Merge branch 'develop' into fix-H5Pset_external-offset

.codespellrc

@@ -0,0 +1,6 @@
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+[codespell]
+skip = .git,*.svg,.codespellrc,./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
+check-hidden = true
+# ignore-regex = 
+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

.devcontainer/Dockerfile

@@ -0,0 +1,5 @@
+FROM mcr.microsoft.com/devcontainers/base:debian
+
+RUN apt-get update && apt-get -y install --no-install-recommends \
+  build-essential cmake cmake-curses-gui doxygen git graphviz \
+  less libtool-bin libyajl-dev mpi-default-dev valgrind wget

.devcontainer/devcontainer.json

@@ -0,0 +1,26 @@
+{
+  "name": "HDF5 Developer",
+  "build": {
+    "context": "..",
+    "dockerfile": "Dockerfile"
+  },
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "ms-python.python",
+        "ms-toolsai.jupyter",
+        "ms-vscode.cpptools",
+        "ms-vscode.live-server",
+        "ms-vscode-remote.remote-containers",
+        "ms-azuretools.vscode-docker",
+        "h5web.vscode-h5web",
+        "davidanson.vscode-markdownlint"
+      ],
+      "settings": {
+        "C_Cpp.default.cppStandard": "c++17",
+        "C_Cpp.default.cStandard": "c99",
+        "terminal.integrated.shell.linux": "/bin/bash"
+      }
+    }
+  }
+}

.devcontainer/noop.txt

@@ -0,0 +1,3 @@
+This file is copied into the container along with environment.yml* from the
+parent folder. This file prevents the Dockerfile COPY instruction from failing
+if no environment.yml is found.

.github/FUNDING.yml

@@ -1,3 +1,3 @@
 # These are supported funding model platforms
 
-custom: "https://hdfgroup.org/about-us/donate-to-the-hdf-group/"
+custom: "https://www.hdfgroup.org/donate"

.github/dependabot.yml

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

.github/workflows/abi-report.yml

@@ -0,0 +1,181 @@
+name: hdf5 Check Application Binary Interface (ABI)
+
+on:
+  workflow_call:
+    inputs:
+      use_tag:
+        description: 'Release version tag'
+        type: string
+        required: false
+        default: snapshot
+      use_environ:
+        description: 'Environment to locate files'
+        type: string
+        required: true
+        default: snapshots
+      file_base:
+        description: "The common base name of the binary"
+        required: true
+        type: string
+      file_ref:
+        description: "The reference name for the release binary"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+
+    steps:
+      - name: Install System dependencies
+        run: |
+          sudo apt update
+          sudo apt install -q -y abi-compliance-checker abi-dumper
+          sudo apt install -q -y japi-compliance-checker
+
+      - name: Convert hdf5 reference name (Linux)
+        id: convert-hdf5lib-refname
+        run:  |
+          FILE_DOTS=$(echo "${{ inputs.file_ref }}" | sed -r "s/([0-9]+)\_([0-9]+)\_([0-9]+).*/\1\.\2\.\3/")
+          echo "HDF5R_DOTS=$FILE_DOTS" >> $GITHUB_OUTPUT
+
+      - uses: actions/checkout@v4.1.1
+
+      - name: Get published binary (Linux)
+        uses: actions/download-artifact@c850b930e6ba138125429b7e5c93fc707a7f8427 # v4.1.4
+        with:
+            name: tgz-ubuntu-2204_gcc-binary
+            path: ${{ github.workspace }}
+
+      - name: List files for the space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}
+
+      - name: Uncompress gh binary (Linux)
+        run: tar -zxvf ${{ github.workspace }}/${{ inputs.file_base }}-ubuntu-2204_gcc.tar.gz
+
+      - name: Uncompress hdf5 binary (Linux)
+        run:  |
+          cd "${{ github.workspace }}/hdf5"
+          tar -zxvf ${{ github.workspace }}/hdf5/HDF5-*-Linux.tar.gz --strip-components 1
+
+      - name: List files for the HDF space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf5
+          ls -l ${{ github.workspace }}/hdf5/HDF_Group/HDF5
+
+      - name: set hdf5lib name
+        id: set-hdf5lib-name
+        run: |
+          HDF5DIR=${{ github.workspace }}/hdf5/HDF_Group/HDF5/
+          FILE_NAME_HDF5=$(ls ${{ github.workspace }}/hdf5/HDF_Group/HDF5)
+          FILE_VERS=$(echo "$FILE_NAME_HDF5" | sed -r "s/([0-9]+\.[0-9]+\.[0-9]+).*/\1/")
+          echo "HDF5_ROOT=$HDF5DIR$FILE_NAME_HDF5" >> $GITHUB_OUTPUT
+          echo "HDF5_VERS=$FILE_VERS" >> $GITHUB_OUTPUT
+
+      - name: Download reference version
+        run: |
+          mkdir "${{ github.workspace }}/hdf5R"
+          cd "${{ github.workspace }}/hdf5R"
+          wget -q https://github.com/HDFGroup/hdf5/releases/download/hdf5-${{ inputs.file_ref }}/hdf5-${{ inputs.file_ref }}-ubuntu-2204.tar.gz
+          tar zxf hdf5-${{ inputs.file_ref }}-ubuntu-2204.tar.gz
+
+      - name: List files for the space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf5R
+
+      - name: Uncompress hdf5 reference binary (Linux)
+        run:  |
+          cd "${{ github.workspace }}/hdf5R"
+          tar -zxvf ${{ github.workspace }}/hdf5R/hdf5/HDF5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}-Linux.tar.gz --strip-components 1
+
+      - name: List files for the HDFR space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf5R
+          ls -l ${{ github.workspace }}/hdf5R/HDF_Group/HDF5
+
+      - name: set hdf5lib reference name
+        id: set-hdf5lib-refname
+        run: |
+          HDF5RDIR=${{ github.workspace }}/hdf5R/HDF_Group/HDF5/
+          FILE_NAME_HDF5R=$(ls ${{ github.workspace }}/hdf5R/HDF_Group/HDF5)
+          echo "HDF5R_ROOT=$HDF5RDIR$FILE_NAME_HDF5R" >> $GITHUB_OUTPUT
+          echo "HDF5R_VERS=$FILE_NAME_HDF5R" >> $GITHUB_OUTPUT
+
+      - name: List files for the lib spaces (Linux)
+        run: |
+          ls -l ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib
+          ls -l ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib
+
+      - name: Run Java API report
+        run: |
+          japi-compliance-checker ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/jarhdf5-${{ steps.convert-hdf5lib-refname.outputs.HDF5R_DOTS }}.jar ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/jarhdf5-${{ steps.set-hdf5lib-name.outputs.HDF5_VERS }}.jar
+
+      - name: Run ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5.so -o ABI-0.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5.so -o ABI-1.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }} -old ABI-0.dump -new ABI-1.dump
+        continue-on-error: true
+
+      - name: Run hl ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5_hl.so -o ABI-2.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5_hl.so -o ABI-3.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}_hl -old ABI-2.dump -new ABI-3.dump
+        continue-on-error: true
+
+      - name: Run cpp ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5_cpp.so -o ABI-4.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5_cpp.so -o ABI-5.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}_cpp -old ABI-4.dump -new ABI-5.dump
+        continue-on-error: true
+
+      - name: Run hl_cpp ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/lib/libhdf5_hl_cpp.so -o ABI-6.dump -public-headers ${{ steps.set-hdf5lib-refname.outputs.HDF5R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/lib/libhdf5_hl_cpp.so -o ABI-7.dump -public-headers ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}_hl_cpp -old ABI-6.dump -new ABI-7.dump
+        continue-on-error: true
+
+      - name: Copy ABI reports
+        run: |
+          cp compat_reports/jarhdf5-/${{ steps.set-hdf5lib-refname.outputs.HDF5R_VERS }}_to_${{ steps.set-hdf5lib-name.outputs.HDF5_VERS }}/compat_report.html ${{ inputs.file_base }}-java_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}_hl/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}_hl/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_hl_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}_cpp/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}_cpp/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_cpp_compat_report.html
+#          ls -l compat_reports/${{ inputs.file_base }}_hl_cpp/X_to_Y
+#          cp compat_reports/${{ inputs.file_base }}_hl_cpp/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf5_hl_cpp_compat_report.html
+
+      - name: List files for the report spaces (Linux)
+        run: |
+          ls -l compat_reports
+          ls -l *.html
+
+      - name: Publish ABI reports
+        id: publish-abi-reports
+        run: |
+          mkdir "${{ runner.workspace }}/buildabi"
+          mkdir "${{ runner.workspace }}/buildabi/hdf5"
+          cp ${{ inputs.file_base }}-hdf5_compat_report.html ${{ runner.workspace }}/buildabi/hdf5
+          cp ${{ inputs.file_base }}-hdf5_hl_compat_report.html ${{ runner.workspace }}/buildabi/hdf5
+          cp ${{ inputs.file_base }}-hdf5_cpp_compat_report.html ${{ runner.workspace }}/buildabi/hdf5
+          cp ${{ inputs.file_base }}-java_compat_report.html ${{ runner.workspace }}/buildabi/hdf5
+          cd "${{ runner.workspace }}/buildabi"
+          tar -zcvf ${{ inputs.file_base }}.html.abi.reports.tar.gz hdf5
+        shell: bash
+
+      - name: Save output as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: abi-reports
+          path: |
+            ${{ runner.workspace }}/buildabi/${{ inputs.file_base }}.html.abi.reports.tar.gz

.github/workflows/aocc-auto.yml

@@ -0,0 +1,102 @@
+name: hdf5 dev PAR autotools aocc ompi
+
+on:
+  workflow_call:
+    inputs:
+      build_mode:
+        description: "release vs. debug build"
+        required: true
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  aocc_build_and_test:
+    name: "aocc ${{ inputs.build_mode }}"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get Sources
+        uses: actions/checkout@v4.1.1
+
+      - name: Install Dependencies
+        shell: bash
+        run: |
+          sudo apt update
+          sudo apt install -y autoconf automake libtool libtool-bin libaec-dev
+          sudo apt install -y doxygen libncurses-dev libquadmath0 libstdc++6 libxml2
+          sudo apt install -y zlib1g-dev libcurl4-openssl-dev libjpeg-dev wget curl bzip2
+          sudo apt install -y m4 flex bison cmake libzip-dev openssl build-essential
+
+      - name: Install AOCC 4.1.0
+        shell: bash
+        run: |
+          wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
+          tar -xvf aocc-compiler-4.1.0.tar
+          cd aocc-compiler-4.1.0
+          bash install.sh
+          source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
+          which clang
+          which flang
+          clang -v
+
+      - name: Cache OpenMPI 4.1.5 installation
+        id: cache-openmpi-4_1_5
+        uses: actions/cache@v4
+        with:
+          path: /home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
+          key: ${{ runner.os }}-${{ runner.arch }}-openmpi-4_1_5-cache
+
+      - name: Install OpenMPI 4.1.5
+        if: ${{ steps.cache-openmpi-4_1_5.outputs.cache-hit != 'true' }}
+        run: |
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
+          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
+          tar zxvf openmpi-4.1.5.tar.gz
+          cd openmpi-4.1.5
+          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install
+          make
+          make install
+
+      - name: Autotools Configure
+        env:
+          NPROCS: 2
+        run: |
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
+          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib:/usr/local/lib
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          sh ./autogen.sh
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          CC=mpicc $GITHUB_WORKSPACE/configure \
+            --prefix=/tmp \
+            --enable-build-mode=${{ inputs.build_mode }} \
+            --enable-shared \
+            --enable-parallel \
+            LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib \
+            -L/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/lib"
+
+      - name: Autotools Build
+        shell: bash
+        env:
+          NPROCS: 2
+        run: |
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          make -j3
+        working-directory: ${{ runner.workspace }}/build
+
+      - name: Autotools Run Tests
+        env:
+          NPROCS: 2
+        run: |
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          make check -j
+        working-directory: ${{ runner.workspace }}/build
+
+      - name: Autotools Install
+        env:
+          NPROCS: 2
+        run: |
+          export PATH=/home/runner/work/hdf5/hdf5/openmpi-4.1.5-install/bin:/usr/local/bin:$PATH
+          make install
+        working-directory: ${{ runner.workspace }}/build