TXTExport refactoring

[KulaginVladimir]

Proposed changes

This PR removes deprecated class TXTExports and fixes issues #819 and #863.

To-do list:

• Add possibility to write data at the last export time
• Define function space depending on the chemical potential conservation flag
• Add filter method to remove duplicates if DG is used
• Tests

Types of changes

What types of changes does your code introduce to FESTIM?

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Code refactoring
• Documentation Update (if none of the other choices apply)
• New tests

Checklist

• Black formatted
• Unit tests pass locally with my changes
• I have added tests that prove my fix is effective or that my feature works
• I have added necessary documentation (if appropriate)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.27%. Comparing base (12628bd) to head (468611d).
Report is 134 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #883      +/-   ##
==========================================
- Coverage   99.56%   99.27%   -0.30%     
==========================================
  Files          61       60       -1     
  Lines        2750     2753       +3     
==========================================
- Hits         2738     2733       -5     
- Misses         12       20       +8     

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[RemDelaporteMathurin]

Hi @KulaginVladimir thanks for taking care of this.

I'm wondering about adding more arguments to the write method.

Could we instead store the information in attributes? For example, instead of calling filter_duplicates at each write we could call it once at the beginning of the simulation (if chemical pot is on) then store combined_indx as an attribute (we would need more explicit variable names ofc).

Then, when we call write we don't need to pass materials and chemical_pot.
If self.combined_indx is None then don't do anything to the data, otherwise filter the data with self.data = self.data[self.combined_indx, :] or something like this.

What do you think?

[KulaginVladimir]

@RemDelaporteMathurin
I refactored the filtering method according to your suggestions. However, there are several points I'd like to adress. Please, see my comments below.

[RemDelaporteMathurin]

This looks good to me! Just some more small comments about documentation, naming...

🚀

[RemDelaporteMathurin]

Suggested change

	# if chemical_pot is True or trap_element_type is DG, get indices of duplicates near interfaces
	# if project_to_DG is True, get indices of duplicates near interfaces

In the scope of this method, there is no such thing as chemica_pot or trap_element_type

[RemDelaporteMathurin]

Hi @KulaginVladimir very sorry for being so late on this... This looks good! A couple of very minor comments, feel free to merge!

[RemDelaporteMathurin]

Suggested change

	else:
	if np.isclose(current_time, self.times[-1], atol=0):
	# write at final time if exports at specific times
	return True
	elif np.isclose(current_time, self.times[-1], atol=0):
	# write at final time if exports at specific times
	return True

[RemDelaporteMathurin]

Suggested change

	If DG1 is used and filter flag is True, the duplicated vertices in the array are filtered except those near interfaces,
	If DG1 is used and ``filter`` flag is True, the duplicated vertices in the array are filtered except those near interfaces,

[RemDelaporteMathurin]

Instead of a print you can do the following:

Suggested change

	print(my_export._unique_indices)
	assert len(my_export.data) == export_len
	assert len(my_export.data) == export_len, f"Wrong export length. Unique indices: {my_export._unique_indices}"

[KulaginVladimir]

Didn't know about such a functionality, but I forgot to delete this print-statement