Feature: Generators (Sourcery refactored)

[sourcery-ai]

Pull Request #866 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/866/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 decrease code quality in the affected files by 0.05%.

Quality metrics	Before	After	Change
Complexity	1.15 ⭐	1.06 ⭐	-0.09 👍
Method Length	51.65 ⭐	51.94 ⭐	0.29 👎
Working memory	6.29 🙂	6.29 🙂	0.00
Quality	78.79% ⭐	78.74% ⭐	-0.05% 👎

Other metrics	Before	After	Change
Lines	3059	2544	-515

Changed files	Quality Before	Quality After	Quality Change
glotaran/init.py	91.44% ⭐	88.07% ⭐	-3.37% 👎
glotaran/builtin/io/folder/test/test_folder_plugin.py	85.18% ⭐	87.00% ⭐	1.82% 👍
glotaran/builtin/io/yml/yml.py	78.43% ⭐	77.86% ⭐	-0.57% 👎
glotaran/builtin/io/yml/test/test_save_model.py	94.31% ⭐	94.31% ⭐	0.00%
glotaran/builtin/io/yml/test/test_save_result.py	83.82% ⭐	87.74% ⭐	3.92% 👍
glotaran/builtin/io/yml/test/test_save_scheme.py	86.35% ⭐	86.35% ⭐	0.00%
glotaran/deprecation/deprecation_utils.py	72.44% 🙂	70.38% 🙂	-2.06% 👎
glotaran/deprecation/modules/test/test_model_model.py	93.30% ⭐	95.01% ⭐	1.71% 👍
glotaran/deprecation/modules/test/test_parameter_parameter_group.py	90.24% ⭐	90.24% ⭐	0.00%
glotaran/deprecation/modules/test/test_project_result.py	94.31% ⭐	95.02% ⭐	0.71% 👍
glotaran/deprecation/modules/test/test_project_scheme.py	75.33% ⭐	74.59% 🙂	-0.74% 👎
glotaran/deprecation/test/test_deprecation_utils.py	87.71% ⭐	87.86% ⭐	0.15% 👍
glotaran/deprecation/test/dummy_package/init.py	94.05% ⭐	89.49% ⭐	-4.56% 👎
glotaran/deprecation/test/dummy_package/deprecated_module_attribute.py	87.99% ⭐	82.07% ⭐	-5.92% 👎
glotaran/model/test/test_model.py	72.61% 🙂	72.68% 🙂	0.07% 👍
glotaran/project/test/test_result.py	80.10% ⭐	93.62% ⭐	13.52% 👍

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/deprecation/deprecation_utils.py	check_qualnames_in_tests.deprecate_dict_entry	11 🙂	135 😞	14 😞	47.35% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/io/yml/yml.py	YmlProjectIo.save_model	15 🙂	106 🙂	13 😞	48.93% 😞	Extract out complex expressions
glotaran/model/test/test_model.py	test_fill	0 ⭐	243 ⛔	7 🙂	62.26% 🙂	Try splitting into smaller methods
glotaran/model/test/test_model.py	test_items	0 ⭐	214 ⛔	7 🙂	64.02% 🙂	Try splitting into smaller methods
glotaran/deprecation/deprecation_utils.py	check_qualnames_in_tests.module_attribute.deprecate_submodule	6 ⭐	123 😞	8 🙂	64.34% 🙂	Try splitting into smaller methods

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]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
2 Code Smells

No Coverage information
0.0% Duplication

[github-actions]

👈 Launch a binder notebook on branch glotaran/pyglotaran/sourcery/pull-866

[github-actions]

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

Benchmark diff v0.5.1 vs. main

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [96b42630]       [6c8cf2ce]
     <v0.5.1>                   
         74.8±4ms         66.7±2ms    ~0.89  BenchmarkOptimize.time_optimize(False, False, False)
         153±20ms         146±20ms     0.95  BenchmarkOptimize.time_optimize(False, False, True)
         74.3±4ms         69.4±4ms     0.93  BenchmarkOptimize.time_optimize(False, True, False)
         157±30ms         141±20ms    ~0.90  BenchmarkOptimize.time_optimize(False, True, True)
         87.9±4ms         82.9±5ms     0.94  BenchmarkOptimize.time_optimize(True, False, False)
        94.5±30ms         88.3±8ms     0.93  BenchmarkOptimize.time_optimize(True, False, True)
         89.1±2ms         89.3±4ms     1.00  BenchmarkOptimize.time_optimize(True, True, False)
        92.5±40ms        99.6±30ms     1.08  BenchmarkOptimize.time_optimize(True, True, True)
             200M             205M     1.03  IntegrationTwoDatasets.peakmem_optimize
-      2.35±0.05s       2.06±0.04s     0.87  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [bde9b19c]       [6c8cf2ce]
         64.5±4ms         66.7±2ms     1.03  BenchmarkOptimize.time_optimize(False, False, False)
         166±10ms         146±20ms    ~0.88  BenchmarkOptimize.time_optimize(False, False, True)
         68.9±4ms         69.4±4ms     1.01  BenchmarkOptimize.time_optimize(False, True, False)
          158±7ms         141±20ms    ~0.89  BenchmarkOptimize.time_optimize(False, True, True)
         85.3±3ms         82.9±5ms     0.97  BenchmarkOptimize.time_optimize(True, False, False)
        92.9±20ms         88.3±8ms     0.95  BenchmarkOptimize.time_optimize(True, False, True)
         86.5±4ms         89.3±4ms     1.03  BenchmarkOptimize.time_optimize(True, True, False)
         153±40ms        99.6±30ms    ~0.65  BenchmarkOptimize.time_optimize(True, True, True)
             204M             205M     1.01  IntegrationTwoDatasets.peakmem_optimize
       1.97±0.05s       2.06±0.04s     1.04  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Merging #962 (6c8cf2c) into main (bde9b19) will decrease coverage by 0.2%.
The diff coverage is 87.0%.

@@           Coverage Diff           @@
##            main    #962     +/-   ##
=======================================
- Coverage   85.4%   85.1%   -0.3%     
=======================================
  Files         87      90      +3     
  Lines       4872    4857     -15     
  Branches     920     912      -8     
=======================================
- Hits        4163    4138     -25     
- Misses       558     571     +13     
+ Partials     151     148      -3     

Impacted Files	Coverage Δ
...lotaran/deprecation/modules/examples/sequential.py	0.0% <0.0%> (ø)
glotaran/project/generators/generator.py	90.4% <90.4%> (ø)
glotaran/__init__.py	100.0% <100.0%> (ø)
glotaran/builtin/io/yml/yml.py	88.6% <100.0%> (-2.0%)	⬇️
glotaran/deprecation/deprecation_utils.py	100.0% <100.0%> (ø)
glotaran/project/generators/__init__.py	100.0% <100.0%> (ø)
.../testing/simulated_data/parallel_spectral_decay.py	100.0% <100.0%> (ø)
...esting/simulated_data/sequential_spectral_decay.py	100.0% <100.0%> (ø)
glotaran/testing/simulated_data/shared_decay.py	100.0% <100.0%> (ø)
glotaran/project/result.py	81.3% <0.0%> (-4.0%)	⬇️
... and 1 more

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