mirror of
https://github.com/HDFGroup/hdf5.git
synced 2026-09-25 04:09:44 +03:00
cde84cdc8f
* Fix MPI Fortran configuration for HDF5Examples (#6206) When building Fortran parallel examples without MPI wrappers, the compiler couldn't find mpi.mod because MPI_Fortran_INCLUDE_DIRS was not populated. This occurred because find_package(MPI) was only called for C, not Fortran. Added enable_language(Fortran) and find_package(MPI REQUIRED COMPONENTS Fortran) to properly configure MPI for Fortran examples, ensuring MPI include directories and libraries are correctly set. * Adds RFCs to the RFC table (#6190) * Added two RFCs to the RFC table "Adding support for digitally signed plugins to HDF5" " Write-Ahead log" * Updated to use the ACM link * Add HDF5 2.0.0 Library Migration Guide (#6183) * Add HDF5 2.0.0 Library Migration Guide * Revise HDF5 migration guide for version 2.0.0 Use 2.0.0 consistently. * Clarify API changes in HDF5 2.0.0 Migration Guide * Fixes the "multiple @param documentation sections" doxygen warnings (#6195) Addresses the "multiple @ param documentation sections" warnings are caused by the interaction of three things: 1. MACRO_EXPANSION = YES with EXPAND_ONLY_PREDEF = NO in Doxyfile.in 2. Versioned API macros in H5version.h like: \def documentation in APIVersions.dox like: 3. \def H5Tarray_create \api_vers_2{H5Tarray_create,H5Tarray_create1,H5Tarray_create2} Because Doxygen expands all macros, it sees H5Tarray_create as an alias for H5Tarray_create1. It then associates documentation from both the \def block (for the macro) and the function's own doc block (with \param entries) with the same function — resulting in "multiple @ param documentation sections." * Update Doxygen version from 1.16.0 to 1.16.1 Use Doxygen 1.16.1 for all platforms. This version includes the latest bug fixes and improvements while maintaining compatibility with our documentation format. * Fix Windows Doxygen installation for version 1.16.1 Handle different Windows binary naming conventions across Doxygen versions: - 1.16.1 uses: doxygen-VERSION.windows.x64.bin.zip - 1.16.0 uses: doxygen-VERSION.x64.bin.zip Try the newer naming convention first, then fall back to the older one if the download fails. This ensures compatibility across versions. * Use ssciwr/doxygen-install in setup-doxygen action Replace direct installation of official Doxygen binaries with ssciwr/doxygen-install action. This avoids Java documentation parsing errors that occur with official binaries but not with distribution builds. The setup-doxygen action now serves as a thin wrapper around ssciwr/doxygen-install@f13be16c83 (v1), using commit hash for security and reproducibility. * Remove redundant version specification from workflows The setup-doxygen action already has a default version (1.16.1), so explicit version specification in workflows is unnecessary. This follows DRY principles and makes version updates simpler. * Updates to #6205 (#6208) * Fix MPI Fortran configuration for HDF5Examples (#6205) When building Fortran parallel examples standalone without MPI wrappers, the compiler cannot find mpi.mod because MPI_Fortran_INCLUDE_DIRS is not populated. * Use MPI::MPI_Fortran imported target instead of raw MPI variables Replace manual MPI_Fortran_LIBRARIES, MPI_Fortran_LINK_FLAGS, and MPI_Fortran_INCLUDE_DIRS usage with the MPI::MPI_Fortran imported target, which transitively carries all include dirs, compile flags, and link flags. This eliminates the CMAKE_Fortran_EXE_LINKER_FLAGS hack and the manual target_include_directories in H5PAR. * Update nvhpc version to 26.1 with CUDA version 13.1. (#6213) # branches: [develop] * Inherit Debug C build flags in Developer build mode (#6182) * Bump the github-actions group across 1 directory with 11 updates (#6215) * Bump the github-actions group across 1 directory with 11 updates Bumps the github-actions group with 11 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/cache](https://github.com/actions/cache) | `5.0.1` | `5.0.3` | | [lukka/get-cmake](https://github.com/lukka/get-cmake) | `4.2.1` | `4.2.3` | | [softwareforgood/check-artifact-v4-existence](https://github.com/softwareforgood/check-artifact-v4-existence) | `0.3.0` | `0.4.1` | | [github/codeql-action](https://github.com/github/codeql-action) | `3.31.9` | `4.32.2` | | [azure/trusted-signing-action](https://github.com/azure/trusted-signing-action) | `0.5.11` | `1.1.0` | | [cygwin/cygwin-install-action](https://github.com/cygwin/cygwin-install-action) | `7d2dc1e241644c3318bed9ec74115d1929baa681` | `2566376092c4e280f21131be027af3f5bb2420a4` | | [aws-actions/configure-aws-credentials](https://github.com/aws-actions/configure-aws-credentials) | `5.1.1` | `6.0.0` | | [vmactions/freebsd-vm](https://github.com/vmactions/freebsd-vm) | `1.3.4` | `1.4.2` | | [vmactions/openbsd-vm](https://github.com/vmactions/openbsd-vm) | `1.3.1` | `1.3.5` | | [mpi4py/setup-mpi](https://github.com/mpi4py/setup-mpi) | `1.4.1` | `1.4.2` | | [actions/setup-python](https://github.com/actions/setup-python) | `6.1.0` | `6.2.0` | vmactions/openbsd-vm@d6c29ce1b4 (`1.3.5`) failed to run ssh on the github runner. 271a1ba62300483cfc58345ff9f425f1349a2cab for v1.3.4 was used instead. * Fix issue with some Subfiling VFD test files not getting deleted (#6212) * CMake: Fix Fortran cross-compilation support Refactor the cross-compilation infrastructure to rely on the standard CMAKE_CROSSCOMPILING_EMULATOR variable instead of the custom CROSSCOMPILING_PATH environment hack. Key changes: - Removed `ENVIRONMENT "${CROSSCOMPILING_PATH}"` from all test definitions. - Updated custom commands (e.g., H5match_types, H5_gen) to invoke the emulator explicitly when cross-compiling. - Updated ConfigureChecks.cmake and HDF5UseFortran.cmake to enable `try_run` checks when an emulator is defined. - Added config/toolchain/mingw-w64-x86-64-wine.sh wrapper to automatically locate MinGW runtime libraries (like libgfortran) for Wine execution. - Cleaned up toolchain files to remove hardcoded emulator paths, deferring configuration to the build environment. * Add Doxygen setup that results in missing Doygen documentation. (#6217) * Added setup-doxygen action in ctest.yml Ubuntu gcc workflow. * Also added actions/checkout for setup-doxygen. * Fixes link checker failure (#6219) Removed https:// as a workaround to avoid error by the link checker. * Remove force-setting of ZLIB_USE_EXTERNAL / SZIP_USE_EXTERNAL (#6222) Removes the force-setting of ZLIB_USE_EXTERNAL and SZIP_USE_EXTERNAL to ON when HDF5_ALLOW_EXTERNAL_SUPPORT is GIT or TGZ so that zlib and szip can be independently built from the system or externally as desired * Truncate Subfiling VFD's stub file when truncating subfiles (#6210) Ensure that the Subfiling VFD's stub file gets truncated when subfiles are being truncated to avoid a potentially unreadable file when the EOF doesn't match the stored EOF value Co-authored-by: Larry Knox <lrknox@hdfgroup.org> * Add CMake function to extract pkg-config info from libraries (#6220) * Consistent extension for C++ (#6214) Except for this file, all use cpp instead of cxx. No obvious reason why the same file types should have different extensions. * Enable Windows ARM64 CTest CI for release binaries (#6177) * ci: add Windows ARM64 MSVC CTest job * ci: add MSYS2 clangarm64 build on Windows ARM64 * cmake: add MSVC ARM64 presets for Windows * zlib: fix MSVC static library flags for ARM64 builds * Renamed .hxx file to .h and updated the #include for it. * Committing clang-format changes --------- Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com> Co-authored-by: Gerd Heber <gheber@hdfgroup.org> Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Julien Schueller <schueller@phimeca.com> Co-authored-by: Martin Diehl <mail@martin-diehl.net> Co-authored-by: Harish RS <harish.rajaselvan@multicorewareinc.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
84 lines
2.6 KiB
YAML
84 lines
2.6 KiB
YAML
name: hdf5 dev julia
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on:
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workflow_call:
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inputs:
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build_mode:
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description: "release vs. debug build"
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required: true
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type: string
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permissions:
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contents: read
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jobs:
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julia_build_and_test:
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name: "julia ${{ inputs.build_mode }}"
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runs-on: ubuntu-latest
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steps:
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- name: Get HDF5 source
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
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- name: Install Dependencies
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shell: bash
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run: |
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sudo apt-get update
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sudo apt-get install ninja-build graphviz
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sudo apt install libssl3 libssl-dev libcurl4 libcurl4-openssl-dev
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sudo apt install -y libaec-dev zlib1g-dev wget curl bzip2 flex bison cmake libzip-dev openssl build-essential
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- name: Configure
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shell: bash
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run: |
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mkdir "${{ runner.workspace }}/build"
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cd "${{ runner.workspace }}/build"
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cmake -C $GITHUB_WORKSPACE/config/cmake/cacheinit.cmake -G Ninja \
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-DCMAKE_BUILD_TYPE=${{ inputs.build_mode }} \
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-DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=OFF \
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-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF \
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-DHDF5_ENABLE_PARALLEL:BOOL=OFF \
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-DHDF5_BUILD_CPP_LIB:BOOL=OFF \
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-DLIBAEC_USE_LOCALCONTENT=OFF \
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-DZLIB_USE_LOCALCONTENT=OFF \
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-DHDF5_BUILD_FORTRAN:BOOL=OFF \
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-DHDF5_BUILD_JAVA:BOOL=OFF \
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-DCMAKE_INSTALL_PREFIX=/tmp \
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$GITHUB_WORKSPACE
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- name: Build
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shell: bash
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run: |
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cmake --build . --parallel 3 --config ${{ inputs.build_mode }}
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working-directory: ${{ runner.workspace }}/build
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- name: Install HDF5
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shell: bash
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run: |
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cmake --install .
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working-directory: ${{ runner.workspace }}/build
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- name: Install julia
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uses: julia-actions/setup-julia@5c9647d97b78a5debe5164e9eec09d653d29bd71 # latest
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with:
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version: '1.6'
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arch: 'x64'
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- name: Get julia hdf5 source
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uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
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with:
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repository: JuliaIO/HDF5.jl
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path: .
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- name: Generate LocalPreferences
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run: |
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echo '[HDF5]' >> LocalPreferences.toml
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echo 'libhdf5 = "/tmp/lib/libhdf5.so"' >> LocalPreferences.toml
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echo 'libhdf5_hl = "/tmp/lib/libhdf5_hl.so"' >> LocalPreferences.toml
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- uses: julia-actions/julia-buildpkg@e3eb439fad4f9aba7da2667e7510e4a46ebc46e1 # latest
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- name: Julia Run Tests
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uses: julia-actions/julia-runtest@d60b785c6f2bdf4ebfb18b2b6f7d93b7dfb0efe3 # latest
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env:
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JULIA_DEBUG: Main
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