Merge branch 'HDFGroup:master' into master

bmribler · Feb 22, 2024 · f1e2f18 · f1e2f18
2 parents cb8f7ef + 0ab5dab
commit f1e2f18
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diff --git a/.gitattributes b/.gitattributes
@@ -66,12 +66,6 @@ hdf/util/testfiles/tvattr.hdf -text
 java/CMakeLists.txt -text
 java/Makefile.am -text
 java/Makefile.in -text
-java/examples/CMakeLists.txt -text
-java/examples/HDF4DatasetCreate.java -text
-java/examples/HDF4FileCreate.java -text
-java/examples/HDF4GroupCreate.java -text
-java/examples/Makefile.am -text
-java/examples/Makefile.in -text
 java/lib/ext/slf4j-nop-1.7.33.jar -text svneol=unset#application/zip
 java/lib/ext/slf4j-simple-1.7.33.jar -text svneol=unset#application/zip
 java/lib/hamcrest-core.jar -text svneol=unset#application/java-archive

diff --git a/.github/workflows/abi-report.yml b/.github/workflows/abi-report.yml
@@ -0,0 +1,152 @@
+name: hdf4 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 hdf4 reference name (Linux)
+        id: convert-hdf4lib-refname
+        run:  |
+          FILE_DOTS=$(echo "${{ inputs.file_ref }}" | sed -r "s/([0-9]+)\_([0-9]+)\_([0-9]+)\-([0-9]+).*/\1\.\2\.\3\-\4/")
+          echo "HDF4R_DOTS=$FILE_DOTS" >> $GITHUB_OUTPUT
+
+      - uses: actions/[email protected]
+
+      - name: Get published binary (Linux)
+        uses: actions/download-artifact@f44cd7b40bfd40b6aa1cc1b9b5b7bf03d3c67110 # v4.1.0
+        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 hdf4 binary (Linux)
+        run:  |
+          cd "${{ github.workspace }}/hdf4"
+          tar -zxvf ${{ github.workspace }}/hdf4/HDF-*-Linux.tar.gz --strip-components 1
+
+      - name: List files for the HDF space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf4
+          ls -l ${{ github.workspace }}/hdf4/HDF_Group/HDF
+
+      - name: set hdf4lib name
+        id: set-hdf4lib-name
+        run: |
+          HDF4DIR=${{ github.workspace }}/hdf4/HDF_Group/HDF/
+          FILE_NAME_HDF4=$(ls ${{ github.workspace }}/hdf4/HDF_Group/HDF)
+          FILE_VERS=$(echo "$FILE_NAME_HDF4" | sed -r "s/([0-9]+\.[0-9]+\.[0-9]+\-[0-9]+)\..*/\1/")
+          echo "HDF4_ROOT=$HDF4DIR$FILE_NAME_HDF4" >> $GITHUB_OUTPUT
+          echo "HDF4_VERS=$FILE_VERS" >> $GITHUB_OUTPUT
+
+      - name: Download reference version
+        run: |
+          mkdir "${{ github.workspace }}/hdf4R"
+          cd "${{ github.workspace }}/hdf4R"
+          wget -q https://github.com/HDFGroup/hdf4/releases/download/hdf-${{ inputs.file_ref }}/hdf-${{ inputs.file_ref }}-ubuntu-2204.tar.gz
+          tar zxf hdf-${{ inputs.file_ref }}-ubuntu-2204.tar.gz
+
+      - name: List files for the space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf4R
+
+      - name: Uncompress hdf4 reference binary (Linux)
+        run:  |
+          cd "${{ github.workspace }}/hdf4R"
+          tar -zxvf ${{ github.workspace }}/hdf4R/hdf4/HDF-${{ steps.convert-hdf4lib-refname.outputs.HDF4R_DOTS }}-Linux.tar.gz --strip-components 1
+
+      - name: List files for the HDFR space (Linux)
+        run: |
+          ls -l ${{ github.workspace }}/hdf4R
+          ls -l ${{ github.workspace }}/hdf4R/HDF_Group/HDF
+
+      - name: set hdf4lib reference name
+        id: set-hdf4lib-refname
+        run: |
+          HDF4RDIR=${{ github.workspace }}/hdf4R/HDF_Group/HDF/
+          FILE_NAME_HDF4R=$(ls ${{ github.workspace }}/hdf4R/HDF_Group/HDF)
+          echo "HDF4R_ROOT=$HDF4RDIR$FILE_NAME_HDF4R" >> $GITHUB_OUTPUT
+          echo "HDF4R_VERS=$FILE_NAME_HDF4R" >> $GITHUB_OUTPUT
+
+      - name: List files for the lib spaces (Linux)
+        run: |
+          ls -l ${{ steps.set-hdf4lib-name.outputs.HDF4_ROOT }}/lib
+          ls -l ${{ steps.set-hdf4lib-refname.outputs.HDF4R_ROOT }}/lib
+
+      - name: Run Java API report
+        run: |
+          japi-compliance-checker ${{ steps.set-hdf4lib-refname.outputs.HDF5R_ROOT }}/lib/jarhdf4-${{ steps.convert-hdf4lib-refname.outputs.HDF4R_DOTS }}.jar ${{ steps.set-hdf4lib-name.outputs.HDF4_ROOT }}/lib/jarhdf4-${{ steps.set-hdf4lib-name.outputs.HDF4_VERS }}.jar
+
+      - name: Run hdf ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf4lib-refname.outputs.HDF4R_ROOT }}/lib/libhdf.so -o ABI-0.dump -public-headers ${{ steps.set-hdf4lib-refname.outputs.HDF4R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf4lib-name.outputs.HDF4_ROOT }}/lib/libhdf.so -o ABI-1.dump -public-headers ${{ steps.set-hdf4lib-name.outputs.HDF4_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}-hdf -old ABI-0.dump -new ABI-1.dump
+        continue-on-error: true
+
+      - name: Run mfhdf ABI report
+        run: |
+          abi-dumper ${{ steps.set-hdf4lib-refname.outputs.HDF4R_ROOT }}/lib/libmfhdf.so -o ABI-2.dump -public-headers ${{ steps.set-hdf4lib-refname.outputs.HDF4R_ROOT }}/include
+          abi-dumper ${{ steps.set-hdf4lib-name.outputs.HDF4_ROOT }}/lib/libmfhdf.so -o ABI-3.dump -public-headers ${{ steps.set-hdf4lib-name.outputs.HDF4_ROOT }}/include
+          abi-compliance-checker -l ${{ inputs.file_base }}-mfhdf -old ABI-2.dump -new ABI-3.dump
+        continue-on-error: true
+
+      - name: Copy ABI reports
+        run: |
+          cp compat_reports/jarhdf4-/${{ steps.set-hdf4lib-refname.outputs.HDF5R_VERS }}_to_${{ steps.set-hdf4lib-name.outputs.HDF4_VERS }}/compat_report.html ${{ inputs.file_base }}-java_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}-hdf/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}-hdf/X_to_Y/compat_report.html ${{ inputs.file_base }}-hdf_compat_report.html
+          ls -l compat_reports/${{ inputs.file_base }}-mfhdf/X_to_Y
+          cp compat_reports/${{ inputs.file_base }}-mfhdf/X_to_Y/compat_report.html ${{ inputs.file_base }}-mfhdf_compat_report.html
+
+      - name: List files for the report spaces (Linux)
+        run: |
+          ls -l compat_reports
+          ls -l *.html
+
+      - name: Save output as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: abi-reports
+          path: |
+            ${{ inputs.file_base }}-hdf_compat_report.html
+            ${{ inputs.file_base }}-mfhdf_compat_report.html
+            ${{ inputs.file_base }}-java_compat_report.html
diff --git a/.github/workflows/aocc-auto.yml b/.github/workflows/aocc-auto.yml
@@ -0,0 +1,150 @@
+name:  hdf4 autotools aocc
+
+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:
+      - uses: actions/[email protected]
+
+      - name: Install System dependencies
+        run: |
+          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 build-essential libncurses-dev libquadmath0 libstdc++6 libxml2
+
+      - name: Install AOCC 4.1.0
+        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/hdf4/hdf4/setenv_AOCC.sh
+          which clang
+          which flang
+          clang -v
+          echo "CC=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/bin/clang" >> $GITHUB_ENV
+          echo "FC=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/bin/flang" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib:/usr/local/lib" >> $GITHUB_ENV
+          echo "LD_RUN_PATH=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib:/usr/local/lib" >> $GITHUB_ENV
+          echo "DESTDIR=/tmp" >> $GITHUB_ENV
+
+      - name: Autotools Configure with aocc
+        shell: bash
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          sh ./autogen.sh
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          $GITHUB_WORKSPACE/configure \
+            --enable-build-mode=${{ inputs.build_mode }} \
+            --enable-netcdf \
+            --enable-shared \
+            --disable-fortran \
+            LDFLAGS="-L/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib"
+
+      # BUILD
+      - name: Autotools Build
+        shell: bash
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          make -j3
+        working-directory: ${{ runner.workspace }}/build
+
+      # RUN TESTS
+      # NORMAL
+      - name: Autotools Run Tests
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          make check -j2
+        working-directory: ${{ runner.workspace }}/build
+
+      # INSTALL (note that this runs even when we don't run the tests)
+      - name: Autotools Install
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          make install
+        working-directory: ${{ runner.workspace }}/build
+
+  aocc_static_build_and_test:
+    name: "aocc static ${{ inputs.build_mode }}"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+
+      - name: Install System dependencies
+        run: |
+          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 build-essential libncurses-dev libquadmath0 libstdc++6 libxml2
+
+      - name: Install AOCC 4.1.0
+        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/hdf4/hdf4/setenv_AOCC.sh
+          which clang
+          which flang
+          clang -v
+          echo "CC=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/bin/clang" >> $GITHUB_ENV
+          echo "FC=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/bin/flang" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib:/usr/local/lib" >> $GITHUB_ENV
+          echo "LD_RUN_PATH=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib:/usr/local/lib" >> $GITHUB_ENV
+          echo "DESTDIR=/tmp" >> $GITHUB_ENV
+
+      - name: Autotools Configure with aocc
+        shell: bash
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          sh ./autogen.sh
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          $GITHUB_WORKSPACE/configure \
+            --enable-build-mode=${{ inputs.build_mode }} \
+            --enable-netcdf \
+            --disable-shared \
+            --enable-fortran \
+            LDFLAGS="-L/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib"
+
+      # BUILD
+      - name: Autotools Build
+        shell: bash
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          make -j3
+        working-directory: ${{ runner.workspace }}/build
+
+      # RUN TESTS
+      # NORMAL
+      - name: Autotools Run Tests
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          make check -j2
+        working-directory: ${{ runner.workspace }}/build
+
+      # INSTALL (note that this runs even when we don't run the tests)
+      - name: Autotools Install
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          make install
+        working-directory: ${{ runner.workspace }}/build
+
diff --git a/.github/workflows/aocc-cmake.yml b/.github/workflows/aocc-cmake.yml
@@ -0,0 +1,77 @@
+name: hdf4 CMake aocc
+
+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:
+      - uses: actions/[email protected]
+
+      - name: Install Linux dependencies
+        shell: bash
+        run: |
+          sudo apt update
+          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+          sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential
+
+      - name: Install AOCC 4.1.0
+        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/hdf4/hdf4/setenv_AOCC.sh
+          which clang
+          which flang
+          clang -v
+          echo "CC=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/bin/clang" >> $GITHUB_ENV
+          echo "FC=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/bin/flang" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib:/usr/local/lib" >> $GITHUB_ENV
+          echo "LD_RUN_PATH=/home/runner/work/hdf4/hdf4/aocc-compiler-4.1.0/lib:/usr/local/lib" >> $GITHUB_ENV
+          echo "DESTDIR=/tmp" >> $GITHUB_ENV
+
+      - name: CMake Configure with aocc
+        shell: bash
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \
+          -DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
+          -DJPEG_USE_LOCALCONTENT=OFF \
+          -DLIBAEC_USE_LOCALCONTENT=OFF \
+          -DZLIB_USE_LOCALCONTENT=OFF \
+          -DHDF4_BUILD_FORTRAN:BOOL=ON \
+          -DHDF4_BUILD_JAVA:BOOL=OFF \
+          $GITHUB_WORKSPACE
+
+      # BUILD
+      - name: CMake Build
+        shell: bash
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
+        working-directory: ${{ runner.workspace }}/build
+
+      # RUN TESTS
+      - name: CMake Run Tests
+        shell: bash
+        run: |
+          source /home/runner/work/hdf4/hdf4/setenv_AOCC.sh
+          export PATH=/usr/local/bin:$PATH
+          ctest . --parallel 2 -C ${{ inputs.build_mode }} -V
+        working-directory: ${{ runner.workspace }}/build