Merge pull request #4940 from HDFGroup/develop

Update feature/sparse_data with latest from develop

.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'

.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'

.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
 

.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) }}
 

.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

.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

.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:

.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:

.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