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Merge remote-tracking branch 'upstream/dev' into 8185-test-refactor-2
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‎.github/CODEOWNERS‎

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/monai/ @KumoLiu @ericspod @Nic-Ma
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/docs/ @KumoLiu @ericspod @Nic-Ma
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/tests/ @KumoLiu @ericspod @Nic-Ma
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/.github/ @KumoLiu
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/monai/networks/schedulers/ @virginiafdez
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/monai/inferers/inferer.py @virginiafdez
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/monai/losses/adversarial_loss.py @virginiafdez
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/monai/losses/perceptual.py @virginiafdez
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/monai/networks/blocks/spade_norm.py @virginiafdez
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/monai/networks/nets/autoencoderkl.py @virginiafdez
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/monai/networks/nets/controlnet.py @virginiafdez
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/monai/networks/nets/diffusion_model_unet.py @virginiafdez
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/monai/networks/nets/patchgan_discriminator.py @virginiafdez
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/monai/networks/nets/spade_autoencoderkl.py @virginiafdez
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/monai/networks/nets/spade_diffusion_model_unet.py @virginiafdez
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/monai/networks/nets/spade_network.py @virginiafdez
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/monai/networks/nets/vqvae.py @virginiafdez

‎.github/codecov.yml‎

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flags: null
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paths: null
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# Disable comments on PR
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comment: false
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comment: # enable code coverage comment on PR
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layout: "diff, flags, files"
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behavior: default
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require_changes: false
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require_base: false
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require_head: true
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hide_project_coverage: true
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ignore:
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- "versioneer.py"

‎.github/workflows/conda.yml‎

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os: [ubuntu-latest]
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python-version: ["3.9", "3.10"]
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runs-on: ${{ matrix.os }}
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timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
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env:
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QUICKTEST: True
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steps:

‎.github/workflows/weekly-preview.yml‎

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export YEAR_WEEK=$(date +'%y%U')
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echo "Year week for tag is ${YEAR_WEEK}"
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if ! [[ $YEAR_WEEK =~ ^[0-9]{4}$ ]] ; then echo "Wrong 'year week' format. Should be 4 digits."; exit 1 ; fi
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git tag "1.5.dev${YEAR_WEEK}"
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git tag "1.6.dev${YEAR_WEEK}"
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git log -1
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git tag --list
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python setup.py sdist bdist_wheel

‎CHANGELOG.md‎

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## [Unreleased]
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## [1.5.0] - 2025-06-13
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## What's Changed
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### Added
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* Add platform-specific constraints to setup.cfg (#8260)
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* Add PythonicWorkflow (#8151)
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* Add SM architecture version check (#8199)
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* Add MedNext implementation (#8004)
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* Added a top button to CONSTRIBUTING.md (#8163)
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* Adding CODEOWNERS (#8457)
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* Restormer Implementation (#8312)
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* Add rectified flow noise scheduler for accelerated diffusion model (#8374)
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* Add prediction type for rflow scheduler (#8386)
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* Add Average Precision to metrics (#8089)
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* Implementation of a Masked Autoencoder for representation learning (#8152)
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* Implement TorchIO transforms wrapper analogous to TorchVision transfo… (#7579)
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* 8328 nnunet bundle integration (#8329)
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* Adding Support Policy + Doc Updates (#8458)
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* Classifier free guidance (#8460)
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### Fixed
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* Fix Ruff Numpy2 deprecation rules (#8179)
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* Fix `torch.load()` frequently warning in PersistentDataset and GDSDataset (#8177)
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* Fix the logging of a nested dictionary metric in MLflow (#8169)
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* Fix ImageFilter to allow Gaussian filter without filter_size (#8189)
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* Fix fold_constants, test_handler switched to onnx (#8211)
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* Fix TypeError in meshgrid (#8252)
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* Fix PatchMerging duplicate merging (#8285)
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* Fix test load image issue (#8297)
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* Fix bundle download error from ngc source (#8307)
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* Fix deprecated usage in zarr (#8313, #8477)
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* Fix DataFrame subsets indexing in CSVDataset() (#8351)
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* Fix `packaging` imports in version comparison logic (#8347)
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* Fix CommonKeys docstring (#8342)
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* Fix: correctly apply fftshift to real-valued data inputs (#8407)
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* Fix OptionalImportError: required package `openslide` is not installed (#8419)
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* Fix cosine noise scheduler (#8427)
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* Fix AutoencoderKL docstrings. (#8445)
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* Inverse Threading Fix (#8418)
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* Fix normalize intensity (#8286)
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* Fix path at test onnx trt export (#8361)
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* Fix broken urls (#8481, #8483)
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### Changed
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* [DOC] Update README.md (#8157)
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* Streamlined Rearrange in SpatialAttentionBlock (#8130)
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* Optimize VISTA3D (#8123)
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* Skip torch trt convert test with torch newer than or equal to 2.5.0 (#8165)
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* Enable redirection of all loggers by configuring a FileHandler within the bundle (#8142)
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* Apply pyupgrade fixes for Python 3.9+ syntax (#8150)
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* Update base image to 2410 (#8164)
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* TRT support for MAISI (#8153)
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* 8134 Add unit test for responsive inference (#8146)
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* SwinUNETR refactor to accept additional parameters (#8212)
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* Allow an arbitrary mask to be used in the self attention (#8235)
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* Bump codecov/codecov-action from 4 to 5 (#8245)
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* Docs: update brats classes description (#8246)
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* Change default value of `patch_norm` to False in `SwinUNETR` (#8249)
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* Modify Dice, Jaccard and Tversky losses (#8138)
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* Modify Workflow to Allow IterableDataset Inputs (#8263)
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* Enhance download_and_extract (#8216)
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* Relax gpu load check (#8282, #8275)
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* Using LocalStore in Zarr v3 (#8299)
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* Enable gpu load nifti (#8188)
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* update pydicom reader to enable gpu load (#8283)
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* Zarr compression tests only with versions before 3.0 (#8319)
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* Changing utils.py to test_utils.py (#8335)
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* Refactor testd (#8231)
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* Recursive Item Mapping for Nested Lists in Compose (#8187)
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* Bump min torch to 1.13.1 to mitigate CVE-2022-45907 unsafe usage of eval (#8296)
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* Inferer modification - save_intermediates clashes with latent shape adjustment in latent diffusion inferers (#8343)
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* Solves path problem in test_bundle_trt_export.py (#8357)
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* Modify ControlNet inferer so that it takes in context when the diffus… (#8360)
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* Update monaihosting download method (#8364)
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* Bump torch minimum to mitigate CVE-2024-31580 & CVE-2024-31583 and enable numpy 2 compatibility (#8368)
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* Auto3DSeg algo_template hash update (#8378)
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* Enable Pytorch 2.6 (#8309)
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* Auto3DSeg algo_template hash update (#8393, #8397)
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* Update Dice Metric Docs (#8388)
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* Auto3DSeg algo_template hash update (#8406)
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* Update bundle download API (#8403)
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* Add Skip test in TestTranschex (#8416)
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* Update get latest bundle version function (#8420)
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* Temporarily Restrict setuptools Version to 79.0.1 (#8441)
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* Update default overlap value in occlusion_sensitivity to 0.6 (#8446)
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* Enable code coverage comments on PRs in codecov configuration (#8402)
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* Migrate to modern Python Logger API (#8449)
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### Deprecated
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### Removed
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* Remove deprecated functionality for v1.5 (#8430)
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* Remove deprecated `return_state_dict ` in bundle `load` (#8454)
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* Remove deprecated `net_name` in test file (#8461)
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* Remove unused test cases in bundle load (#8463)
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* selfattention block: Remove the fc linear layer if it is not used (#8325)
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* Removed outdated `torch` version checks from transform functions (#8359)
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## [1.4.0] - 2024-10-17
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### Added
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[highlights]: https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md
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[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.4.0...HEAD
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[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.5.0...HEAD
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[1.5.0]: https://github.com/Project-MONAI/MONAI/compare/1.4.0...1.5.0
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[1.4.0]: https://github.com/Project-MONAI/MONAI/compare/1.3.2...1.4.0
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[1.3.2]: https://github.com/Project-MONAI/MONAI/compare/1.3.1...1.3.2
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[1.3.1]: https://github.com/Project-MONAI/MONAI/compare/1.3.0...1.3.1

‎CITATION.cff‎

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abstract: "AI Toolkit for Healthcare Imaging"
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authors:
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- name: "MONAI Consortium"
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date-released: 2024-10-17
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version: "1.4.0"
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date-released: 2025-06-13
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version: "1.5.0"
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identifiers:
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- description: "This DOI represents all versions of MONAI, and will always resolve to the latest one."
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type: doi

‎CONTRIBUTING.md‎

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A bash script (`runtests.sh`) is provided to run all tests locally.
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Please run ``./runtests.sh -h`` to see all options.
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To run a particular test, for example `tests/losses/test_dice_loss.py`:
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```
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python -m tests.test_dice_loss
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python -m tests.losses.test_dice_loss
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Before submitting a pull request, we recommend that all linting and unit tests

‎README.md‎

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- customizable design for varying user expertise;
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- multi-GPU multi-node data parallelism support.
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## Requirements
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MONAI works with the [currently supported versions of Python](https://devguide.python.org/versions), and depends directly on NumPy and PyTorch with many optional dependencies.
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* Major releases of MONAI will have dependency versions stated for them. The current state of the `dev` branch in this repository is the unreleased development version of MONAI which typically will support current versions of dependencies and include updates and bug fixes to do so.
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* PyTorch support covers [the current version](https://github.com/pytorch/pytorch/releases) plus three previous minor versions. If compatibility issues with a PyTorch version and other dependencies arise, support for a version may be delayed until a major release.
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* Our support policy for other dependencies adheres for the most part to [SPEC0](https://scientific-python.org/specs/spec-0000), where dependency versions are supported where possible for up to two years. Discovered vulnerabilities or defects may require certain versions to be explicitly not supported.
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* See the `requirements*.txt` files for dependency version information.
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[MedNIST demo](https://colab.research.google.com/drive/1wy8XUSnNWlhDNazFdvGBHLfdkGvOHBKe) and [MONAI for PyTorch Users](https://colab.research.google.com/drive/1boqy7ENpKrqaJoxFlbHIBnIODAs1Ih1T) are available on Colab.
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[MedNIST demo](https://colab.research.google.com/github/Project-MONAI/tutorials/blob/main/2d_classification/mednist_tutorial.ipynb) and [MONAI for PyTorch Users](https://colab.research.google.com/github/Project-MONAI/tutorials/blob/main/modules/developer_guide.ipynb) are available on Colab.
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Examples and notebook tutorials are located at [Project-MONAI/tutorials](https://github.com/Project-MONAI/tutorials).
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## Community
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Join the conversation on Twitter/X [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join our [Slack channel](https://forms.gle/QTxJq3hFictp31UM9).
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Join the conversation on Twitter/X [@ProjectMONAI](https://twitter.com/ProjectMONAI), [LinkedIn](https://www.linkedin.com/company/projectmonai), or join our [Slack channel](https://forms.gle/QTxJq3hFictp31UM9).
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Ask and answer questions over on [MONAI's GitHub Discussions tab](https://github.com/Project-MONAI/MONAI/discussions).
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‎docs/images/maisi_infer.png‎

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‎docs/requirements.txt‎

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-f https://download.pytorch.org/whl/cpu/torch-2.4.1%2Bcpu-cp39-cp39-linux_x86_64.whl
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torch>=2.4.1, <2.7.0
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pytorch-ignite==0.4.11
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numpy>=1.20

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