspod@users.noreply.github.com>, hereby add my Signed-off-by to this commit: 566c2bc Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

DCO Remediation Commit for Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

4e7d7c5

I, Eric Kerfoot <eric.kerfoot@kcl.ac.uk>, hereby add my Signed-off-by to this commit: 510987d Signed-off-by: Eric Kerfoot <eric.kerfoot@kcl.ac.uk>

Merge branch 'dev' into docker_slim

cd88b32

Fix

3cdf717

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Project-MONAI deleted a comment from coderabbitai bot Nov 23, 2025

Cleanup

4d6e1bb

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

ericspod mentioned this pull request Dec 1, 2025

Test erros on PyTorch Release 25.08 on Series 50 #8587

Open

ericspod and others added 4 commits December 4, 2025 23:25

Experimenting with stages without CUDA toolkit

fc937d0

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Nearly final version of dockerfile, all but 9 tests pass

90fb7ef

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

Merge branch 'dev' into docker_slim

7421580

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>

[pre-commit.ci] auto fixes from pre-commit.com hooks

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for more information, see https://pre-commit.ci

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