Feature/project/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.

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-866

[codecov]

Codecov Report

Merging #867 (999cf2e) into main (d1e36a9) will increase coverage by 0.3%.
The diff coverage is 92.9%.

❗ Current head 999cf2e differs from pull request most recent head 821bd3b. Consider uploading reports for the commit 821bd3b to get more accurate results

@@           Coverage Diff           @@
##            main    #867     +/-   ##
=======================================
+ Coverage   84.5%   84.9%   +0.3%     
=======================================
  Files         79      86      +7     
  Lines       4522    4681    +159     
  Branches     826     853     +27     
=======================================
+ Hits        3824    3976    +152     
- Misses       556     560      +4     
- Partials     142     145      +3     

Impacted Files	Coverage Δ
...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)
...n/analysis/optimization_group_calculator_linked.py	96.5% <96.7%> (ø)
glotaran/analysis/optimization_group_calculator.py	100.0% <100.0%> (ø)
... and 13 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...821bd3b. Read the comment docs.

[github-actions]

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

Benchmark diff v0.4.1 vs. main

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [21ba272a]       [821bd3b1]
     <v0.4.1>                   
+      49.2±0.9ms       56.7±0.5ms     1.15  BenchmarkOptimize.time_optimize(False, False, False)
-         298±3ms         61.7±7ms     0.21  BenchmarkOptimize.time_optimize(False, False, True)
-        68.6±3ms       57.4±0.8ms     0.84  BenchmarkOptimize.time_optimize(False, True, False)
         73.6±5ms         60.8±2ms    ~0.83  BenchmarkOptimize.time_optimize(False, True, True)
+        49.7±2ms         68.7±1ms     1.38  BenchmarkOptimize.time_optimize(True, False, False)
-         302±5ms         73.1±3ms     0.24  BenchmarkOptimize.time_optimize(True, False, True)
         68.3±1ms         70.1±1ms     1.03  BenchmarkOptimize.time_optimize(True, True, False)
         71.4±2ms        91.5±50ms    ~1.28  BenchmarkOptimize.time_optimize(True, True, True)
             193M             193M     1.00  IntegrationTwoDatasets.peakmem_optimize
-      4.63±0.05s       1.82±0.05s     0.39  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [d1e36a93]       [821bd3b1]
+      33.3±0.6ms       56.7±0.5ms     1.70  BenchmarkOptimize.time_optimize(False, False, False)
+        38.7±1ms         61.7±7ms     1.60  BenchmarkOptimize.time_optimize(False, False, True)
         56.8±2ms       57.4±0.8ms     1.01  BenchmarkOptimize.time_optimize(False, True, False)
         60.3±1ms         60.8±2ms     1.01  BenchmarkOptimize.time_optimize(False, True, True)
+      43.3±0.9ms         68.7±1ms     1.59  BenchmarkOptimize.time_optimize(True, False, False)
         115±60ms         73.1±3ms    ~0.64  BenchmarkOptimize.time_optimize(True, False, True)
       66.6±0.4ms         70.1±1ms     1.05  BenchmarkOptimize.time_optimize(True, True, False)
        75.3±50ms        91.5±50ms    ~1.21  BenchmarkOptimize.time_optimize(True, True, True)
             193M             193M     1.00  IntegrationTwoDatasets.peakmem_optimize
       1.82±0.05s       1.82±0.05s     1.00  IntegrationTwoDatasets.time_optimize

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 1.75%.

Quality metrics	Before	After	Change
Complexity	3.72 ⭐	3.68 ⭐	-0.04 👍
Method Length	74.03 🙂	80.97 🙂	6.94 👎
Working memory	9.18 🙂	9.34 🙂	0.16 👎
Quality	65.36% 🙂	63.61% 🙂	-1.75% 👎

Other metrics	Before	After	Change
Lines	4984	3295	-1689

Changed files	Quality Before	Quality After	Quality Change
benchmark/benchmarks/integration/ex_two_datasets/benchmark.py	85.49% ⭐	89.66% ⭐	4.17% 👍
glotaran/analysis/optimize.py	46.86% 😞	40.69% 😞	-6.17% 👎
glotaran/analysis/test/test_constraints.py	57.15% 🙂	57.48% 🙂	0.33% 👍
glotaran/analysis/test/test_grouping.py	50.01% 🙂	49.67% 😞	-0.34% 👎
glotaran/analysis/test/test_optimization.py	34.60% 😞	34.53% 😞	-0.07% 👎
glotaran/analysis/test/test_penalties.py	64.87% 🙂	67.55% 🙂	2.68% 👍
glotaran/analysis/test/test_relations.py	57.85% 🙂	58.25% 🙂	0.40% 👍
glotaran/builtin/io/yml/test/test_save_model.py	94.31% ⭐	94.31% ⭐	0.00%
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	59.16% 🙂	59.54% 🙂	0.38% 👍
glotaran/builtin/megacomplexes/decay/test/test_k_matrix.py	65.74% 🙂	71.77% 🙂	6.03% 👍
glotaran/deprecation/modules/test/init.py	80.32% ⭐	75.41% ⭐	-4.91% 👎
glotaran/deprecation/modules/test/test_project_scheme.py	71.23% 🙂	71.69% 🙂	0.46% 👍
glotaran/examples/init.py	%	%	%
glotaran/examples/test/test_example.py	100.00% ⭐	99.17% ⭐	-0.83% 👎
glotaran/model/init.py	%	%	%
glotaran/model/model.py	73.26% 🙂	72.40% 🙂	-0.86% 👎
glotaran/model/test/test_model.py	70.89% 🙂	72.38% 🙂	1.49% 👍
glotaran/project/scheme.py	89.88% ⭐	81.10% ⭐	-8.78% 👎
glotaran/project/test/test_result.py	80.28% ⭐	89.36% ⭐	9.08% 👍
glotaran/project/test/test_scheme.py	80.82% ⭐	78.28% ⭐	-2.54% 👎
glotaran/test/test_spectral_decay.py	51.45% 🙂	53.88% 🙂	2.43% 👍
glotaran/test/test_spectral_decay_full_model.py	55.21% 🙂	55.92% 🙂	0.71% 👍
glotaran/test/test_spectral_penalties.py	46.60% 😞	45.01% 😞	-1.59% 👎

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
4 Code Smells

No Coverage information
6.2% Duplication