[hdf5] Update HDF5 to 1.12 (#11747)

* [hdf5] Update HDF5 to 1.12 and use github live-clones instead of binary download

* [hdf5] bump control

* [hdf5] fix szip and typo about linkage

* [hdf5] add missing package namespace.... they somehow missed to set it?

* [hdf5] retry without "

* [field3d] fix regression and update. Remove windows as unsupported since the cmakelists tries to support windows

* fix typo

* remove ws

Co-authored-by: NancyLi1013 <46708020+NancyLi1013@users.noreply.github.com>

* linebreak first patch

Co-authored-by: NancyLi1013 <46708020+NancyLi1013@users.noreply.github.com>

* ws change

Co-authored-by: NancyLi1013 <46708020+NancyLi1013@users.noreply.github.com>

* [field3d] update copying installation

* [hdf5] use official github repo

* clean baseline

Co-authored-by: NancyLi1013 <46708020+NancyLi1013@users.noreply.github.com>
Co-authored-by: Jack·Boos·Yu <47264268+JackBoosY@users.noreply.github.com>

ports/field3d/CONTROL

@@ -1,6 +1,6 @@
 Source: field3d
-Version: 1.7.2
+Version: 1.7.3
 Homepage: https://github.com/imageworks/Field3D
 Description: An open source library for storing voxel data. It provides C++ classes that handle in-memory storage and a file format based on HDF5 that allows the C++ objects to be written to and read from disk.
-Build-Depends: hdf5, boost-regex, boost-thread, boost-program-options, boost-system, openexr, boost-foreach, boost-test, boost-timer, boost-format
+Build-Depends: hdf5[core], boost-regex, boost-thread, boost-program-options, boost-system, openexr, boost-foreach, boost-test, boost-timer, boost-format
 Supports: !(windows|arm|uwp)

ports/field3d/hdf5.api.patch

@@ -0,0 +1,14 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1e608b3ec..5ff2c3c31 100644
+--- a/CMakeLists.txt	
++++ b/CMakeLists.txt
+@@ -34,7 +34,8 @@
+ CMAKE_MINIMUM_REQUIRED( VERSION 2.8 )
+ 
+ PROJECT ( field3d )
+-
++add_definitions(-UH5_USE_112_API_DEFAULT)
++add_definitions(-DH5_USE_110_API_DEFAULT)
+ set( CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake )
+ 
+ FIND_PACKAGE (Doxygen)

ports/field3d/portfile.cmake

@@ -1,8 +1,5 @@
-include(vcpkg_common_functions)
 
-if (VCPKG_TARGET_IS_WINDOWS)
+if (TRIPLET_SYSTEM_ARCH MATCHES "arm")
-	message(FATAL_ERROR "Windows is currently not supported.")
-elseif (TRIPLET_SYSTEM_ARCH MATCHES "arm")
     message(FATAL_ERROR "ARM is currently not supported.")
 elseif(VCPKG_CMAKE_SYSTEM_NAME STREQUAL WindowsStore)
     message(FATAL_ERROR "Error: UWP builds are currently not supported.")
@@ -11,16 +8,19 @@ endif()
 vcpkg_from_github(
     OUT_SOURCE_PATH SOURCE_PATH
     REPO imageworks/Field3D
-    REF v1.7.2
+    REF v1.7.3
-    SHA512 e4ea51310105980f759dce48830db8ae3592ce32a02b246214d8aed9df7a7f5c500314f2daf92196b7a76d648f2909b18112df4c5c3c8949c0676d710dfbf1f2
+    SHA512 de3f10ff120420925de67064b2169f2a30c9180e308acc9090d70567b45be5423f4b1f7eb32bb376c887cea1364803cf7b2db66c2bc49f8a39a1037bbf0e5f39
     HEAD_REF master
     PATCHES
         fix-build_error.patch
+        hdf5.api.patch # Switches the HDF5 default API for this port to 1.10
 )
 
 vcpkg_configure_cmake(
     SOURCE_PATH ${SOURCE_PATH}
     PREFER_NINJA
+    OPTIONS
+        "-DINSTALL_DOCS:BOOL=OFF"
 )
 
 vcpkg_install_cmake()
@@ -31,5 +31,5 @@ endif()
 file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/include)
 
 # Handle copyright
-file(COPY ${SOURCE_PATH}/COPYING ${SOURCE_PATH}/README DESTINATION ${CURRENT_PACKAGES_DIR}/share/field3d)
+file(INSTALL "${SOURCE_PATH}/COPYING" DESTINATION "${CURRENT_PACKAGES_DIR}/share/${PORT}" RENAME copyright)
-file(RENAME ${CURRENT_PACKAGES_DIR}/share/field3d/COPYING ${CURRENT_PACKAGES_DIR}/share/field3d/copyright)
+file(INSTALL "${SOURCE_PATH}/README" DESTINATION "${CURRENT_PACKAGES_DIR}/share/${PORT}")

ports/hdf5/CONTROL

@@ -1,5 +1,5 @@
 Source: hdf5
-Version: 1.10.5-12
+Version: 1.12.0
 Homepage: https://www.hdfgroup.org/downloads/hdf5/
 Description: HDF5 is a data model, library, and file format for storing and managing data
 Default-Features: szip, zlib

ports/hdf5/export-private.patch

@@ -1,15 +0,0 @@
-diff --git a/hdf5-1.10.5/hl/src/H5LDprivate.h b/hdf5-1.10.5/hl/src/H5LDprivate.h
-index b52928b53..5f02ea781 100644
---- a/hdf5-1.10.5/hl/src/H5LDprivate.h
-+++ b/hdf5-1.10.5/hl/src/H5LDprivate.h
-@@ -40,8 +40,8 @@ typedef struct H5LD_memb_t {
-  * #2: these two routines are too specific to be made as public routines
-  * Decide to do #3 at this point of time after some discussion.
-  */
--void H5LD_clean_vector(H5LD_memb_t *listv[]);
--int H5LD_construct_vector(char *fields, H5LD_memb_t *listv[], hid_t par_tid);
-+H5_HLDLL void H5LD_clean_vector(H5LD_memb_t *listv[]);
-+H5_HLDLL int H5LD_construct_vector(char *fields, H5LD_memb_t *listv[], hid_t par_tid);
- 
- #endif /* end _H5LDprivate_H */
- 

ports/hdf5/hdf5_config.patch

@@ -1,24 +1,31 @@
-diff --git a/hdf5-1.10.5/config/cmake/hdf5-config.cmake.in b/hdf5-1.10.5/config/cmake/hdf5-config.cmake.in
+diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in
-index 3bd9e1d..7f6699c 100644
+index b5a12a650..a8cbacb1c 100644
---- a/hdf5-1.10.5/config/cmake/hdf5-config.cmake.in
+--- a/config/cmake/hdf5-config.cmake.in	
-+++ b/hdf5-1.10.5/config/cmake/hdf5-config.cmake.in
++++ b/config/cmake/hdf5-config.cmake.in
-@@ -108,11 +108,15 @@ set (HDF5_VERSION_MINOR  @HDF5_VERSION_MINOR@)
+@@ -54,7 +54,10 @@ set (${HDF5_PACKAGE_NAME}_PARALLEL_FILTERED_WRITES "@PARALLEL_FILTERED_WRITES@")
- # project which has already built hdf5 as a subproject
+ #-----------------------------------------------------------------------------
- #-----------------------------------------------------------------------------
+ # Dependencies
- if (NOT TARGET "@HDF5_PACKAGE@")
+ #-----------------------------------------------------------------------------
--  if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS AND NOT TARGET "zlib")
++include(CMakeFindDependencyMacro)
--    include (@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@/@ZLIB_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
++
-+  if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT AND NOT TARGET ZLIB::ZLIB)
+ if (${HDF5_PACKAGE_NAME}_ENABLE_PARALLEL)
-+    find_package(ZLIB REQUIRED)
++  find_dependency(MPI)
-   endif ()
+   set (${HDF5_PACKAGE_NAME}_MPI_C_INCLUDE_PATH "@MPI_C_INCLUDE_DIRS@")
--  if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS AND NOT TARGET "szip")
+   set (${HDF5_PACKAGE_NAME}_MPI_C_LIBRARIES    "@MPI_C_LIBRARIES@")
--    include (@PACKAGE_SHARE_INSTALL_DIR@/@SZIP_PACKAGE_NAME@/@SZIP_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
+   if (${HDF5_PACKAGE_NAME}_BUILD_FORTRAN)
-+  if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND NOT TARGET "szip")
+@@ -110,11 +113,11 @@ set (${HDF5_PACKAGE_NAME}_VERSION_MINOR  @HDF5_VERSION_MINOR@)
-+    if(${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
+ # project which has already built hdf5 as a subproject
-+      include (@PACKAGE_SHARE_INSTALL_DIR@/@SZIP_PACKAGE_NAME@/@SZIP_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
+ #-----------------------------------------------------------------------------
-+    else()
+ if (NOT TARGET "@HDF5_PACKAGE@")
-+      find_package(@SZIP_PACKAGE_NAME@ REQUIRED)
+-  if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
-+    endif()
+-    include (@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@/@ZLIB_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
-   endif ()
++  if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT)
-   include (@PACKAGE_SHARE_INSTALL_DIR@/@HDF5_PACKAGE@/@HDF5_PACKAGE@@HDF_PACKAGE_EXT@-targets.cmake)
++    find_dependency(ZLIB)
- endif ()
+   endif ()
+-  if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS)
+-    include (@PACKAGE_SHARE_INSTALL_DIR@/@SZIP_PACKAGE_NAME@/@SZIP_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake)
++  if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT)
++    find_dependency(szip)
+   endif ()
+   include (@PACKAGE_SHARE_INSTALL_DIR@/@HDF5_PACKAGE@/@HDF5_PACKAGE@@HDF_PACKAGE_EXT@-targets.cmake)
+ endif ()

ports/hdf5/portfile.cmake

@@ -1,20 +1,14 @@
 vcpkg_fail_port_install(ON_TARGET "UWP")
 
-vcpkg_download_distfile(ARCHIVE
+vcpkg_from_github(
-    URLS "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/CMake-hdf5-1.10.5.tar.gz"
-    FILENAME "CMake-hdf5-1.10.5.tar.gz"
-    SHA512 a25ea28d7a511f9184d97b5b8cd4c6d52dcdcad2bffd670e24a1c9a6f98b03108014a853553fa2b00d4be7523128b5fd6a4454545e3b17ff8c66fea16a09e962
-)
-
-vcpkg_extract_source_archive_ex(
     OUT_SOURCE_PATH SOURCE_PATH
-    ARCHIVE ${ARCHIVE}
+    REPO  HDFGroup/hdf5 
-    REF hdf5
+    REF hdf5-1_12_0
-    PATCHES
+    SHA512 d84df1ea72dc6fa038440a370e1b1ff523364474e7f214b967edc26d3191b2ef4fe1d9273c4a086a5945f1ad1ab6aa8dbcda495898e7967b2b73fd93dd5071e0
-        hdf5_config.patch       
+    HEAD_REF develop
-        fix-generate.patch      # removes the build of static targets in shared builds
+    PATCHES 
-        static-targets.patch    # maps the internal static tagets to the shared targets if building as a dynamic library
+       hdf5_config.patch
-        export-private.patch    # exports two additional functions in shared builds to make hl/tools/h5watch build in shared builds. 
+       szip.patch
 )
 
 if ("parallel" IN_LIST FEATURES AND "cpp" IN_LIST FEATURES)
@@ -42,11 +36,17 @@ if(FEATURES MATCHES "tools" AND VCPKG_CRT_LINKAGE STREQUAL "static")
     list(APPEND FEATURE_OPTIONS -DBUILD_STATIC_EXECS=ON)
 endif()
 
+if(NOT VCPKG_LIBRARY_LINKAGE STREQUAL "static")
+    list(APPEND FEATURE_OPTIONS
+                    -DBUILD_STATIC_LIBS=OFF
+                    -DONLY_SHARED_LIBS=ON)
+endif()
+
 find_library(SZIP_RELEASE NAMES libsz libszip szip sz PATHS "${CURRENT_INSTALLED_DIR}/lib" NO_DEFAULT_PATH)
 find_library(SZIP_DEBUG NAMES libsz libszip szip sz libsz_D libszip_D szip_D sz_D szip_debug PATHS "${CURRENT_INSTALLED_DIR}/debug/lib" NO_DEFAULT_PATH)
 
 vcpkg_configure_cmake(
-    SOURCE_PATH ${SOURCE_PATH}/hdf5-1.10.5
+    SOURCE_PATH ${SOURCE_PATH}
     DISABLE_PARALLEL_CONFIGURE
     PREFER_NINJA
     OPTIONS
@@ -55,8 +55,7 @@ vcpkg_configure_cmake(
         -DHDF5_BUILD_EXAMPLES=OFF
         -DHDF5_INSTALL_DATA_DIR=share/hdf5/data
         -DHDF5_INSTALL_CMAKE_DIR=share
-        "-DSZIP_LIBRARY_DEBUG:PATH=${SZIP_DEBUG}"
+        -DHDF_PACKAGE_NAMESPACE:STRING=hdf5::
-        "-DSZIP_LIBRARY_RELEASE:PATH=${SZIP_RELEASE}"
 )
 
 vcpkg_install_cmake()

ports/hdf5/static-targets.patch

@@ -1,37 +0,0 @@
-diff --git a/hdf5-1.10.5/CMakeLists.txt b/hdf5-1.10.5/CMakeLists.txt
-index 6ca2f5c54..f7a4db9e5 100644
---- a/hdf5-1.10.5/CMakeLists.txt	
-+++ b/hdf5-1.10.5/CMakeLists.txt
-@@ -150,6 +150,7 @@ set (HDF5_JAVA_TEST_LIB_NAME    "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_JAVA_TEST_LIB
- #-----------------------------------------------------------------------------
- # Set the target names of all the libraries
- #-----------------------------------------------------------------------------
-+if(NOT BUILD_SHARED_LIBS)
- set (HDF5_LIB_TARGET              "${HDF5_LIB_CORENAME}-static")
- set (HDF5_TEST_LIB_TARGET         "${HDF5_TEST_LIB_CORENAME}-static")
- set (HDF5_CPP_LIB_TARGET          "${HDF5_CPP_LIB_CORENAME}-static")
-@@ -162,9 +163,24 @@ set (HDF5_F90_TEST_LIB_TARGET     "${HDF5_F90_TEST_LIB_CORENAME}-static")
- set (HDF5_F90_C_TEST_LIB_TARGET   "${HDF5_F90_C_TEST_LIB_CORENAME}-static")
- set (HDF5_HL_F90_LIB_TARGET       "${HDF5_HL_F90_LIB_CORENAME}-static")
- set (HDF5_HL_F90_C_LIB_TARGET     "${HDF5_HL_F90_C_LIB_CORENAME}-static")
-+else()
-+set (HDF5_LIB_TARGET              "${HDF5_LIB_CORENAME}-shared")
-+set (HDF5_TEST_LIB_TARGET         "${HDF5_TEST_LIB_CORENAME}-shared")
-+set (HDF5_CPP_LIB_TARGET          "${HDF5_CPP_LIB_CORENAME}-shared")
-+set (HDF5_HL_LIB_TARGET           "${HDF5_HL_LIB_CORENAME}-shared")
-+set (HDF5_HL_CPP_LIB_TARGET       "${HDF5_HL_CPP_LIB_CORENAME}-shared")
-+set (HDF5_TOOLS_LIB_TARGET        "${HDF5_TOOLS_LIB_CORENAME}-shared")
-+set (HDF5_F90_LIB_TARGET          "${HDF5_F90_LIB_CORENAME}-shared")
-+set (HDF5_F90_C_LIB_TARGET        "${HDF5_F90_C_LIB_CORENAME}-shared")
-+set (HDF5_F90_TEST_LIB_TARGET     "${HDF5_F90_TEST_LIB_CORENAME}-shared")
-+set (HDF5_F90_C_TEST_LIB_TARGET   "${HDF5_F90_C_TEST_LIB_CORENAME}-shared")
-+set (HDF5_HL_F90_LIB_TARGET       "${HDF5_HL_F90_LIB_CORENAME}-shared")
-+set (HDF5_HL_F90_C_LIB_TARGET     "${HDF5_HL_F90_C_LIB_CORENAME}-shared")
-+endif()
- set (HDF5_JAVA_JNI_LIB_TARGET     "${HDF5_JAVA_JNI_LIB_CORENAME}")
- set (HDF5_JAVA_HDF5_LIB_TARGET    "${HDF5_JAVA_HDF5_LIB_CORENAME}")
- set (HDF5_JAVA_TEST_LIB_TARGET    "${HDF5_JAVA_TEST_LIB_CORENAME}")
-+
- set (HDF5_LIBSH_TARGET            "${HDF5_LIB_CORENAME}-shared")
- set (HDF5_TEST_LIBSH_TARGET       "${HDF5_TEST_LIB_CORENAME}-shared")
- set (HDF5_CPP_LIBSH_TARGET        "${HDF5_CPP_LIB_CORENAME}-shared")

ports/hdf5/szip.patch

@@ -0,0 +1,13 @@
+diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake
+index 5a8956456..997bb8e81 100644
+--- a/CMakeFilters.cmake	
++++ b/CMakeFilters.cmake
+@@ -100,7 +100,7 @@ option (HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF)
+ if (HDF5_ENABLE_SZIP_SUPPORT)
+   option (HDF5_ENABLE_SZIP_ENCODING "Use SZip Encoding" OFF)
+   if (NOT SZIP_USE_EXTERNAL)
+-    find_package (SZIP NAMES ${SZIP_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
++    find_package (SZIP NAMES ${SZIP_PACKAGE_NAME}${HDF_PACKAGE_EXT})
+     if (NOT SZIP_FOUND)
+       find_package (SZIP) # Legacy find
+       if (SZIP_FOUND)

scripts/ci.baseline.txt

@@ -445,9 +445,6 @@ fdlibm:arm-uwp=fail
 fdlibm:x64-uwp=fail
 fftw3:arm-uwp=fail
 fftw3:x64-uwp=fail
-field3d:x64-windows=fail
-field3d:x64-windows-static=fail
-field3d:x86-windows=fail
 flint:x64-linux=fail
 flint:x64-osx=fail
 fltk:arm-uwp=fail