✨ Add configuration for plot functions

[s-weigand]

Here is the long overdue PR that adds the plot config.
The main goal is to reduce repetitive boilerplate code (I.e. when changing plot labels).

See the difference in code to get the same resulting plot (CONFIG._reset(project_config) is just needed in the docs to show the differences.)

With the corresponding config:

plotting:
  general:
    default_args_override:
      linlog: true
      use_svd_number: true
      linthresh: 2
    axis_label_override:
      time: "Time (ps)"
      spectral: "Wavelength (nm)"
      data_left_singular_vectors: ""
      data_singular_values: "Singular Value (a.u.)"
      data_right_singular_vectors: ""

Change summary

• ✨ Add configuration for plot functions
• ⬆️🧰 Update tooling
• 🧰📚 Change notebook doc parser to myst-nb (this allows support for mermaid)

Checklist

• ✔️ Passing the tests (mandatory for all PR's)

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[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran-extras/plot-config

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[codecov]

Codecov Report

Attention: Patch coverage is 95.25862% with 22 lines in your changes missing coverage. Please review.

Project coverage is 58.26%. Comparing base (b880df9) to head (3b6133c).
Report is 27 commits behind head on main.

Files with missing lines	Patch %	Lines
pyglotaran_extras/config/config.py	94.33%	6 Missing and 3 partials ⚠️
pyglotaran_extras/config/plot_config.py	95.87%	4 Missing and 5 partials ⚠️
pyglotaran_extras/plotting/plot_svd.py	80.00%	2 Missing ⚠️
tests/io/test_load_data.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #288       +/-   ##
===========================================
+ Coverage   44.77%   58.26%   +13.48%     
===========================================
  Files          27       31        +4     
  Lines        1043     1598      +555     
  Branches      162      290      +128     
===========================================
+ Hits          467      931      +464     
- Misses        568      651       +83     
- Partials        8       16        +8     

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[s-weigand]

After this PR got merged our docs will have the config schema for the builtin functions under <root_url>/_static/pygta_config.schema.json and we can use it to add it to the schema store.
See for PR built of docs

[jsnel]

As we say in dutch "Het heeft even geduurd, maar nu hebben we ook wat!". 👍
Loosely translated: "It (sure) took a while, but it was (well) worth it!"

To illlustrate what can be done with it, here the plot_overview from the fluorescence case study without config and with.

# yaml-language-server: $schema=pygta_config.schema.json

plotting:
  general:
    default_args_override:
      linlog: false
      use_svd_number: false
      linthresh: 2
    axis_label_override:
      time: Time (ps)
      spectral: Wavelength (nm)
      data_left_singular_vectors: ''
      data_singular_values: Singular Value (a.u.)
      data_right_singular_vectors: ''
  plot_data_overview:
    default_args_override: 
      use_svd_number: false
  plot_svd:
    default_args_override:
      use_svd_number: true
  plot_overview:
    default_args_override:
      show_data: false

... which may not seem, until you realize all axis labels have now almost effortlessly been replaced (spectral -> Wavelength (nm), time -> Time (ps), etc).

The autocompletion, due to the (autogenerated) pygta_config.schema.json being present (which is created after calling CONFIG.init_project() works very well in VS Code.

from pyglotaran_extras import CONFIG

CONFIG.init_project()

All in all, an impressive piece of work, and clearly a labor of love, which I'm sure out community will ❤️ as well.

[jsnel]

Reviewed and tested ok. The docs can still do with some polishing here and there, but this is more than good enough for the pyglotaran_extras CONFIG v1 release. 👍

For the effort and pushing to finish in conjunction with the pyglotaran 0.7.3 release, I award you a gold medal 🥇 !