Sync develop changes July 19 - July 29 to hdf5_1_14 (#4678)

* publish msi binary (#4663) * Add publish from branch workflow (#4664) * Replace incorrect use of an internal function (#4668) * Replace incorrect use of an internal function In some API functions, the internal function H5I_object() was used instead of H5I_object_verify(), which verifies the type of an ID argument. So when an inappropriate ID was passed in to the affected API, it was accepted. This behavior can cause issues at a later time, including a segfault, as reported in issue #GH-4656. The fix was applied to the following functions: H5Fget_intent() H5Fget_fileno() H5Fget_freespace() H5Fget_create_plist() H5Fget_access_plist() H5Fget_vfd_handle() H5Dvlen_get_buf_size() H5Fget_mdc_config() H5Fset_mdc_config() H5Freset_mdc_hit_rate_stats() Fixes GH-4662 * Fix incorrect indentation for permissions. (#4669) * Remove outdated line from Copyright header in new files. (#4676) * Fix binary examples process (#4666) --------- Co-authored-by: Allen Byrne <[email protected]> Co-authored-by: bmribler <[email protected]>
HDFGroup · Jul 30, 2024 · 7481563 · 7481563
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diff --git a/.github/workflows/cmake-bintest.yml b/.github/workflows/cmake-bintest.yml
@@ -147,7 +147,7 @@ jobs:
   # MacOS w/ Clang + CMake
   #
     name: "MacOS Clang Binary Test"
-    runs-on: macos-latest
+    runs-on: macos-13
     steps:
       - name: Install Dependencies (MacOS)
         run: brew install ninja doxygen
@@ -161,7 +161,7 @@ jobs:
       - name: Get published binary (MacOS)
         uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
         with:
-              name: tgz-osx-${{ inputs.build_mode }}-binary
+              name: tgz-osx13-${{ inputs.build_mode }}-binary
               path: ${{ github.workspace }}
 
       - name: Uncompress hdf5 binary (MacOS)
@@ -204,3 +204,64 @@ jobs:
           cmake --workflow --preset=ci-StdShar-OSX-Clang --fresh
         shell: bash
 
+  test_binary_mac_latest:
+  # MacOS w/ Clang + CMake
+  #
+    name: "MacOS Clang Binary Test"
+    runs-on: macos-latest
+    steps:
+      - name: Install Dependencies (MacOS_latest)
+        run: brew install ninja doxygen
+
+      - name: Set up JDK 21
+        uses: actions/setup-java@v4
+        with:
+          java-version: '21'
+          distribution: 'temurin'
+
+      - name: Get published binary (MacOS_latest)
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+        with:
+          name: tgz-osx-${{ inputs.build_mode }}-binary
+          path: ${{ github.workspace }}
+
+      - name: Uncompress hdf5 binary (MacOS_latest)
+        run:  |
+          cd "${{ github.workspace }}"
+          tar -zxvf ${{ github.workspace }}/HDF5-*-Darwin.tar.gz --strip-components 1
+
+      - name: set hdf5lib name
+        id: set-hdf5lib-name
+        run: |
+          HDF5DIR=${{ github.workspace }}/HDF_Group/HDF5/
+          FILE_NAME_HDF5=$(ls ${{ github.workspace }}/HDF_Group/HDF5)
+          echo "HDF5_ROOT=$HDF5DIR$FILE_NAME_HDF5" >> $GITHUB_OUTPUT
+          echo "HDF5_PLUGIN_PATH=$HDF5_ROOT/lib/plugin" >> $GITHUB_OUTPUT
+
+      - name: List files for the binaries (MacOS_latest)
+        run: |
+          ls -l ${{ github.workspace }}/HDF_Group/HDF5
+
+      - name: List files for the space (MacOS_latest)
+        run: |
+          ls ${{ github.workspace }}
+          ls ${{ runner.workspace }}
+
+      # symlinks the compiler executables to a common location 
+      - name: Setup GNU Fortran
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 12
+
+      - name: Run ctest (MacOS_latest)
+        id: run-ctest
+        env:
+          HDF5_ROOT: ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}
+          HDF5_PLUGIN_PATH: ${{ steps.set-hdf5lib-name.outputs.HDF5_PLUGIN_PATH }}
+        run: |
+          cd "${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/share/HDF5Examples"
+          cmake --workflow --preset=ci-StdShar-OSX-Clang --fresh
+        shell: bash
+
diff --git a/.github/workflows/cmake-ctest.yml b/.github/workflows/cmake-ctest.yml
@@ -86,11 +86,15 @@ jobs:
           cmake --workflow --preset=${{ inputs.preset_name }}-MSVC --fresh
         shell: bash
 
-      - name: Publish binary (Windows)
-        id: publish-ctest-binary
+      - name: Create build folders (Windows)
         run: |
           mkdir "${{ runner.workspace }}/build114"
           mkdir "${{ runner.workspace }}/build114/hdf5"
+        shell: bash
+
+      - name: Publish binary (Windows)
+        id: publish-ctest-binary
+        run: |
           Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING -Destination ${{ runner.workspace }}/build114/hdf5/
           Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING_LBNL_HDF5 -Destination ${{ runner.workspace }}/build114/hdf5/
           Copy-Item -Path ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-MSVC/README.md -Destination ${{ runner.workspace }}/build114/hdf5/
@@ -99,6 +103,17 @@ jobs:
           7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_cl.zip hdf5
         shell: pwsh
 
+      - name: Publish msi binary (Windows)
+        id: publish-ctest-msi-binary
+        run: |
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING_LBNL_HDF5 -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-MSVC/README.md -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-MSVC/* -Destination ${{ runner.workspace }}/build/hdf5/ -Include *.msi
+          cd "${{ runner.workspace }}/build"
+          7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_cl.msi.zip hdf5
+        shell: pwsh
+
       - name: List files in the space (Windows)
         run: |
               Get-ChildItem -Path ${{ github.workspace }}
@@ -113,6 +128,13 @@ jobs:
               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`
 
+      - name: Save published msi binary (Windows)
+        uses: actions/upload-artifact@v4
+        with:
+              name: msi-vs2022_cl-binary
+              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_cl.msi.zip
+              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
+
   build_and_test_linux:
   # Linux (Ubuntu) w/ gcc + CMake
   #
@@ -253,6 +275,12 @@ jobs:
         with:
           version: "1.9.7"
 
+      - name: Set up JDK 19
+        uses: actions/setup-java@v4
+        with:
+          java-version: '19'
+          distribution: 'temurin'
+
       - name: Set file base name (MacOS)
         id: set-file-base
         run: |
@@ -306,7 +334,7 @@ jobs:
           cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Clang/README.md ${{ runner.workspace }}/build114/hdf5
           cp ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Clang/*.tar.gz ${{ runner.workspace }}/build114/hdf5
           cd "${{ runner.workspace }}/build114"
-          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx.tar.gz hdf5
+          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx13.tar.gz hdf5
         shell: bash
 
       - name: List files in the space (MacOS)
@@ -316,6 +344,95 @@ jobs:
 
       # Save files created by ctest script
       - name: Save published binary (MacOS)
+        uses: actions/upload-artifact@v4
+        with:
+              name: tgz-osx13-binary
+              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-osx13.tar.gz
+              if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
+
+  build_and_test_mac_latest:
+  # MacOS w/ Clang + CMake
+  #
+    name: "MacOS Clang CMake"
+    runs-on: macos-latest
+    steps:
+      - name: Install Dependencies (MacOS_latest)
+        run: brew install ninja
+
+      - name: Install Dependencies
+        uses: ssciwr/doxygen-install@v1
+        with:
+          version: "1.9.7"
+
+      - name: Set up JDK 19
+        uses: actions/setup-java@v4
+        with:
+          java-version: '21'
+          distribution: 'temurin'
+
+      - name: Set file base name (MacOS_latest)
+        id: set-file-base
+        run: |
+          FILE_NAME_BASE=$(echo "${{ inputs.file_base }}")
+          echo "FILE_BASE=$FILE_NAME_BASE" >> $GITHUB_OUTPUT
+          if [[ '${{ inputs.use_environ }}' == 'release' ]]
+          then
+            SOURCE_NAME_BASE=$(echo "${{ inputs.snap_name }}")
+          else
+            SOURCE_NAME_BASE=$(echo "hdfsrc")
+          fi
+          echo "SOURCE_BASE=$SOURCE_NAME_BASE" >> $GITHUB_OUTPUT
+
+      # Get files created by release script
+      - name: Get tgz-tarball (MacOS_latest)
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+        with:
+              name: tgz-tarball
+              path: ${{ github.workspace }}
+
+      - name: List files for the space (MacOS_latest)
+        run: |
+              ls ${{ github.workspace }}
+              ls ${{ runner.workspace }}
+
+      - name: Uncompress source (MacOS_latest)
+        run: tar -zxvf ${{ github.workspace }}/${{ steps.set-file-base.outputs.FILE_BASE }}.tar.gz
+
+      # symlinks the compiler executables to a common location 
+      - name: Setup GNU Fortran
+        uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 12
+
+      - name: Run ctest (MacOS_latest)
+        id: run-ctest
+        run: |
+          cd "${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}"
+          cmake --workflow --preset=${{ inputs.preset_name }}-OSX-Clang --fresh
+        shell: bash
+
+      - name: Publish binary (MacOS_latest)
+        id: publish-ctest-binary
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          mkdir "${{ runner.workspace }}/build/hdf5"
+          cp ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING ${{ runner.workspace }}/build/hdf5
+          cp ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING_LBNL_HDF5 ${{ runner.workspace }}/build/hdf5
+          cp ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-Clang/README.md ${{ runner.workspace }}/build/hdf5
+          cp ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-Clang/*.tar.gz ${{ runner.workspace }}/build/hdf5
+          cd "${{ runner.workspace }}/build"
+          tar -zcvf ${{ steps.set-file-base.outputs.FILE_BASE }}-osx.tar.gz hdf5
+        shell: bash
+
+      - name: List files in the space (MacOS_latest)
+        run: |
+              ls ${{ github.workspace }}
+              ls -l ${{ runner.workspace }}
+
+      # Save files created by ctest script
+      - name: Save published binary (MacOS_latest)
         uses: actions/upload-artifact@v4
         with:
               name: tgz-osx-binary
@@ -457,11 +574,15 @@ jobs:
           cmake --workflow --preset=${{ inputs.preset_name }}-win-Intel --fresh
         shell: pwsh
 
-      - name: Publish binary (Windows_intel)
-        id: publish-ctest-binary
+      - name: Create build folders (Windows_intel)
         run: |
           mkdir "${{ runner.workspace }}/build114"
           mkdir "${{ runner.workspace }}/build114/hdf5"
+        shell: bash
+
+      - name: Publish binary (Windows_intel)
+        id: publish-ctest-binary
+        run: |
           Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING -Destination ${{ runner.workspace }}/build114/hdf5/
           Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING_LBNL_HDF5 -Destination ${{ runner.workspace }}/build114/hdf5/
           Copy-Item -Path ${{ runner.workspace }}/hdf5/build114/${{ inputs.preset_name }}-Intel/README.md -Destination ${{ runner.workspace }}/build114/hdf5/
@@ -470,6 +591,17 @@ jobs:
           7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_intel.zip hdf5
         shell: pwsh
 
+      - name: Publish msi binary (Windows_intel)
+        id: publish-ctest-msi-binary
+        run: |
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/${{ steps.set-file-base.outputs.SOURCE_BASE }}/COPYING_LBNL_HDF5 -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-Intel/README.md -Destination ${{ runner.workspace }}/build/hdf5/
+          Copy-Item -Path ${{ runner.workspace }}/hdf5/build/${{ inputs.preset_name }}-Intel/* -Destination ${{ runner.workspace }}/build/hdf5/ -Include *.msi
+          cd "${{ runner.workspace }}/build"
+          7z a -tzip ${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_intel.msi.zip hdf5
+        shell: pwsh
+
       - name: List files in the space (Windows_intel)
         run: |
               Get-ChildItem -Path ${{ github.workspace }}
@@ -484,6 +616,13 @@ jobs:
               path: ${{ runner.workspace }}/build114/${{ 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`
 
+      - name: Save published msi binary (Windows_intel)
+        uses: actions/upload-artifact@v4
+        with:
+              name: msi-vs2022_intel-binary
+              path: ${{ runner.workspace }}/build/${{ steps.set-file-base.outputs.FILE_BASE }}-win-vs2022_intel.msi.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
   #

diff --git a/.github/workflows/main-cmake.yml b/.github/workflows/main-cmake.yml
@@ -286,6 +286,14 @@ jobs:
         if:  ${{ (matrix.os == 'ubuntu-latest') && (inputs.thread_safety != 'TS') }}
 
       - name: Save published binary (Mac)
+        uses: actions/upload-artifact@v4
+        with:
+            name: tgz-osx13-${{ inputs.build_mode }}-binary
+            path: ${{ runner.workspace }}/build/HDF5-*-Darwin.tar.gz
+            if-no-files-found: error # 'warn' or 'ignore' are also available, defaults to `warn`
+        if: ${{ (matrix.os == 'macos-13') && (inputs.thread_safety != 'TS') }}
+
+      - name: Save published binary (Mac_latest)
         uses: actions/upload-artifact@v4
         with:
               name: tgz-osx-${{ inputs.build_mode }}-binary

diff --git a/.github/workflows/publish-branch.yml b/.github/workflows/publish-branch.yml
@@ -0,0 +1,45 @@
+name: hdf5 publish files in HDF5 folder from branch to S3
+
+# Triggers the workflow on demand
+on:
+  workflow_dispatch:
+    inputs:
+      local_dir:
+        description: 'HDF5 local directory'
+        type: string
+        required: true
+      target_dir:
+        description: 'hdf5 target bucket directory'
+        type: string
+        required: true
+
+permissions:
+  contents: read
+
+jobs:
+  publish-tag:
+    runs-on: ubuntu-latest
+    steps:
+        # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+        - name: Get Sources
+          uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+          with:
+            fetch-depth: 0
+            ref: '${{ github.head_ref || github.ref_name }}'
+
+        - name: List files for the space
+          run: |
+              ls -l ${{ github.workspace }}
+              ls ${{ github.workspace }}/HDF5
+
+        - name: Setup AWS CLI
+          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 }}
+                 aws-region: ${{ secrets.AWS_REGION }}
+
+        - name: Sync dir to S3 bucket
+          run: |
+                aws s3 sync ./HDF5/${{ inputs.local_dir }} s3://${{ secrets.AWS_S3_BUCKET }}/${{ vars.TARGET_PATH }}/${{ inputs.target_dir }}
+
diff --git a/.github/workflows/publish-release.yml b/.github/workflows/publish-release.yml
@@ -12,8 +12,9 @@ on:
         description: 'HDF5 target bucket directory'
         type: string
         required: true
-    permissions:
-      contents: read
+
+permissions:
+  contents: read
 
 jobs:
   publish-tag:
@@ -47,9 +48,9 @@ jobs:
                 aws s3 sync ./HDF5 s3://${{ secrets.AWS_S3_BUCKET }}/${{ vars.TARGET_PATH }}/${{ inputs.target_dir }}/downloads --delete
 
         - name: Uncompress source (Linux)
-          run: tar -zxvf ${{ github.workspace }}/${{ inputs.use_hdf }}.doxygen.tar.gz
+          run: tar -zxvf ${{ github.workspace }}/HDF5/${{ inputs.use_hdf }}.doxygen.tar.gz
 
         - name: Sync userguide to S3 bucket
           run: |
-                aws s3 sync ./doxygen s3://${{ secrets.AWS_S3_BUCKET }}/${{ vars.TARGET_PATH }}/${{ inputs.target_dir }}/documentation --delete
+                aws s3 sync ./HDF5/doxygen s3://${{ secrets.AWS_S3_BUCKET }}/${{ vars.TARGET_PATH }}/${{ inputs.target_dir }}/documentation/doxygen --delete