jwallwork23 commented 4 months ago

Wrap XIOS functionality for reading from file

Fixes #577

Task List

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

Change Description

So far we have only considered writing to file in the XIOS integration work. This PR enables reading from file, too.

XIOS' read methods are wrapped, as well as methods for setting file attributes related to the file mode (read vs. write) and parallel access mode.

Test Description

A XiosRead_test.cpp script is added, which reads from a input.nc file and checks its dimensions and values are as expected.

Question for reviewer: is it okay to add a NetCDF file to the repo? (I notice such files are ignored by default so had to force-add it.)

This PR also modifies XiosFile_test.cpp to test the newly wrapped parts of the XIOS API related to file attributes, as well as modifying XiosWrite_test.cpp to check the existence of output.nc and delete it at the end of the test.

Pre-Request Checklist

[x] 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
[x] No new warnings are generated
[x] The documentation has been updated (or an issue has been created to track the corresponding change)
[x] Methods and Tests are commented such that they can be understood without having to obtain additional context
[x] This PR/Issue is labelled as a bug/feature/enhancement/breaking change
[x] File dates have been updated to reflect modification date
[x] This change conforms to the conventions described in the README

jwallwork23 commented 4 months ago

The commit history is rather nonlinear given a couple of merges from develop so (as mentioned above) I advocate squash-merging this PR rather than going through a rebase.

jwallwork23 commented 3 months ago

This has now been updated to use CDL files rather than NetCDF. Would you mind taking a look to re-review @timspainNERSC?

jwallwork23 commented 3 months ago

Reverted to standard = initialisation as discussed in the meeting.

Managed to do the rebase in the end so no need to squash-merge.

Ready for re-review now @timspainNERSC, thanks.

nextsimhub / nextsimdg