Merge pull request #84 from HDFGroup/feature/sparse_data

Feature/sparse data
vchoi-hdfgroup · Oct 10, 2024 · 06a16f0 · 06a16f0
2 parents 76f0589 + 892d866
commit 06a16f0
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Showing 341 changed files with 15,070 additions and 9,044 deletions.
diff --git a/.github/workflows/clang-format-check.yml b/.github/workflows/clang-format-check.yml
@@ -18,6 +18,6 @@ jobs:
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp,java'
-        clangFormatVersion: 13
+        clangFormatVersion: 17
         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'
diff --git a/.github/workflows/clang-format-fix.yml b/.github/workflows/clang-format-fix.yml
@@ -30,7 +30,7 @@ jobs:
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp,java'
-        clangFormatVersion: 13
+        clangFormatVersion: 17
         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'

diff --git a/.github/workflows/cmake-bintest.yml b/.github/workflows/cmake-bintest.yml
@@ -201,6 +201,6 @@ jobs:
           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-MACOS-Clang --fresh
+          cmake --workflow --preset=ci-StdShar-macos-Clang --fresh
         shell: bash
 
diff --git a/.github/workflows/cmake-script.yml b/.github/workflows/cmake-script.yml
diff --git a/.github/workflows/daily-build.yml b/.github/workflows/daily-build.yml
@@ -3,6 +3,12 @@ name: hdf5 dev daily build
 # Triggers the workflow on a schedule or on demand
 on:
   workflow_dispatch:
+    inputs:
+      use_ignore:
+        description: 'Ignore has_changes check'
+        type: string
+        required: false
+        default: check
   schedule:
     - cron: "6 0 * * *"
 
@@ -14,6 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     outputs:
       hdf5-name: ${{ steps.gethdf5base.outputs.HDF5_NAME_BASE }}
+      run-ignore: ${{ steps.getinputs.outputs.INPUTS_IGNORE }}
 
     steps:
     - uses: actions/checkout@v4.1.7
@@ -23,21 +30,39 @@ jobs:
       with:
         version: 'tags/snapshot'
         file: 'last-file.txt'
+      continue-on-error: true
 
     - name: Read base-name file
       id: gethdf5base
       run: echo "HDF5_NAME_BASE=$(cat last-file.txt)" >> $GITHUB_OUTPUT
 
     - run: echo "hdf5 base name is ${{ steps.gethdf5base.outputs.HDF5_NAME_BASE }}."
 
+    - name: Read inputs
+      id: getinputs
+      run: |
+        echo "INPUTS_IGNORE=${{ inputs.use_ignore }}" >> $GITHUB_OUTPUT
+
+    - run: echo "use_ignore is ${{ steps.getinputs.outputs.INPUTS_IGNORE }}."
+
   call-workflow-tarball:
+    needs: [get-old-names]
     uses: ./.github/workflows/tarball.yml
     with:
+      use_ignore: ${{ needs.get-old-names.outputs.run-ignore }}
       use_tag: snapshot
       use_environ: snapshots
 
+  call-workflow-c-script:
+    needs: [get-old-names, call-workflow-tarball]
+    uses: ./.github/workflows/cmake-script.yml
+    with:
+      file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
+      use_environ: snapshots
+    if: ${{ ((needs.call-workflow-tarball.outputs.has_changes == 'true') || (needs.get-old-names.outputs.run-ignore == 'ignore')) }}
+
   call-workflow-ctest:
-    needs: call-workflow-tarball
+    needs: [get-old-names, call-workflow-tarball]
     uses: ./.github/workflows/cmake-ctest.yml
     with:
       preset_name: ci-StdShar
@@ -54,17 +79,17 @@ jobs:
         AZURE_ENDPOINT: ${{ secrets.AZURE_ENDPOINT }}
         AZURE_CODE_SIGNING_NAME: ${{ secrets.AZURE_CODE_SIGNING_NAME }}
         AZURE_CERT_PROFILE_NAME: ${{ secrets.AZURE_CERT_PROFILE_NAME }}
-    if: ${{ needs.call-workflow-tarball.outputs.has_changes == 'true' }}
+    if: ${{ ((needs.call-workflow-tarball.outputs.has_changes == 'true') || (needs.get-old-names.outputs.run-ignore == 'ignore')) }}
 
   call-workflow-abi:
-    needs: [call-workflow-tarball, call-workflow-ctest]
+    needs: [get-old-names, call-workflow-tarball, call-workflow-ctest]
     uses: ./.github/workflows/abi-report.yml
     with:
-      file_ref: '1.14.4.3'
+      file_ref: '1.14.5'
       file_base: ${{ needs.call-workflow-tarball.outputs.file_base }}
       use_tag: snapshot
       use_environ: snapshots
-    if: ${{ needs.call-workflow-tarball.outputs.has_changes == 'true' }}
+    if: ${{ ((needs.call-workflow-tarball.outputs.has_changes == 'true') || (needs.get-old-names.outputs.run-ignore == 'ignore')) }}
 
   call-workflow-release:
     needs: [get-old-names, call-workflow-tarball, call-workflow-ctest, call-workflow-abi]
@@ -77,7 +102,7 @@ jobs:
       file_sha: ${{ needs.call-workflow-tarball.outputs.file_sha }}
       use_tag: snapshot
       use_environ: snapshots
-    if: ${{ needs.call-workflow-tarball.outputs.has_changes == 'true' }}
+    if: ${{ ((needs.call-workflow-tarball.outputs.has_changes == 'true') || (needs.get-old-names.outputs.run-ignore == 'ignore')) }}
 
   call-workflow-remove:
     needs: [get-old-names, call-workflow-tarball, call-workflow-ctest, call-workflow-abi, call-workflow-release]
@@ -88,5 +113,5 @@ jobs:
       file_base: ${{ needs.get-old-names.outputs.hdf5-name }}
       use_tag: snapshot
       use_environ: snapshots
-    if: ${{ (needs.call-workflow-tarball.outputs.has_changes == 'true') && (needs.get-old-names.outputs.hdf5-name != needs.call-workflow-tarball.outputs.file_base) }}
+    if: ${{ ((needs.call-workflow-tarball.outputs.has_changes == 'true') || (needs.get-old-names.outputs.run-ignore == 'ignore')) && (needs.get-old-names.outputs.hdf5-name != needs.call-workflow-tarball.outputs.file_base) }}
 
diff --git a/.github/workflows/h5py.yml b/.github/workflows/h5py.yml
@@ -24,8 +24,8 @@ jobs:
         sed -i 's/hdf5@1.10.4:1.14/hdf5@1.10.4:/g' \
         ./spack/var/spack/repos/builtin/packages/py-h5py/package.py
         . ./spack/share/spack/setup-env.sh
-        ./spack/bin/spack spec py-h5py@master+mpi ^hdf5@develop-1.15
-        ./spack/bin/spack install py-h5py@master+mpi ^hdf5@develop-1.15
+        ./spack/bin/spack spec py-h5py@master+mpi ^hdf5@develop-1.17
+        ./spack/bin/spack install py-h5py@master+mpi ^hdf5@develop-1.17
         ./spack/bin/spack install py-pytest
         ./spack/bin/spack install py-ipython
         spack load py-h5py

diff --git a/.github/workflows/hdfeos5.yml b/.github/workflows/hdfeos5.yml
@@ -0,0 +1,51 @@
+name: hdfeos5 dev
+
+# Triggers the workflow on push or pull request or on demand
+on:
+  workflow_dispatch:
+  push:
+  pull_request:
+    branches: [ develop ]
+    paths-ignore:
+      - '.github/CODEOWNERS'
+      - '.github/FUNDING.yml'
+      - 'doc/**'
+      - 'release_docs/**'
+      - 'ACKNOWLEDGEMENTS'
+      - 'COPYING**'
+      - '**.md'
+
+# Using concurrency to cancel any in-progress job or run
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build hdfeos5
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4.1.7
+
+      - name: Install Autotools Dependencies (Linux)
+        run: |
+          sudo apt update
+          sudo apt install automake autoconf libtool libtool-bin
+      - name: Install HDF5
+        run: |
+          ./autogen.sh
+          ./configure --prefix=/usr/local --disable-tests --with-default-api-version=v16
+          make
+          sudo make install
+      - name: Install HDF-EOS5
+        run: |
+          wget -O HDF-EOS5.2.0.tar.gz "https://git.earthdata.nasa.gov/projects/DAS/repos/hdfeos5/raw/hdf-eos5-2.0-src.tar.gz?at=refs%2Fheads%2FHDFEOS5_2.0"
+          tar zxvf HDF-EOS5.2.0.tar.gz
+          cd hdf-eos5-2.0
+          ./configure CC=/usr/local/bin/h5cc --prefix=/usr/local/ --enable-install-include
+          make
+          make check
+          sudo make install
diff --git a/.github/workflows/intel-auto.yml b/.github/workflows/intel-auto.yml
@@ -1,4 +1,4 @@
-name: hdf5 dev autotools icx
+name: hdf5 dev autotools icx CI
 
 # Triggers the workflow on a call from another workflow
 on:

diff --git a/.github/workflows/intel-cmake.yml b/.github/workflows/intel-cmake.yml
@@ -1,4 +1,4 @@
-name: hdf5 dev CMake icx
+name: hdf5 dev CMake icx CI
 
 # Triggers the workflow on a call from another workflow
 on:

diff --git a/.github/workflows/main-cmake-spc.yml b/.github/workflows/main-cmake-spc.yml
@@ -77,6 +77,66 @@ jobs:
       #
 #      - name: CMake Run Tests
 #        run: ctest . --parallel 2 -C Debug -V
+#        working-directory: ${{ runner.workspace }}/build
+
+  build_v1_8:
+    name: "gcc DBG v1.8 default API"
+    runs-on: ubuntu-latest
+    steps:
+      # SETUP
+      - name: Install Linux Dependencies
+        run: |
+           sudo apt-get update
+           sudo apt-get install ninja-build doxygen graphviz
+           sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+           sudo apt install gcc-12 g++-12 gfortran-12
+           echo "CC=gcc-12" >> $GITHUB_ENV
+           echo "CXX=g++-12" >> $GITHUB_ENV
+           echo "FC=gfortran-12" >> $GITHUB_ENV
+ 
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Get Sources
+        uses: actions/checkout@v4.1.7
+
+      #
+      # CMAKE CONFIGURE
+      #
+      - name: CMake Configure
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            -G Ninja \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DBUILD_SHARED_LIBS=ON \
+            -DHDF5_ENABLE_ALL_WARNINGS=ON \
+            -DHDF5_ENABLE_PARALLEL:BOOL=OFF \
+            -DHDF5_BUILD_CPP_LIB:BOOL=ON \
+            -DHDF5_BUILD_FORTRAN=ON \
+            -DHDF5_BUILD_JAVA=ON \
+            -DHDF5_BUILD_DOC=OFF \
+            -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 \
+            -DH5_NO_DEPRECATED_SYMBOLS:BOOL=OFF \
+            -DDEFAULT_API_VERSION:STRING=v18 \
+            $GITHUB_WORKSPACE
+        shell: bash
+
+      #
+      # BUILD
+      #
+      - name: CMake Build
+        run: cmake --build . --parallel 3 --config Debug
+        working-directory: ${{ runner.workspace }}/build
+
+      #
+      # RUN TESTS - disable until some tests are fixed
+      #
+#      - name: CMake Run Tests
+#        run: ctest . --parallel 2 -C Debug -V
 #        working-directory: ${{ runner.workspace }}/build
 
   build_v1_10:
@@ -199,6 +259,126 @@ jobs:
         run: ctest . --parallel 2 -C Debug -V
         working-directory: ${{ runner.workspace }}/build
 
+  build_v1_14:
+    name: "gcc DBG v1.14 default API"
+    runs-on: ubuntu-latest
+    steps:
+      # SETUP
+      - name: Install Linux Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+          sudo apt install gcc-12 g++-12 gfortran-12
+          echo "CC=gcc-12" >> $GITHUB_ENV
+          echo "CXX=g++-12" >> $GITHUB_ENV
+          echo "FC=gfortran-12" >> $GITHUB_ENV
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Get Sources
+        uses: actions/checkout@v4.1.7
+
+      #
+      # CMAKE CONFIGURE
+      #
+      - name: CMake Configure
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            -G Ninja \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DBUILD_SHARED_LIBS=ON \
+            -DHDF5_ENABLE_ALL_WARNINGS=ON \
+            -DHDF5_ENABLE_PARALLEL:BOOL=OFF \
+            -DHDF5_BUILD_CPP_LIB:BOOL=ON \
+            -DHDF5_BUILD_FORTRAN=ON \
+            -DHDF5_BUILD_JAVA=ON \
+            -DHDF5_BUILD_DOC=OFF \
+            -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 \
+            -DH5_NO_DEPRECATED_SYMBOLS:BOOL=OFF \
+            -DDEFAULT_API_VERSION:STRING=v114 \
+            $GITHUB_WORKSPACE
+        shell: bash
+
+      #
+      # BUILD
+      #
+      - name: CMake Build
+        run: cmake --build . --parallel 3 --config Debug
+        working-directory: ${{ runner.workspace }}/build
+
+      #
+      # RUN TESTS
+      #
+      - name: CMake Run Tests
+        run: ctest . --parallel 2 -C Debug -V
+        working-directory: ${{ runner.workspace }}/build
+
+  build_v1_16:
+    name: "gcc DBG v1.16 default API"
+    runs-on: ubuntu-latest
+    steps:
+      # SETUP
+      - name: Install Linux Dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install ninja-build doxygen graphviz
+          sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
+          sudo apt install gcc-12 g++-12 gfortran-12
+          echo "CC=gcc-12" >> $GITHUB_ENV
+          echo "CXX=g++-12" >> $GITHUB_ENV
+          echo "FC=gfortran-12" >> $GITHUB_ENV
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - name: Get Sources
+        uses: actions/checkout@v4.1.7
+
+      #
+      # CMAKE CONFIGURE
+      #
+      - name: CMake Configure
+        run: |
+          mkdir "${{ runner.workspace }}/build"
+          cd "${{ runner.workspace }}/build"
+          cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake \
+            -G Ninja \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DBUILD_SHARED_LIBS=ON \
+            -DHDF5_ENABLE_ALL_WARNINGS=ON \
+            -DHDF5_ENABLE_PARALLEL:BOOL=OFF \
+            -DHDF5_BUILD_CPP_LIB:BOOL=ON \
+            -DHDF5_BUILD_FORTRAN=ON \
+            -DHDF5_BUILD_JAVA=ON \
+            -DHDF5_BUILD_DOC=OFF \
+            -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 \
+            -DH5_NO_DEPRECATED_SYMBOLS:BOOL=OFF \
+            -DDEFAULT_API_VERSION:STRING=v116 \
+            $GITHUB_WORKSPACE
+        shell: bash
+
+      #
+      # BUILD
+      #
+      - name: CMake Build
+        run: cmake --build . --parallel 3 --config Debug
+        working-directory: ${{ runner.workspace }}/build
+
+      #
+      # RUN TESTS
+      #
+      - name: CMake Run Tests
+        run: ctest . --parallel 2 -C Debug -V
+        working-directory: ${{ runner.workspace }}/build
+
   build_zlibng:
     name: "gcc use zlib-ng filter"
     runs-on: ubuntu-latest