feature: introduce config file for JPK tags

[ns-rse]

Off the back of #118 (thanks @derollins) I've parameterised the JPK tags that were introduced into
AFMReader/default_config.yaml and load these by default when using AFMReader.load_jpk(). A parameter is introduced
to that function (confi_path) which allows users to specify their own configuration file should they wish to use alternative tags.

• Copies the read_yaml() function and tests from TopoStats.
• Brief description of configuration file and structure added to docs/usage.md (where some tables were also aligned by
  Emacs).

Exiting tests/test_jpk.py pass.

I envisage this being an extensible and flexible way of users being able to handle parameters changing the array of file types that
exist now and in the future and it should be easy to extend to other file formats.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 91.89189% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.74%. Comparing base (ac9753c) to head (5a5674b).
⚠️ Report is 248 commits behind head on main.

Files with missing lines	Patch %	Lines
AFMReader/io.py	72.72%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #124      +/-   ##
==========================================
+ Coverage   74.62%   75.74%   +1.11%     
==========================================
  Files           8        9       +1     
  Lines         607      705      +98     
==========================================
+ Hits          453      534      +81     
- Misses        154      171      +17     

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[derollins]

Only suggestion is to add an extra value for completeness, have done it myself locally but don't know if I can change it here.

[ns-rse]

Brilliant, thanks for the feedback @derollins 👍

I've added in slot_size to the configuration file, updated AFMReader/jpk.py to use this parameter and included it in the documentation.

[derollins]

Captures all the .jpk file tags used to read the files and has a clear config file for the values of these tags. I'm just unsure about how alternative config files can be used, since this is a library rather than an executable programme.