Refactoring

[thisFreya]

Refactored according to Nina's requests - reorganized file structure and renamed many functions accordingly.

[codecov]

Codecov Report

Merging #46 (ee100db) into master (1bc504f) will decrease coverage by 1.50%.
The diff coverage is 97.15%.

@@            Coverage Diff             @@
##           master      #46      +/-   ##
==========================================
- Coverage   95.32%   93.83%   -1.49%     
==========================================
  Files           7        6       -1     
  Lines         363      259     -104     
==========================================
- Hits          346      243     -103     
+ Misses         17       16       -1     

Impacted Files	Coverage Δ
ioSPI/micrographs.py	96.43% <96.43%> (ø)
ioSPI/particle_metadata.py	97.23% <97.23%> (ø)
ioSPI/atomic_models.py	98.22% <100.00%> (ø)
ioSPI/fourier.py	98.51% <0.00%> (-1.49%)	⬇️

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[ninamiolane]

First comment, will finish the review later :) thanks!

[geoffwoollard]

overall looks good. files and functions more specific and informative.

[geoffwoollard]

resolve that linting error. I'm fine merging when Nina is.

[ninamiolane]

Very nice, thank you!

BTW: are you using pycharm or vscode with the functionality that allows refactoring quickly? E.g. vscode has an option "change all occurences", which is convention for this (see screenshot).

It is looking much better, thank you very much for your patience in this!

I have made some comments on the conventions regarding the names of the input parameters in the functions now (which is in the same spirit of my previous remarks on the file names and function names, now we're looking more granularly at the parameters' names).

The parameter names should also follow a consistent convention (otherwise the user gets crazy because they needs to remember that write_atomic_model_* takes output_path as first parameter, but write_micrograph_* takes path as first parameter and write_metadata_* takes path as second parameter : not a great experience.

I have made comments along these lines, but I'll let you go through the files to see if, in this spirit, everything can be made rigorously consistent.

Thanks!

[ninamiolane]

And yes, please fix the linting error. It might be coming from an update in black, it has been popping up on other projects that I manage.

It could be fixed by running black . in the root of this repo.

[thisFreya]

@ninamiolane Changes implemented, please let me know if there's anything else that can be better represented!

[ninamiolane]

LGTM! Thank you for the changes.