👌 Add option to deactivate data/residual plotting in overview plots

[s-weigand]

Especially for big datasets the 2D plots (data/residual) in plot_overview or plot_simple_overview can take a long time (up to 1 minute). This change adds None as a possible value for show_data which allows switching off this part of the plot altogether, instead "Skipped" will be written to the middle of the axis (subplot).

The following code will generate the plot below it

from glotaran.testing.simulated_data.sequential_spectral_decay import SCHEME
from glotaran.optimization.optimize import optimize
from pyglotaran_extras import plot_overview

result = optimize(SCHEME)

plot_overview(
    result.data["dataset_1"],
    figure_only=False,
    nr_of_data_svd_vectors=3,
    nr_of_residual_svd_vectors=1,
    show_data=None,
    linlog=True,
    linthresh=50,
)

Change summary

• 👌 Added option to deactivate 2D plotting for performance improvement

Checklist

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

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 1.39%.

Quality metrics	Before	After	Change
Complexity	4.74 ⭐	5.13 ⭐	0.39 👎
Method Length	163.67 😞	167.67 😞	4.00 👎
Working memory	15.83 ⛔	16.01 ⛔	0.18 👎
Quality	49.75% 😞	48.36% 😞	-1.39% 👎

Other metrics	Before	After	Change
Lines	310	324	14

Changed files	Quality Before	Quality After	Quality Change
pyglotaran_extras/plotting/plot_overview.py	50.54% 🙂	50.01% 🙂	-0.53% 👎
pyglotaran_extras/plotting/plot_residual.py	47.68% 😞	44.75% 😞	-2.93% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
pyglotaran_extras/plotting/plot_overview.py	plot_overview	5 ⭐	263 ⛔	26 ⛔	34.93% 😞	Try splitting into smaller methods. Extract out complex expressions
pyglotaran_extras/plotting/plot_residual.py	plot_residual	8 ⭐	199 😞	15 😞	42.76% 😞	Try splitting into smaller methods. Extract out complex expressions
pyglotaran_extras/plotting/plot_overview.py	plot_simple_overview	3 ⭐	203 😞	14 😞	48.58% 😞	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

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[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran-extras/deactivate-2d-plot-option

[codecov]

Codecov Report

Base: 40.66% // Head: 40.61% // Decreases project coverage by -0.05% ⚠️

Coverage data is based on head (65a578d) compared to base (0411135).
Patch coverage: 0.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #118      +/-   ##
==========================================
- Coverage   40.66%   40.61%   -0.06%     
==========================================
  Files          24       24              
  Lines         718      719       +1     
  Branches       98       98              
==========================================
  Hits          292      292              
- Misses        426      427       +1     

Impacted Files	Coverage Δ
pyglotaran_extras/plotting/plot_overview.py	37.50% <0.00%> (+1.29%)	⬆️
pyglotaran_extras/plotting/plot_residual.py	27.58% <0.00%> (-3.19%)	⬇️

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[jsnel]

LGTM. In the future we can think about a more efficient use of the real estate rather than printing skipped in rather large font. ;)