This is an automatic packaging of SimpleITK based on the main branch. It contains the latest features and experimental developments.

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/latest

What's Changed

• ENH: Add support for ITK SingleMultiThreader by @blowekamp in #2590
• ENH: Add Python examples and documentation for Elastix by @blowekamp in #2598
• BUG: Fix Elastix SuperBuild dep when using system ITK by @blowekamp in #2600
• ENH: Add C#, Java, Lua, and R examples for Elastix by @blowekamp in #2599
• FIX: Correct build names to match enabled languages by @blowekamp in #2603
• BUG: Add virtual destructor to ImageViewer by @blowekamp in #2602
• ENH: Update CMake version to 3.31.0 by @blowekamp in #2601
• DOC: Add release notes for v3.0.0b1 by @blowekamp in #2597
• Simplify wrapping logic by setting WRAP_ in each wrapper by @blowekamp in #2604
• Updates to R wrapping. by @zivy in #2605
• Fix swapped C and C++ CMake flag variables in manylinux cmd.sh by @blowekamp in #2608
• Restructure Elastix ParameterMaps documentation and examples by @blowekamp in #2606
• Update ITK to current development version. by @blowekamp in #2607
• Fix C# string interpolation in ParameterMaps.cs for older C# version compatibility by @blowekamp in #2609
• Use reshape over setting ndarray shape by @blowekamp in #2611
• Add r parameter map interface by @blowekamp in #2612
• Adding CITATION file for R package. by @zivy in #2614
• Update instructions for R binary distribution. by @zivy in #2616
• Bump actions/checkout from 6 to 7 by @dependabot[bot] in #2613
• Bump actions/cache from 5 to 6 by @dependabot[bot] in #2615
• Split publish job into publish-github and publish-pypi by @blowekamp in #2617
• GHA: Add Python sdist job to Package workflow by @blowekamp in #2618
• BUG: Use the enum type name CoherenceEnhancingDiffusionImageFilter declares by @hjmjohnson in #2621
• Disable Ruby on OSX by @blowekamp in #2620
• Bump actions/checkout from 6.0.2 to 7.0.0 by @dependabot[bot] in #2622
• Update Elastix git tag by @blowekamp in #2623
• Update ITK has to July 8 2026 hash by @blowekamp in #2624
• Improve documentation for composite transform. by @zivy in #2628
• BUG: Fix license-expression metadata breaking twine check by @blowekamp in #2632
• Update GitHub download stats script. by @zivy in #2633
• Add sitk-upload-binary-data skill by @blowekamp in #2637
• Improvements to the statistics scripts. by @zivy in #2644
• Replace buggy bash commit-msg hook with Python implementation by @blowekamp in #2640
• Bump pypa/gh-action-pypi-publish from 1.14.0 to 1.14.1 by @dependabot[bot] in #2647
• Document filter test image comparison and baseline data workflow by @blowekamp in #2643
• ENH: Add NoMask test case for NormalizedCorrelationImageFilter by @blowekamp in #2634
• Slim down kw-pre-commit: drop dead code, delegate to standard hooks by @blowekamp in #2641
• CI: move WRAP_RUBY testing from macOS to Linux batch build job by @blowekamp in #2648
• BUG: Fix LabelMapMaskImageFilter BackgroundValue cast through label type by @blowekamp in #2629
• Add setup-externaldata script to configure .ExternalData clone by @blowekamp in #2642
• Update ITK version to 5.4.7 by @blowekamp in #2649
• BUG: Remove copy=False kwarg from reshape in GetArrayViewFromImage by @blowekamp in #2654
• CI: Migrate BatchBuild macOS jobs off deprecated macos-13 runner by @blowekamp in #2653
• CI: Fix always-truthy if expression in BatchBuild.yml by @blowekamp in #2658
• Bump actions/checkout from 7.0.0 to 7.0.1 by @dependabot[bot] in #2656
• BUG: Pin numpy <2.5 for manylinux2014 python test venv by @blowekamp in #2659
• Updated documentaiton to reflect new R distro. by @zivy in #2661
• CI: Enable dependabot for GitHub Actions on release branch by @blowekamp in #2662
• Bump pyp...

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.6

What's Changed

• Use reshape over setting ndarray shape by @blowekamp in #2611
• Update ITK version to 5.4.7 by @blowekamp in #2649
• BUG: Remove copy=False kwarg from reshape in GetArrayViewFromImage by @blowekamp in #2654
• CI: Migrate BatchBuild macOS jobs off deprecated macos-13 runner by @blowekamp in #2653
• CI: Fix always-truthy if expression in BatchBuild.yml by @blowekamp in #2658
• BUG: Pin numpy <2.5 for manylinux2014 python test venv by @blowekamp in #2659

Full Changelog: v2.5.5...v2.5.6

This is an automatic packaging of SimpleITK based on the v3.0.0b1 tag.

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v3.0.0b1

What's Changed

• Align Elastix/Transformix API with elastix PR #1417 by @blowekamp in #2526
• Remove outdated cdash exceptions for warnings and errors by @blowekamp in #2528
• Use additional PR branch name in ccache key by @blowekamp in #2529
• DOC: Update Sphinx docs for v3.0.0a3 changes by @blowekamp in #2530
• Add migration guide for version 3.0 by @blowekamp in #2533
• DOC: Add release notes and update documentation infrastructure by @blowekamp in #2534
• COMP: Update ITK to release-5.4 branch hash 2026-02-26 by @blowekamp in #2535
• Add myst_parser to Sphinx Docs requirements by @blowekamp in #2537
• DOC: Update requirements and ReadTheDocs config by @blowekamp in #2538
• Separately backport gersemi CMake formatting for FindR.cmake by @blowekamp in #2541
• Update FindR to detect R.dll on windows. by @blowekamp in #2542
• Update Elastix to Superbuild 5.3.1 by @blowekamp in #2540
• Coverage image by @blowekamp in #2532
• Update FindR to detect R.dll on windows. - for release by @blowekamp in #2546
• DOC: Update phrasing in documentation. by @zivy in #2548
• Merge ElastixImageFilter and TransformixImageFilter into SimpleElastix by @blowekamp in #2547
• Add GHA batch builds which use fetch content by @blowekamp in #2545
• DOC: Add FAQ entry for Windows pip build path length error by @blowekamp in #2551
• BUG: Replace deprecated macos-13 runner with macos-15-intel by @blowekamp in #2553
• Create an Elastix FetchContent build option by @blowekamp in #2543
• Release into main by @blowekamp in #2554
• Remove manylinux 2014. by @blowekamp in #2559
• Update elastix to af47e22, and use target based properties by @blowekamp in #2558
• Fix continue-on-error in composite actions to use boolean expression by @blowekamp in #2557
• Bump pypa/gh-action-pypi-publish from 1.13.0 to 1.14.0 by @dependabot[bot] in #2560
• ENH: Add free-threaded Python 3.14t package builds by @blowekamp in #2552
• Enable SimpleElastix in doxygen build by @blowekamp in #2562
• Package with elastix by @blowekamp in #2555
• Declare Python module as GIL-free for free-threaded CPython by @blowekamp in #2565
• Update actions/setup-python from v5 to v6 by @blowekamp in #2567
• SWIG use doxygen flag for automatic docs by @blowekamp in #2566
• Update ITK Superbuild version to 5.4.6 by @blowekamp in #2570
• COMP: Link ITKRegistrationCommonModule for elastix pyramid headers by @blowekamp in #2569
• DOC: Add release notes for v2.5.4 by @blowekamp in #2571
• ENH: Use file glob for external data cache key in GHA workflows by @blowekamp in #2572
• ENH: Simplify ccache key in Build.yml GHA workflow by @blowekamp in #2573
• GHA: Pin R version to 4.5 by @blowekamp in #2575
• Update Superbuild SWIG to 4.4.1 by @blowekamp in #2577
• COMP: Remove KWStyle style checking by @blowekamp in #2578
• ENH: Fix free-threaded Python linking with CMake >= 3.30 by @blowekamp in #2581
• ENH: Add free-threaded Python (3.14t) packaging support - for release by @blowekamp in #2580
• BUG: Remove duplicate Python packaging steps in Package workflow by @blowekamp in #2582
• ENH: Update macOS CI runner from macos-13 to macos-14 by @blowekamp in #2584
• Fix R CLOENV - for release and master by @blowekamp in #2585
• BUG: Patch SWIG superbuild for R 4.6.0 API removals by @blowekamp in #2587
• BUG: Patch SWIG superbuild for R 4.6.0 API removals - for main by @blowekamp in #2589
• ENH: Add R wrapping CI coverage to Build and BatchBuild workflows by @blowekamp in #2586
• BUG: Fix DicomSeriesReader test for ITK PR#5357 direction fix by @blowekamp in #2591
• DOC: Add release notes for v2.5.5 by @blowekamp in #2592
• DOC: Expand v2.5.5 release notes with highlights and installation ins… by @blowekamp in #2594
• GHA packaging use mac-15 ARM by @blowekamp in #2595
• ci: harden Package workflow against supply-chain and injection risks by @blowekamp in #2596

Full Changelog: v3.0.0a3...v3.0.0b1

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.5

What's Changed

• ENH: Add free-threaded Python (3.14t) packaging support - for release by @blowekamp in #2580
• ENH: Update macOS CI runner from macos-13 to macos-14 by @blowekamp in #2584
• Fix R CLOENV - for release and master by @blowekamp in #2585
• BUG: Patch SWIG superbuild for R 4.6.0 API removals by @blowekamp in #2587

Full Changelog: v2.5.4...v2.5.5

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.4

What's Changed

• COMP: Update ITK to release-5.4 branch hash 2026-02-26 by @blowekamp in #2535
• Separately backport gersemi CMake formatting for FindR.cmake by @blowekamp in #2541
• Update FindR to detect R.dll on windows. - for release by @blowekamp in #2546
• BUG: Replace deprecated macos-13 runner with macos-15-intel by @blowekamp in #2553
• Update ITK Superbuild version to 5.4.6 by @blowekamp in #2570

Full Changelog: v2.5.3...v2.5.4

This is an automatic packaging of SimpleITK based on the v3.0.0a3 tag.

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v3.0.0a3

What's Changed

• Install required locale for ITK testing by @blowekamp in #2525
• Add UseLegacyOperatorCoefficients to SobelEdgeDetectionImageFilter by @blowekamp in #2515
• ENH: Use CMake TIMESTAMP by @blowekamp in #2527

Full Changelog: v3.0.0a2...v3.0.0a3

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v3.0.0a2

What's Changed

• Use rossetta arch command to run python executable - for release by @blowekamp in #2419
• BUG: Remove '%' from tmp file names by @dave3d in #2432
• Update ITK version to v6.0b01 by @blowekamp in #2431
• Template tweaks by @blowekamp in #2437
• Use macos-15-intel for intel binaries by @blowekamp in #2435
• Adjust white space in filter templates by @blowekamp in #2438
• Add wrapping for ContourExtractor2D by @blowekamp in #2436
• Bump actions/upload-artifact from 4 to 5 by @dependabot[bot] in #2439
• Bump actions/download-artifact from 5 to 6 by @dependabot[bot] in #2440
• Update to latest versions of packages. by @zivy in #2441
• Script for analyzing GitHub release downloads. by @zivy in #2442
• Replace the environment.yml file with usage of uv. by @zivy in #2444
• COMP: Address CMake warning related to empty elseif by @blowekamp in #2443
• FOR RELEASE - Update docker based package builds to use external source by @blowekamp in #2446
• Fix generation of checksums by @blowekamp in #2448
• Fix generation of checksums - FOR RELEASE by @blowekamp in #2450
• Update superbuild ITK version to 5.4.5 release by @blowekamp in #2449
• Add PyBuffer interface to Image (PEP 688) and numpy array conversion by @blowekamp in #2447
• Bump actions/checkout from 5 to 6 by @dependabot[bot] in #2452
• Update tutorials page. by @zivy in #2453
• Move Python package metadata to pyproject.toml by @blowekamp in #2451
• Add ContainerManageMemory method to the PimpleImage by @blowekamp in #2455
• Utilities for download analysis. by @zivy in #2454
• Use pip wheel for PEP 571 python build system by @blowekamp in #2456
• Remove cmake checks for unsupported MSVC compilers. by @blowekamp in #2457
• Use CMake's ContentFetch for GoogleTest by @blowekamp in #2458
• check the used GTest::gtest target for existing package by @blowekamp in #2461
• Add CMake block to Source Version script by @blowekamp in #2462
• Set unique file name for the SimpleIO examples. by @zivy in #2464
• Specify SWIG 4.3.0 as minimum required by @blowekamp in #2418
• Propagate used CMake git version variables by @blowekamp in #2468
• Various CMake improvements by @blowekamp in #2466
• Add SWIG 4.3.0 version requirement to superbuild by @blowekamp in #2472
• Add optional --output flag to expand script by @blowekamp in #2467
• Fix extension for Python module on windows by @blowekamp in #2474
• GHA in Build and Test CI, use pip for SimpleITK python build environment. by @blowekamp in #2471
• Tune and fix options in GitHub Actions by @blowekamp in #2473
• Bump actions/upload-artifact from 5 to 6 by @dependabot[bot] in #2477
• Bump actions/download-artifact from 6 to 7 by @dependabot[bot] in #2479
• Bump actions/cache from 4 to 5 by @dependabot[bot] in #2478
• Use CMAKE_LINKER_TYPE to set ld as gold by @blowekamp in #2480
• Add support for pyyaml C based loaders by @blowekamp in #2481
• Standardize Module_ITKReview option in Superbuild by @blowekamp in #2482
• GH fix missing matrix to environment variable propagation by @blowekamp in #2483
• Fix compile options for Lua wrapping. by @blowekamp in #2485
• Add uv installer for powershell by @blowekamp in #2487
• Fix setup-precommit to support Windows venv paths by @blowekamp in #2489
• Fix if logic when using IS_EXECUTABLE before cmake 3.29 by @blowekamp in #2488
• Fix path to uv in SuperBuild on non-windows by @blowekamp in #2490
• Refactor to use scikit-build-core with installation script by @blowekamp in #2484
• Use a funciton over block for CMake version compatibility by @blowekamp in #2491
• Fix python dist by @blowekamp in #2492
• GHA enable Lua wrapping in batch build by @blowekamp in #2486
• Move ITK link and flags properties to targets by @blowekamp in #2493
• Add manylinux_2_28 Python Packages by @blowekamp in #2496
• Remove extra find_package for ITK by @blowekamp in #2495
• Update ITK Superbuild version to 6.0b2 by @blowekamp in #2498
• Add using ITK with CMake's FetchContent module by @blowekamp in #2475
• Prefer usage of CMake foreach with IN LISTS by @blowekamp in #2503
• Update Doxygen build to use ITK FetchContent by @blowekamp in #2501
• ENH: Migrate to CMake 3.23+ FILE_SET for header management by @blowekamp in #2502
• Address missing SimpleITKBasicFiltersGeneratedHeaders.i file by @blowekamp in #2506
• Create BasicFilters/src directory for output of generated code. by @blowekamp in #2507
• Stop support packaging for Python 3.9 by @blowekamp in #2508
• Add toplevel pyproject.toml by @blowekamp in https://github.com/SimpleITK/S...

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.3

What's Changed

• Use rossetta arch command to run python executable - for release by @blowekamp in #2419
• FOR RELEASE - Update docker based package builds to use external source by @blowekamp in #2446
• Fix generation of checksums - FOR RELEASE by @blowekamp in #2450
• Update superbuild ITK version to 5.4.5 release by @blowekamp in #2449

Security Fixes

• Addresses Out-of-Bounds vulnerability with a malformed DICOM file containing encapsulated PixelData fragments. The fix is contained in ITK 5.4.5.

Full Changelog: v2.5.2...v2.5.3

This is SimpleITK 3.0.0 Alpha Release 1.

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v3.0.0a1

What's Changed

• Update Superbuild SWIG version to 4.3.1 by @blowekamp in #2279
• Use CodeBuild runners in nightly. by @blowekamp in #2280
• Json tweaks by @blowekamp in #2282
• Add Clion default build paths and venvs to gitignore by @blowekamp in #2285
• Address compilation error when building ruby on OSX by @blowekamp in #2287
• Use target compile options over source properties by @blowekamp in #2288
• Add permision restriction to actions by @blowekamp in #2284
• use nullptr by @blowekamp in #2290
• Add ForceOrthogonalDirection and ReverseOrder options by @blowekamp in #2293
• Use O1 optimization flag for ITK valgrind by @blowekamp in #2295
• Update itk to 6.0a3 for development by @blowekamp in #2289
• Use ITK valgrind suppression file for Ubuntu 22.04 LTS by @blowekamp in #2298
• STYLE: Upgrade to comment_spell_check v0.4.0 by @dave3d in #2300
• Add key word only options to ReadImage by @blowekamp in #2296
• Remove return self functionality by @blowekamp in #2278
• Add flag to suppress sprintf warning in SWIG build on OSX by @blowekamp in #2303
• Fix Docker FromAs error by @blowekamp in #2305
• Fix CMake version policy max is now correctly 3.20 by @blowekamp in #2304
• DOC: Correct minor spelling mistake. by @zivy in #2307
• Use boolean types for boolean attributes in JSON by @blowekamp in #2302
• Json conformance by @blowekamp in #2308
• Update to windows-2022 by @blowekamp in #2309
• More pre-commit by @blowekamp in #2312
• Add formal JSON schema by @blowekamp in #2310
• DOC: improving documentation for basic DICOM series reader example by @zivy in #2313
• Add pretty-format-json to pre-commit by @blowekamp in #2315
• Allow measurements results parameters to be numbers. by @blowekamp in #2316
• ENH: Address changes in Fiji installation on windows. by @zivy in #2317
• Replace template code generation with a JINJA and Python based system. by @blowekamp in #2318
• Update the getting started page to point to the virtual tutorial. by @zivy in #2321
• Update JSONBeautify Python script. by @blowekamp in #2326
• Update typing for Resample in extra.py by @chris-rapson-formus in #2323
• Change JSON values to numbers from strings by @blowekamp in #2325
• Restore removal of GHA Nightly ITK build requirements. by @blowekamp in #2324
• Add Superbuild target to create Python virtual environment by @blowekamp in #2322
• Update build docucmentation for Python JINJA2 by @blowekamp in #2327
• Fix requirement of Python in superbuild by @blowekamp in #2328
• Fixes for Dockerfiles used in the Package GHA workflow by @blowekamp in #2329
• Add additional support for a main branch by @blowekamp in #2330
• Jinja improvements by @blowekamp in #2331
• DOC: Add C# and java versions to the DemonsRegistration1 example. by @zivy in #2334
• Add gersemi cmake formatter by @blowekamp in #2332
• Use uv to create python venv for SimpleITK Python by @blowekamp in #2338
• DOC: Add C# and java versions to the DemonsRegistration2 example. by @zivy in #2335
• Fix using IS_EXECUTABLE with older CMake versions by @blowekamp in #2340
• Convert the Python unit tests to use pytest by @blowekamp in #2337
• DOC: Update url to ITK 5.0 migration guide. by @zivy in #2342
• ENH: create a spell checking pre-commit by @dave3d in #2333
• DOC: Add C#, C++ and java versions to the DicomImagePrintTags example. by @zivy in #2344
• Disable uv modifying shell environments by @blowekamp in #2343
• Document usage of uv in build process by @blowekamp in #2341
• Keep uv install XDG receipt local to build. by @blowekamp in #2346
• BUG: inverting intensity for MONOCHROME1 not needed. by @zivy in #2348
• Disable passing filename on some local pre-commit hooks by @blowekamp in #2350
• DOC: Add C#, C++ and java versions to the DicomConvert example. by @zivy in #2336
• Fixes for Nightly Package builds by @blowekamp in #2349
• Refactor the function factories to not take pointer in constructor by @blowekamp in #2351
• Adding DICOM reading failure question to FAQ. by @zivy in #2353
• Make the Addressor constexpr by @blowekamp in #2354
• COMP: address issue with recursive_directory_iterator on OSX CI. by @zivy in #2356
• Convert to a smart pointer for member. by @blowekamp in #2358
• Address CMP0175 warnings by @blowekamp in #2359
• Add export specification for ProcessObjectDeleter by @blowekamp in #2362
• Use copy mode for ...

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.2

What's Changed

• Add ForceOrthogonalDirection and ReverseOrder options - for release by @blowekamp in #2294
• Fix Docker FromAsCasing error for Doxygen - for RELEASE by @blowekamp in #2306
• Update ITK Superbuild version to 5.4.4 by @blowekamp in #2319

Full Changelog: v2.5.0...v2.5.2