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XIOS implementation of ParaGridIO (take 2) #751

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XIOS implementation of ParaGridIO (take 2) #751

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XIOS implementation of ParaGridIO (take 2)

Fixes #552
Supersedes #667

Task List

  • Defined the tests that specify a complete and functioning change (It may help to create a design specification & test specification)
  • Implemented the source code change that satisfies the tests
  • Documented the feature by providing worked example
  • Updated the README or other documentation
  • Completed the pre-Request checklist below

Change Description

Reimplementation of the ParaGridIO class using XIOS for I/O. It will automatically be used if nextSIM-DG is compiled with XIOS enabled.

The read and write methods formerly in the Xios handler class are moved to the XIOS implementation of ParaGridIO. This is because ModelArray is going to get XIOS-related functionality and we need to avoid circular dependencies.

Test Description

...

Pre-Request Checklist

  • The requirements of this pull request are fully captured in an issue or design specification and are linked and summarised in the description of this PR
  • No new warnings are generated
  • The documentation has been updated (or an issue has been created to track the corresponding change)
  • Methods and Tests are commented such that they can be understood without having to obtain additional context
  • This PR/Issue is labelled as a bug/feature/enhancement/breaking change
  • File dates have been updated to reflect modification date
  • This change conforms to the conventions described in the README

@jwallwork23
Draft ParaGridIO_Xios
9c4997c
@jwallwork23
Update comment
e383cd8
@jwallwork23
Temporarily comment out tests - DO NOT MERGE
fbb8557
@jwallwork23
Temporarily comment out ParaGridIO_Xios code - DO NOT MERGE
8c66ea5
@jwallwork23
Set pointer outside of class
6211430
@jwallwork23
Don't pass contextId to ParaGridIO
62a48c6
@jwallwork23
Pass pointers to Xios in test
7d85cce
@jwallwork23
TODOs for desired refactoring
2159ba7
@jwallwork23
Temporarily make setupXios public - DO NOT MERGE
361be4d
@jwallwork23
Setup xy_domain and z_axis in setupXios method
311c19d
@jwallwork23
Setup file in setupXios method
a03c491
@jwallwork23
Have setupXiosHandler create ModelState object
6ab05c8
@jwallwork23
Setup field_2D and field_3D in setupXios method
beede75
@jwallwork23
Pass ModelState to testFileWrite, not ModelArray
b63bbff
@jwallwork23
Pass ModelState to readFile, not ModelArray
e6a031a
@jwallwork23
Define PIO outside of setupXiosHandler
b9be37d
@jwallwork23
Pass PIO pointer to read/write tests
4b7bcfc
@jwallwork23
Do the write in dumpModelState
3750030
@jwallwork23
Don't pass metadata to setupXios method; tidying
044fc5e
@jwallwork23
Make XIOS available in build
9086964
@jwallwork23
Add catch for undefined timestep
48f3acb
@jwallwork23
Add incrementCalendar method
b90e25c
@jwallwork23
Set up ModelMetadata so that calendar can be updated during write
00bfc76
@jwallwork23
Add check for if calendar timestep is already defined
16a8649
@jwallwork23
Set default timestep; allow calendar specification
cd73448
@jwallwork23
Merge branch 'init-timestep' into issue552_xios-paragrid-io_take2
d5aaed8
@jwallwork23
Fix typo
b48e947
@jwallwork23
Warning rather than error for already set timestep
02c9419
@jwallwork23
Set default calendar origin and start
03fe783
@jwallwork23
Merge branch 'init-timestep' into issue552_xios-paragrid-io_take2
e895409
@jwallwork23 jwallwork23 added enhancement New feature or request ICCS Tasks or reviews for the ICCS team labels Dec 4, 2024
@jwallwork23 jwallwork23 self-assigned this Dec 4, 2024
This was referenced Dec 4, 2024
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jwallwork23 added a commit that referenced this pull request Dec 10, 2024
@jwallwork23
Allow timestep to be set when XIOS handler is created (#750)
225adcf 
Refinement of #751

# Allow timestep to be set when XIOS handler is created

This PR makes a few minor modifications to the `Xios` handler object:
* Improve clarity of docstrings related to configuration.
* Allow the user to set the timestep, calendar type and context ID when
creating the `Xios` instance.
* Set the calendar origin and start as part of the configuration.
* Update tests accordingly.

These steps should make it easier to set up XIOS and reduce the amount
of additional boilerplate when using it to drive I/O rather than the
existing approach.
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Reimplement ParaGridIO using XIOS
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