Execute intermediate data wrapper in output recon file naming tests

[yousefmoazzam]

Fixes #577

Based on information in the hdf5 docs on file locks saying that the locks are not needed when running multiple processes working together (such as when running processes using MPI), I had noted that running the 6 offending tests in test_save_intermediate_data under mpirun -n 1 never produced the error, and chalked it off as some anomaly where those tests needed to be run under MPI to pass locally.

However, since then, I noticed that those offending tests only ever create the hdf5 file for saving, and the execute() method on the wrapper object is never called.

This test is parameterised to have 4 of the 6 failing cases:

httomo/tests/method_wrappers/test_save_intermediate.py

Lines 340 to 353 in c0036b9

	wrp = make_method_wrapper(
	make_mock_repo(mocker, implementation="cpu"),
	"httomo.methods",
	"save_intermediate_data",
	MPI.COMM_WORLD,
	make_mock_preview_config(mocker),
	loader=loader,
	prev_method=prev_method,
	)
	assert isinstance(wrp, SaveIntermediateFilesWrapper)
	files = get_files(tmp_path)
	assert len(files) == 1
	assert Path(files[0]).name == expected_filename

and this test is parameterised with 2 of the 6 failing cases:

httomo/tests/method_wrappers/test_save_intermediate.py

Lines 401 to 414 in c0036b9

	wrp = make_method_wrapper(
	make_mock_repo(mocker, implementation="cpu"),
	"httomo.methods",
	"save_intermediate_data",
	MPI.COMM_WORLD,
	make_mock_preview_config(mocker),
	loader=loader,
	prev_method=prev_method,
	)
	assert isinstance(wrp, SaveIntermediateFilesWrapper)
	files = get_files(tmp_path)
	assert len(files) == 1
	assert Path(files[0]).name == EXPECTED_FILENAME

where the absence of wrp.execute() should be noted.

The execute() method is what actually closes the hdf5 file:

httomo/httomo/method_wrappers/save_intermediate.py

Lines 94 to 95 in c0036b9

	if block.is_last_in_chunk:
	self._file.close()

This was confirmed to indeed be the issue, where simply running the execute() method on the intermediate data wrapper objects makes the hdf5 file locks not appear anymore when running tests locally.

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