full pipelines tests fix and agnostic loader changes to tests

[dkazanc]

Agnostic loader template is currently substituted by default in tests for full pipelines. Some datasets, however, do not adhere to NXTomo standard, hence the changes bellow.

Checklist

• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• I have made corresponding changes to the documentation

[dkazanc]

This PR fixes all tests with respect to changes in the backends here.
All tests pass apart from the sweeping CoR one, which is a different issue.

[dkazanc]

@yousefmoazzam OK, I think this is done now with the small data and framework (ui_layer) tests fixed. The only one test in the framework that is failing for me is:
FAILED tests/test_cli.py::test_cli_noargs_shows_help - assert 0 == 2
Any ideas why? Thanks

[yousefmoazzam]

@yousefmoazzam OK, I think this is done now with the small data and framework (ui_layer) tests fixed. The only one test in the framework that is failing for me is: FAILED tests/test_cli.py::test_cli_noargs_shows_help - assert 0 == 2 Any ideas why? Thanks

If you mean that the test is failing for you when running locally, can you try updating click to version 8.2.0 (see #587 for more details).

[dkazanc]

thanks, that resolved it!