Release 0.14.4 backports #1177

ax3l · 2022-01-19T19:32:08Z

https://github.com/openPMD/openPMD-api/milestone/3

Increased Compatibility & Python Install Bug

This release fixes various read/parsing bugs and increases compatibility with upcoming versions of ADIOS and old releases of Intel icpc. An installation issue for pip-based installs from source in the last release was fixed and Python 3.10 support added. Various documentation and installation warnings have been fixed.

Thanks to @ax3l and @franzpoeschel for contributing to this release!

Which version am I running?

Python

import openpmd_api
print(openpmd_api.__version__)

C++

#include <openPMD/openPMD.hpp>
#include <iostream>

int main() {
    // query compile-time macros:
    std::cout << OPENPMDAPI_VERSION_MAJOR << "."
              << OPENPMDAPI_VERSION_MINOR << "."
              << OPENPMDAPI_VERSION_PATCH << std::endl;
    // there is also: OPENPMDAPI_VERSION_LABEL (e.g. "alpha")

    // or query the runtime API (since 0.12.0):
    std::cout << openPMD::getVersion() << std::endl;
    return 0;
}

CLI

# command line option (since 0.12.0):
openpmd-ls --version

Forgot to add in openPMD#1128, which is then missing in Python sdist files for pip from-source builds.

Add support for Python 3.10.

musllinux uses the musl libc on an Alpine stack, especially for docker-ish containers. Let's add coverage while also covering CPython 3.10

Fix a typo in the `__repr__` of `Iteration` in Python.

Until now, the half-parsed records were not deleted. Our sanity checks in `Series::~Series()` caught up on that and threw errors.

No idea why this PR triggers that error

Happened so far in variable-based iteration encoding

The `Attribute` constructors with implicit variant conversion sometimes do not work in ICC 19.1.2. ``` openPMD-api/src/RecordComponent.cpp(226): error: no instance of constructor "openPMD::Attribute::Attribute" matches the argument list argument types are: (openPMD::Extent) Attribute a(getExtent()); ^ openPMD-api/include/openPMD/backend/Attribute.hpp(50): note: this candidate was rejected because arguments do not match class Attribute : ^ openPMD-api/include/openPMD/backend/Attribute.hpp(50): note: this candidate was rejected because arguments do not match class Attribute : ^ openPMD-api/include/openPMD/backend/Attribute.hpp(79): note: this candidate was rejected because arguments do not match Attribute(resource r) : Variant(std::move(r)) ^ ``` Same work-around as for NVCC in openPMD#1103

Fix a warning with CMake 3.22+. We use simple syntax in cmake_dependent_option, so we are compatible with the extended syntax in CMake 3.22+: https://cmake.org/cmake/help/v3.22/policy/CMP0127.html

Fix minor warnings in the docs: - double reference (make 2nd ref annonymous) - misaligned reference

Fix misnamed filename and misnamed prefix in text.

Add `.bib` blocks for easier citation of standard and API.

Fix a highlighting issue for `openPMD-ls` in the docs. Explicitly use `python3` for module calls.

If we append them, then we overwrite flags like `-Wno-...` from environment variables.

Referes to post-`2.7.1` `master` branch of ADIOS2. Catch new ADIOS2 error type: string getCompressionOperator Dirtily catch ADIOS2 exception in automatically_deactivate_span Cleanly destruct a Series that errored during flushing Problem was that IO tasks that do not return cleanly but throw an exception must be removed from the IO queue, otherwise the task will be tried again during destruction. Usually, this means that anything will happen. SerialIOTest: Remove Comments (resolved) Print warning when removing task from IO queue std::string and fix warning

ax3l · 2022-01-19T19:57:25Z

test/SerialIOTest.cpp

+                    new int[ size ]{}, []( auto * ptr ) { delete[] ptr; } );
+            } );
+
+        REQUIRE( spanWorkaround );


@franzpoeschel does this test require the new JSON re-work or so? In that case, I would need to remove it from the backport.

It does, though it might actually make sense to backport the workaround too. I'll have a look

I've opened the backport as a PR: ax3l#2

CHANGELOG.rst

ax3l and others added 17 commits January 19, 2022 11:01

Add cmake/ to MANIFEST.in

365c668

Forgot to add in openPMD#1128, which is then missing in Python sdist files for pip from-source builds.

Add failing test

f4c36d7

Read gridSpacing also from long doubles

e830053

Python: 3.10

02ebba7

Add support for Python 3.10.

CI: Python 3.10 on Alpine Linux

f3c96c8

musllinux uses the musl libc on an Alpine stack, especially for docker-ish containers. Let's add coverage while also covering CPython 3.10

Fix: Python Iteration Repr Typo

2d46334

Fix a typo in the `__repr__` of `Iteration` in Python.

Remove invalid records from our data structure entirely

6510ceb

Until now, the half-parsed records were not deleted. Our sanity checks in `Series::~Series()` caught up on that and threw errors.

Fix doxygen?

72ad569

No idea why this PR triggers that error

Don't apply compression operators multipe times

a53d905

Happened so far in variable-based iteration encoding

CMake 3.22+: Policy CMP0127

385f737

Fix a warning with CMake 3.22+. We use simple syntax in cmake_dependent_option, so we are compatible with the extended syntax in CMake 3.22+: https://cmake.org/cmake/help/v3.22/policy/CMP0127.html

Docs: Minor Warnings

f7e961f

Fix minor warnings in the docs: - double reference (make 2nd ref annonymous) - misaligned reference

Docs: Fix HDF5 JSON File

00ffa3b

Fix misnamed filename and misnamed prefix in text.

Docs: Update Citation & Add BibTeX

6db6560

Add `.bib` blocks for easier citation of standard and API.

Docs: Fix CLI Highlighting

540f0fa

Fix a highlighting issue for `openPMD-ls` in the docs. Explicitly use `python3` for module calls.

CMake: Warning Flags First in CXXFLAGS

52ac8e1

If we append them, then we overwrite flags like `-Wno-...` from environment variables.

ax3l added bug affects latest release labels Jan 19, 2022

ax3l added this to the 0.14.4 milestone Jan 19, 2022

ax3l changed the base branch from dev to release-0.14.4 January 19, 2022 19:32

ax3l closed this Jan 19, 2022

ax3l reopened this Jan 19, 2022

ax3l commented Jan 19, 2022

View reviewed changes

ax3l requested a review from franzpoeschel January 19, 2022 19:57

ax3l commented Jan 19, 2022

View reviewed changes

CHANGELOG.rst Outdated Show resolved Hide resolved

Automatically deactivate span-based API when operators are present

858236e

ax3l force-pushed the release-0.14.4-backports branch 2 times, most recently from 9bd6a28 to 7262fc1 Compare January 21, 2022 21:33

Add .pre-commit-config.yaml

30109a9

Release: 0.14.4

de420f6

ax3l force-pushed the release-0.14.4-backports branch from 7262fc1 to de420f6 Compare January 21, 2022 21:34

ax3l merged commit 756bffc into openPMD:release-0.14.4 Jan 21, 2022

ax3l deleted the release-0.14.4-backports branch January 21, 2022 22:40

ax3l mentioned this pull request Jan 23, 2022

openpmd-api v0.14.4 conda-forge/openpmd-api-feedstock#85

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Release 0.14.4 backports #1177

Release 0.14.4 backports #1177

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ax3l commented Jan 19, 2022

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ax3l Jan 19, 2022 •

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franzpoeschel Jan 20, 2022

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franzpoeschel Jan 20, 2022

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Release 0.14.4 backports #1177

Release 0.14.4 backports #1177

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Conversation

ax3l commented Jan 19, 2022

Increased Compatibility & Python Install Bug

Which version am I running?

Python

C++

CLI

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franzpoeschel Jan 20, 2022

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ax3l Jan 19, 2022 •

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