ENH: Update SimpleITK to 0.11.0.dev110, Swig 3.0.10 and PCRE 8.38
SimpleITK changes reported below:
$ git shortlog ee2a30c..aeada7a --no-merges
Bradley Lowekamp (246):
Adding script to run doxyall for generate SWIG .i files
Adding script to update JSON with ITK doxygen
Moving documentation generations scripts to separate directory
Adding common variable/config file for scripts
Generalizing script to generate Swig .i documentation files
Adding README for the GenerateDocs directory
Adding overview of the documentation process
COMP: Adress Ununsed typenames in Common
Update to ITK 4.9 release tag
BUG: Do not link against specific Python version on OS X
Add CMake option to build eggs
Move Python virtualenv to Superbuild
Prefer the use of distutils over setuptools
Use virtualenv's setuptools and wheel, remove ez_setup
Correctly add superbuild dependency on virtualenv
Add find package for Python virtualenv
Tweak virtualenv creation options
Adding JSON validation on precommit and during code generation
Correct JSON syntax errors detected by validation
Adding missing needed changes for JSON validation.
Adding initial description for MultiLableSTAPLEImageFilter
In Python use open over file
Improving order and utilizing default magic values for "unset" state.
Adding test to verify that the input and output buffers are different
Removing procedural methods for filters with not image output.
Add Python support for Get/SetPixel for tuple arguments
Adding support for CMake STRINGS property to superbuild variables.
Fixing unused typedef reported by clang
Updating virtualenv version to 15.0.1
Use PYTHON_EXECUTABLE to call virtualenv
Rename PYTHON_VIRTUALENV_EXECUTABLE to SCRIPT
Fix TemplateComponent active member parameter name
try_compile test for allowing undefined symbols in shared libraries
Improve flag hashing with C++11 try_compiles
Use localized cmake list variable for paths.
Don't link to language libraries on linux
Check for name of current project in stead of related variable
Split FORBID_DOWNLOADS cmake flag into separate file
Move Strip option and function to separate file
Remove WRAP_PYTHON conditional in Python sub-directory for dist
Move Java variables to sub-directory
Moving CSharp Java dependencies to individual file generations step.
Moved location of org_itk_simple_jar target.
Make wrapped languages independent projects.
Moved location of CMake sitk_target_link_libraries_with_dynamic_lookup
Moved location of CMake sitk_target_link_libraries_with_dynamic_lookup
Update name of CMake file for linking with dynamic lookup
Explicitly use required ITK modules
Update Superbuild download URLs to use https
Update upload data script to use https
Replace sitkExtra with now TargetLink CMake module in top-level
Rename some CMake file with sitkPrefix
Rename UseSWIGLocal to sitkUseSWIG
Update ITK Superbuild version along release towards 4.9.1
Adding ConfusionMatrix measurement
Fix the path of setupegg.py used for packaging
Make R's DESCRIPTION file configured
Remove unneeded LOCATION property of SimpleITKR library
Move md5 data files into R packaging directory
Remove empty R library check
Remove message statement with debug information.
Restore using hash in variable name
Remove unneeded include of DynamicLookup cmake module
Remove checking for warning flags at the Superbuild level
Check if C++11 is require at the Superbuild level.
Update ITK to v4.9.1 release tag
Fix CMP0042 Warning in try compile
Splitting the Wrapping directory into separate language directories
Correct typeo ImageSeriesWriter's Doxygen reference to procedural method
Renaming file with sitk prefix
Replace '=' in CMake variable name
Fix "dist/dist" path for output of whl and eggs
Only add Example tests when testing is enabled
Restore missing dist target
Enable Python wheels over eggs by default
Adding Powell optimizer to registration
BUG: Remove implicit deep copy in ImportImageFilter
Documenting SetDisplacementField method "steals" the image
Fix typo in IntegerLabelPixelIDTypeList type
Updating Swig git version
BUG: Adding missing return value to SetOptimizerAsPowell
Update Superbuild ITK version to 4.10rc1
Fix Euler3D test top support 4 fixed parameters
Use exception in sitkSTLToITKDirection macro
BUG: Adjust itk.org ExternalData URL.
Fix number of expected Euler3D fixed parameters
Update ITK Superbuild version toward ITK v4.10
Fix CMake CMP0042 in TargetLinkLibrariesWithDynamicLookup
Suppress libraries as being required for wrapped languages
CMake recently add LUA_MATH_LIBRARY as an additional variable
Require python 2.6 for running JSON validation script
Updating Superbuild ITK version to 4.10 rc 2
Do not require Python libs if weak linking is going to be used
Use current binary directory for Python packaging working directory
Update ITK Superbuild version along RC
Adding SimpleITK version components to Config file
Adding correct version variables to CPack
Fix setup.py using hash with empty string
Updating ITK Superbuild version to 4.10
Reuse ImageIO from reading initial information
Adding option to read DICOM private tags
Adding Set/Get testing for LoadPrivateTags
Adding example to print DICOM tags after reading file
Updating to SWIG 3.0.9 release
Add R tests for new features with SWIG
Fix setting using git vs https protocol for ITK superbuild
Fix PEP 440 compliance with "+" for local identifier
Address CMP0058 issue with configure time generated files
Fix Output path for GTEST library with Ninja
Address narrowing conversion warnings
Updating Superbuild version of virtualenv to 15.0.2
Removing unused typedef of Self causing SWIG warnings
Better suppress self warnings from SWIG
Restore missing warnings flags to compilation
Removing usage of return self from tests
Remove usage or return self define from testing utility.
Remove Self typedef in PyCommand
Move hidden required MSVC flags to common required flags file.
Adding flags for mingw to create big object files
Adding missing SWIG dependency on SimpleITK_Common.i
Move language specific Swig into language files
Replacing Self return declarations with macro
Remove unneeded private copy operators in Command classes
Defining self return value
Adding Doxygen macro for the return by self value.
Adding option for no_size_check to named inputs
Reducing check to expect from assert
Changing to Named inputs for NormalizedCorrelation filter.
Updating Masked FFT Normalized Correlation with named inputs
Don't check size of Moving images
Updating SimpleITK JSON from ITK doxygen
Updating Java and Python swig documentation files
Updating ITK version along 4.10 release branch
Update testing functions with properties and generator expressions
Moving Java test to global namespace
Fix bug of missing JAR_FILE variable
Remove C++ based driver for languages tests
Add support for generated CSharp files with full paths
Removing TestHarness support with language tests
Add Expand template generation for language tests
Restore multiple tests for language generated tests.
Correct language test names to use "." over "[ ]".
Adding missing new line after end of function.
Updating ITK tag with a couple more patches with 4.10 release
Adding link type specification to SimpleITK libraries
Remove dead CMake code
Add CMAKE_LINKER to propagate from Superbuild
Create Python SimpleITK library in wrapping directory
Override default output paths for language wrapping
Updating Swig superbuild version to 3.0.10
CMake version 3 is now required
Install generated headers and ".i" files in generation function
Remove wrapping projects dependency on SimpleITK binary directory.
Corrected installation of headers
Address CMP0058 issue with generate CSharp files
Updating ITK superbuild version along 4.10 release
Prepend SimpleITK CMake module directory to search path
Only set POSITION_INDEPENDENT_CODE flag if not already set
Remove unused cmake macro
Remove SKIP_BUILD_RPATH property for SimpleITK libraries.
Disable build RPATHs for wrapped languages.
Remove visibility flags in superbuild for CMAKE property defaults
Always build ITK with hidden visibility with static libraries
Enable CMP0042 and CMP0063 to New
Remove Segmentation examples as separate project
Don't use per-configuration output directory for Python library.
Move DataFinder implementation to cxx file.
Added missing library dependencies in Testing.
Adding missing library linkage to SimpleITKExplicit
Default the visibility of SimpleITK libraries to hidden
Adding Image methods to set meta-data and erase a key
Use generator expression for itkTestDriver
Print command when Expand generation fails for ctest generation
Minimize headers included in SimpleITKTestHarness.h
Updating ITK Superbuild version to just before 4.10.1 release
Replace sitkTransformCompareDriver with sitkCompareDriver
Remove creation for MetaDataDictionary array in ImageSeriesReader
Explict Library only needs default visibility with shared libraries
Correct CMake module path for independent language projects
Updating ITK Superbuild version to include CMP0063 fix for vxl
Fix MSVC double to float conversion warnings
Adding wrapper for std::unique_ptr as nsstd::auto_ptr
Renaming std::auto_ptr to nsstd::auto_ptr
Adding alias for nsstd namespace in testing
Update the Swig docs from generation scripts
Update to use python from future for py3 compatibility
Fix disabling using virtualenv from superbuild
Fix missing arguments when setting CMake CACHE variable
Enable policies to be set in sitkProjectLanguageCommon
Add check for alias template to use unique_ptr
Prefer C++11 over tr1
Explicitly add GTest libraries to avoid pthread linking issue.
Append LUA test ENVIRONMENT instead of overwriting in
Fix incorrect logic for dist target dependency on virtualenv
Correct PYTHONPATH when not using virtualenv
Add missing language file extensions to example glob
Only conditionally add ITK tag dependency
Bumping version 0.11.0 for development
Update the SimpleITK version the Super Examples use.
Include Fiji in Show documentation
Adding SimpleITK 0.10.0 wheels to the Python Downloads page
Fixing Download page list to include a space
Fix dependency for InsightDoxygen.tag
Update ExternalProjects to use variable for URL
Use CMake ExternalData module to download ExternalProject source
Use ExternalData download for lua source
Prefer ExternalProject_Add_StepDependencies for project dependencies on data
Adding circle.yml for continuous integration with CircleCi
Don't implicitly set SimpleITK version variable via CMake find_project
Adding comment documentation to Config version change
Replacing 0.10.0 manylinux wheels with build 1.
Move compilation to dependencies for CircleCi
Reducing number of compilations per container
Reducing number of compilations on node 0
explicitly required ITK components for BasicFilters libraries
Fix R language link in readme
Adding CircleCi badge for master branch.
Enable shared libraries for CircleCi build
Use git mirror for cached ITK repository
Remove errant code it GTest external project file.
Do not cache ITK git repository use github
Use SEMICOLON generator expression in arg list
Remove double underscore in header guards from ITK headers
Fix namespace for auto_ptr
Add missing argument to gtest_add_test
Adding tests for Image::GetNumberOfPixels
Correct tests for Image::EraseMetaData
Adding examples of using R with dicom files
Remove CircleCI rsync and distributed testing
Ignore non-code branches
Adding SSH multiplexing to prevent change host ID warnings distcc
Separate R Array functions into separate file
Fix command line argument error handing.
Add basic JavaRegistration example
Adding CSharp port of ImageRegistration1 example
Use UNINITIALIZED CMake variable type when undefined.
Use named inputs for LabelMapOverlayImageFilter
Remove generated warning from committed files
Add missing parameter for scaling input
Add uint8_t support for dim_vec test parameter for lua and ruby
Adding SetColormap parameter to Label colormap based filters.
Fix incorrect Java array type for uint8_t
BUG: Fix missing sitkSourceVersionVars.cmake file from archives
COMP: Include iostream before R
Do not warn about python version when python not found
Only use exact if python interpreter has been found
Dave Chen (4):
Build a loadable Lua module
Added return values for sitkShowTest
Fix ITK TAGS_DEPENDS bug
Simplified the show command
David T. Chen (23):
Remove Clang warnings when building Lua
COMP: CLang Warning Remediation
COMP: Macros to suppress clang warnings
COMP: Removed anonymous namespace
ENH: Added debugging message option to Show
New image tests for Java
Added BigIntegerFix class
Fix for CMake's semicolon issue on Windows
Reverting deleted line
Check for cmake version
Fixed the timeout value for Show on Windows
Refactored semi-colon hack
Remove old python virtualenv on rebuild
Updated Lua examples to load SimpleITK module
Save LUA_EXECUTABLE cmake variable
Old CMake Uppercase Expression Fix
Updated filter.csv
Update the SimpleDerivative.lua example
Set SITK_NOSHOW env var for Lua tests
Added Lua sub-directory
Added SimpleDerivative example test.
Updated filter.csv
Initial checkin of .travis.yml
Gabriel A. Devenyi (1):
Pass ITK module options into Superbuild
Hans Johnson (6):
DOC: s/treaded/treated/g spelling fix
COMP: Use Self typedef
COMP: Typedef not used, so not tested.
ENH: Add ignore for CLion editior temp files
Document how to Use SimpleITK from C++ need operators
ENH: Add GetNumberOfPixels to Images
Kasper Marstal (2):
BUG: Fix Java 1.8 javadoc linting breaking the java build
BUG: Fix JoinSeriesImageFilter GoogleTest should be fixture
Matt McCormick (2):
DOC: Update itk.org URL's for HTTPS support.
DOC: Correct issue tracker URL to https://issues.itk.org
Paolo Zaffino (1):
ENH: add SITK_GIT_PROTOCOL to enable user selection of the protocol
Richard Beare (16):
Support for more indexing operations.
SimpleITK methods returning void are returning NULL when called from R, and the NULL gets printed, which is annoying.
Missing tests of PixelType enumeration
A nicer way of dealing with the PixelIDValue enumeration.
R documentation from doxygen.
Support for building swig from a git repository.
R vectors of images
R documentation for procedural interface.
Single functions for pixel access
Advances in bracket operator/slicing
Correct R doc linking.
Improvements to Rd file generation
Remove extra new lines generated in Python and Java Swig Docs file.
Move Rdefines and Rversions outside the extern C.
Void returns from method calls.
Disable pthreads in GTest
Ziv Yaniv (6):
Adding test for BSplineTransformInitializer.
Separated the BSplineTransformInitializer test in two.
Adding test for meta data dictionary.
Adding example illustrating changes in DICOM tags.
Updated readme to reflect current state of SimpleITK.
Added missing curly brace in Cmakelists file.
git-svn-id: http://svn.slicer.org/Slicer4/trunk@25524 3bd1e089-480b-0410-8dfb-8563597acbee |
