Refactor/refactor project after 807 (Sourcery refactored)

[sourcery-ai]

Pull Request #825 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/825/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.

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[sourcery-ai]

Sourcery Code Quality Report

✅  Merging this PR will increase code quality in the affected files by 1.25%.

Quality metrics	Before	After	Change
Complexity	6.90 ⭐	6.69 ⭐	-0.21 👍
Method Length	50.43 ⭐	48.57 ⭐	-1.86 👍
Working memory	7.53 🙂	7.30 🙂	-0.23 👍
Quality	69.86% 🙂	71.11% 🙂	1.25% 👍

Other metrics	Before	After	Change
Lines	4998	5392	394

Changed files	Quality Before	Quality After	Quality Change
glotaran/analysis/optimize.py	45.91% 😞	45.71% 😞	-0.20% 👎
glotaran/analysis/problem.py	80.36% ⭐	80.44% ⭐	0.08% 👍
glotaran/analysis/simulation.py	64.20% 🙂	64.20% 🙂	0.00%
glotaran/builtin/io/folder/folder_plugin.py	71.72% 🙂	61.82% 🙂	-9.90% 👎
glotaran/builtin/io/folder/test/test_folder_plugin.py	86.72% ⭐	93.57% ⭐	6.85% 👍
glotaran/builtin/io/netCDF/netCDF.py	79.78% ⭐	87.18% ⭐	7.40% 👍
glotaran/builtin/io/yml/yml.py	52.74% 🙂	78.42% ⭐	25.68% 👍
glotaran/builtin/io/yml/test/test_save_result.py	88.48% ⭐	95.76% ⭐	7.28% 👍
glotaran/examples/sequential.py	46.88% 😞	43.68% 😞	-3.20% 👎
glotaran/io/init.py	87.99% ⭐	87.99% ⭐	0.00%
glotaran/io/interface.py	97.71% ⭐	97.52% ⭐	-0.19% 👎
glotaran/model/dataset_model.py	81.03% ⭐	80.93% ⭐	-0.10% 👎
glotaran/model/item.py	55.63% 🙂	56.94% 🙂	1.31% 👍
glotaran/model/model.py	72.67% 🙂	73.25% 🙂	0.58% 👍
glotaran/model/property.py	43.98% 😞	48.19% 😞	4.21% 👍
glotaran/model/test/test_model.py	71.05% 🙂	70.88% 🙂	-0.17% 👎
glotaran/parameter/parameter_group.py	69.30% 🙂	69.30% 🙂	0.00%
glotaran/plugin_system/data_io_registration.py	92.67% ⭐	92.43% ⭐	-0.24% 👎
glotaran/plugin_system/project_io_registration.py	89.03% ⭐	87.08% ⭐	-1.95% 👎
glotaran/plugin_system/test/test_project_io_registration.py	91.22% ⭐	91.22% ⭐	0.00%
glotaran/project/init.py	%	%	%
glotaran/project/result.py	69.15% 🙂	68.30% 🙂	-0.85% 👎
glotaran/project/scheme.py	90.75% ⭐	90.05% ⭐	-0.70% 👎
glotaran/project/test/test_result.py	80.10% ⭐	82.44% ⭐	2.34% 👍
glotaran/project/test/test_scheme.py	76.59% ⭐	76.97% ⭐	0.38% 👍

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/model/item.py	_create_mprint_func	45 ⛔	275 ⛔	10 😞	25.00% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
glotaran/model/property.py	ModelProperty.validate	44 ⛔	187 😞	13 😞	25.34% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
glotaran/parameter/parameter_group.py	ParameterGroup.from_dataframe	28 😞	267 ⛔	13 😞	26.41% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/optimize.py	_create_result	15 🙂	256 ⛔	23 ⛔	27.13% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/model/item.py	_create_mprint_func.mprint_item	35 ⛔	270 ⛔	10 😞	28.28% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

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• 🙂 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]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
5 Code Smells

No Coverage information
0.0% Duplication

[github-actions]

👈 Launch a binder notebook on branch glotaran/pyglotaran/sourcery/pull-825

[github-actions]

Benchmark is done. Checkout the benchmark result page.
Benchmark differences below 5% might be due to CI noise.

Benchmark diff

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [dc00e6da]       [55a61c96]
     <v0.4.0>                   
-        64.0±1ms         46.0±1ms     0.72  BenchmarkOptimize.time_optimize(False, False, False)
-         367±2ms        60.8±30ms     0.17  BenchmarkOptimize.time_optimize(False, False, True)
-        94.9±1ms       79.3±0.9ms     0.84  BenchmarkOptimize.time_optimize(False, True, False)
         95.8±1ms         91.2±3ms     0.95  BenchmarkOptimize.time_optimize(False, True, True)
       63.3±0.6ms         61.4±1ms     0.97  BenchmarkOptimize.time_optimize(True, False, False)
-         369±3ms         68.3±1ms     0.19  BenchmarkOptimize.time_optimize(True, False, True)
         97.6±1ms        100±0.9ms     1.03  BenchmarkOptimize.time_optimize(True, True, False)
         97.6±1ms         138±50ms    ~1.41  BenchmarkOptimize.time_optimize(True, True, True)
             179M             181M     1.01  IntegrationTwoDatasets.peakmem_create_result
             195M             199M     1.02  IntegrationTwoDatasets.peakmem_optimize
-         301±3ms          237±3ms     0.79  IntegrationTwoDatasets.time_create_result
-      6.10±0.01s       2.13±0.07s     0.35  IntegrationTwoDatasets.time_optimize

[lgtm-com]

This pull request introduces 1 alert when merging 55a61c9 into 2f1afe7 - view on LGTM.com

new alerts:

• 1 for Variable defined multiple times