New upstream version 1.1.0 (841fbad9) · Commits · Debian Med / simpleitk

.circleci/circleci.cmake

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		# set_from_env
		# ------------
		#
		# Sets a CMake variable from an environment variable. If the
		# environment variable is not defined then either a fatal error is
		# generated or the CMake variable is not modified.
		#
		# set_from_env( <variable> <environment variable> [REQUIRED\|DEFAULT value] )
		function(set_from_env var env_var)
		if(NOT DEFINED ENV{${env_var}})
		if (ARGV2 STREQUAL "REQUIRED")
		message(FATAL_ERROR "Required environment variable \"${env_var}\" not defined.")
		elseif (ARGV2 STREQUAL "DEFAULT")
		set(${var} ${ARGV3} PARENT_SCOPE)
		endif()
		else()
		set(${var} $ENV{${env_var}} PARENT_SCOPE)
		endif()
		endfunction()

		set(CTEST_SITE "CircleCI")
		set(CTEST_UPDATE_VERSION_ONLY 1)


		# Make environment variables to CMake variables for CTest
		set_from_env(CTEST_CMAKE_GENERATOR "CTEST_CMAKE_GENERATOR" DEFAULT "Unix Makefiles" )
		set_from_env(CTEST_BINARY_DIRECTORY "CTEST_BINARY_DIRECTORY")
		set_from_env(CTEST_DASHBOARD_ROOT "CTEST_DASHBOARD_ROOT" REQUIRED)
		set_from_env(CTEST_SOURCE_DIRECTORY "CTEST_SOURCE_DIRECTORY" REQUIRED)
		set_from_env(CTEST_CONFIGURATION_TYPE "CTEST_CONFIGURATION_TYPE" DEFAULT "Release")
		set_from_env(CTEST_BUILD_FLAGS "CTEST_BUILD_FLAGS")
		set_from_env(CTEST_BUILD_TARGET "CTEST_BUILD_TARGET")
		set_from_env(CTEST_TEST_ARGS "CTEST_TEST_ARGS")


		set_from_env(PARALLEL_LEVEL "PARALLEL_LEVEL" DEFAULT 2 )
		set( CTEST_TEST_ARGS ${CTEST_TEST_ARGS} PARALLEL_LEVEL ${PARALLEL_LEVEL})

		set_from_env(DASHBOARD_BRANCH_DIRECTORY "DASHBOARD_BRANCH_DIRECTORY" REQUIRED)

		# Construct build name based on what is being built
		string(SUBSTRING $ENV{CIRCLE_SHA1} 0 7 commit_sha1)
		set(CTEST_BUILD_NAME "CircleCI-$ENV{CIRCLE_BRANCH}-$ENV{CIRCLE_STAGE}-${commit_sha1}")

		set_from_env(dashboard_git_branch "CIRCLE_BRANCH")
		set_from_env(dashboard_model "DASHBOARD_MODEL" DEFAULT "Experimental" )
		set(dashboard_loop 0)


		if ( EXISTS "${CTEST_SOURCE_DIRECTORY}/circle.yml")
		list(APPEND CTEST_NOTES_FILES
		"${CTEST_SOURCE_DIRECTORY}/circle.yml"
		)
		endif()

		if ( EXISTS "${CTEST_SOURCE_DIRECTORY}/.circleci/config.yml")
		list(APPEND CTEST_NOTES_FILES
		"${CTEST_SOURCE_DIRECTORY}/.circleci/config.yml"
		)
		endif()


		SET (_dashboard_cache "
		BUILD_DOCUMENTATION:BOOL=OFF
		BUILD_EXAMPLES:BOOL=OFF
		BUILD_SHARED_LIBS:BOOL=ON
		BUILD_TESTING:BOOL=ON

		SimpleITK_USE_SYSTEM_LUA:BOOL=ON
		SimpleITK_EXPLICIT_INSTANTIATION:BOOL=OFF

		WRAP_DEFAULT:BOOL=OFF
		" )

		set_from_env(dashboard_cache "CTEST_CACHE" DEFAULT ${_dashboard_cache})


		if (DEFINED ENV{DISTCC_DIR})
		SET (dashboard_cache "${dashboard_cache}
		CMAKE_CXX_COMPILER_LAUNCHER:STRING=distcc
		CMAKE_C_COMPILER_LAUNCHER:STRING=distcc
		" )
		endif()



		include("${DASHBOARD_BRANCH_DIRECTORY}/simpleitk_common.cmake")

		if(NOT ${configure_return} EQUAL 0 OR
		NOT ${build_return} EQUAL 0 OR
		NOT ${build_errors} EQUAL 0 OR
		NOT ${build_warnings} EQUAL 0 OR
		NOT ${test_return} EQUAL 0)
		message(FATAL_ERROR
		"Build did not complete without warnings, errors, or failures.")
		else()
		return(0)
		endif()

.circleci/config.yml

0 → 100644

+198 −0

Original line number	Diff line number	Diff line
		referenced:
		defaults: &defaults
		docker:
		- image: circleci/python:2.7
		working_directory: ~/
		resource_class: large
		environment:
		CTEST_DASHBOARD_ROOT: /home/circleci
		CTEST_SOURCE_DIRECTORY: /home/circleci/SimpleITK
		CTEST_BINARY_DIRECTORY: /home/circleci/SimpleITK-build
		CTEST_BUILD_FLAGS: "-j 4"
		CTEST_CONFIGURATION_TYPE: "Release"
		CTEST_OUTPUT_ON_FAILURE: 1
		ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS: 2
		PARALLEL_LEVEL: 4
		DASHBOARD_BRANCH_DIRECTORY: /home/circleci/dashboard
		ExternalData_OBJECT_STORES: /home/circleci/.ExternalData
		CCACHE_NODIRECT: 1
		dependencies: &dependencies
		run:
		name: Dependencies
		command: \|
		sudo apt-get install -y rsync lua5.1 ccache kwstyle swig
		sudo pip install --upgrade pip
		sudo pip install numpy scikit-ci-addons
		ci_addons circle/install_cmake.py 3.10.2
		generate-hash-step: &generate-hash-step
		run:
		name: Generate external data hash
		command: \|
		cd SimpleITK
		git log -n 1 ${CTEST_SOURCE_DIRECTORY}/Testing/Data/ \| tee /home/circleci/external-data.hashable
		restore-data-step: &restore-data-step
		restore_cache:
		keys:
		- 'v1-external-data-{{ checksum "/home/circleci/external-data.hashable" }}'
		- 'v1-external-data'
		restore-ccache-step: &restore-ccache-step
		restore_cache:
		keys:
		- ccache-{{ arch }}-{{ .Branch }}
		- ccache-{{ arch }}-master
		clone-dashboard-step: &clone-dashboard-step
		run:
		name: Cloning dashboard branch
		command: \|
		git clone --single-branch ${CIRCLE_REPOSITORY_URL} -b dashboard ${DASHBOARD_BRANCH_DIRECTORY}
		env-step: &env-step
		run:
		name: Additional Environment Variables
		command: \|
		echo 'export DASHBOARD_MODEL=$( [[ "$CIRCLE_BRANCH" = "master" \|\| "$CIRCLE_BRANCH" = "next" \|\| "$CIRCLE_BRANCH" = "release" ]] && echo Continuous \|\| echo Experimental )' >> $BASH_ENV
		echo 'export PATH=/usr/lib/ccache:${PATH}' >> $BASH_ENV

		version: 2
		jobs:
		build-and-test:
		<<: *defaults
		steps:
		- checkout:
		path : ~/SimpleITK
		- *generate-hash-step
		- *restore-data-step
		- *restore-ccache-step
		- *clone-dashboard-step
		- *dependencies
		- *env-step
		- run:
		name: CCache initialization
		command: \|
		ccache --show-stats
		ccache --zero-stats
		ccache --max-size=2.0G
		- run:
		name: Build and Testing with CTest
		no_output_timeout: 20.0m
		command: \|
		export LD_LIBRARY_PATH="${CTEST_BINARY_DIRECTORY}/ITK-prefix/lib/:${CTEST_BINARY_DIRECTORY}/SimpleITK-build/lib"
		export CTEST_CACHE="
		BUILD_DOCUMENTATION:BOOL=OFF
		BUILD_EXAMPLES:BOOL=OFF
		BUILD_SHARED_LIBS:BOOL=ON

		SimpleITK_USE_SYSTEM_LUA:BOOL=ON
		SimpleITK_EXPLICIT_INSTANTIATION:BOOL=OFF

		WRAP_DEFAULT:BOOL=OFF"
		ctest -V -S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
		- run:
		name: ccache stats
		when: always
		command: \|
		ccache --show-stats
		- run:
		name: Formatting CTest for JUnit
		when: always
		command: \|
		env
		mkdir -p /tmp/test-results
		ci_addons ctest_junit_formatter ${CTEST_BINARY_DIRECTORY} > /tmp/test-results/JUnit-${CIRCLE_NODE_INDEX}.xml
		- store_test_results:
		path: /tmp/test-results
		destination: ctest
		- save_cache:
		key: 'ccache-{{ arch }}-{{ .Branch }}-{{ epoch }}'
		paths: [ "/home/circleci/.ccache" ]
		- save_cache:
		key: 'v1-external-data-{{ checksum "/home/circleci/external-data.hashable" }}'
		paths: [ "/home/circleci/.ExternalData" ]
		- run:
		name: Cleanup build
		command: \|
		rm -rf "${CTEST_BINARY_DIRECTORY}/ITK" "${CTEST_BINARY_DIRECTORY}/ITK-build"
		rm -rf "${CTEST_BINARY_DIRECTORY}/SimpleITK" "${CTEST_BINARY_DIRECTORY}/SimpleITK-build"
		- persist_to_workspace:
		root: /home/circleci/SimpleITK-build
		paths:
		- "*"
		python-and-test:
		<<: *defaults
		steps:
		- checkout:
		path : ~/SimpleITK
		- *generate-hash-step
		- *restore-data-step
		- *clone-dashboard-step
		- *dependencies
		- *env-step
		- attach_workspace:
		at: /home/circleci/SimpleITK-build
		- run:
		name: Build Python and Testing with CTest
		no_output_timeout: 20.0m
		command: \|
		export LD_LIBRARY_PATH="${CTEST_BINARY_DIRECTORY}/ITK-prefix/lib/:${CTEST_BINARY_DIRECTORY}/lib"
		export CTEST_CACHE="CMAKE_PREFIX_PATH:PATH=${CTEST_BINARY_DIRECTORY}
		SWIG_EXECUTABLE:PATH=${CTEST_BINARY_DIRECTORY}/Swig/bin/swig"
		export CTEST_BINARY_DIRECTORY="/home/circleci/SimpleITK-py"
		ctest -V -Ddashboard_source_config_dir:PATH="Wrapping/Python" -S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
		docs:
		<<: *defaults
		steps:
		- checkout:
		path : ~/SimpleITK
		- *generate-hash-step
		- *restore-data-step
		- *restore-ccache-step
		- *clone-dashboard-step
		- *dependencies
		- *env-step
		- run:
		name: Additional Dependencies
		command: \|
		sudo apt-get install -y doxygen
		- run:
		name: Building and Generating Doxygen
		no_output_timeout: 20.0m
		command: \|
		export CTEST_BUILD_TARGET=SimpleITK-doc
		export CTEST_CACHE="
		BUILD_SHARED_LIBS:BOOL=ON
		WRAP_DEFAULT=OFF
		BUILD_DOXYGEN=ON
		SimpleITK_USE_SYSTEM_LUA:BOOL=ON"
		ctest -V -Ddashboard_no_test:BOOL=1\
		-Ddashboard_track:BOOL=Doxygen\
		-S "${CTEST_SOURCE_DIRECTORY}/.circleci/circleci.cmake"
		- run:
		name: Archiving directory for artifact
		command: \|
		cd ${CTEST_BINARY_DIRECTORY}/SimpleITK-build/Documentation/
		tar -zcvf simpleitk_doxygen_html.tar.gz html
		- store_artifacts:
		path: /home/circleci/SimpleITK-build/SimpleITK-build/Documentation/simpleitk_doxygen_html.tar.gz
		workflows:
		version: 2
		build_and_test:
		jobs:
		- build-and-test:
		filters:
		branches:
		ignore:
		- gh-pages
		- dashboard
		- hooks
		- python-and-test:
		requires:
		- build-and-test
		nightly:
		triggers:
		- schedule:
		cron: "0 3 * * *"
		filters:
		branches:
		only:
		- master
		jobs:
		- docs

CMake/CTestCustom.cmake.in

+1 −0

Original line number	Diff line number	Diff line
		@@ -54,6 +54,7 @@ SET(CTEST_CUSTOM_WARNING_EXCEPTION
		# Ignore CSharp invalid version warning for dev
		"warning CS1607.The version number.dev.*is invalid"
		"warning CS1607.The version.dev.*is not in the normal"
		"warning CS7035.The specified version string.does not conform"

		# Warning when building R, issue related to make file
		"warning: jobserver unavailable:"

CMake/configure_file_build_time.cmake

0 → 100644

+1 −0

Original line number	Diff line number	Diff line
		configure_file( "${CONFIGUREBUILDTIME_filename}" "${CONFIGUREBUILDTIME_out_filename}" )

CMake/sitkAddTest.cmake

+77 −41

Original line number	Diff line number	Diff line
		@@ -2,6 +2,7 @@ include(sitkExternalData)
		include(CMakeParseArguments)

		set(SimpleITK_DATA_ROOT ${SimpleITK_SOURCE_DIR}/Testing/Data)
		set(SimpleITK_TEST_OUTPUT_DIR ${CMAKE_BINARY_DIR}/Testing/Temporary)

		#-----------------------------------------------------------------------------
		# SimpleITK wrapper for add_test that adds support for external data,
		@@ -13,16 +14,26 @@ set(SimpleITK_DATA_ROOT ${SimpleITK_SOURCE_DIR}/Testing/Data)
		# The first arguments are passed to cmake's add_test function with
		# support for the DATA{} references to external data
		# TRANSFORM_COMPARE <test transform> <baseline displacement> [tolerance]
		# IMAGE_COMPARE <test image> <baseline image> [tolerance]
		# IMAGE_MD5_COMPARE <test image> <md5 hash>
		function(sitk_add_test)
		set(options "")
		set(oneValueArgs "NAME")
		set(multiValueArgs COMMAND TRANSFORM_COMPARE)
		set(multiValueArgs COMMAND TRANSFORM_COMPARE IMAGE_COMPARE IMAGE_MD5_COMPARE)
		cmake_parse_arguments("_" "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN} )

		if ( NOT "${__TRANSFORM_COMPARE}" STREQUAL "" )
		set(COMPARE_ARGS ${COMPARE_ARGS} --compareTransform ${__TRANSFORM_COMPARE})
		endif()

		if ( NOT "${__IMAGE_COMPARE}" STREQUAL "" )
		set(COMPARE_ARGS ${COMPARE_ARGS} --compare ${__IMAGE_COMPARE})
		endif()

		if ( NOT "${__IMAGE_MD5_COMPARE}" STREQUAL "" )
		set(COMPARE_ARGS ${COMPARE_ARGS} --compare-MD5 ${__IMAGE_MD5_COMPARE})
		endif()

		if (COMPARE_ARGS)
		set(__COMMAND $<TARGET_FILE:sitkCompareDriver> ${COMPARE_ARGS} -- ${__COMMAND})
		endif()
		@@ -30,7 +41,6 @@ function(sitk_add_test)
		# Add test with data in the SimpleITKData group.
		ExternalData_add_test(SimpleITKData NAME ${__NAME} COMMAND ${__COMMAND} ${__UNPARSED_ARGUMENTS})


		endfunction()


		@@ -52,16 +62,21 @@ function(sitk_add_python_test name)
		endif()

		sitk_add_test(NAME Python.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		${command}
		${ARGN}
		)
		set_property(TEST Python.${name}
		PROPERTY LABELS Python
		)
		if (SimpleITK_TESTING_NOSHOW)
		set_property(TEST Python.${name}
		PROPERTY ENVIRONMENT SITK_NOSHOW=YES
		)
		endif()
		if (NOT SimpleITK_PYTHON_USE_VIRTUALENV)
		set_property(TEST Python.${name}
		APPEND PROPERTY ENVIRONMENT PYTHONPATH=${SimpleITK_BINARY_DIR}/Wrapping/Python
		APPEND PROPERTY ENVIRONMENT PYTHONPATH=${SimpleITK_Python_BINARY_DIR}
		)
		endif()

		@@ -86,16 +101,21 @@ function(sitk_add_lua_test name)
		endif()

		sitk_add_test(NAME Lua.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		${command}
		${ARGN}
		)
		set_property(TEST Lua.${name}
		PROPERTY LABELS Lua
		)
		set_property(TEST Lua.${name}
		PROPERTY ENVIRONMENT LUA_CPATH=$<TARGET_FILE:SimpleITKLuaModule_LUA>
		)
		if (SimpleITK_TESTING_NOSHOW)
		set_property(TEST Lua.${name}
		APPEND PROPERTY ENVIRONMENT SITK_NOSHOW=YES
		)
		endif()
		endfunction()


		@@ -117,11 +137,13 @@ function(sitk_add_ruby_test name)
		endif()

		sitk_add_test(NAME Ruby.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		${command}
		${ARGN}
		)

		set_property(TEST Ruby.${name}
		PROPERTY LABELS Ruby
		)
		set_property(TEST Ruby.${name}
		PROPERTY ENVIRONMENT RUBYLIB=$<TARGET_FILE_DIR:simpleitk_RUBY>
		)
		@@ -146,10 +168,13 @@ function(sitk_add_tcl_test name)
		endif()

		sitk_add_test(NAME Tcl.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		${command}
		${ARGN}
		)
		set_property(TEST Tcl.${name}
		PROPERTY LABELS Tcl
		)
		endfunction()


		@@ -170,9 +195,9 @@ function(sitk_add_java_test name java_file)

		set( _JAVA_LIBRARY_PATH "$<TARGET_FILE_DIR:SimpleITKJava_JAVA>")
		if(WIN32)
		set( _JAVA_CLASSPATH "${SimpleITK_BINARY_DIR}/Wrapping/Java/${JAR_FILE}$<SEMICOLON>${_class_path}" )
		set( _JAVA_CLASSPATH "${SimpleITK_Java_BINARY_DIR}/${JAR_FILE}$<SEMICOLON>${_class_path}" )
		else()
		set( _JAVA_CLASSPATH "${SimpleITK_BINARY_DIR}/Wrapping/Java/${JAR_FILE}:${_class_path}" )
		set( _JAVA_CLASSPATH "${SimpleITK_Java_BINARY_DIR}/${JAR_FILE}:${_class_path}" )
		endif()

		if (NOT TARGET ${_java_class}Java)
		@@ -196,13 +221,16 @@ function(sitk_add_java_test name java_file)


		sitk_add_test(NAME Java.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		"${Java_JAVA_EXECUTABLE}"
		"-Djava.library.path=${_JAVA_LIBRARY_PATH}"
		"-classpath" "${_JAVA_CLASSPATH}"
		"${_java_class}"
		${ARGN}
		)
		set_property(TEST Java.${name}
		PROPERTY LABELS Java
		)
		endfunction()


		@@ -215,7 +243,8 @@ function(sitk_add_r_test name)
		return()
		endif()

		set(command "${R_COMMAND}")
		set(command "${RSCRIPT_EXECUTABLE}" "--no-save" "--no-restore"
		"--no-site-file" "--no-init-file")

		# add extra command which may be needed on some systems
		if(CMAKE_OSX_ARCHITECTURES)
		@@ -224,12 +253,17 @@ function(sitk_add_r_test name)
		endif()

		sitk_add_test(NAME R.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		${command}
		${ARGN}
		)

		file(TO_NATIVE_PATH "${SimpleITK_BINARY_DIR}/Wrapping/R/R_libs" _native_path)
		set_property(TEST R.${name}
		PROPERTY LABELS R
		)

		file(TO_NATIVE_PATH "${SimpleITK_R_BINARY_DIR}/R_libs" _native_path)

		set_property(TEST R.${name}
		PROPERTY ENVIRONMENT R_LIBS=${_native_path}
		)
		@@ -274,17 +308,19 @@ function(sitk_add_csharp_test name csharp_file)
		# the interpreter is set to "" when none is needed
		if( CSHARP_INTERPRETER )
		sitk_add_test(NAME CSharp.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		"${CSHARP_INTERPRETER}"
		"${CSHARP_BINARY_DIRECTORY}/${CSHARP_EXECUTABLE}.exe"
		${ARGN}
		)
		else ()
		sitk_add_test(NAME CSharp.${name}
		COMMAND "${ITK_TEST_DRIVER}"
		COMMAND
		"${CSHARP_BINARY_DIRECTORY}/${CSHARP_EXECUTABLE}.exe"
		${ARGN}
		)
		endif()

		set_property(TEST CSharp.${name}
		PROPERTY LABELS CSharp
		)
		endfunction()