dev-remove-gwyddion: Other Bruker formats not parsed

[Max-Gamill]

Describe the bug Alternative to .spm files there are .001 file formats too, and currently these are not analysed when using this branch.

To Reproduce Run with any non-.spm AFM file.

Expected behavior It should analyse these files.

Additional context Should be able to be solved with by inserting the code below into the "# search recursively for files" section (there may be a nicer way to do it with glob in one line):

file_list1 = list(path_base.glob('**/*' + '.spm'))
file_list2 = list(path_base.glob('**/*' + '.[0-9][0-9][0-9]'))
file_list = file_list1 + file_list2

[ns-rse]

In IAA meeting 2022-05-12 @alicepyne raised the need to support other formats.

As well as the above proposal this can be done relatively easily by extending the YAML configuration file to include a list of file types...

file_ext:
  - .spm
  - .jpk
  - .other

Then in the code when we glob files to find them (currently in topostats/utils/find_images) with something similar to (solution)...

    return list(base_dir.glob(f'**/*[{ext[0]}][{ext[1]}][{ext[2]}]' + file_ext))

...although some thought will need to be given to how to handle the length of the list of file extensions.

[ns-rse]

@MaxGamill-Sheffield : Can we close this issue now? Is supporting the .001 etc. file formats something that is still required?