HDF5: Delete and re-create attribute when overwriting with diff. type #1697
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franzpoeschel
commented
Dec 4, 2024
| @@ -7522,6 +7522,8 @@ void groupbased_read_write(std::string const &ext) | |||
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| E_x.setAttribute("updated_in_run", 0); | |||
| E_y.setAttribute("updated_in_run", 0); | |||
| E_y.setAttribute("changed_datatype_in_run", 0); | |||
| write.close(); | |||
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.close() calls added for stricter error check, the destructors will swallow exceptions.
Somehow truncation test is broken by this
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Dec 20, 2024
…openPMD#1697) * HDF5: Delete and re-create attribute when overwriting with diff. type * WIP: Change datatype in test Somehow truncation test is broken by this * Add forgotten H5Aclose() call
ax3l
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Jan 16, 2025
* Release: 0.16.1 Signed-off-by: Axel Huebl <axel.huebl@plasma.ninja> * Fix new_version.py * Update version in windows.yml * Reformat with yapf3 * Fix greedy Regex parsing * Changelog: Add PRs #1681 #1679 #1678 * Fix: CMake Internal Control (#1678) The `openPMD_USE_INTERNAL_*` options are for general internal/external control. They were accidentally overwritten by new tar flags and sometimes incomplete. Signed-off-by: Axel Huebl <axel.huebl@plasma.ninja> * Revert "CMake Tar: TOML11 3.7.1 (#1673)" (#1679) This reverts commit aea4b72. * Replace deprecated makeSuite with loadTestsFromTestCase (#1681) Removed with Python 3.13 * Doc: Fix Shipped Internally (#1682) Downloaded now. Signed-off-by: Axel Huebl <axel.huebl@plasma.ninja> * `PYBIND11_FINDPYTHON=ON` (#1684) Reuse our `find_package(Python ...)` call and use new CMake logic in pybind11. https://pybind11.readthedocs.io/en/stable/compiling.html#modules-with-cmake https://cmake.org/cmake/help/latest/command/find_package.html#config-mode-version-selection Signed-off-by: Axel Huebl <axel.huebl@plasma.ninja> * Fix ICX build (#1690) Error was: /home/runner/work/openPMD-api/openPMD-api/include/openPMD/backend/Container.hpp:262:32: error: no member named 'm_container' in 'Container<T, T_key, T_container>' 262 | container().swap(other.m_container); * Fix Leftover ADIOS1 Mentions (#1683) * Fix Leftover ADIOS1 Mentions Signed-off-by: Axel Huebl <axel.huebl@plasma.ninja> * Remove ADIOS1 from examples --------- Signed-off-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Franz Pöschel <franz.poeschel@gmail.com> * Explicitly specify ADIOS2 components in openPMDConfig.cmake (#1693) * Explicitly specify ADIOS2 components in openPMDConfig.cmake When including openPMD in downstream CMake and that CMake script contains Fortran, ADIOS2 will automatically detect that. But since we do not reexport the ADIOS2 headers, we only need the components that openPMD explicitly uses: CXX and MPI. * Same in CMakeLists.txt * Remove mpirun_workaround.sh (#1698) Seems to no longer be necessary in the affected CI runs * Properly check for empty HDF5_VERSION in CMake (#1702) The old test apparently invoked some weird CMake legacy behavior. This should make the pinned HDF5 Conda version unnecessary (#1701) since the version with missing HDF5_VERSION is correctly dealt with. * HDF5: Delete and re-create attribute when overwriting with diff. type (#1697) * HDF5: Delete and re-create attribute when overwriting with diff. type * WIP: Change datatype in test Somehow truncation test is broken by this * Add forgotten H5Aclose() call * TOUCH IOTask: Avoid setting files as dirty in non-write modes (#1704) * Bugfix: Consider dirty upon touch() only in write modes * Add error check to avoid writing in read-only mode * Changelog * Use ULONG for particle patches * Upgrade appleclang14 build to MacOS 13 > The macOS-12 environment is deprecated, consider switching to macOS-13, macOS-14 (macos-latest) or macOS-15. For more details, see actions/runner-images#10721 * Update Changelog * Release Date --------- Signed-off-by: Axel Huebl <axel.huebl@plasma.ninja> Co-authored-by: Franz Pöschel <franz.poeschel@gmail.com>
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Seen in a file that was originally create with
h5pyand the opened in R/W-mode with openPMD-api. Since h5py and openPMD-api apparently use different vec-string types, this leads to corrupted files.Since we do support attributes with multiple possible types, the type of an existing attribute should be checked before reuse.
TODO: