Release 0.14.5 backports (#1282)

* 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 #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 (#1260)

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

Follow-up to #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>

Author: 4 people

.clang-format

@@ -0,0 +1,72 @@
+---
+Language:  Cpp
+
+BasedOnStyle:  LLVM
+AccessModifierOffset: -4
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+# AlignEscapedNewlinesLeft: false
+AlignEscapedNewlines: Right
+AlignOperands: false
+AlignTrailingComments: false
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLambdasOnASingleLine: true
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+
+BreakBeforeBraces:  Custom
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: true
+  AfterEnum: true
+  AfterExternBlock: true
+  AfterFunction: true
+  AfterNamespace: true
+  AfterStruct: true
+  AfterUnion: true
+  BeforeCatch: true
+  BeforeElse: true
+  # BeforeLambdaBody: true
+  SplitEmptyFunction: false
+  SplitEmptyNamespace: false
+  SplitEmptyRecord: false
+
+BreakConstructorInitializers: BeforeComma
+BreakInheritanceList: BeforeComma
+ColumnLimit: 80
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth:  4
+ContinuationIndentWidth: 4
+FixNamespaceComments: true
+IndentWidth: 4
+NamespaceIndentation: Inner
+PointerAlignment: Right
+SortUsingDeclarations: false
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesInAngles: false
+SpacesInContainerLiterals: false
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: Auto
+StatementMacros: ["OPENPMD_private", "OPENPMD_protected"]
+
+---
+Language: Json
+BasedOnStyle: llvm
+...

.github/ISSUE_TEMPLATE/install_problem.md

@@ -5,7 +5,7 @@ labels: install
 ---
 
 **Performed steps**
-The following steps 
+The following steps
 
 ```commandline
 ...

.github/ci/sanitizer/clang/Leak.supp

@@ -15,3 +15,4 @@ leak:adios_inq_var
 # ADIOS2
 leak:adios2::core::engine::SstReader::*
 leak:adios2::core::engine::SstWriter::*
+leak:ps_make_timer_name_

.github/ci/spack-envs/clang10_nopy_ompi_h5_ad1_ad2/spack.yaml

@@ -20,26 +20,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
@@ -63,3 +63,5 @@ spack:
   config:
     build_jobs: 2
 
+  mirrors:
+    E4S: https://cache.e4s.io

.github/ci/spack-envs/clang5_nopy_nompi_h5/spack.yaml

@@ -10,7 +10,7 @@ spack:
 
   packages:
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~mpi ~fortran
       compiler: [[email protected]]
 
@@ -32,3 +32,5 @@ spack:
   config:
     build_jobs: 2
 
+  mirrors:
+    E4S: https://cache.e4s.io

.github/ci/spack-envs/clang5_nopy_ompi_h5_ad1_ad2_bp3/spack.yaml

@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
@@ -61,3 +61,5 @@ spack:
   config:
     build_jobs: 2
 
+  mirrors:
+    E4S: https://cache.e4s.io

.github/ci/spack-envs/clang8_py38_mpich_h5_ad1_ad2/spack.yaml

@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     mpich:
       externals:
-      - spec: "mpich"
+      - spec: mpich@3.3
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [mpich]
@@ -61,3 +61,5 @@ spack:
   config:
     build_jobs: 2
 
+  mirrors:
+    E4S: https://cache.e4s.io

.github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad1_ad2/spack.yaml

@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.8.0
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       providers:
         mpi: [openmpi]
@@ -61,3 +61,5 @@ spack:
   config:
     build_jobs: 2
 
+  mirrors:
+    E4S: https://cache.e4s.io

.github/ci/spack-envs/gcc5_py36_ompi_h5_ad1_ad2/spack.yaml

@@ -18,26 +18,26 @@ spack:
       variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
     cmake:
       externals:
-      - spec: "cmake"
+      - spec: cmake@3.23.0
         prefix: /usr
       buildable: False
     openmpi:
       externals:
-      - spec: "openmpi"
+      - spec: openmpi@2.1.1
         prefix: /usr
       buildable: False
     perl:
       externals:
-      - spec: "perl"
+      - spec: perl@5.26.1
         prefix: /usr
       buildable: False
     python:
       externals:
-      - spec: "python"
+      - spec: python@3.6.3
         prefix: /usr
       buildable: False
     all:
-      target: ['x86_64']
+      target: [x86_64]
       variants: ~fortran
       compiler: [[email protected]]
 
@@ -59,3 +59,5 @@ spack:
   config:
     build_jobs: 2
 
+  mirrors:
+    E4S: https://cache.e4s.io