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build(deps): bump monai from 1.3.2 to 1.4.0 in /requirements #2795

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merged 2 commits into from
Oct 22, 2024

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@dependabot dependabot bot commented on behalf of github Oct 21, 2024

Bumps monai from 1.3.2 to 1.4.0.

Release notes

Sourced from monai's releases.

1.4.0

Added

  • Implemented Conjugate Gradient Solver to generate confidence maps. (#7876)
  • Added norm parameter to ResNet (#7752, #7805)
  • Introduced alpha parameter to DiceFocalLoss for improved flexibility (#7841)
  • Integrated Tailored ControlNet Implementations (#7875)
  • Integrated Tailored Auto-Encoder Model (#7861)
  • Integrated Tailored Diffusion U-Net Model (7867)
  • Added Maisi morphological functions (#7893)
  • Added support for downloading bundles from NGC private registry (#7907, #7929, #8076)
  • Integrated generative refactor into the core (#7886, #7962)
  • Made ViT and UNETR models compatible with TorchScript (#7937)
  • Implemented post-download checks for MONAI bundles and compatibility warnings (#7938)
  • Added NGC prefix argument when downloading bundles (7974)
  • Added flash attention support in the attention block for improved performance (#7977)
  • Enhanced MLPBlock for compatibility with VISTA-3D (#7995)
  • Added support for Neighbor-Aware Calibration Loss (NACL) for calibrated models in segmentation tasks (#7819)
  • Added label_smoothing parameter to DiceCELoss for enhanced model calibration (#8000)
  • Add include_fc and use_combined_linear argument in the SABlock (#7996)
  • Added utilities, networks, and an inferer specific to VISTA-3D (#7999, #7987, #8047, #8059, #8021)
  • Integrated a new network, CellSamWrapper, for cell-based applications (#7981)
  • Introduced WriteFileMapping transform to map between input image paths and their corresponding output paths (#7769)
  • Added TrtHandler to accelerate models using TensorRT (#7990, #8064)
  • Added box and points conversion transforms for more flexible spatial manipulation (#8053)
  • Enhanced RandSimulateLowResolutiond transform with deterministic support (#8057)
  • Added a contiguous argument to the Fourier class to facilitate contiguous tensor outputs (#7969)
  • Allowed ApplyTransformToPointsd to receive a sequence of reference keys for more versatile point manipulation (#8063)
  • Made MetaTensor an optional print in DataStats and DataStatsd for more concise logging (#7814)

misc.

  • Refactored Dataset to utilize Compose for handling transforms. (#7784)
  • Combined map_classes_to_indices and generate_label_classes_crop_centers into a unified function (#7712)
  • Introduced metadata schema directly into the codebase for improved structure and validation (#7409)
  • Renamed optional_packages_version to required_packages_version for clearer package dependency management. (#7253)
  • Replaced pkg_resources with the more modern packaging module for package handling (#7953)
  • Refactored MAISI-related networks to align with the new generative components (#7989, #7993, #8005)
  • Added a badge displaying monthly download statistics to enhance project visibility (#7891)

Fixed

transforms

  • Ensured deterministic behavior in MixUp, CutMix, and CutOut transforms (#7813)
  • Applied a minor correction to AsDiscrete transform (#7984)
  • Fixed handling of integer weightmaps in RandomWeightedCrop (#8097)
  • Resolved data type bug in ScaleIntensityRangePercentile (#8109)

data

  • Fixed negative strides issue in the NrrdReader (#7809)
  • Addressed wsireader issue with retrieving MPP (7921)
  • Ensured location is returned as a tuple in wsireader (#8007)
  • Corrected interpretation of space directions in nrrd reader (#8091)

metrics and losses

  • Improved memory management for NACLLoss (#8020)
  • Fixed reduction logic in GeneralizedDiceScore (#7970)

... (truncated)

Changelog

Sourced from monai's changelog.

[1.4.0] - 2024-10-17

What's Changed

Added

  • Implemented Conjugate Gradient Solver to generate confidence maps. (#7876)
  • Added norm parameter to ResNet (#7752, #7805)
  • Introduced alpha parameter to DiceFocalLoss for improved flexibility (#7841)
  • Integrated Tailored ControlNet Implementations (#7875)
  • Integrated Tailored Auto-Encoder Model (#7861)
  • Integrated Tailored Diffusion U-Net Model (7867)
  • Added Maisi morphological functions (#7893)
  • Added support for downloading bundles from NGC private registry (#7907, #7929, #8076)
  • Integrated generative refactor into the core (#7886, #7962)
  • Made ViT and UNETR models compatible with TorchScript (#7937)
  • Implemented post-download checks for MONAI bundles and compatibility warnings (#7938)
  • Added NGC prefix argument when downloading bundles (#7974)
  • Added flash attention support in the attention block for improved performance (#7977)
  • Enhanced MLPBlock for compatibility with VISTA-3D (#7995)
  • Added support for Neighbor-Aware Calibration Loss (NACL) for calibrated models in segmentation tasks (#7819)
  • Added label_smoothing parameter to DiceCELoss for enhanced model calibration (#8000)
  • Add include_fc and use_combined_linear argument in the SABlock (#7996)
  • Added utilities, networks, and an inferer specific to VISTA-3D (#7999, #7987, #8047, #8059, #8021)
  • Integrated a new network, CellSamWrapper, for cell-based applications (#7981)
  • Introduced WriteFileMapping transform to map between input image paths and their corresponding output paths (#7769)
  • Added TrtHandler to accelerate models using TensorRT (#7990, #8064)
  • Added box and points conversion transforms for more flexible spatial manipulation (#8053)
  • Enhanced RandSimulateLowResolutiond transform with deterministic support (#8057)
  • Added a contiguous argument to the Fourier class to facilitate contiguous tensor outputs (#7969)
  • Allowed ApplyTransformToPointsd to receive a sequence of reference keys for more versatile point manipulation (#8063)
  • Made MetaTensor an optional print in DataStats and DataStatsd for more concise logging (#7814)

misc.

  • Refactored Dataset to utilize Compose for handling transforms. (#7784)
  • Combined map_classes_to_indices and generate_label_classes_crop_centers into a unified function (#7712)
  • Introduced metadata schema directly into the codebase for improved structure and validation (#7409)
  • Renamed optional_packages_version to required_packages_version for clearer package dependency management. (#7253)
  • Replaced pkg_resources with the more modern packaging module for package handling (#7953)
  • Refactored MAISI-related networks to align with the new generative components (#7989, #7993, #8005)
  • Added a badge displaying monthly download statistics to enhance project visibility (#7891)

Fixed

transforms

  • Ensured deterministic behavior in MixUp, CutMix, and CutOut transforms (#7813)
  • Applied a minor correction to AsDiscrete transform (#7984)
  • Fixed handling of integer weightmaps in RandomWeightedCrop (#8097)
  • Resolved data type bug in ScaleIntensityRangePercentile (#8109)

data

  • Fixed negative strides issue in the NrrdReader (#7809)
  • Addressed wsireader issue with retrieving MPP (7921)
  • Ensured location is returned as a tuple in wsireader (#8007)
  • Corrected interpretation of space directions in nrrd reader (#8091)

metrics and losses

  • Improved memory management for NACLLoss (#8020)

... (truncated)

Commits

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📚 Documentation preview 📚: https://torchmetrics--2795.org.readthedocs.build/en/2795/

@dependabot dependabot bot added the test / CI testing or CI label Oct 21, 2024
@dependabot dependabot bot requested a review from a team October 21, 2024 23:28
Bumps [monai](https://github.com/Project-MONAI/MONAI) from 1.3.2 to 1.4.0.
- [Release notes](https://github.com/Project-MONAI/MONAI/releases)
- [Changelog](https://github.com/Project-MONAI/MONAI/blob/dev/CHANGELOG.md)
- [Commits](Project-MONAI/MONAI@1.3.2...1.4.0)

---
updated-dependencies:
- dependency-name: monai
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot force-pushed the dependabot-pip-requirements-monai-1.4.0 branch from ba459e7 to 947282d Compare October 22, 2024 06:00
@stancld stancld self-requested a review October 22, 2024 08:05
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@SkafteNicki SkafteNicki left a comment

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I can see that tests related to monai are failing so I am going to block this for now

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codecov bot commented Oct 22, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 34%. Comparing base (06f2015) to head (e966a14).
Report is 1 commits behind head on master.

Additional details and impacted files
@@           Coverage Diff            @@
##           master   #2795     +/-   ##
========================================
- Coverage      69%     34%    -34%     
========================================
  Files         336     336             
  Lines       18215   18215             
========================================
- Hits        12494    6276   -6218     
- Misses       5721   11939   +6218     

@Borda Borda enabled auto-merge (squash) October 22, 2024 09:27
@Borda Borda merged commit d1d3242 into master Oct 22, 2024
64 of 65 checks passed
@Borda Borda deleted the dependabot-pip-requirements-monai-1.4.0 branch October 22, 2024 09:40
@mergify mergify bot added the ready label Oct 22, 2024
Borda pushed a commit that referenced this pull request Oct 22, 2024
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nicki Skafte <skaftenicki@gmail.com>
(cherry picked from commit d1d3242)
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3 participants