Merge examples and workflows from develop (HDFGroup#3918)

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"

.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/checkout@v4
+    - uses: actions/checkout@v4.1.1
     - name: Run clang-format style check for C and Java code
       uses: DoozyX/[email protected]
       with:

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

@@ -21,17 +21,17 @@ jobs:
     permissions:
         contents: write # In order to allow EndBug/add-and-commit to commit changes
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
     - name: Fix C and Java formatting issues detected by clang-format
-      uses: DoozyX/[email protected]
+      uses: DoozyX/clang-format-lint-action@9ea72631b74e61ce337d0839a90e76180e997283 # v0.13
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp,java'
         clangFormatVersion: 13
         inplace: True
         style: file
         exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'
-    - uses: EndBug/add-and-commit@v9
+    - uses: EndBug/add-and-commit@1bad3abcf0d6ec49a5857d124b0bfb52dc7bb081 # v9.1.3
       with:
           author_name: github-actions
           author_email: 41898282+github-actions[bot]@users.noreply.github.com

.github/workflows/cmake-ctest.yml

@@ -25,7 +25,7 @@ jobs:
         run: choco install ninja
 
       - name: Enable Developer Command Prompt
-        uses: ilammy/msvc-dev-cmd@v1.12.1
+        uses: ilammy/msvc-dev-cmd@v1.13.0
 
       - name: Set file base name (Windows)
         id: set-file-base
@@ -36,7 +36,7 @@ jobs:
 
       # Get files created by release script
       - name: Get zip-tarball (Windows)
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
               name: zip-tarball
               path: ${{ github.workspace }}
@@ -72,7 +72,7 @@ jobs:
           Copy-Item -Path ${{ runner.workspace }}/hdf5/hdfsrc/README.md -Destination ${{ runner.workspace }}/build114/hdf5/
           Copy-Item -Path ${{ runner.workspace }}/hdf5/build114/ci-StdShar-MSVC/* -Destination ${{ runner.workspace }}/build114/hdf5/ -Include *.zip
           cd "${{ runner.workspace }}/build114"
-          7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win_vs2022.zip hdf5
+          7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_cl.zip hdf5
         shell: pwsh
 
       - name: List files in the space (Windows)
@@ -85,8 +85,8 @@ jobs:
       - name: Save published binary (Windows)
         uses: actions/upload-artifact@v3
         with:
-              name: zip-vs2022-binary
-              path: ${{ runner.workspace }}/build114/${{ steps.set-file-base.outputs.FILE_BASE }}-win_vs2022.zip
+              name: zip-vs2022_cl-binary
+              path: ${{ runner.workspace }}/build114/${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_cl.zip
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
   build_and_test_linux:
@@ -106,7 +106,7 @@ jobs:
 
       # Get files created by release script
       - name: Get tgz-tarball (Linux)
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
               name: tgz-tarball
               path: ${{ github.workspace }}
@@ -135,7 +135,7 @@ jobs:
           cp ${{ runner.workspace }}/hdf5/hdfsrc/README.md ${{ runner.workspace }}/build114/hdf5
           cp ${{ runner.workspace }}/hdf5/build114/ci-StdShar-GNUC/*.tar.gz ${{ runner.workspace }}/build114/hdf5
           cd "${{ runner.workspace }}/build114"
-          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204.tar.gz hdf5
+          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz hdf5
         shell: bash
 
       - name: List files in the space (Linux)
@@ -147,8 +147,8 @@ jobs:
       - name: Save published binary (Linux)
         uses: actions/upload-artifact@v3
         with:
-              name: tgz-ubuntu-2204-binary
-              path: ${{ runner.workspace }}/build114/${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204.tar.gz
+              name: tgz-ubuntu-2204_gcc-binary
+              path: ${{ runner.workspace }}/build114/${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204_gcc.tar.gz
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
       # Save doxygen files created by ctest script
@@ -176,7 +176,7 @@ jobs:
 
       # Get files created by release script
       - name: Get tgz-tarball (MacOS)
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
               name: tgz-tarball
               path: ${{ github.workspace }}
@@ -227,6 +227,164 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
               name: tgz-osx12-binary
-              path: ${{ runner.workspace }}/build114/${{ steps.set-file-base.outputs.FILE_BASE }}-osx12.tar.gz
+              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-osx12.tar.gz
               if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
 
+####### intel builds
+  build_and_test_win_intel:
+  # Windows w/ OneAPI + CMake
+  #
+    name: "Windows Intel CTest"
+    runs-on: windows-latest
+    steps:
+      - name: Install Dependencies (Windows_intel)
+        run: choco install ninja
+
+      - name: add oneAPI to env
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: intel
+          version: '2023.2'
+
+      - name: Enable Developer Command Prompt
+        uses: ilammy/[email protected]
+
+      - name: Set file base name (Windows_intel)
+        id: set-file-base
+        run: |
+          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
+          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
+        shell: bash
+
+      # Get files created by release script
+      - name: Get zip-tarball (Windows_intel)
+        uses: actions/download-artifact@v4
+        with:
+              name: zip-tarball
+              path: ${{ github.workspace }}
+
+      - name: using powershell
+        shell: pwsh
+        run: Get-Location
+
+      - name: List files for the space (Windows_intel)
+        run: |
+              Get-ChildItem -Path ${{ github.workspace }}
+              Get-ChildItem -Path ${{ runner.workspace }}
+        shell: pwsh
+
+      - name: Uncompress source (Windows_intel)
+        working-directory: ${{ github.workspace }}
+        run: 7z x ${{ steps.set-file-base.outputs.FILE_BASE }}.zip
+        shell: bash
+
+      - name: Run ctest (Windows_intel) with oneapi
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
+        run: |
+          cd "${{ runner.workspace }}/hdf5/hdfsrc"
+          cmake --workflow --preset=ci-StdShar-Intel --fresh
+        shell: pwsh
+
+      - name: Publish binary (Windows_intel)
+        id: publish-ctest-binary
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          mkdir "${{ runner.workspace }}/build/hdf5"
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/hdfsrc/COPYING -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/hdfsrc/COPYING_LBNL_HDF5 -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/hdfsrc/README.md -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/build/ci-StdShar-Intel/* -Destination ${{ runner.workspace }}/build/hdf5/ -Include *.zip
+          cd "${{ runner.workspace }}/build"
+          7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip hdf5
+        shell: pwsh
+
+      - name: List files in the space (Windows_intel)
+        run: |
+              Get-ChildItem -Path ${{ github.workspace }}
+              Get-ChildItem -Path ${{ runner.workspace }}
+        shell: pwsh
+
+      # Save files created by ctest script
+      - name: Save published binary (Windows_intel)
+        uses: actions/upload-artifact@v3
+        with:
+              name: zip-vs2022_intel-binary
+              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip
+              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
+
+  build_and_test_linux_intel:
+  # Linux (Ubuntu) w/ OneAPI + CMake
+  #
+    name: "Ubuntu Intel CMake"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install CMake Dependencies (Linux_intel)
+        run: sudo apt-get install ninja-build doxygen graphviz
+
+      - name: add oneAPI to env
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: intel
+          version: '2023.2'
+
+      - name: Set file base name (Linux_intel)
+        id: set-file-base
+        run: |
+          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
+          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
+
+      # Get files created by release script
+      - name: Get tgz-tarball (Linux_intel)
+        uses: actions/download-artifact@v4
+        with:
+              name: tgz-tarball
+              path: ${{ github.workspace }}
+
+      - name: List files for the space (Linux_intel)
+        run: |
+              ls -l ${{ github.workspace }}
+              ls ${{ runner.workspace }}
+
+      - name: Uncompress source (Linux_intel)
+        run: tar -zxvf ${{ github.workspace }}/${{ steps.set-file-base.outputs.FILE_BASE }}.tar.gz
+
+      - name: Run ctest (Linux_intel)
+        env:
+          FC: ${{ steps.setup-fortran.outputs.fc }}
+          CC: ${{ steps.setup-fortran.outputs.cc }}
+          CXX: ${{ steps.setup-fortran.outputs.cxx }}
+        run: |
+          cd "${{ runner.workspace }}/hdf5/hdfsrc"
+          cmake --workflow --preset=ci-StdShar-Intel --fresh
+        shell: bash
+
+      - name: Publish binary (Linux_intel)
+        id: publish-ctest-binary
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          mkdir "${{ runner.workspace }}/build/hdf5"
+          cp ${{ runner.workspace }}/hdf5/hdfsrc/COPYING ${{ runner.workspace }}/build/hdf5
+          cp ${{ runner.workspace }}/hdf5/hdfsrc/COPYING_LBNL_HDF5 ${{ runner.workspace }}/build/hdf5
+          cp ${{ runner.workspace }}/hdf5/hdfsrc/README.md ${{ runner.workspace }}/build/hdf5
+          cp ${{ runner.workspace }}/hdf5/build/ci-StdShar-Intel/*.tar.gz ${{ runner.workspace }}/build/hdf5
+          cd "${{ runner.workspace }}/build"
+          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204_intel.tar.gz hdf5
+        shell: bash
+
+      - name: List files in the space (Linux_intel)
+        run: |
+              ls ${{ github.workspace }}
+              ls -l ${{ runner.workspace }}
+
+      # Save files created by ctest script
+      - name: Save published binary (Linux_intel)
+        uses: actions/upload-artifact@v3
+        with:
+              name: tgz-ubuntu-2204_intel-binary
+              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-ubuntu-2204_intel.tar.gz
+              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`

.github/workflows/cmake.yml

@@ -11,6 +11,10 @@ permissions:
 # in parallel. We just have one job, but the matrix items defined below will
 # run in parallel.
 jobs:
+    call-workflow-special-cmake:
+      name: "CMake Special Workflows"
+      uses: ./.github/workflows/main-cmake-spc.yml
+
     call-debug-thread-cmake:
         name: "CMake Debug Thread-Safety Workflows"
         uses: ./.github/workflows/main-cmake.yml

.github/workflows/codespell.yml

@@ -10,8 +10,8 @@ jobs:
     name: Check for spelling errors
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.1
       - uses: codespell-project/actions-codespell@master
         with:
-          skip: ./.github/workflows/codespell.yml,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html
+          skip: ./.github/workflows/codespell.yml,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp
           ignore_words_list: ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos

.github/workflows/cve.yml

@@ -27,7 +27,7 @@ jobs:
     name: CVE regression
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.1
 
       - name: Install Autotools Dependencies (Linux)
         run: |
@@ -40,7 +40,7 @@ jobs:
           make
           sudo make install
       - name: Checkout CVE test repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.1.1
         with:
           repository: HDFGroup/cve_hdf5
           path: cve_hdf5

.github/workflows/hdfeos5.yml

@@ -27,7 +27,7 @@ jobs:
     name: Build hdfeos5
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.1
 
       - name: Install Autotools Dependencies (Linux)
         run: |

.github/workflows/intel-auto.yml

@@ -16,7 +16,7 @@ jobs:
     name: "Intel ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.1
 
       - name: Install Dependencies
         run: |

.github/workflows/intel-cmake.yml

@@ -19,7 +19,7 @@ jobs:
     name: "ubuntu-oneapi ${{ inputs.build_mode }}"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.1
 
       # Only CMake need ninja-build, but we just install it unilaterally
       # libssl, etc. are needed for the ros3 VFD
@@ -77,7 +77,7 @@ jobs:
     name: "windows-oneapi ${{ inputs.build_mode }}"
     runs-on: windows-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.1
 
       - name: Install Dependencies (Windows)
         run: choco install ninja

.github/workflows/linux-auto-aocc-ompi.yml

@@ -26,7 +26,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.1.1
 
       - name: Install System dependencies
         run: |

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

@@ -40,7 +40,7 @@ jobs:
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Get Sources
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.1.1
 
       # 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/checkout@v4
+        uses: actions/checkout@v4.1.1
 
       # AUTOTOOLS CONFIGURE
       - name: Autotools Configure