Merge remote-tracking branch 'canonical/develop' into refactor_h5fd_a…

…nd_packages

.github/workflows/julia-auto.yml

@@ -16,9 +16,17 @@ jobs:
     name: "julia ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - name: Get Sources
+      - name: Get HDF5 source
         uses: actions/[email protected]
 
+        # Checking out the Julia HDF5 wrappers will clobber the HDF5 checkout
+        # NOTE: Remove this when the Julia wrappers have been patched
+      - name: Save the Julia patch file
+        shell: bash
+        run: |
+          mkdir "${{ runner.workspace }}/julia_patch"
+          cp .github/workflows/julia_ci.patch "${{ runner.workspace }}/julia_patch"
+
       - name: Install Dependencies
         shell: bash
         run: |
@@ -65,6 +73,11 @@ jobs:
           repository: JuliaIO/HDF5.jl
           path: .
 
+        # NOTE: Remove this when the Julia wrappers have been patched
+      - name: Patch Julia CI
+        run:  |
+          git apply "${{ runner.workspace }}/julia_patch/julia_ci.patch" -v
+
       - name: Generate LocalPreferences
         run: |
           echo '[HDF5]' >> LocalPreferences.toml

.github/workflows/julia-cmake.yml

@@ -16,9 +16,17 @@ jobs:
     name: "julia ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - name: Get Sources
+      - name: Get HDF5 source
         uses: actions/[email protected]
 
+        # Checking out the Julia HDF5 wrappers will clobber the HDF5 checkout
+        # NOTE: Remove this when the Julia wrappers have been patched
+      - name: Save the Julia patch file
+        shell: bash
+        run: |
+          mkdir "${{ runner.workspace }}/julia_patch"
+          cp .github/workflows/julia_ci.patch "${{ runner.workspace }}/julia_patch"
+
       - name: Install Dependencies
         shell: bash
         run: |
@@ -68,6 +76,11 @@ jobs:
           repository: JuliaIO/HDF5.jl
           path: .
 
+        # NOTE: Remove this when the Julia wrappers have been patched
+      - name: Patch Julia CI
+        run:  |
+          git apply "${{ runner.workspace }}/julia_patch/julia_ci.patch" -v
+
       - name: Generate LocalPreferences
         run: |
           echo '[HDF5]' >> LocalPreferences.toml

.github/workflows/julia_ci.patch

@@ -0,0 +1,19 @@
+diff --git a/test/objects.jl b/test/objects.jl
+index d68dd749..0541e91a 100644
+--- a/test/objects.jl
++++ b/test/objects.jl
+@@ -16,7 +16,13 @@ using HDF5.API
+     h5open(fn, "r") do h5f
+         @test API.h5o_exists_by_name(h5f, "data")
+         @test API.h5o_exists_by_name(h5f, "lore")
+-        @test_throws API.H5Error API.h5o_exists_by_name(h5f, "noonian")
++        @static if HDF5.API.h5_get_libversion() <= v"1.14.5"
++            # Buggy behavior in earlier versions of HDF5 returns FAIL (-1)
++            @test_throws API.H5Error API.h5o_exists_by_name(h5f, "noonian")
++        else
++            # The correct behavior is to return false (0)
++            @test API.h5o_exists_by_name(h5f, "noonian") == 0
++        end
+
+         loc_id = API.h5o_open(h5f, "data", API.H5P_DEFAULT)
+         try

CMakeFilters.cmake

@@ -101,7 +101,11 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
       endif ()
       set(H5_ZLIB_FOUND ${ZLIB_FOUND})
       if (H5_ZLIB_FOUND)
-        set (H5_ZLIB_HEADER "zlib.h")
+        if (HDF5_USE_ZLIB_NG)
+          set (H5_ZLIB_HEADER "zlib-ng.h")
+        else ()
+          set (H5_ZLIB_HEADER "zlib.h")
+        endif ()
         set (H5_ZLIB_INCLUDE_DIR_GEN ${ZLIB_INCLUDE_DIR})
         set (H5_ZLIB_INCLUDE_DIRS ${H5_ZLIB_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIR})
         # The FindZLIB.cmake module does not set an OUTPUT_NAME
@@ -125,6 +129,9 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
   if (H5_ZLIB_FOUND)
     set (H5_HAVE_FILTER_DEFLATE 1)
     set (H5_HAVE_ZLIB_H 1)
+    if (HDF5_USE_ZLIB_NG)
+      set (H5_HAVE_ZLIBNG_H 1)
+    endif ()
     set (H5_HAVE_LIBZ 1)
     if (H5_HAVE_FILTER_DEFLATE)
       set (EXTERNAL_FILTERS "${EXTERNAL_FILTERS} DEFLATE")
@@ -135,6 +142,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
     set (HDF5_ENABLE_Z_LIB_SUPPORT OFF CACHE BOOL "" FORCE)
     message (WARNING " ZLib support in HDF5 was enabled but not found")
   endif ()
+  message(STATUS "H5_ZLIB_HEADER=${H5_ZLIB_HEADER}")
 endif ()
 
 #-----------------------------------------------------------------------------

CMakePresets.json

@@ -18,11 +18,11 @@
       "hidden": true,
       "cacheVariables": {
         "ZLIB_PACKAGE_NAME": {"type": "STRING", "value": "zlib"},
-        "ZLIB_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/madler/zlib/releases/download/v1.3"},
-        "ZLIB_TGZ_NAME": {"type": "STRING", "value": "zlib-1.3.tar.gz"},
+        "ZLIB_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/madler/zlib/releases/download/v1.3.1"},
+        "ZLIB_TGZ_NAME": {"type": "STRING", "value": "zlib-1.3.1.tar.gz"},
         "ZLIBNG_PACKAGE_NAME": {"type": "STRING", "value": "zlib-ng"},
         "ZLIBNG_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/zlib-ng/zlib-ng/archive/refs/tags"},
-        "ZLIBNG_TGZ_NAME": {"type": "STRING", "value": "2.1.6.tar.gz"},
+        "ZLIBNG_TGZ_NAME": {"type": "STRING", "value": "2.2.2.tar.gz"},
         "LIBAEC_PACKAGE_NAME": {"type": "STRING", "value": "libaec"},
         "LIBAEC_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/MathisRosenhauer/libaec/releases/download/v1.1.3"},
         "LIBAEC_TGZ_NAME": {"type": "STRING", "value": "libaec-1.1.3.tar.gz"}

config/cmake/H5pubconf.h.in

@@ -366,6 +366,9 @@
 /* Define to 1 if you have the <zlib.h> header file. */
 #cmakedefine H5_HAVE_ZLIB_H @H5_HAVE_ZLIB_H@
 
+/* Define to 1 if you have the <zlib.h> header file. */
+#cmakedefine H5_HAVE_ZLIBNG_H @H5_HAVE_ZLIBNG_H@
+
 /* Define to 1 if you have the `_getvideoconfig' function. */
 #cmakedefine H5_HAVE__GETVIDEOCONFIG @H5_HAVE__GETVIDEOCONFIG@
 

config/cmake/HDFLibMacros.cmake

@@ -40,6 +40,11 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type)
   add_library(${HDF_PACKAGE_NAMESPACE}zlib-static ALIAS zlib-static)
   set (H5_ZLIB_STATIC_LIBRARY "${HDF_PACKAGE_NAMESPACE}zlib-static")
   set (H5_ZLIB_LIBRARIES ${H5_ZLIB_STATIC_LIBRARY})
+  if (HDF5_USE_ZLIB_NG)
+    set (H5_ZLIB_HEADER "zlib-ng.h")
+  else ()
+    set (H5_ZLIB_HEADER "zlib.h")
+  endif ()
 
   set (H5_ZLIB_INCLUDE_DIR_GEN "${hdf5_zlib_BINARY_DIR}")
   set (H5_ZLIB_INCLUDE_DIR "${hdf5_zlib_SOURCE_DIR}")

config/cmake/LIBAEC/CMakeLists.txt

@@ -151,7 +151,7 @@ target_include_directories (${LIBAEC_LIB_TARGET} PUBLIC
   "$<BUILD_INTERFACE:${LIBAEC_SOURCE_DIR}/include>"
   "$<BUILD_INTERFACE:${CMAKE_BINARY_DIR}>"
   "$<INSTALL_INTERFACE:include>")
-if (CMAKE_C_COMPILER_ID MATCHES "IntelLLVM" OR CMAKE_C_COMPILER_ID MATCHES "[Cc]lang")
+if (CMAKE_C_COMPILER_ID MATCHES "IntelLLVM" OR (CMAKE_C_COMPILER_ID MATCHES "[Cc]lang" AND NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 15.0))
   target_compile_options(${LIBAEC_LIB_TARGET} PRIVATE -Wno-deprecated-non-prototype)
 endif ()
 if (CMAKE_C_COMPILER_ID STREQUAL "GNU")

config/cmake/ZLIB/CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required (VERSION 3.18)
 set (CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
 project (ZLIB C)
 
-set (VERSION "1.3")
+set(VERSION "1.3.1")
 
 #-----------------------------------------------------------------------------
 # Basic ZLIB stuff here
@@ -131,6 +131,7 @@ set_directory_properties (PROPERTIES INCLUDE_DIRECTORIES
 if (MSVC)
   set(CMAKE_DEBUG_POSTFIX "d")
   add_definitions (-D_BIND_TO_CURRENT_VCLIBS_VERSION=1)
+  add_definitions (-D_CRT_SECURE_NO_DEPRECATE)
   add_definitions (-D_CRT_SECURE_NO_WARNINGS)
   add_definitions (-D_CONSOLE)
   add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
@@ -191,7 +192,10 @@ set(ZLIB_SRCS
 )
 
 add_library(${ZLIB_LIB_TARGET} STATIC ${ZLIB_SRCS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
-target_include_directories(${ZLIB_LIB_TARGET} PRIVATE "${CMAKE_BINARY_DIR}")
+target_include_directories(${ZLIB_LIB_TARGET}
+    PRIVATE "${CMAKE_BINARY_DIR}"
+    PUBLIC "${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}"
+)
 if (MSVC AND CMAKE_CL_64)
   set_target_properties (${ZLIB_LIB_TARGET} PROPERTIES STATIC_LIBRARY_FLAGS "/machine:x64")
 endif ()