Refactor/save result (Sourcery refactored)

[sourcery-ai]

Pull Request #874 refactored by Sourcery.

Since the original Pull Request was opened as a fork in a contributor's
repository, we are unable to create a Pull Request branching from it.

To incorporate these changes, you can either:

1. Merge this Pull Request instead of the original, or

2. Ask your contributor to locally incorporate these commits and push them to
   the original Pull Request

   Incorporate changes via command line

   git fetch https://github.com/glotaran/pyglotaran pull/874/head
   git merge --ff-only FETCH_HEAD
   git push

NOTE: As code is pushed to the original Pull Request, Sourcery will
re-run and update (force-push) this Pull Request with new refactorings as
necessary. If Sourcery finds no refactorings at any point, this Pull Request
will be closed automatically.

See our documentation here.

Run Sourcery locally

Reduce the feedback loop during development by using the Sourcery editor plugin:

• VS Code
• PyCharm

Help us improve this pull request!

[github-actions]

👈 Launch a binder notebook on branch glotaran/pyglotaran/sourcery/pull-874

[sourcery-ai]

Sourcery Code Quality Report

✅  Merging this PR will increase code quality in the affected files by 0.75%.

Quality metrics	Before	After	Change
Complexity	3.05 ⭐	2.98 ⭐	-0.07 👍
Method Length	57.62 ⭐	55.56 ⭐	-2.06 👍
Working memory	8.32 🙂	8.13 🙂	-0.19 👍
Quality	69.57% 🙂	70.32% 🙂	0.75% 👍

Other metrics	Before	After	Change
Lines	6276	6053	-223

Changed files	Quality Before	Quality After	Quality Change
benchmark/benchmarks/integration/ex_two_datasets/benchmark.py	89.66% ⭐	89.66% ⭐	0.00%
glotaran/analysis/optimization_group_calculator.py	99.90% ⭐	99.90% ⭐	0.00%
glotaran/analysis/optimize.py	39.79% 😞	40.69% 😞	0.90% 👍
glotaran/analysis/test/test_constraints.py	57.48% 🙂	57.48% 🙂	0.00%
glotaran/analysis/test/test_grouping.py	49.67% 😞	49.67% 😞	0.00%
glotaran/analysis/test/test_multiple_goups.py	56.70% 🙂	56.70% 🙂	0.00%
glotaran/analysis/test/test_optimization.py	34.53% 😞	34.53% 😞	0.00%
glotaran/analysis/test/test_penalties.py	67.27% 🙂	67.55% 🙂	0.28% 👍
glotaran/analysis/test/test_relations.py	58.25% 🙂	58.25% 🙂	0.00%
glotaran/builtin/io/ascii/wavelength_time_explicit_file.py	78.10% ⭐	78.01% ⭐	-0.09% 👎
glotaran/builtin/io/folder/folder_plugin.py	55.31% 🙂	51.37% 🙂	-3.94% 👎
glotaran/builtin/io/folder/test/test_folder_plugin.py	85.18% ⭐	88.86% ⭐	3.68% 👍
glotaran/builtin/io/yml/yml.py	78.34% ⭐	78.42% ⭐	0.08% 👍
glotaran/builtin/io/yml/test/test_save_model.py	94.31% ⭐	94.31% ⭐	0.00%
glotaran/builtin/io/yml/test/test_save_result.py	88.79% ⭐	96.72% ⭐	7.93% 👍
glotaran/builtin/io/yml/test/test_save_scheme.py	78.73% ⭐	78.73% ⭐	0.00%
glotaran/builtin/megacomplexes/decay/init.py	%	%	%
glotaran/builtin/megacomplexes/decay/decay_megacomplex.py	70.00% 🙂	86.65% ⭐	16.65% 👍
glotaran/builtin/megacomplexes/decay/initial_concentration.py	83.93% ⭐	88.17% ⭐	4.24% 👍
glotaran/builtin/megacomplexes/decay/k_matrix.py	78.25% ⭐	79.00% ⭐	0.75% 👍
glotaran/builtin/megacomplexes/decay/util.py	53.83% 🙂	53.97% 🙂	0.14% 👍
glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py	59.54% 🙂	59.54% 🙂	0.00%
glotaran/builtin/megacomplexes/decay/test/test_k_matrix.py	65.74% 🙂	71.77% 🙂	6.03% 👍
glotaran/deprecation/modules/test/init.py	75.41% ⭐	75.41% ⭐	0.00%
glotaran/deprecation/modules/test/test_project_result.py	94.31% ⭐	95.29% ⭐	0.98% 👍
glotaran/deprecation/modules/test/test_project_scheme.py	75.33% ⭐	71.69% 🙂	-3.64% 👎
glotaran/examples/init.py	%	%	%
glotaran/examples/test/test_example.py	100.00% ⭐	99.17% ⭐	-0.83% 👎
glotaran/io/init.py	87.99% ⭐	87.99% ⭐	0.00%
glotaran/io/interface.py	97.71% ⭐	92.06% ⭐	-5.65% 👎
glotaran/model/init.py	%	%	%
glotaran/model/dataset_group.py	93.03% ⭐	93.03% ⭐	0.00%
glotaran/model/model.py	72.40% 🙂	72.40% 🙂	0.00%
glotaran/model/test/test_model.py	72.38% 🙂	72.38% 🙂	0.00%
glotaran/plugin_system/data_io_registration.py	92.43% ⭐	92.40% ⭐	-0.03% 👎
glotaran/plugin_system/project_io_registration.py	87.08% ⭐	88.67% ⭐	1.59% 👍
glotaran/plugin_system/test/test_data_io_registration.py	92.24% ⭐	92.11% ⭐	-0.13% 👎
glotaran/plugin_system/test/test_project_io_registration.py	91.22% ⭐	91.16% ⭐	-0.06% 👎
glotaran/project/result.py	76.37% ⭐	76.25% ⭐	-0.12% 👎
glotaran/project/scheme.py	72.83% 🙂	81.10% ⭐	8.27% 👍
glotaran/project/test/test_result.py	80.28% ⭐	82.52% ⭐	2.24% 👍
glotaran/project/test/test_scheme.py	80.83% ⭐	78.28% ⭐	-2.55% 👎
glotaran/test/test_spectral_decay.py	53.88% 🙂	53.88% 🙂	0.00%
glotaran/test/test_spectral_decay_full_model.py	55.92% 🙂	55.92% 🙂	0.00%
glotaran/test/test_spectral_penalties.py	45.01% 😞	45.01% 😞	0.00%

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/analysis/optimize.py	_create_result	16 🙂	280 ⛔	26 ⛔	24.30% ⛔	Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/test/test_optimization.py	test_optimization	19 😞	514 ⛔	15 😞	25.11% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
glotaran/test/test_spectral_penalties.py	test_equal_area_penalties	5 ⭐	783 ⛔	17 ⛔	34.81% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/megacomplexes/decay/util.py	calculate_decay_matrix_gaussian_irf	11 🙂	183 😞	18 ⛔	38.30% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/megacomplexes/decay/util.py	retrieve_decay_associated_data	1 ⭐	255 ⛔	17 ⛔	44.04% 😞	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

• ⭐ excellent
• 🙂 good
• 😞 poor
• ⛔ very poor

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

---

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

[sonarqubecloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
5.9% Duplication

[codecov]

Codecov Report

Merging #875 (94cd6ca) into main (d1e36a9) will increase coverage by 0.4%.
The diff coverage is 93.2%.

@@           Coverage Diff           @@
##            main    #875     +/-   ##
=======================================
+ Coverage   84.5%   85.0%   +0.4%     
=======================================
  Files         79      86      +7     
  Lines       4522    4686    +164     
  Branches     826     853     +27     
=======================================
+ Hits        3824    3985    +161     
+ Misses       556     554      -2     
- Partials     142     147      +5     

Impacted Files	Coverage Δ
.../builtin/io/ascii/wavelength_time_explicit_file.py	58.6% <ø> (ø)
glotaran/plugin_system/data_io_registration.py	100.0% <ø> (ø)
...n/builtin/megacomplexes/decay/decay_megacomplex.py	79.3% <69.2%> (-3.3%)	⬇️
glotaran/analysis/optimization_group.py	87.6% <78.2%> (ø)
glotaran/project/scheme.py	88.0% <79.1%> (-2.8%)	⬇️
glotaran/project/generators/generator.py	88.8% <88.8%> (ø)
...ltin/megacomplexes/decay/decay_megacomplex_base.py	92.0% <92.0%> (ø)
glotaran/model/model.py	84.9% <92.3%> (+1.7%)	⬆️
glotaran/analysis/optimize.py	86.3% <92.5%> (+1.2%)	⬆️
...analysis/optimization_group_calculator_unlinked.py	94.3% <96.5%> (ø)
... and 23 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d1e36a9...94cd6ca. Read the comment docs.