🩹🗑️ Fixed usage of deprecated functionality and syntax

[s-weigand]

This upgrades the model files to use the pyglotaran 0.5.0 syntax and the script files to use the pyglotaran-extras 0.5.0rc1 syntax.

Best reviewed commit by commit.

All deprecations up to the current main of pyglotaran were removed.

[s-weigand]

Maybe the functionality from scripts/run_examples.py to throw errors on deprecations would be nice to have in the pyglotaran_extras, since it allows you to fix them step by step mostly at model parsing time or import time. The only exception is code that comes after the optimization, e.g. plotting functions, but you wouldn't need for the plots to finish.

[s-weigand]

I made it a draft for now, since we have no consistency check on the examples themselves. I guess the best place to implement that functionality would be a separate repository, where we could also implement it as an action. What do you think?

[jsnel]

I suggest borrowing from the pyglotaran repo the Run Examples + Compare results actions, and compare the incoming PR against main against the latest released version of the software and/or (optionally) main.

[s-weigand]

The problem is that the result comparison code lives inside of pyglotaran, so we either add the result consistency checking action to the pyglotaran repo or make it a standalone repo (my preferred solution).

[jsnel]

The problem is that the result comparison code lives inside of pyglotaran, so we either add the result consistency checking action to the pyglotaran repo or make it a standalone repo (my preferred solution).

Let's do that (make it a stand alone repo). Do we use pyglotaran-validation for this, or yet another repo?

[jsnel]

This PR has been stale for some time, but it would be nice to have the examples updates to non-deprecated code. Perhaps to work around the validation issues, we can do a one time manual check.

[s-weigand]

This PR has been stale for some time, but it would be nice to have the examples updates to non-deprecated code. Perhaps to work around the validation issues, we can do a one time manual check.

I will factor out the validation code to a separate repository this weekend since this is a blocker for a potential release of pyglotaran=0.7.0 (see due deprecations for 0.7.0)

[sourcery-ai[bot]]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.30%.

Quality metrics	Before	After	Change
Complexity	1.09 ⭐	1.13 ⭐	0.04 👎
Method Length	124.95 😞	127.50 😞	2.55 👎
Working memory	13.02 😞	12.96 😞	-0.06 👍
Quality	52.88% 🙂	52.58% 🙂	-0.30% 👎

Other metrics	Before	After	Change
Lines	1139	1129	-10

Changed files	Quality Before	Quality After	Quality Change
pyglotaran_examples/ex_doas_beta/ex_doas_beta.py	59.62% 🙂	59.16% 🙂	-0.46% 👎
pyglotaran_examples/ex_doas_beta/ex_doas_beta_ascii.py	59.62% 🙂	59.61% 🙂	-0.01% 👎
pyglotaran_examples/ex_spectral_constraints/ex_spectral_constraints.py	48.48% 😞	48.36% 😞	-0.12% 👎
pyglotaran_examples/ex_spectral_guidance/ex_spectral_guidance.py	80.76% ⭐	80.47% ⭐	-0.29% 👎
pyglotaran_examples/ex_two_datasets/ex_two_datasets.py	36.53% 😞	36.47% 😞	-0.06% 👎
pyglotaran_examples/quick_start/quickstart.py	50.52% 🙂	50.45% 🙂	-0.07% 👎
pyglotaran_examples/study_fluorescence/target_analysis_script.py	38.79% 😞	38.82% 😞	0.03% 👍
pyglotaran_examples/study_transient_absorption/target_analysis_script.py	45.88% 😞	45.77% 😞	-0.11% 👎
pyglotaran_examples/study_transient_absorption/two_dataset_analysis.py	38.47% 😞	38.40% 😞	-0.07% 👎
pyglotaran_examples/test/simultaneous_analysis_3d_disp/sim_analysis_script_3d_disp.py	44.15% 😞	43.87% 😞	-0.28% 👎
pyglotaran_examples/test/simultaneous_analysis_3d_nodisp/sim_analysis_script_3d.py	44.15% 😞	43.87% 😞	-0.28% 👎
pyglotaran_examples/test/simultaneous_analysis_3d_weight/sim_analysis_script_3d_weight.py	44.05% 😞	43.78% 😞	-0.27% 👎
pyglotaran_examples/test/simultaneous_analysis_6d_disp/sim_analysis_script_6d_disp.py	39.04% 😞	38.84% 😞	-0.20% 👎
scripts/run_examples.py	78.80% ⭐	76.82% ⭐	-1.98% 👎

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
scripts/run_examples.py	script_run_wrapper	11 🙂	178 😞		49.78% 😞	Try splitting into smaller methods
pyglotaran_examples/ex_doas_beta/ex_doas_beta.py	run_doas_model	1 ⭐	284 ⛔	10 😞	52.78% 🙂	Try splitting into smaller methods. Extract out complex expressions
pyglotaran_examples/ex_doas_beta/ex_doas_beta_ascii.py	run_doas_model	1 ⭐	276 ⛔	10 😞	53.09% 🙂	Try splitting into smaller methods. Extract out complex expressions
pyglotaran_examples/ex_spectral_guidance/ex_spectral_guidance.py	load_and_plot_results	0 ⭐	143 😞	5 ⭐	75.32% ⭐	Try splitting into smaller methods
scripts/run_examples.py	github_format_warning	0 ⭐	33 ⭐	10 😞	79.25% ⭐	Extract out complex expressions

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