✨ Add Folder plugin for save result

[s-weigand]

This plugin adds back the functionality from glotaran.analysis.result.Result.save(result_path) of pyglotaran 0.3.x.
For glotaran.io.save_result it also adds inferring of format_name=="folder" if the provided result_path doesn't have an extension.
If result_path is a file it will raise a ValueError.

Usage equivalent to result.save(result_path)

save_result(result_path=str(output_folder), result=result, allow_overwrite=True)
# or if format must be given:
save_result(result_path=str(output_folder), result=result, format_name="folder", allow_overwrite=True)
save_result(result_path=str(output_folder), result=result, format_name="pyglotaran-legacy", allow_overwrite=True)

Also, the plugin is registered under the names folder and pyglotaran-legacy, thus if we want to fundamentally change the folder-plugin we can keep the old implementation around as pyglotaran-legacy for backward compatibility.

Testing

Passing the tests is mandatory.

Closing issues

closes #619

[codecov]

Codecov Report

Merging #620 (826555e) into main (b188047) will increase coverage by 0.1%.
The diff coverage is 100.0%.

@@           Coverage Diff           @@
##            main    #620     +/-   ##
=======================================
+ Coverage   77.8%   78.0%   +0.1%     
=======================================
  Files         63      64      +1     
  Lines       3537    3564     +27     
  Branches     658     663      +5     
=======================================
+ Hits        2753    2781     +28     
+ Misses       655     654      -1     
  Partials     129     129             

Impacted Files	Coverage Δ
glotaran/builtin/io/folder/folder_plugin.py	100.0% <100.0%> (ø)
glotaran/plugin_system/io_plugin_utils.py	100.0% <100.0%> (ø)
glotaran/plugin_system/project_io_registration.py	100.0% <100.0%> (ø)
glotaran/parameter/parameter_group.py	88.6% <0.0%> (+0.4%)	⬆️

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[jsnel]

Tested OK.

[jsnel]

Please change 'pyglotaran-legacy' to 'legacy' in the context of pyglotaran plugins that should be sufficient.

[sourcery-ai]

Sourcery Code Quality Report

✅  Merging this PR will increase code quality in the affected files by 4.85%.

Quality metrics	Before	After	Change
Complexity	1.53 ⭐	1.12 ⭐	-0.41 👍
Method Length	34.65 ⭐	31.37 ⭐	-3.28 👍
Working memory	6.77 🙂	5.80 ⭐	-0.97 👍
Quality	82.70% ⭐	87.55% ⭐	4.85% 👍

Other metrics	Before	After	Change
Lines	732	738	6

Changed files	Quality Before	Quality After	Quality Change
glotaran/builtin/io/yml/test/test_save_result.py	47.52% 😞	85.79% ⭐	38.27% 👍
glotaran/plugin_system/io_plugin_utils.py	84.39% ⭐	82.41% ⭐	-1.98% 👎
glotaran/plugin_system/project_io_registration.py	86.84% ⭐	86.66% ⭐	-0.18% 👎
glotaran/plugin_system/test/test_io_plugin_utils.py	92.70% ⭐	92.19% ⭐	-0.51% 👎

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/plugin_system/io_plugin_utils.py	protect_from_overwrite	4 ⭐	52 ⭐	11 😞	70.29% 🙂	Extract out complex expressions

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The emojis denote the absolute quality of the code:

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• 😞 poor
• ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

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[sonarcloud]

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[s-weigand]

Admittedly the importing of the fixture and that for added noqas look a bit ugly, but since the tests are inside of the package and not in a separate folder we can just use a global conftest.py so all fixtures are known to all pytest tests.

[jsnel]

LGTM. More✨ for pyglotaran