Vamas sub-reader: enhance data extraction, add IRREGULAR parsing

[lukaspie]

This enhances the capabilities of the existing Vamas XPS reader. The Vamas reader reads .vms files, which is the current ISO standard data transfer format (ISO 14976).

VMS specific:

• [x] Write CPS data to file
• [x] Extract units for quantities
• [x] Parse header comments -> additional metadata (depends on spectrometer software that writes the vms file)
• [x] Parse comment lines -> data analysis
• [x] Parse vamas files of type IRREGULAR
• [x] Update config file (will be done again when we have the [*] syntax from the MultiFormatReader

General:

• [x] align mapper dictionary keys

[coveralls]

Pull Request Test Coverage Report for Build 8294709433

Details

• 356 of 480 (74.17%) changed or added relevant lines in 8 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+14.8%) to 48.748%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pynxtools_xps/sle/sle_specs.py	0	2	0.0%
pynxtools_xps/txt/txt_scienta.py	0	2	0.0%
pynxtools_xps/txt/txt_vamas_export.py	0	2	0.0%
pynxtools_xps/xy/xy_specs.py	0	2	0.0%
pynxtools_xps/reader_utils.py	27	31	87.1%
pynxtools_xps/vms/vamas.py	198	239	82.85%
pynxtools_xps/vms/casa_data_model.py	93	164	56.71%
<!--	Total:	356	480	74.17%	-->

Totals
Change from base Build 8293922186:	14.8%
Covered Lines:	1285
Relevant Lines:	2636

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💛 - Coveralls

[RubelMozumder]

Here are the some change requests. I see this is a big code base. So, you can add some tests specific to the reader according to the file extension.

[lukaspie]

Here are the some change requests. I see this is a big code base. So, you can add some tests specific to the reader according to the file extension.

I have added test data for the Vamas format that is addressed by this PR. Data for other file extensions will be added later.

[lukaspie]

One small comment on the test: You could parametrise it with the reader directories. That way you would get a single run for each specific reader and would immediately see which of them fails. It's maybe something we could also introduce in the plugin template

Good idea. I think I will address this in another PR since I want to add some more tests for the individual readers anyway.

[RubelMozumder]

Sorry for the confusion. I reviewed some code on the first review but some of them submitted and some of them I did not submit. So, now you see new change requests. Which I am going to resolve now. I think there a few comment you may add in the future especially pynxtools_xps/vms/vamas.py where you assumed all the data will come in a chain. But if one of them is broken or missing other fields will read the wrong data. So in another PR you can take care of it.

[lukaspie]

Sorry for the confusion. I reviewed some code on the first review but some of them submitted and some of them I did not submit. So, now you see new change requests. Which I am going to resolve now. I think there a few comment you may add in the future especially pynxtools_xps/vms/vamas.py where you assumed all the data will come in a chain. But if one of them is broken or missing other fields will read the wrong data. So in another PR you can take care of it.

There is really no other way around then reading the data in a list. The Vamas format does not allow for keywords in the file and it alway assumes that all of the elements are at the correct positions (it is an ISO standard afterall, so if you don't have the right structure, it cannot be a vamas file).