Files
hdf5/.github/workflows/bintest.yml
T
cde84cdc8f Update hdf5 2.1.0 with 17commits from develop since 2/5/2026 (#6229)
* 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>
2026-02-20 17:03:09 -06:00

296 lines
10 KiB
YAML

name: hdf5 examples bintest runs
# Triggers the workflow on a call from another workflow
on:
workflow_call:
inputs:
build_mode:
description: "release vs. debug build"
required: true
type: string
save_binary:
description: "binary-ext-name or missing"
required: true
default: "skip"
type: string
java_version:
description: "Java version to use for testing (19, 21, 24, 25, latest)"
required: false
default: "19"
type: string
permissions:
contents: read
env:
CTEST_OUTPUT_ON_FAILURE: 1
jobs:
test_binary_win:
# Windows w/ MSVC
#
name: "Windows MSVC Binary Test"
runs-on: windows-latest
steps:
- name: Install Dependencies (Windows)
run: choco install ninja
- name: Set up JDK ${{ inputs.java_version }}
uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
with:
java-version: |
${{
inputs.save_binary == 'ffm' && '25' ||
inputs.java_version == 'latest' && '24' ||
inputs.java_version
}}
distribution: ${{ inputs.save_binary == 'ffm' && 'oracle' || 'temurin' }}
- name: Enable Developer Command Prompt
uses: ilammy/msvc-dev-cmd@0b201ec74fa43914dc39ae48a89fd1d8cb592756 # v1.13.0
# Get files created by cmake-ctest script
- name: Get published binary (Windows)
uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
with:
name: zip-vs2022_cl-${{ inputs.build_mode }}-${{ inputs.save_binary }}-binary
path: ${{ github.workspace }}/hdf5
- name: Uncompress hdf5 binary (Win)
working-directory: ${{ github.workspace }}/hdf5
run: 7z x HDF5-*-win64.zip
shell: bash
- name: List files for the space (Win)
run: |
ls -l ${{ github.workspace }}
ls -l ${{ github.workspace }}/hdf5
- name: create hdf5 location (Win)
working-directory: ${{ github.workspace }}/hdf5
run: |
New-Item -Path "${{ github.workspace }}/HDF_Group/HDF5" -ItemType Directory
Copy-Item -Path "${{ github.workspace }}/hdf5/HDF*/*" -Destination "${{ github.workspace }}/HDF_Group/HDF5" -Recurse
shell: pwsh
- name: List files for the space (Win)
run: ls -l ${{ github.workspace }}/HDF_Group/HDF5
- name: set hdf5lib name
id: set-hdf5lib-name
run: |
HDF5DIR="${{ github.workspace }}/HDF_Group/HDF5"
echo "HDF5_ROOT=$HDF5DIR$FILE_NAME_HDF5" >> $GITHUB_OUTPUT
echo "HDF5_PLUGIN_PATH=$HDF5_ROOT/lib/plugin" >> $GITHUB_OUTPUT
shell: bash
- name: List files for the binaries (Win)
run: |
ls -l ${{ github.workspace }}/HDF_Group/HDF5
- name: using powershell
shell: pwsh
run: Get-Location
- name: List files for the space (Windows)
run: |
Get-ChildItem -Path ${{ github.workspace }}
Get-ChildItem -Path ${{ runner.workspace }}
shell: pwsh
- name: Run CTest (Windows)
env:
HDF5_ROOT: ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}
HDF5_PLUGIN_PATH: ${{ steps.set-hdf5lib-name.outputs.HDF5_PLUGIN_PATH }}
run: |
cd "${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/HDF5Examples"
cmake --workflow --preset=ci-StdShar-MSVC --fresh
shell: bash
test_binary_linux:
# Linux (Ubuntu) w/ gcc
#
name: "Ubuntu gcc Binary Test"
runs-on: ubuntu-latest
steps:
- name: Install Dependencies (Linux)
run: |
sudo apt-get update
sudo apt-get install ninja-build graphviz
- name: Set up JDK ${{ inputs.java_version }}
uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
with:
java-version: |
${{
inputs.save_binary == 'ffm' && '25' ||
inputs.java_version == 'latest' && '24' ||
inputs.java_version
}}
distribution: ${{ inputs.save_binary == 'ffm' && 'oracle' || 'temurin' }}
- name: Get published binary (Linux)
uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
with:
name: tgz-ubuntu-2404_gcc-${{ inputs.build_mode }}-${{ inputs.save_binary }}-binary
path: ${{ github.workspace }}
- name: Uncompress hdf5 binary (Linux)
run: |
cd "${{ github.workspace }}"
tar -zxvf ${{ github.workspace }}/HDF5-*-Linux.tar.gz --strip-components 1
- name: set hdf5lib name
id: set-hdf5lib-name
run: |
HDF5DIR=${{ github.workspace }}/HDF_Group/HDF5/
FILE_NAME_HDF5=$(ls ${{ github.workspace }}/HDF_Group/HDF5)
echo "HDF5_ROOT=$HDF5DIR$FILE_NAME_HDF5" >> $GITHUB_OUTPUT
echo "HDF5_PLUGIN_PATH=$HDF5_ROOT/lib/plugin" >> $GITHUB_OUTPUT
- name: List files for the binaries (Linux)
run: |
ls -l ${{ github.workspace }}/HDF_Group/HDF5
- name: List files for the space (Linux)
run: |
ls -l ${{ github.workspace }}
ls ${{ runner.workspace }}
- name: Run CTest (Linux)
env:
HDF5_ROOT: ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}
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-GNUC --fresh
shell: bash
test_binary_mac_latest:
# MacOS w/ Clang
#
name: "MacOS Clang Binary Test"
runs-on: macos-latest
steps:
- name: Install Dependencies (MacOS_latest)
run: brew install ninja
- name: Set up JDK ${{ inputs.java_version }}
uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
with:
java-version: |
${{
inputs.save_binary == 'ffm' && '25' ||
inputs.java_version == 'latest' && '24' ||
inputs.java_version
}}
distribution: ${{ inputs.save_binary == 'ffm' && 'oracle' || 'temurin' }}
- name: Get published binary (MacOS_latest)
uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
with:
name: tgz-macos14_clang-${{ inputs.build_mode }}-${{ inputs.save_binary }}-binary
path: ${{ github.workspace }}
- name: Uncompress hdf5 binary (MacOS_latest)
run: |
cd "${{ github.workspace }}"
tar -zxvf ${{ github.workspace }}/HDF5-*-Darwin.tar.gz --strip-components 1
- name: set hdf5lib name
id: set-hdf5lib-name
run: |
HDF5DIR=${{ github.workspace }}/HDF_Group/HDF5/
FILE_NAME_HDF5=$(ls ${{ github.workspace }}/HDF_Group/HDF5)
echo "HDF5_ROOT=$HDF5DIR$FILE_NAME_HDF5" >> $GITHUB_OUTPUT
echo "HDF5_PLUGIN_PATH=$HDF5_ROOT/lib/plugin" >> $GITHUB_OUTPUT
- name: List files for the binaries (MacOS_latest)
run: |
ls -l ${{ github.workspace }}/HDF_Group/HDF5
- name: List files for the space (MacOS_latest)
run: |
ls ${{ github.workspace }}
ls ${{ runner.workspace }}
# symlinks the compiler executables to a common location
- name: Setup GNU Fortran
uses: fortran-lang/setup-fortran@47809fdb6e637da656ce9ada436527b240c1287f # v1
id: setup-fortran
with:
compiler: gcc
version: 14
- name: Run CTest (MacOS_latest)
id: run-ctest
env:
HDF5_ROOT: ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}
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
shell: bash
test_h5cc_linux:
# Linux (Ubuntu) w/ gcc
#
name: "Ubuntu h5cc Binary Test"
runs-on: ubuntu-latest
steps:
- name: Install Dependencies (Linux)
run: |
sudo apt-get update
sudo apt-get install ninja-build graphviz
- name: Set up JDK ${{ inputs.java_version }}
uses: actions/setup-java@f2beeb24e141e01a676f977032f5a29d81c9e27e # v5
with:
java-version: |
${{
inputs.save_binary == 'ffm' && '25' ||
inputs.java_version == 'latest' && '24' ||
inputs.java_version
}}
distribution: ${{ inputs.save_binary == 'ffm' && 'oracle' || 'temurin' }}
- name: Get published binary (Linux)
uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
with:
name: tgz-ubuntu-2404_gcc-${{ inputs.build_mode }}-${{ inputs.save_binary }}-binary
path: ${{ github.workspace }}
- name: Uncompress hdf5 binary (Linux)
run: |
cd "${{ github.workspace }}"
tar -zxvf ${{ github.workspace }}/HDF5-*-Linux.tar.gz --strip-components 1
- name: set hdf5lib name
id: set-hdf5lib-name
run: |
HDF5DIR=${{ github.workspace }}/HDF_Group/HDF5/
FILE_NAME_HDF5=$(ls ${{ github.workspace }}/HDF_Group/HDF5)
echo "HDF5_ROOT=$HDF5DIR$FILE_NAME_HDF5" >> $GITHUB_OUTPUT
echo "HDF5_PLUGIN_PATH=$HDF5_ROOT/lib/plugin" >> $GITHUB_OUTPUT
- name: List files for the binaries (Linux)
run: |
ls -l ${{ github.workspace }}/HDF_Group/HDF5
- name: List files for the space (Linux)
run: |
ls -l ${{ github.workspace }}
ls ${{ runner.workspace }}
- name: Run testpc (Linux)
env:
HDF5_HOME: ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}
HDF5_PLUGIN_PATH: ${{ steps.set-hdf5lib-name.outputs.HDF5_PLUGIN_PATH }}
run: |
mkdir "${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/share/build"
cd "${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/share/HDF5Examples"
sh ./test-pc.sh ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/share/HDF5Examples ${{ steps.set-hdf5lib-name.outputs.HDF5_ROOT }}/share/build .
shell: bash