…se or on other configs options.

…ide other plugins (trace, mpi, Decl'HDF5, etc.)

…s in the YML file!

…ch element requiring any metadata value uses depends_on YAML attribute to ensure an update of its attributes value to Damaris lib once the metadata are exposed (using Damaris Parameters in the background)!

…ding auto initialize without on_init event, and adding some cmake instruction in enforce finding of Damaris when Damaris_ROOT is provided.

The condition to do that is to always have this sequence at the end of the simulation:
PDI_finalize();
MPI_Finalize();
Or provide in the yml conf the code following PDI_finalize();
Code like the following could not be handled:
PDI_finalize();
PC_tree_destroy(&conf);
free(cur);
free(next);
MPI_Finalize();

This reverts commit db29c2c.

Fix-local-install-1

)

* Hide is_client from user, and ending damaris server in background:
- The  condition to do that is to always have this sequence at the end of the simulation:

PDI_finalize();
MPI_Finalize();

- Or provide in the yml conf the code following PDI_finalize();

- Code like the following could not be handled for the moment. But in the future by providing the instructions to execute...:

PDI_finalize();
PC_tree_destroy(&conf);
free(cur);
free(next);
MPI_Finalize();

* update copyright

* Removing on_init and on_finalize

* Example with only Damaris API (resolves #10)

* Datasets as regex (pdidev#583)

* First version with regex

* fix pdidev#582, update authors README and indent

* update changelog

* adding class for test

* fix indent

* fix indent

* fix spdlog

* adding test in parallel

* fix error on file

* Update plugins/decl_hdf5/README.md

Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com>

* Update plugins/decl_hdf5/README.md

Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com>

* fix pdidev#582, fix request change

---------

Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com>

* Add macOS CI (pdidev#576)

* Add macOS CI
* Remove chunking check on a non-chunked dataset
* Use MPI oversubscription
* Disable unqualified std cast call
* Use float type instead of integer
* Use storage instead of computation
* Disable zsh test
* use `H5Pget_layout` to check if dataset is chunked
* remove warning : cast hsize_t to int before `printf`
* Re-enable zsh test with a new env.bash path
* add call to `build_and_run_all_tests` and add workaround for macos
* add netcdf
* initialize CMAKE_FLAGS
* disable PYTHON for macos
* install hdf5-mpi on macos 14 and 15
* build hdf5 from source + add -j4
* Update copyright headers
* Update AUTHORS
* Update CHANGELOG.md

fixes pdidev#556, fixes pdidev#565, fixes pdidev#587, fixes pdidev#588

---------

Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com>
Co-authored-by: yushan wang <yushan.wang@cea.fr>
Co-authored-by: Benoit Martin <bmartin@cea.fr>
Co-authored-by: Julien Bigot <julien.bigot@cea.fr>

* Fix libyaml cmake policy version (pdidev#594)

* add CMAKE_POLICY_VERSION_MINIMUM to 3.5 when building libyaml
* fix pdidev#593
* update changelog and add comment

* Fix github action (CI) access issue of tests.xml (pdidev#584)

* Fix github action (CI) access issue of tests.xml

* Fix pdidev#585 github action (CI) access issue of tests.xml, and go through PR checklist

* Fix pdidev#585 github action (CI) access issue of tests.xml, using an other folder 'tmp_dir_test' containing the tests output, rather than docker's tmpfs

* Update AUTHORS

---------

Co-authored-by: Benoit Martin <bmartin@cea.fr>

* Add CODEOWNERS (pdidev#591)

* Add CODEOWNERS

---------

Co-authored-by: Benoit Martin <bmartin@cea.fr>
Co-authored-by: yushan wang <yushan.wang@cea.fr>

* Check of the HDF5 API version to use in error handler (pdidev#600)

* Ensuring the use of a compatible HDF5 API versions during errors handling

Fix pdidev#567

---------

Co-authored-by: Anida Khizar <anida.khizar@cea.fr>
Co-authored-by: Julien Bigot <julien.bigot@cea.fr>
Co-authored-by: yushan wang <yushan.wang@cea.fr>

* 592 improvement hdf5 dataset as regex (pdidev#597)

* fix#592, comment about dataset as regex

* Fix pdidev#592, reduce the interior loop

* fix copyright

* add fmt/range

* fix indent

* sort name of dataset in case of multiple regex found

* fix indent

* Fix pdidev#592, dsets as vector, introduce struct for explicit dataset

* change Dataset_explicit_type to class

* Apply suggestion from @jbigot

* Update plugins/decl_hdf5/dataset_explicit_type.h

* Update plugins/decl_hdf5/dataset_explicit_type.h

* Update plugins/decl_hdf5/dataset_explicit_type.h

* Update plugins/decl_hdf5/dataset_explicit_type.h

* add std:optional and remove unnecessary comment

---------

Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com>

* Add workflow_dispatch in pages

* Fix pdidev#598, add workflow_dispatch in pages

* fix in PC parser

* fix in PC parser
* add test for catching possible error
* catch config error in google test
* Use GTest's 'ASSERT_NO_FATAL_FAILURE' to catch a write failure

Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com>
* code cleaning
* Using PDI_NULL_Handler for error catching.

Co-authored-by: Benoit Martin <bmartin@cea.fr>
* add rwx right to tmp_dir_test


---------

Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com>
Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com>

* PDI Release 1.9.3

Update the embedded versions of paraconf, pybind11 & zpp to fix a build issue 
with recent cmake. (pdidev#632) 

Sort Doxyfile for easier update

Update to be compatible with latest Doxygen (pdidev#629)
* Make all pages subpages of the About page
* Remove the hand-crafted module page and use the generated topics page instead
* Update the layout file
* Add missing options in the Doxyfile
* Set MARKDOWN_STRICT=NO to prevent backquote errors
* Set PAGE_OUTLINE_PANEL=NO to prevent generation of a useless index
* Minor CSS update to handle the additional level in the generated HTML
* Fix two minor doc bugs

Fix pdidev#631
Fix pdidev#629

* Cleanup changelogs before release

* Fix HDF5 compression test for MacOS 26

Fix pdidev#627

Co-authored-by: Julian Auriac <julian.auriac@cea.fr>

* Indent

* Remove Deisa plugin (pdidev#639)

* Update the version of dependencies

Update the version of dependencies according to our policy: oldest supported
Debian, Fedora & Ubuntu, as well as spack 0.19. The new requirements are:
CMake 3.22, Doxygen 1.9.1, HDF5 1.10.7, mpi4py 3.1.3, NetCDF 4.8.1,
numpy 1.21.5, pyyaml 5.4.1 pybind11 2.9.1, Python 3.10.6, spdlog 1.9.2

* Rely on standard Find* from cmake as much as possible
* Add policy(PUSH) in cmake to prevent leaks
* Include FindHDF5 from CMake 4.1 and backport it to 3.22 to use its fix for HL

Fix pdidev#613

* Fix default CMAKE_BUILD_TYPE value (pdidev#619)

* Fix default CMAKE_BUILD_TYPE value

* Mock PDI

Fix pdidev#438

Co-authored-by: Julian Auriac <julian.auriac@cea.fr>
Co-authored-by: Benoit Martin <benoit.martin2@cea.fr>

* Update dependencies on googletest & benchmark

* PDI Release 1.10.0

* Changelog minor fix

* Adding missing LICENSE files and fix some minor indent

* Support multiple consecutive calls to `find_package(PDI)`

Fix pdidev#526

Co-authored-by: Benoit Martin <benoit.martin2@cea.fr>

* add-compression-in-decl_netcdf (pdidev#604)

Add deflate and chunking to Decl'NetCDF

* Enable hdf5 subfiling2 (pdidev#650)

enable HDF5 subfiling support, add test.
note: to set the subfiling stripe size (64Mo for example), use `export H5FD_SUBFILING_STRIPE_SIZE= 67108864`.

* add type check for reading data from netCDF file (pdidev#646)

* add type and sign check for integer read

* add size check for float and double variable read

* Disable unit tests for JSON dependency (pdidev#651)

* Update versions of the langagues standard we use (pdidev#659)

Update the versions of the languages standard we use

* We require versions of compilers that support more recent versions of the standard already. This is not a user facing change.

* Fix for C++ 20
  - some incorrect use of fmt:: are only detected now with the use of C++ 20
  - C++ 20 introduced mirror operator == that lead to some abiguous calls
  - Bump embedded spdlog to 1.15 because 1.14 had issues with C++ 20

Fix pdidev#660

* fix pybind11 on macos (pdidev#655)

* fix pybind11 linking error on macos and enable Python based plugins for macOS CI

* enable netcdf in macos CI (pdidev#667)

* enable netcdf in macos CI

* Update clang-format to version 18 (pdidev#673)

Match the version in test_env:v4

* Renamed some error codes and deprecated the old ones (pdidev#671)

Fix pdidev#670

* Finish moving to clang-format 18

* Fully qualify `std::move` calls (pdidev#676)

Prevent a compilation warning and incorrect usages
Fix pdidev#675

Co-authored-by: yushan wang <yushan.wang@cea.fr>

* Enhance subfiling environment checking and update usage notes (pdidev#654)

* Enhance README with subfiling usage notes

Added important notes for using subfiling correctly.

* add MPI thread level check

* update readme

* fix

* fix

* update test for subfiling counting

* add subfiling stripe size in test

* make subfiling_stripe_size configurable in yaml

* update readme

* make subfiling a new class and add stripe size configuration

* update readme

* indent

* Add subfiling.cxx to decl_hdf5 plugin sources

* update upon review notes

* enable subfiling check test only if supported

* remove subfiling check count test

* pass subfiling test from c to cxx

* indent

* update readme [skip ci]

* remove unnecessary headers fropm test

* add header in test

* throw an error if stripe_size is negative

* fix indent [skip ci]

* use warning when stripe_size is 0

* Replace Config_error with Spectree_error

* Move Spectree_error usage to a consistent location

* Improved testing framework (pdidev#669)

* Added `pdi/testing.h` that should be used t test plugins.
* Ported `plugins/decl_hdf5/tests/decl_hdf5_tests.cxx` as an example.
* Fixed a minor bug discovered along the way in Decl'HDF5

Fix pdidev#668

* Do some tests in sequential to not use all CI if everything fails (pdidev#674)

* Do some tests in sequential to not use all CI if everything fails

* Do not run benchmarks by default

Fix pdidev#679

* Fix a bug that was introduced in mock PDI with the (unreleased) move to C++ 20

mock PDI now relies on C++ 20 features when compiling in C++ but did not advertize it

* Fix target_compile_features syntax for PDI_C

---------

Co-authored-by: jmorice91 <jacques.morice@cea.fr>
Co-authored-by: Benoit Martin <benoitmartin88.pro@gmail.com>
Co-authored-by: Thomas Padioleau <thomas.padioleau@cea.fr>
Co-authored-by: Julien Bigot <jbigot@users.noreply.github.com>
Co-authored-by: Benoit Martin <bmartin@cea.fr>
Co-authored-by: Julien Bigot <julien.bigot@cea.fr>
Co-authored-by: JAuriac <56091659+JAuriac@users.noreply.github.com>
Co-authored-by: AnidaKhizar <anida-khizar@hotmail.fr>
Co-authored-by: Anida Khizar <anida.khizar@cea.fr>
Co-authored-by: Julian Auriac <julian.auriac@cea.fr>
Co-authored-by: Benoit Martin <benoit.martin2@cea.fr>

* fix missing change in new error of pdi

* fix indent

…o damaris_plugin

rename the example

* Cleaning the code, removing meshes, paraview and python

… file paths for storage