[med-svn] [Git][med-team/camitk][master] 6 commits: remove doxygen xml output to improve reproducibility
Emmanuel Promayon (@promayon-guest)
gitlab at salsa.debian.org
Sat Mar 15 14:12:27 GMT 2025
Emmanuel Promayon pushed to branch master at Debian Med / camitk
Commits:
9f4d8b90 by Emmanuel Promayon at 2025-03-14T18:11:29+01:00
remove doxygen xml output to improve reproducibility
- - - - -
d3992289 by Emmanuel Promayon at 2025-03-15T13:43:41+01:00
use VTK9 modules to remove java dependencies
- - - - -
35e9932f by Emmanuel Promayon at 2025-03-15T13:52:52+01:00
fix path of two missing files using wildcard instead of camitk version number
- - - - -
a18dc01d by Emmanuel Promayon at 2025-03-15T14:03:34+01:00
fix patch formats
- - - - -
07c0bd04 by Emmanuel Promayon at 2025-03-15T14:08:44+01:00
Fix Java unrequired dependency
- - - - -
b7ebf05b by Emmanuel Promayon at 2025-03-15T14:39:45+01:00
fix d/changelog contact name
- - - - -
10 changed files:
- debian/changelog
- debian/not-installed
- + debian/patches/0004-remove-XML-output-to-improve-reproducibility.patch
- + debian/patches/0005-use-VTK-modules-to-remove-useless-java-dependencies.patch
- debian/patches/0007-disable-graph-generation-in-api.patch
- debian/patches/0210-vtk-9.3.patch
- debian/patches/series
- debian/rules
- debian/tests/cepgenerator-test.sh
- debian/tests/config-test.sh
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+camitk (5.2.0-4) UNRELEASED; urgency=medium
+
+ [ Emmanuel Promayon ]
+ * use VTK9 modules to remove unneeded java dependencies
+ * remove doxygen xml output to improve reproducibility
+ * fix dh_missing and patch format warnings
+
+ -- Emmanuel Promayon <Emmanuel.Promayon at univ-grenoble-alpes.fr> Sat, 15 Mar 2025 14:05:12 +0100
+
camitk (5.2.0-3) unstable; urgency=medium
* Team upload.
=====================================
debian/not-installed
=====================================
@@ -1,4 +1,3 @@
-usr/include/camitk-5.1/libraries/shakerlib/ShakerLib.h
usr/bin/camitk-pmltest
usr/bin/camitk-testloggercrash
usr/bin/camitk-basic
@@ -10,4 +9,5 @@ usr/bin/camitk-lmltest
usr/bin/camitk-testlogger
usr/bin/camitk-fancy
usr/bin/camitk-simple
-usr/share/camitk-5.1/cmake/macros/NSIS.template.in
+usr/share/camitk-*/cmake/macros/NSIS.template.in
+usr/include/camitk-*/libraries/shakerlib/ShakerLib.h
=====================================
debian/patches/0004-remove-XML-output-to-improve-reproducibility.patch
=====================================
@@ -0,0 +1,89 @@
+From: Emmanuel Promayon <Emmanuel.Promayon at univ-grenoble-alpes.fr>
+Date: Fri, 14 Mar 2025 18:08:23 +0100
+Subject: remove XML output to improve reproducibility
+
+---
+ sdk/doc/doxygen.conf.in | 33 ++++++++++++++++-----------------
+ 1 file changed, 16 insertions(+), 17 deletions(-)
+
+diff --git a/sdk/doc/doxygen.conf.in b/sdk/doc/doxygen.conf.in
+index 9d7702c..3e6b660 100644
+--- a/sdk/doc/doxygen.conf.in
++++ b/sdk/doc/doxygen.conf.in
+@@ -62,8 +62,8 @@ SORT_MEMBERS_CTORS_1ST = NO
+ SORT_GROUP_NAMES = NO
+ SORT_BY_SCOPE_NAME = NO
+ GENERATE_TODOLIST = NO
+-GENERATE_TESTLIST = YES
+-GENERATE_BUGLIST = YES
++GENERATE_TESTLIST = NO
++GENERATE_BUGLIST = NO
+ GENERATE_DEPRECATEDLIST= YES
+ ENABLED_SECTIONS =
+ MAX_INITIALIZER_LINES = 30
+@@ -119,7 +119,6 @@ VERBATIM_HEADERS = YES
+ # configuration options related to the alphabetical class index
+ #---------------------------------------------------------------------------
+ ALPHABETICAL_INDEX = YES
+-COLS_IN_ALPHA_INDEX = 5
+ IGNORE_PREFIX = MYPROJECT
+
+ #---------------------------------------------------------------------------
+@@ -159,7 +158,7 @@ GENERATE_CHI = NO
+ CHM_INDEX_ENCODING =
+ BINARY_TOC = NO
+ TOC_EXPAND = NO
+-GENERATE_QHP = YES
++GENERATE_QHP = NO
+ QCH_FILE = camitk
+ QHP_NAMESPACE = camitk
+ QHP_VIRTUAL_FOLDER = doc
+@@ -191,9 +190,9 @@ MAN_LINKS = NO
+ #---------------------------------------------------------------------------
+ # configuration options related to the XML output
+ #---------------------------------------------------------------------------
+-GENERATE_XML = YES
++GENERATE_XML = NO
+ XML_OUTPUT = xml
+-XML_PROGRAMLISTING = YES
++XML_PROGRAMLISTING = NO
+
+ #---------------------------------------------------------------------------
+ # configuration options for the AutoGen Definitions output
+@@ -235,25 +234,25 @@ EXTERNAL_GROUPS = YES
+ CLASS_DIAGRAMS = NO
+ HIDE_UNDOC_RELATIONS = YES
+ HAVE_DOT = YES
+-INTERACTIVE_SVG = NO
++INTERACTIVE_SVG = YES
+ DOT_NUM_THREADS = 0
+ DOT_FONTNAME = Helvetica
+ DOT_FONTSIZE = 10
+ DOT_FONTPATH =
+-CLASS_GRAPH = NO
+-COLLABORATION_GRAPH = NO
+-GROUP_GRAPHS = NO
++CLASS_GRAPH = YES
++COLLABORATION_GRAPH = YES
++GROUP_GRAPHS = YES
+ #For doxygen 1.8 UML_LOOK = YES
+ UML_LOOK = YES
+ #For doxygen 1.8
+ UML_LIMIT_NUM_FIELDS = 5
+-TEMPLATE_RELATIONS = NO
+-INCLUDE_GRAPH = NO
+-INCLUDED_BY_GRAPH = NO
+-CALL_GRAPH = NO
+-CALLER_GRAPH = NO
+-GRAPHICAL_HIERARCHY = NO
+-DIRECTORY_GRAPH = NO
++TEMPLATE_RELATIONS = YES
++INCLUDE_GRAPH = YES
++INCLUDED_BY_GRAPH = YES
++CALL_GRAPH = YES
++CALLER_GRAPH = YES
++GRAPHICAL_HIERARCHY = YES
++DIRECTORY_GRAPH = YES
+ DOT_IMAGE_FORMAT = svg
+ DOT_PATH = @DOT_PATH@
+ DOTFILE_DIRS =
=====================================
debian/patches/0005-use-VTK-modules-to-remove-useless-java-dependencies.patch
=====================================
@@ -0,0 +1,191 @@
+From: Emmanuel Promayon <Emmanuel.Promayon at univ-grenoble-alpes.fr>
+Date: Fri, 14 Mar 2025 19:08:28 +0100
+Subject: use VTK modules to remove useless java dependencies
+
+Forwarded: not-needed
+
+---
+ .../cepgenerator/testing/cepgenerator-test.sh | 4 --
+ sdk/applications/config/testing/config-test.sh | 4 --
+ sdk/cmake/modules/CamiTKConfig.cmake.in | 53 ++++++++++++++++++++--
+ .../modules/macros/camitk/CamiTKApplication.cmake | 6 ++-
+ .../modules/macros/camitk/CamiTKExtension.cmake | 6 ++-
+ .../modules/macros/camitk/CamiTKLibrary.cmake | 6 +++
+ sdk/libraries/core/CMakeLists.txt | 5 ++
+ 7 files changed, 71 insertions(+), 13 deletions(-)
+
+diff --git a/sdk/applications/cepgenerator/testing/cepgenerator-test.sh b/sdk/applications/cepgenerator/testing/cepgenerator-test.sh
+index 067c043..ca778ef 100755
+--- a/sdk/applications/cepgenerator/testing/cepgenerator-test.sh
++++ b/sdk/applications/cepgenerator/testing/cepgenerator-test.sh
+@@ -330,10 +330,6 @@ testcepfile() {
+ # if a problem occurs, call the clean method
+ trap "cleanup" 0 INT QUIT ABRT PIPE TERM EXIT
+
+-# add java to LD_LIBRARY_PATH to fix strange dependency (is it due to VTK9 package?)
+-export JAVA_HOME=/usr/lib/jvm/default-java
+-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${JAVA_HOME}/lib/:${JAVA_HOME}/lib/server/
+-
+ init $*
+ cd $workingDir
+ $scriptDir/generate-coreschema-files.sh
+diff --git a/sdk/applications/config/testing/config-test.sh b/sdk/applications/config/testing/config-test.sh
+index 4f20303..83c5664 100755
+--- a/sdk/applications/config/testing/config-test.sh
++++ b/sdk/applications/config/testing/config-test.sh
+@@ -275,10 +275,6 @@ checkValue() {
+ # if a problem occurs, call the clean method
+ trap "cleanup" 0 INT QUIT ABRT PIPE TERM EXIT
+
+-# add java to LD_LIBRARY_PATH to fix strange dependency (is it due to VTK9 package?)
+-export JAVA_HOME=/usr/lib/jvm/default-java
+-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${JAVA_HOME}/lib/:${JAVA_HOME}/lib/server/
+-
+ declareTestData
+ initTestData
+ init $*
+diff --git a/sdk/cmake/modules/CamiTKConfig.cmake.in b/sdk/cmake/modules/CamiTKConfig.cmake.in
+index 46323f0..f983994 100644
+--- a/sdk/cmake/modules/CamiTKConfig.cmake.in
++++ b/sdk/cmake/modules/CamiTKConfig.cmake.in
+@@ -42,7 +42,49 @@ else()
+ endif()
+
+ # Find VTK
+-find_package(VTK REQUIRED)
++if("${CAMITK_VERSION_MAJOR}.${CAMITK_VERSION_MINOR}" VERSION_LESS 5.2)
++ find_package(VTK REQUIRED)
++else()
++ set(CAMITK_VTK_COMPONENTS CommonCore
++ CommonDataModel
++ CommonExecutionModel
++ CommonMath
++ CommonTransforms
++ FiltersCore
++ FiltersExtraction
++ FiltersGeneral
++ FiltersSources
++ GUISupportQt
++ IOImage
++ ImagingCore
++ InteractionWidgets
++ RenderingAnnotation
++ RenderingCore
++ RenderingOpenGL2
++ # Adding suggested modules as well
++ FiltersParallel # implements VTK::FiltersCore
++ InteractionStyle # implements VTK::RenderingCore
++ #RenderingCellGrid # implements VTK::RenderingCore
++ RenderingFreeType # implements VTK::RenderingCore
++ RenderingGL2PSOpenGL2 # implements VTK::RenderingOpenGL2
++ RenderingUI
++ # Manually added for CamiTK CE
++ IOGeometry # required by basicmesh action
++ FiltersParallelVerdict # required by CamiTK basicmesh action
++ ImagingStencil # required by CamiTK basicmesh action
++ RenderingVolume # required by CamiTK volumerendering action
++ RenderingVolumeOpenGL2 # required by CamiTK volumerendering action
++ IOImport # required by CamiTK core
++ IOExport # required by CamiTK vrml component
++ IOExportGL2PS # required by CamiTK core
++ )
++ find_package(VTK REQUIRED
++ COMPONENTS ${CAMITK_VTK_COMPONENTS}
++ )
++ # add VTK:: to the component names (used later in target_link_libraries)
++ string(REGEX REPLACE "([^;]+)" "VTK::\\1" CAMITK_VTK_LIBRARIES "${CAMITK_VTK_COMPONENTS}")
++endif()
++
+ if(NOT VTK_FOUND)
+ message(SEND_ERROR "Failed to find VTK. VTK is required.")
+ endif()
+@@ -51,7 +93,12 @@ if("${VTK_VERSION}" VERSION_LESS 7.1)
+ endif()
+ message(STATUS "Found suitable version of VTK : ${VTK_VERSION} (VTK 7.1 or above required)")
+ set(CAMITK_VTK_VERSION ${VTK_VERSION_MAJOR}.${VTK_VERSION_MINOR})
+-include(${VTK_USE_FILE}) # This automatically set the include dirs (remain the link_directories and target_link_libraries)
++if("${VTK_VERSION}" VERSION_LESS 9.0)
++ include(${VTK_USE_FILE}) # This automatically set the include dirs (remain the link_directories and target_link_libraries)
++else()
++ # nothing to do.
++endif()
++
+ set(VTK_LIBRARY_DIR ${VTK_DIR}/../..)
+
+ #-- supply default values for CMake
+@@ -224,7 +271,7 @@ else()
+
+ # list of all core dependencies
+ set(CAMITK_LIBRARIES
+- ${VTK_LIBRARIES} # no need to add more libraries in the list, CMake & VTK handle it correclty on Linux & Apple
++ ${CAMITK_VTK_LIBRARIES} # no need to add more libraries in the list, CMake & VTK handle it correclty on Linux & Apple
+ # QVTK
+ qtpropertybrowser
+ )
+diff --git a/sdk/cmake/modules/macros/camitk/CamiTKApplication.cmake b/sdk/cmake/modules/macros/camitk/CamiTKApplication.cmake
+index eca1f0b..322c1c4 100644
+--- a/sdk/cmake/modules/macros/camitk/CamiTKApplication.cmake
++++ b/sdk/cmake/modules/macros/camitk/CamiTKApplication.cmake
+@@ -515,7 +515,11 @@ macro(camitk_application)
+ #########################################################################
+ # LINKING LIBRARIES
+ target_link_libraries(${APPLICATION_TARGET_NAME} ${CAMITK_CORE_LIBRARIES} ${CAMITK_LIBRARIES} ${COMPONENT_EXTENSION_LIBRARIES} ${ACTION_EXTENSION_LIBRARIES} ${VIEWER_EXTENSION_LIBRARIES} ${CEP_LIBRARIES} ${XERCESC_LIBRARY} ${CAMITK_ITK_LIBRARIES} ${PYTHON_LIBRARIES} ${EXTERNAL_LIBRARIES})
+-
++ if("${VTK_VERSION}" VERSION_GREATER_EQUAL 9.0)
++ vtk_module_autoinit(
++ TARGETS ${APPLICATION_TARGET_NAME}
++ MODULES ${CAMITK_VTK_LIBRARIES})
++ endif()
+
+
+ #########################################################################
+diff --git a/sdk/cmake/modules/macros/camitk/CamiTKExtension.cmake b/sdk/cmake/modules/macros/camitk/CamiTKExtension.cmake
+index acc6a71..1c1e429 100644
+--- a/sdk/cmake/modules/macros/camitk/CamiTKExtension.cmake
++++ b/sdk/cmake/modules/macros/camitk/CamiTKExtension.cmake
+@@ -677,7 +677,11 @@ macro(camitk_extension)
+ # LINKING LIBRARIES
+ # Any component or action has to be linked with ${CAMITK_CORE_LIBRARIES} and with all its dependencies
+ target_link_libraries(${${TYPE_EXTENSION_CMAKE}_TARGET_NAME} ${CAMITK_CORE_LIBRARIES} ${CAMITK_LIBRARIES} ${COMPONENT_EXTENSION_LIBRARIES} ${ACTION_EXTENSION_LIBRARIES} ${VIEWER_EXTENSION_LIBRARIES} ${CEP_LIBRARIES} ${CAMITK_ITK_LIBRARIES} ${LIBXML2_LIBRARY} ${OpenCV_LIBRARIES} ${IGSTK_LIBRARIES} ${XERCESC_LIBRARIES} ${GDCM_LIBRARIES} ${EXTERNAL_LIBRARIES})
+-
++ if("${VTK_VERSION}" VERSION_GREATER_EQUAL 9.0)
++ vtk_module_autoinit(
++ TARGETS ${${TYPE_EXTENSION_CMAKE}_TARGET_NAME}
++ MODULES ${CAMITK_VTK_LIBRARIES})
++ endif()
+
+
+ #########################################################################
+diff --git a/sdk/cmake/modules/macros/camitk/CamiTKLibrary.cmake b/sdk/cmake/modules/macros/camitk/CamiTKLibrary.cmake
+index 3eb245f..5dbea7e 100644
+--- a/sdk/cmake/modules/macros/camitk/CamiTKLibrary.cmake
++++ b/sdk/cmake/modules/macros/camitk/CamiTKLibrary.cmake
+@@ -428,6 +428,12 @@ macro(camitk_library)
+ #########################################################################
+ # LINKING LIBRARIES
+ target_link_libraries(${LIBRARY_TARGET_NAME} ${CAMITK_LIBRARIES_DEPENDENCIES} ${CEP_LIBRARIES} ${LINKER_EXTERNAL_LIBRARIES} ${LIBXML2_LIBRARY} ${CAMITK_ITK_LIBRARIES} ${XERCESC_LIBRARIES})
++ if("${VTK_VERSION}" VERSION_GREATER_EQUAL 9.0)
++ vtk_module_autoinit(
++ TARGETS ${LIBRARY_TARGET_NAME}
++ MODULES ${CAMITK_VTK_LIBRARIES})
++ endif()
++
+
+
+
+diff --git a/sdk/libraries/core/CMakeLists.txt b/sdk/libraries/core/CMakeLists.txt
+index d4c68d0..89c2631 100644
+--- a/sdk/libraries/core/CMakeLists.txt
++++ b/sdk/libraries/core/CMakeLists.txt
+@@ -65,6 +65,11 @@ if (WIN32 AND MSVC)
+ endif()
+
+ target_link_libraries(${CAMITK_CORE_LIB_TARGET_NAME} ${CAMITK_LIBRARIES})
++if("${VTK_VERSION}" VERSION_GREATER_EQUAL 9.0)
++ vtk_module_autoinit(
++ TARGETS ${CAMITK_CORE_LIB_TARGET_NAME}
++ MODULES ${CAMITK_VTK_LIBRARIES})
++endif()
+
+ # output directory
+ if (MSVC)
=====================================
debian/patches/0007-disable-graph-generation-in-api.patch
=====================================
@@ -1,14 +1,11 @@
From: Emmanuel Promayon <Emmanuel.Promayon at univ-grenoble-alpes.fr>
Date: Fri, 28 Feb 2025 10:46:49 +0100
Subject: Disable graph generation in apidoc
-
-Forwarded: not-needed
-Last-Update: 2023-07-27
-
Generating graphs in apidoc takes a lot of resources.
It is not particularly needed as it is available
online and can be generated from the sources if
needed.
+Forwarded: not-needed
Last-Update: 2023-07-27
---
sdk/doc/doxygen.conf.in | 22 +++++++++++-----------
=====================================
debian/patches/0210-vtk-9.3.patch
=====================================
@@ -1,11 +1,10 @@
+Subject: Followup with deprecated vtkConfigure.h header, renaming of SetQuadQualityMeasureToMaxEdgeRatios into SetQuadQualityMeasureToMaxEdgeRatio and removal of SetTetQualityMeasureToAspectBeta
From: Gianfranco Costamagna <locutusofborg at debian.org>
+Last-Update: 2024-06-20
+
Date: Fri, 28 Feb 2025 10:46:49 +0100
-Subject: Followup with deprecated vtkConfigure.h header,
- renaming of SetQuadQualityMeasureToMaxEdgeRatios into
- SetQuadQualityMeasureToMaxEdgeRatio and removal of
- SetTetQualityMeasureToAspectBeta
-Last-Update: 2024-06-20
+
---
sdk/actions/mesh/basicmesh/MeshQuality.cpp | 18 +++++++++---------
sdk/components/vtkimage/RawDataDialog.cpp | 4 +++-
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
0007-disable-graph-generation-in-api.patch
0210-vtk-9.3.patch
0003-FIX-FTBFS-disabling-culprit-itk-test-for-now.patch
+0004-remove-XML-output-to-improve-reproducibility.patch
+0005-use-VTK-modules-to-remove-useless-java-dependencies.patch
=====================================
debian/rules
=====================================
@@ -80,7 +80,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# to know about all camitk extension directories and properly manage inner-dependencies
# between extensions (i.e., mml component extension depends on physicalmodel component extensions)
# Lib dependencies can be in any extensions (viewers, component and action extensions) lib directory
- export LD_LIBRARY_PATH=$(LIB_BUILD_DIR)/:$(PRIVATE_LIB_BUILD_DIR)/viewers/:$(PRIVATE_LIB_BUILD_DIR)/components/:$(PRIVATE_LIB_BUILD_DIR)/actions/:$(PRIVATE_LIB_BUILD_DIR)/:$(JAVA_HOME)/lib/:$(JAVA_HOME)/lib/server/ ; \
+ export LD_LIBRARY_PATH=$(LIB_BUILD_DIR)/:$(PRIVATE_LIB_BUILD_DIR)/viewers/:$(PRIVATE_LIB_BUILD_DIR)/components/:$(PRIVATE_LIB_BUILD_DIR)/actions/:$(PRIVATE_LIB_BUILD_DIR)/ ; \
(cd camitk-build && xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" ctest -V --timeout 1800)
endif
=====================================
debian/tests/cepgenerator-test.sh
=====================================
@@ -330,10 +330,6 @@ testcepfile() {
# if a problem occurs, call the clean method
trap "cleanup" 0 INT QUIT ABRT PIPE TERM EXIT
-# add java to LD_LIBRARY_PATH to fix strange dependency (is it due to VTK9 package?)
-export JAVA_HOME=/usr/lib/jvm/default-java
-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${JAVA_HOME}/lib/:${JAVA_HOME}/lib/server/
-
init $*
cd $workingDir
$scriptDir/generate-coreschema-files.sh
=====================================
debian/tests/config-test.sh
=====================================
@@ -275,10 +275,6 @@ checkValue() {
# if a problem occurs, call the clean method
trap "cleanup" 0 INT QUIT ABRT PIPE TERM EXIT
-# add java to LD_LIBRARY_PATH to fix strange dependency (is it due to VTK9 package?)
-export JAVA_HOME=/usr/lib/jvm/default-java
-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${JAVA_HOME}/lib/:${JAVA_HOME}/lib/server/
-
declareTestData
initTestData
init $*
View it on GitLab: https://salsa.debian.org/med-team/camitk/-/compare/4d34703170a91e30b94044a6a3638933c3728232...b7ebf05bca2f97808cbf0006e11c35b682ce30c1
--
View it on GitLab: https://salsa.debian.org/med-team/camitk/-/compare/4d34703170a91e30b94044a6a3638933c3728232...b7ebf05bca2f97808cbf0006e11c35b682ce30c1
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