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ax3l merged 9 commits into from
Jun 6, 2022
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Release 0.14.5 conflicting backports #6

ax3l merged 9 commits into from
Jun 6, 2022

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@franzpoeschel franzpoeschel commented May 30, 2022 •
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ax3l commented May 30, 2022

@franzpoeschel thanks a lot! After merging #5, this has a small conflict in include/openPMD/backend/Attributable.hpp

@ax3l ax3l self-requested a review May 30, 2022 17:59
@ax3l ax3l self-assigned this May 30, 2022
@ax3l ax3l added the bug label May 30, 2022
@franzpoeschel franzpoeschel force-pushed the release-0.14.5-conflicting-backports branch from d82aa6d to bb3061f Compare May 31, 2022 08:12
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franzpoeschel commented May 31, 2022

@franzpoeschel thanks a lot! After merging #5, this has a small conflict in include/openPMD/backend/Attributable.hpp

Now resolved

@ax3l ax3l merged commit 55edd42 into ax3l:release-0.14.5-backports Jun 6, 2022
This was referenced Jun 6, 2022
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ax3l added a commit that referenced this pull request Jun 8, 2022
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@franzpoeschel @pre-commit-ci
Release 0.14.5 backports (openPMD#1282)
ce25526 
* Improve write time

* Print warning if mpi4py is not found in openpmd-pipe

* ADIOS1: Remove task from IO queue if it fails with exception

* `setup.py`: Extra CMake Arg Control

* EMSCRIPTEN: Skip Py Extension

* g++/clang++: Add `-Wsign-compare`

* python/RecordComponent: fix `-Wsign-compare`

* Patch MSVC pybind11 bug

Improve patch comment

* Python: Do Not Strip Symbols In Debug

Avoid stripping symbols for Python debug builds, so we can see lines
in coredumps and debugger runs.

* CI: NVHPC New Apt Repo

Update the NVHPC install instructions to the latest and greatest.
Fix failing CI (dependency install).

Also upgrade to 21.11 as on Perlmutter.

* clang-format & pre-commit & python include

* run pre-commit

* ps_make_timer_name_: add memory leak suppression

* Fix: Missing HDF5 Include

This tries to fix a compile error on Maxwell (DESY).
```
/home/diederse/software/hipace_4GPU/hipace/build/_deps/fetchedopenpmd-src/src/IO/HDF5/HDF5IOHandler.cpp: In member function 'virtual void openPMD::HDF5IOHandlerImpl::readAttribute(openPMD::Writable*, openPMD::Parameter<openPMD::Operation::READ_ATT>&)':
/home/diederse/software/hipace_4GPU/hipace/build/_deps/fetchedopenpmd-src/src/IO/HDF5/HDF5IOHandler.cpp:1586:17: error: 'H5free_memory' was not declared in this scope
 1586 |                 H5free_memory(m1);
      |                 ^~~~~~~~~~~~~
/home/diederse/software/hipace_4GPU/hipace/build/_deps/fetchedopenpmd-src/src/IO/HDF5/HDF5IOHandler.cpp:1609:17: error: 'H5free_memory' was not declared in this scope
 1609 |                 H5free_memory(m1);
      |                 ^~~~~~~~~~~~~
/home/diederse/software/hipace_4GPU/hipace/build/_deps/fetchedopenpmd-src/src/IO/HDF5/HDF5IOHandler.cpp:1628:17: error: 'H5free_memory' was not declared in this scope
 1628 |                 H5free_memory(m2);
      |                 ^~~~~~~~~~~~~
```

* Increase reference count also in other load_chunk overload

Don't know if it is necessary, but looks like we forgot it earlier

Add comment

* Spack: Remove Old Files

* Spack: v0.17.1

* Update Env Files

* Python Iteration: Fix __repr__ (time)

Small numbers, as common for iterations, were flushed to zero
in `std::to_string(double)` of the representation of `Iteration`
variables:
```
step    __repr__
100     <openPMD.Iteration at t = '0.000000 s'>
was:    8.687655225973454e-14 * 1.0
```

* CI: Update CUDA repo key

Nvidia has made changes in the signing keys.

https://forums.developer.nvidia.com/t/notice-cuda-linux-repository-key-rotation/212771

* CI: Switch to Mamba

* Doc: Update HDF5 Coll. Metadata Versions

Update the documentation about HDFFV-11260 and the newly released
fixes in release lines.

* HDF5 Coll. MD Reads: Simplify Wording

* Tiny wording improvement and a +

* Remove deprecated debug parameter in ADIOS2

* HDF5IOHandler: Clang-Format/Clang-Tidy

```
/home/runner/work/openPMD-api/openPMD-api/src/IO/HDF5/HDF5IOHandler.cpp:1835:21:
  warning: repeated branch in conditional chain [bugprone-branch-clone]
                    isLegacyLibSplashAttr =
                    ^
```

* `conda.yaml`: add `pre-commit`

* Fix: Python Variant Issue on Conda

* Test: Demonstrate Pattern Issue

As in openPMD#1173

* JSON: Improve File Open Error Message

Include path to file

* Upon parsing, store each iteration's filename

If the padding is inconsistent, a later Iteration::open() needs the
original filename. Trying to compute the filename from the expansion
pattern will lead to wrong filenames.

* Backport: fix-open-iteration (#5)

* Pass-through flushing parameters

* CI fixes

* Test

* Don't flush when opening an iteration

* CI fixes

* FlushLevel: Use default base class in NVC++

* clang-tidy: Define member defaults of Writable in-class

* Update include/openPMD/IO/AbstractIOHandler.hpp

Co-authored-by: Axel Huebl <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Release 0.14.5 conflicting backports (#6)

* Don't safeguard empty strings while reading

* Update TODO Comment

* Add missing update for VEC_CLONG_DOUBLE

* Ignore deprecated AccessType in SerialIOTest

* SerialIOTest: Fix GCC Pragma Check (openPMD#1260)

There was a typo in `__GNUC_MINOR__`, causing the test not to work on all GCC versions.

Follow-up to openPMD#1213

* Clearly fail when users select a wrong backend

* ICC: Unreachable end of function

* Fix use after free in ADIOS1IOHandler

* Remove unavailable_backend_test

Hard to trigger without explicit backend selection, and test coverage is
present on dev anyway

Co-authored-by: Axel Huebl <[email protected]>

* Version: 0.14.5

including Changelog

Co-authored-by: Jean Luca Bez <[email protected]>
Co-authored-by: Franz Pöschel <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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