Sync develop changes July 2 - July 19 to hdf5_1_14 (#4665)

* Test fixes for log-based vol (#4618)

* fixes to address failures in the log-based VOL

* moved file cleanup to tests proper

* skipped index API test if not supported

* Add 'try' parameter to H5Z_find, and remove calls to H5E_clear_stack() (#4609)

* Bump the github-actions group with 4 updates (#4620)

Bumps the github-actions group with 4 updates: [actions/checkout](https://github.com/actions/checkout), [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials), [softprops/action-gh-release](https://github.com/softprops/action-gh-release) and [github/codeql-action](https://github.com/github/codeql-action).

Updates `actions/checkout` from 4.1.1 to 4.1.7
- [Release notes](https://github.com/actions/checkout/releases)
- [Commits](actions/checkout@v4.1.1...v4.1.7)

Updates `aws-actions/configure-aws-credentials` from 1 to 4
- [Release notes](https://github.com/aws-actions/configure-aws-credentials/releases)
- [Changelog](https://github.com/aws-actions/configure-aws-credentials/blob/main/CHANGELOG.md)
- [Commits](aws-actions/configure-aws-credentials@v1...v4)

Updates `softprops/action-gh-release` from 2.0.5 to 2.0.6
- [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@69320db...a74c6b7)

Updates `github/codeql-action` from 3.25.7 to 3.25.11
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](github/codeql-action@f079b84...b611370)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: github-actions
- dependency-name: aws-actions/configure-aws-credentials
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: github-actions
- dependency-name: softprops/action-gh-release
  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 a stack size warning in ros3 VFD code (#4625)

Just makes a stack array dynamic. Valgrind shows no memory leaks.

* Reworked cleaning up API test files (#4626)

* Reworked cleaning up test files, only removing test files if present to account for skipped tests

* changed to using H5Fis_accessible

* update to full use of remove_test_file

* corrected offset type in C wrapper (#4622)

* Remove some internal use of API calls and H5E_BEGIN_TRY/H5E_END_TRY (#4624)

* Remove auto NSIS check because of issues with CI (#4646)

* Add python testing for examples (#4628)

* Clean up Fortran __float128 configure-time checks (#4649)

* Always use DECIMAL_DIG instead of LDBL_DIG. This was controlled by
  an ifdef that is always true in C99 or greater

It's confusing to use float.h C constants as variable names in
configure.ac and the PAC_FC_LDBL_DIG macro.

* Directly compare MY_FLT128_DIG and MY_LDBL_DIG

* Make uniform across CMake and Autotools
* Don't export quadmath.h variables to H5pubconf.h

* Feature/awesome (#4604)

* Added Doxygen Awesome and fixed a few quirks.

* Fixed unterminated strings.

* Added Doxygen Awesome by copy.

* Add tools usage text as doxygen  for Tools UG (#4602)

* Add h5* compiler wrapper testing for CMake #4605 (#4613)

* Add show option

* remove non-static libs and correct names of static libs

* Fixup the pkg-config libs and comp builds

* Fix commands and add fortran pkg-config test scripts

* Add help usage option

* Add temporary fix for ARM64 Mac _Float16 build failure (#4639)

* Correct H5VL_t ref count on H5O_refresh_metadata failure (#4636)

* Fix bad H5VL_t rc on H5O_refresh_metadata fail

* Decrement nrefs before raising error

* Update doxygen Learn Basics / example refs. Add Reference sections (#4640)

* Fixed messed up table captions.  (#4653)

* Fixed messed up table captions. Browsers don't seem to respect relative values for width. Hardcoding 800px for now.

* Fixed FetchContent usage for new CMake reqs. (#4650)

CMake version 3.30 changed the behavior of the FetchContent module to deprecate
the use of FetchContent_Populate() in favor of FetchContent_MakeAvailable(). Therefore,
the copying of HDF specialized CMakeLists.txt files to the dependent project's source
was implemented in the FetchContent_Declare() call.

* Fixed usage issue with FindZLIB.cmake module (#4655)

* Add a comment on the FindZLIB.cmake module usage

* Allow choice of static/shared compression libs for Find Module

* Added new option to INSTALL_CMake file and changed option text

* Eliminate more H5E_BEGIN/END_TRY macros and H5E_clear_stack() calls (#4648)

* Correct name of zlib_ng option (#4658)

* Fix the examples for testing java with binaries (#4660)

* Update filename in RELEASE_PROCESS.md to current name
INSTALL_autotools.txt.

* Remove reference to V116 in tools/src/h5repack/h5repack.h.

.github/workflows/abi-report.yml

@@ -46,7 +46,7 @@ jobs:
           FILE_DOTSMAIN=$(echo "${{ inputs.file_ref }}" | sed -r "s/([0-9]+)\.([0-9]+)\.([0-9]+).*/\1\.\2\.\3/")
           echo "HDF5R_DOTSMAIN=$FILE_DOTSMAIN" >> $GITHUB_OUTPUT
 
-      - uses: actions/[email protected].1
+      - uses: actions/[email protected].7
 
       - name: Get published binary (Linux)
         uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7

.github/workflows/aocc-auto.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Dependencies
         shell: bash

.github/workflows/aocc-cmake.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Dependencies
         shell: bash

.github/workflows/clang-format-check.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
-    - uses: actions/[email protected].1
+    - uses: actions/[email protected].7
     - name: Run clang-format style check for C and Java code
       uses: DoozyX/[email protected]
       with:

.github/workflows/clang-format-fix.yml

@@ -21,7 +21,7 @@ jobs:
     permissions:
         contents: write # In order to allow EndBug/add-and-commit to commit changes
     steps:
-    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
     - name: Fix C and Java formatting issues detected by clang-format
       uses: DoozyX/clang-format-lint-action@9ea72631b74e61ce337d0839a90e76180e997283 # v0.13
       with:

.github/workflows/codespell.yml

@@ -10,5 +10,5 @@ jobs:
     name: Check for spelling errors
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/[email protected].1
+      - uses: actions/[email protected].7
       - uses: codespell-project/actions-codespell@master

.github/workflows/cve.yml

@@ -28,7 +28,7 @@ jobs:
     name: CVE regression
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/[email protected].1
+      - uses: actions/[email protected].7
 
       - name: Install Autotools Dependencies (Linux)
         run: |
@@ -41,7 +41,7 @@ jobs:
           make
           sudo make install
       - name: Checkout CVE test repository
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
         with:
           repository: HDFGroup/cve_hdf5
           path: cve_hdf5

.github/workflows/cygwin-auto.yml

@@ -23,7 +23,7 @@ jobs:
           git config --global core.autocrlf input
 
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Cygwin
         uses: cygwin/cygwin-install-action@master

.github/workflows/cygwin-cmake.yml

@@ -23,7 +23,7 @@ jobs:
           git config --global core.autocrlf input
 
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Cygwin
         uses: cygwin/cygwin-install-action@master

.github/workflows/daily-build.yml

@@ -16,7 +16,7 @@ jobs:
       hdf5-name: ${{ steps.gethdf5base.outputs.HDF5_NAME_BASE }}
 
     steps:
-    - uses: actions/[email protected].1
+    - uses: actions/[email protected].7
 
     - name: Get hdf5 release base name
       uses: dsaltares/fetch-gh-release-asset@master

.github/workflows/hdfeos5.yml

@@ -28,7 +28,7 @@ jobs:
     name: Build hdfeos5
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/[email protected].1
+      - uses: actions/[email protected].7
 
       - name: Install Autotools Dependencies (Linux)
         run: |

.github/workflows/intel-auto.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Dependencies
         shell: bash

.github/workflows/intel-cmake.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Get Sources (Linux)
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Dependencies (Linux)
         shell: bash
@@ -76,7 +76,7 @@ jobs:
     runs-on: windows-latest
     steps:
       - name: Get Sources (Windows)
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Dependencies (Windows)
         run: choco install ninja

.github/workflows/main-auto-par-spc.yml

@@ -40,7 +40,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -98,7 +98,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure

.github/workflows/main-auto-par.yml

@@ -48,7 +48,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure

.github/workflows/main-auto-spc.yml

@@ -43,7 +43,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -104,7 +104,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -165,7 +165,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -226,7 +226,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -287,7 +287,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -348,7 +348,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -409,7 +409,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure
@@ -472,7 +472,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure

.github/workflows/main-auto.yml

@@ -46,7 +46,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Autotools Configure
         run: |

.github/workflows/main-cmake-par.yml

@@ -23,7 +23,7 @@ jobs:
     name: "Parallel GCC-${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/[email protected].1
+      - uses: actions/[email protected].7
 
       - name: Install Linux Dependencies
         run: |
@@ -42,6 +42,7 @@ jobs:
           mkdir "${{ runner.workspace }}/build"
           cd "${{ runner.workspace }}/build"
           CC=mpicc cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            --log-level=VERBOSE \
             -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
             -DBUILD_SHARED_LIBS=ON \
             -DHDF5_ENABLE_ALL_WARNINGS=ON \

.github/workflows/main-cmake-spc.yml

@@ -36,7 +36,7 @@ jobs:
  
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       #
       # CMAKE CONFIGURE
@@ -96,7 +96,7 @@ jobs:
  
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       #
       # CMAKE CONFIGURE
@@ -156,7 +156,7 @@ jobs:
  
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       #
       # CMAKE CONFIGURE
@@ -216,7 +216,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       #
       # CMAKE CONFIGURE
@@ -227,6 +227,7 @@ jobs:
           cd "${{ runner.workspace }}/build"
           cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
             -G Ninja \
+            --log-level=VERBOSE \
             -DCMAKE_BUILD_TYPE=Release \
             -DBUILD_SHARED_LIBS=ON \
             -DHDF5_ENABLE_ALL_WARNINGS=ON \
@@ -235,12 +236,12 @@ jobs:
             -DHDF5_BUILD_FORTRAN=ON \
             -DHDF5_BUILD_JAVA=ON \
             -DHDF5_BUILD_DOC=OFF \
-            -DLIBAEC_USE_LOCALCONTENT=ON \
-            -DZLIB_USE_LOCALCONTENT=ON \
+            -DLIBAEC_USE_LOCALCONTENT=OFF \
+            -DZLIB_USE_LOCALCONTENT=OFF \
             -DHDF5_ENABLE_MIRROR_VFD:BOOL=ON \
             -DHDF5_ENABLE_DIRECT_VFD:BOOL=ON \
             -DHDF5_ENABLE_ROS3_VFD:BOOL=ON \
-            -DHDF5_USE_ZLIBNG:BOOL=ON \
+            -DHDF5_USE_ZLIB_NG:BOOL=ON \
             $GITHUB_WORKSPACE
         shell: bash
 

.github/workflows/main-cmake.yml

@@ -110,7 +110,7 @@ jobs:
           # but that seems unnecessary
           - name: "MacOS Clang"
             os: macos-latest
-            cpp: OFF
+            cpp: ON
             fortran: ON
             java: ON
             docs: ON
@@ -180,7 +180,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       #
       # CMAKE CONFIGURE

.github/workflows/msys2-auto.yml

@@ -32,7 +32,7 @@ jobs:
         shell: msys2 {0}
     steps:
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: '${{ matrix.icon }} Setup MSYS2'
         uses: msys2/setup-msys2@v2

.github/workflows/netcdf.yml

@@ -32,15 +32,15 @@ jobs:
         sudo apt update
         sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen openssl libtool libtool-bin
     - name: Checkout HDF5
-      uses: actions/[email protected].1
+      uses: actions/[email protected].7
     - name: Install HDF5
       run: |
         ./autogen.sh
         ./configure --prefix=/usr/local --disable-tests --disable-static --enable-shared --enable-hl --with-szlib
         make -j
         sudo make install -j
     - name: Checkout netCDF
-      uses: actions/[email protected].1
+      uses: actions/[email protected].7
       with:
         repository: unidata/netcdf-c
         path: netcdf-c

.github/workflows/nvhpc-auto.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Dependencies
         shell: bash

.github/workflows/nvhpc-cmake.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Get Sources
-        uses: actions/[email protected].1
+        uses: actions/[email protected].7
 
       - name: Install Dependencies
         shell: bash

.github/workflows/publish-release.yml

@@ -21,7 +21,7 @@ jobs:
     steps:
         # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
         - name: Get Sources
-          uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+          uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
           with:
             fetch-depth: 0
             ref: '${{ github.head_ref || github.ref_name }}'
@@ -36,7 +36,7 @@ jobs:
             file: '${{ inputs.use_hdf }}-*.*'
 
         - name: Setup AWS CLI
-          uses: aws-actions/configure-aws-credentials@v1
+          uses: aws-actions/configure-aws-credentials@v4
           with:
                  aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
                  aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}