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: Exclude _deps directory from coverage reports by @blowekamp in #2521
• Update ITK version and refactor variables by @blowekamp in #2522
• GHA Package Fixes by @blowekamp in #2520
• GHA: Add ccache support for Linux builds by @blowekamp in #2523
• Bump actions/download-artifact from 7 to 8 by @dependabot[bot] in #2517
• Bump actions/upload-artifact from 6 to 7 by @dependabot[bot] in #2518
• 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
• 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• Remove outdated cdash exceptions for warnings and errors by @blowekamp in #2528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

Full Changelog: v3.0.0a2...latest

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

Release Notes

Announcing the SimpleITK 2.5.0 Release!

The release includes critical bug fixes and compilation issues including an update to ITK v5.4.2.

Installing SimpleITK

Complete instructions on getting started with SimpleITK including downloading binaries or building SimpleITK can be found on the SimpleITK Read the Docs web page.

Python Binary Downloads

• Python binary wheels are available for download. It is important to have the latest version of pip for correct wheel compatibility and installation. To install the latest SimpleITK package from PyPI:

  python -m pip install --upgrade pip
  python -m pip install SimpleITK
  

NOTE: The Python package filename now follows the enforced name normalization on PyPI. That is the name of the file is now simpleitk....whl. PyPI is case insensitive with regards to names of packages. However, the name of the Python package when importing is still case and should be import SimpleITK.

The binary distribution contains wheels built on the Python 3.11 stable API ( see PEP 384 ) and should work with Python versions including and after 3.11.

Anaconda Binary Downloads

SimpleITK Conda binaries are available for the conda-forge ecosystem. To get started run the following command:

conda create --name sitk python=3.12 simpleitk --channel conda-forge --override-channels

Getting Started

To get started with pre-compiled Java or C# bindings, building the R binding via a devtools installer or building SimpleITK from source code see the Getting Started Guide.

Release Notes

New Features

• Added support for up to 5D images in MinimumProjectionImageFilter.
• Introduced wrapping for ReinitializeLevelSetImageFilter.
• Enabled external ITK module LabelErodeDilate by default.

Updates

• Removed packaging of Python 3.8 (EOL) in manylinux wheels and GitHub Actions.
• Updated ITK to version 5.4.3.
• Upgraded Superbuild components:
  • PCRE2 to version 10.44.
  • Lua to version 5.4.7.
  • SWIG to version 4.3.0.
  • GTest to version 1.15.2.

Bug Fixes

• Resolved Valgrind issues in LabelErodeDilate module.
• Fixed syntax warnings for Python 3.12 compatibility.

Documentation

• Updated R documentation.
• Conformed to Python package name normalization in documentation.
• Fixed dead URLs in the read-the-docs documentation.

What's Changed

• Use SimpleITK_BUILD_DISTRIBUTE in Mac ARM build scrip by @blowekamp in #2180
• Remove CircleCI from readme by @blowekamp in #2179
• Instruct on creating isolated conda-forge ecosystem by @blowekamp in #2182
• Additional clarification on using conda-forge by @blowekamp in #2183
• STYLE: Fixes to the python examples for pylint by @dave3d in #2178
• Update Superbuild GTest to 1.15.2 by @blowekamp in #2185
• Update docs by @zivy in #2181
• Add mac-arm64 to Build.yml by @jwj019 in #2158
• DOC: Fixes for pylint by @dave3d in #2187
• Fix SyntaxWarning in Python 3.12 by @fepegar in #2190
• Update for 2.5.0 development by @blowekamp in #2192
• Remove Python 3.8 from GHA by @blowekamp in #2194
• BUG: Correct SITK_MAX_DIMENSION usage by @blowekamp in #2193
• Use constexpr statements over enable_if dispatched functions by @blowekamp in #2196
• Address unused variable warning related to constexpr by @blowekamp in #2198
• Use maybe_unused directive over Unsed function. by @blowekamp in #2199
• Use variadic template for function traits and bindings by @blowekamp in #2197
• Use SimpleITK_BUILD_STRIP for mac packages by @blowekamp in #2201
• Use protected member function for safe GetIndex method by @blowekamp in #2204
• ENH: Handle error strings in a way that doesn't produce compile warnings by @richardbeare in #2205
• Update Superbuild to PCRE 10.44 by @blowekamp in #2210
• Update to SWIG 4.3.0 by @blowekamp in #2208
• Update Superbuild to lua 5.4.7 by @blowekamp in #2209
• Remove legacy RUBY CMake variables by @blowekamp in #2212
• Separate SimpleITKFilters tests by @blowekamp in #2211
• Use Image::AllocateInitialized by @blowekamp in #2213
• Update along ITK release_5.4 branch by @blowekamp in #2216
• ENH: Add wrapping for ReinitializeLevelSetImageFilter by @blowekamp in #2215
• Use cmake_minimum_required with ...max_policy by @blowekamp in #2217
• Update ITK Superbuild version to 5.4.1 by @blowekamp in #2223
• Update ITK to include vector image accessor patch by @blowekamp in #2224
• Use build-in xml package by @blowekamp in #2219
• Remove CircleCI configuration by @blowekamp in #2150
• Add dependabot to update github actions by @blowekamp in #2228
• Replace macos-12 batch builds by @blowekamp in #2230
• DOC: Update R documentation. by @zivy in #2232
• Backport patches made in Slicer fork by @blowekamp in #2137
• Slicer backport for release by @blowekamp in #2233
• Enable external ITK module LabelErodeDilate by default by @dyollb in #2235
• Add upto 5D support to MinimumProjectionImageFilter by @blowekamp in #2236
• Use loop and list for enabling ITK modules by @blowekamp in #2237
• Update clang format by @blowekamp in #2238
• Address Doxygen build issue with no python executable by @blowekamp in #2242
• Use pre-commit GHA action by @blowekamp in https://github....

To upgrade to this Python binary package run:
pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.0rc3

What's Changed

• BUG: Normalize Python package name to simpleitk by @blowekamp in #2257
• Image reader base dox by @blowekamp in #2248
• Make GHA packaging case insensitive for python wheels by @blowekamp in #2258
• Update documentation for python package name normalization by @blowekamp in #2260
• Normalize Python package name for latest release notes by @blowekamp in #2262
• Don't use head.sha for ci group by @blowekamp in #2263
• Replace self-hosted runners with GH hosted runners by @blowekamp in #2259

Full Changelog: v2.5.0rc2...v2.5.0rc3

To upgrade to this Python binary package run:
pip install --upgrade --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.0rc2

What's Changed

• Update Superbuild ITK version to v5.4.3 tag by @blowekamp in #2256

Full Changelog: v2.5.0rc1...v2.5.0rc2

This is SimpleITK 2.5.0 Release Candidate 1.

To upgrade to this Python binary package run:
pip install --upgrade --pre SimpleITK --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.0rc1

What's Changed

• Use SimpleITK_BUILD_DISTRIBUTE in Mac ARM build scrip by @blowekamp in #2180
• Remove CircleCI from readme by @blowekamp in #2179
• Instruct on creating isolated conda-forge ecosystem by @blowekamp in #2182
• Additional clarification on using conda-forge by @blowekamp in #2183
• STYLE: Fixes to the python examples for pylint by @dave3d in #2178
• Update Superbuild GTest to 1.15.2 by @blowekamp in #2185
• Update docs by @zivy in #2181
• Add mac-arm64 to Build.yml by @jwj019 in #2158
• DOC: Fixes for pylint by @dave3d in #2187
• Fix SyntaxWarning in Python 3.12 by @fepegar in #2190
• Update for 2.5.0 development by @blowekamp in #2192
• Remove Python 3.8 from GHA by @blowekamp in #2194
• BUG: Correct SITK_MAX_DIMENSION usage by @blowekamp in #2193
• Use constexpr statements over enable_if dispatched functions by @blowekamp in #2196
• Address unused variable warning related to constexpr by @blowekamp in #2198
• Use maybe_unused directive over Unsed function. by @blowekamp in #2199
• Use variadic template for function traits and bindings by @blowekamp in #2197
• Use SimpleITK_BUILD_STRIP for mac packages by @blowekamp in #2201
• Use protected member function for safe GetIndex method by @blowekamp in #2204
• ENH: Handle error strings in a way that doesn't produce compile warnings by @richardbeare in #2205
• Update Superbuild to PCRE 10.44 by @blowekamp in #2210
• Update to SWIG 4.3.0 by @blowekamp in #2208
• Update Superbuild to lua 5.4.7 by @blowekamp in #2209
• Remove legacy RUBY CMake variables by @blowekamp in #2212
• Separate SimpleITKFilters tests by @blowekamp in #2211
• Use Image::AllocateInitialized by @blowekamp in #2213
• Update along ITK release_5.4 branch by @blowekamp in #2216
• ENH: Add wrapping for ReinitializeLevelSetImageFilter by @blowekamp in #2215
• Use cmake_minimum_required with ...max_policy by @blowekamp in #2217
• Update ITK Superbuild version to 5.4.1 by @blowekamp in #2223
• Update ITK to include vector image accessor patch by @blowekamp in #2224
• Use build-in xml package by @blowekamp in #2219
• Remove CircleCI configuration by @blowekamp in #2150
• Add dependabot to update github actions by @blowekamp in #2228
• Replace macos-12 batch builds by @blowekamp in #2230
• DOC: Update R documentation. by @zivy in #2232
• Backport patches made in Slicer fork by @blowekamp in #2137
• Enable external ITK module LabelErodeDilate by default by @dyollb in #2235
• Add upto 5D support to MinimumProjectionImageFilter by @blowekamp in #2236
• Use loop and list for enabling ITK modules by @blowekamp in #2237
• Update clang format by @blowekamp in #2238
• Address Doxygen build issue with no python executable by @blowekamp in #2242
• Use pre-commit GHA action by @blowekamp in #2240
• Publish test pypi by @blowekamp in #2231
• Test using GHA host linux arm by @blowekamp in #2239
• Adress failing Doxygen builds in Packaging CI by @blowekamp in #2243
• Update CSVtoTable arguments in CMake by @blowekamp in #2244
• Add permissions to create release for publish action by @blowekamp in #2246
• Explicitly set OSX_ARCHITECTURES on osx java package by @blowekamp in #2247
• Bump pypa/gh-action-pypi-publish from 1.12.3 to 1.12.4 by @dependabot in #2245
• Override LabelErodeDilate module hash to fix valgrind defect by @blowekamp in #2249
• Update ITK valgrind to include module used by simpleITK by @blowekamp in #2250
• Second attempt to resolve valgrind issues in LabelErodeDilate by @blowekamp in #2253

New Contributors

• @fepegar made their first contribution in #2190
• @dependabot made their first contribution in #2245

Full Changelog: v2.4.1...v2.5.0rc1