Sync develop changes May 20 - June 6 to hdf5_1_14 (#4553)

* Fix daily-build CI and correct use of *_FOUND settings for filters (#4504) * Correct examples tests to just run under dynamic analysis (#4505) * Remove trailing extra whitespace in hyperlink (#4509) * Set H5 specific vars immediately if legacy find (#4512) * Set H5 specific vars immediately if legacy find * Correct find process vars (vs in-line build) * Correct SZIP find * Everything is libaec 1.0.6 or newer * Correct option help text * Don't update 'pos' and 'op' fields when using pread/pwrite (#4492) Instead of reading the absolute minimal possible, use the likely value of a v2+ superblock w/8-byte addresses & lengths. * Fix spelling (#4522) * Fix typo in DAPL callback documentation (#4523) * Move/rename libhdf5.settings input files (#4525) Move without other changes: src/libhdf5.settings.in -> src/libhdf5.settings.autotools.in config/cmake/libhdf5.settings.cmake.in -> src/libhdf5.settings.cmake.in * Disable UNITY_BUILD for now - globally (#4515) * Fix function name in USAGE for H5Pencode2() (#4519) * Allow HDF5_LIB_INFIX to work with DLL (#4500) * Allow HDF5_LIB_INFIX to work with DLL * Separate individual library name into parts and add suffix option * Java cannot use alternative names and removed extra setting * Incorporate the underscore into the CORE name * Fix typos in property callback documentation (#4532) * Fix wrong int type as some systems have int as 64-bit wide (#4534) * H5FDquery return value (#4530) * Switch H5FDquery() return values to use library's FAIL / SUCCEED macros * Update return value also * Refactor to reduce code duplication (#4531) * Update error output w/new routine name * Fix a few function names in USAGE comments that don't match the actual (#4533) * Fix a few function names in USAGE comments that don't match the actual function names. * Remove typo '[' * Switch to working url for api-compatibility-macros.html. * Remove julia CI actions (#4540) These have been failing for a week or two for unclear reasons, both in the Autotools and CMake. No obvious library changes triggered this. See GitHub issue #4539 for more info/discussion The Julia tests will be disabled until the root cause is found. * Bump the github-actions group with 3 updates (#4538) Bumps the github-actions group with 3 updates: [softprops/action-gh-release](https://github.com/softprops/action-gh-release), [ossf/scorecard-action](https://github.com/ossf/scorecard-action) and [github/codeql-action](https://github.com/github/codeql-action). Updates `softprops/action-gh-release` from 2.0.4 to 2.0.5 - [Release notes](https://github.com/softprops/action-gh-release/releases) - [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md) - [Commits](softprops/action-gh-release@9d7c94c...69320db) Updates `ossf/scorecard-action` from 2.3.1 to 2.3.3 - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](ossf/scorecard-action@0864cf1...dc50aa9) Updates `github/codeql-action` from 3.25.3 to 3.25.7 - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@d39d31e...f079b84) --- updated-dependencies: - dependency-name: softprops/action-gh-release dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: ossf/scorecard-action dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch dependency-group: github-actions ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix various mistakes in doxygen docs (#4541) * Fix a dead link and example file names * Add the missing content of a section * Export HDF5 parallel status for CMake FetchContent'ed VOL connectors (#4542) * Remove an unnecessary check for parallel and thread-safety from examples (#4543) * Add option to use zlib-ng as zlib library (#4487) * Export HDF5 version for CMake FetchContent'ed VOL connectors (#4548) * Adjust h5repack userblock option to allow reserve size (#4544) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Allen Byrne <[email protected]> Co-authored-by: H. Joe Lee <[email protected]> Co-authored-by: Quincey Koziol <[email protected]> Co-authored-by: jhendersonHDF <[email protected]> Co-authored-by: mattjala <[email protected]> Co-authored-by: Dana Robinson <[email protected]> Co-authored-by: Peter Chang <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: bmribler <[email protected]> Co-authored-by: Scot Breitenfeld <[email protected]>
HDFGroup · Jun 8, 2024 · ad50867 · ad50867
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diff --git a/.github/workflows/autotools.yml b/.github/workflows/autotools.yml
@@ -99,12 +99,6 @@ jobs:
       with:
             build_mode: "production"
 
-    call-release-auto-julia:
-        name: "Autotools Julia Workflows"
-        uses: ./.github/workflows/julia-auto.yml
-        with:
-            build_mode: "production"
-
     call-release-auto-xpr:
         name: "Autotools TestExpress Workflows"
         uses: ./.github/workflows/testxpr-auto.yml

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
@@ -102,12 +102,6 @@ jobs:
         with:
             build_mode: "Release"
 
-    call-release-cmake-julia:
-        name: "CMake Julia Workflows"
-        uses: ./.github/workflows/julia-cmake.yml
-        with:
-            build_mode: "Release"
-
     call-release-cmake-xpr:
         name: "CMake TestExpress Workflows"
         uses: ./.github/workflows/testxpr-cmake.yml

diff --git a/.github/workflows/julia-auto.yml b/.github/workflows/julia-auto.yml
diff --git a/.github/workflows/julia-cmake.yml b/.github/workflows/julia-cmake.yml
diff --git a/.github/workflows/main-cmake-spc.yml b/.github/workflows/main-cmake-spc.yml
@@ -80,7 +80,7 @@ jobs:
 #        working-directory: ${{ runner.workspace }}/build
 
   build_v1_10:
-    name: "gcc DBG v1.10 default API (build only)"
+    name: "gcc DBG v1.10 default API"
     runs-on: ubuntu-latest
     steps:
       # SETUP
@@ -140,7 +140,7 @@ jobs:
         working-directory: ${{ runner.workspace }}/build
 
   build_v1_12:
-    name: "gcc DBG v1.12 default API (build only)"
+    name: "gcc DBG v1.12 default API"
     runs-on: ubuntu-latest
     steps:
       # SETUP
@@ -198,3 +198,62 @@ jobs:
       - name: CMake Run Tests
         run: ctest . --parallel 2 -C Debug -V
         working-directory: ${{ runner.workspace }}/build
+
+  build_zlibng:
+    name: "gcc use zlib-ng filter"
+    runs-on: ubuntu-latest
+    steps:
+      # SETUP
+      - name: Install Linux Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+          sudo apt install gcc-12 g++-12 gfortran-12
+          echo "CC=gcc-12" >> $GITHUB_ENV
+          echo "CXX=g++-12" >> $GITHUB_ENV
+          echo "FC=gfortran-12" >> $GITHUB_ENV
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Get Sources
+        uses: actions/[email protected]
+
+      #
+      # CMAKE CONFIGURE
+      #
+      - name: CMake Configure
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DBUILD_SHARED_LIBS=ON \
+            -DHDF5_ENABLE_ALL_WARNINGS=ON \
+            -DHDF5_ENABLE_PARALLEL:BOOL=OFF \
+            -DHDF5_BUILD_CPP_LIB:BOOL=ON \
+            -DHDF5_BUILD_FORTRAN=ON \
+            -DHDF5_BUILD_JAVA=ON \
+            -DHDF5_BUILD_DOC=OFF \
+            -DLIBAEC_USE_LOCALCONTENT=ON \
+            -DZLIB_USE_LOCALCONTENT=ON \
+            -DHDF5_ENABLE_MIRROR_VFD:BOOL=ON \
+            -DHDF5_ENABLE_DIRECT_VFD:BOOL=ON \
+            -DHDF5_ENABLE_ROS3_VFD:BOOL=ON \
+            -DHDF5_USE_ZLIBNG:BOOL=ON \
+            $GITHUB_WORKSPACE
+        shell: bash
+
+      #
+      # BUILD
+      #
+      - name: CMake Build
+        run: cmake --build . --parallel 3 --config Release
+        working-directory: ${{ runner.workspace }}/build
+
+      #
+      # RUN TESTS
+      #
+      - name: CMake Run Tests
+        run: ctest . --parallel 2 -C Release -V
+        working-directory: ${{ runner.workspace }}/build
diff --git a/.github/workflows/release-files.yml b/.github/workflows/release-files.yml
@@ -178,6 +178,7 @@ jobs:
           sha256sum ${{ steps.get-file-base.outputs.FILE_BASE }}.html.abi.reports.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
 
       - name: Create sha256 sums for files  for nonversioned files
+        if: ${{ (inputs.use_environ == 'release') }}
         run: |
           sha256sum hdf5.zip >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
           sha256sum hdf5.tar.gz >> ${{ steps.get-file-base.outputs.FILE_BASE }}.sha256sums.txt
@@ -199,7 +200,7 @@ jobs:
       - name: PreRelease tag
         id: create_prerelease
         if: ${{ (inputs.use_environ == 'snapshots') }}
-        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
+        uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # v2.0.5
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: true
@@ -224,7 +225,7 @@ jobs:
       - name: Release tag
         id: create_release
         if: ${{ (inputs.use_environ == 'release') }}
-        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
+        uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # v2.0.5
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: false

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -37,7 +37,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
+        uses: ossf/scorecard-action@dc50aa9510b46c811795eb24b2f1ba02a914e534 # v2.3.3
         with:
           results_file: results.sarif
           results_format: sarif
@@ -67,6 +67,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@d39d31e687223d841ef683f52467bd88e9b21c14 # v3.25.3
+        uses: github/codeql-action/upload-sarif@f079b8493333aace61c81488f8bd40919487bd9f # v3.25.7
         with:
           sarif_file: results.sarif
diff --git a/CMakeFilters.cmake b/CMakeFilters.cmake
@@ -9,14 +9,23 @@
 # If you do not have access to either file, you may request a copy from
 # [email protected].
 #
-option (USE_LIBAEC_STATIC "Use static AEC library" OFF)
-option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB else search" OFF)
-option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP else search" OFF)
+option (HDF5_USE_ZLIB_NG "Use zlib-ng library as zlib library" OFF)
+option (HDF5_USE_LIBAEC_STATIC "Use static AEC library" OFF)
+option (ZLIB_USE_EXTERNAL "Use External Library Building for ZLIB" OFF)
+option (SZIP_USE_EXTERNAL "Use External Library Building for SZIP" OFF)
 
 if (NOT ZLIB_USE_LOCALCONTENT)
-  set (ZLIB_URL ${ZLIB_TGZ_ORIGPATH}/${ZLIB_TGZ_NAME})
+  if (HDF5_USE_ZLIB_NG)
+    set (ZLIB_URL ${ZLIBNG_TGZ_ORIGPATH}/${ZLIBNG_TGZ_NAME})
+  else ()
+    set (ZLIB_URL ${ZLIB_TGZ_ORIGPATH}/${ZLIB_TGZ_NAME})
+  endif ()
 else ()
-  set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
+  if (HDF5_USE_ZLIB_NG)
+    set (ZLIB_URL ${TGZPATH}/${ZLIBNG_TGZ_NAME})
+  else ()
+    set (ZLIB_URL ${TGZPATH}/${ZLIB_TGZ_NAME})
+  endif ()
 endif ()
 message (VERBOSE "Filter ZLIB file is ${ZLIB_URL}")
 
@@ -71,8 +80,13 @@ option (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON)
 if (HDF5_ENABLE_Z_LIB_SUPPORT)
   if (NOT H5_ZLIB_HEADER)
     if (NOT ZLIB_USE_EXTERNAL)
+      if (HDF5_USE_ZLIB_NG)
+        set (PACKAGE_NAME ${ZLIBNG_PACKAGE_NAME}${HDF_PACKAGE_EXT})
+      else ()
+        set (PACKAGE_NAME ${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT})
+      endif ()
       set(ZLIB_FOUND FALSE)
-      find_package (ZLIB NAMES ${ZLIB_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
+      find_package (ZLIB NAMES ${PACKAGE_NAME} COMPONENTS static shared)
       if (NOT ZLIB_FOUND)
         find_package (ZLIB) # Legacy find
       endif ()
@@ -119,9 +133,14 @@ if (HDF5_ENABLE_SZIP_SUPPORT)
   if (NOT SZIP_USE_EXTERNAL)
     set(libaec_USE_STATIC_LIBS ${HDF5_USE_LIBAEC_STATIC})
     set(SZIP_FOUND FALSE)
-    find_package (SZIP NAMES ${LIBAEC_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
-    if (NOT SZIP_FOUND)
-      find_package (SZIP) # Legacy find
+    find_package (libaec 1.0.5 CONFIG)
+    if (SZIP_FOUND)
+      set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${H5_SZIP_LIBRARIES})
+    else ()
+      find_package (SZIP NAMES ${LIBAEC_PACKAGE_NAME}${HDF_PACKAGE_EXT} COMPONENTS static shared)
+      if (NOT SZIP_FOUND)
+        find_package (SZIP) # Legacy find
+      endif ()
     endif ()
     set(H5_SZIP_FOUND ${SZIP_FOUND})
     if (H5_SZIP_FOUND)

diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
@@ -120,7 +120,7 @@ else ()
   set (BYTESEX little-endian)
 endif ()
 configure_file (
-    ${HDF_RESOURCES_DIR}/libhdf5.settings.cmake.in
+    ${HDF5_SOURCE_DIR}/src/libhdf5.settings.cmake.in
     ${HDF5_SRC_BINARY_DIR}/libhdf5.settings ESCAPE_QUOTES @ONLY
 )
 install (