Feature: Add SavingOptions to save_result API

[joernweissenborn]

This PR adds the SavingOption to the save_result function. It also adds more tests for the result.

Checklist

• ✔️ Passing the tests (mandatory for all PR's)
• 👌 Closes issue (mandatory for ✨ feature and 🩹 bug fix PR's)
• 🧪 Adds new tests for the feature (mandatory for ✨ feature and 🩹 bug fix PR's)
• 📚 Adds documentation of the feature

Closes issues

closes #XXXX

[github-actions]

👈 Launch a binder notebook on branch joernweissenborn/pyglotaran/refactor/save_result

[sonarqubecloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
5.9% Duplication

[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]       [fdb35f91]
     <v0.5.1>                   
       60.4±0.6ms       59.4±0.4ms     0.98  BenchmarkOptimize.time_optimize(False, False, False)
         64.1±1ms         65.5±3ms     1.02  BenchmarkOptimize.time_optimize(False, False, True)
       59.6±0.6ms       59.4±0.4ms     1.00  BenchmarkOptimize.time_optimize(False, True, False)
        67.2±30ms        79.7±30ms    ~1.19  BenchmarkOptimize.time_optimize(False, True, True)
       71.5±0.9ms         71.7±1ms     1.00  BenchmarkOptimize.time_optimize(True, False, False)
        77.3±30ms        80.3±20ms     1.04  BenchmarkOptimize.time_optimize(True, False, True)
         71.4±1ms         71.5±1ms     1.00  BenchmarkOptimize.time_optimize(True, True, False)
         109±40ms         76.5±4ms    ~0.70  BenchmarkOptimize.time_optimize(True, True, True)
             202M             201M     1.00  IntegrationTwoDatasets.peakmem_optimize
       2.00±0.04s       1.92±0.04s     0.96  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [09de6b26]       [fdb35f91]
       59.6±0.6ms       59.4±0.4ms     1.00  BenchmarkOptimize.time_optimize(False, False, False)
        78.4±30ms         65.5±3ms    ~0.84  BenchmarkOptimize.time_optimize(False, False, True)
       58.6±0.4ms       59.4±0.4ms     1.01  BenchmarkOptimize.time_optimize(False, True, False)
        64.0±20ms        79.7±30ms    ~1.24  BenchmarkOptimize.time_optimize(False, True, True)
       71.4±0.6ms         71.7±1ms     1.00  BenchmarkOptimize.time_optimize(True, False, False)
        82.7±30ms        80.3±20ms     0.97  BenchmarkOptimize.time_optimize(True, False, True)
       71.8±0.4ms         71.5±1ms     1.00  BenchmarkOptimize.time_optimize(True, True, False)
         111±30ms         76.5±4ms    ~0.69  BenchmarkOptimize.time_optimize(True, True, True)
             204M             201M     0.99  IntegrationTwoDatasets.peakmem_optimize
       1.94±0.03s       1.92±0.04s     0.99  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Merging #874 (fdb35f9) into main (09de6b2) will increase coverage by 0.1%.
The diff coverage is 96.4%.

@@           Coverage Diff           @@
##            main    #874     +/-   ##
=======================================
+ Coverage   85.3%   85.5%   +0.1%     
=======================================
  Files         90      90             
  Lines       4857    4870     +13     
  Branches     912     913      +1     
=======================================
+ Hits        4147    4166     +19     
+ Misses       561     553      -8     
- Partials     149     151      +2     

Impacted Files	Coverage Δ
.../builtin/io/ascii/wavelength_time_explicit_file.py	58.6% <ø> (ø)
glotaran/plugin_system/data_io_registration.py	97.2% <ø> (ø)
glotaran/builtin/io/folder/folder_plugin.py	95.8% <93.9%> (-1.8%)	⬇️
glotaran/builtin/io/yml/yml.py	89.0% <100.0%> (+0.4%)	⬆️
glotaran/io/__init__.py	100.0% <100.0%> (ø)
glotaran/io/interface.py	100.0% <100.0%> (ø)
glotaran/plugin_system/project_io_registration.py	100.0% <100.0%> (ø)
glotaran/project/result.py	88.4% <100.0%> (+7.0%)	⬆️

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[sonarqubecloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
17.5% Duplication

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.52%.

Quality metrics	Before	After	Change
Complexity	1.56 ⭐	1.61 ⭐	0.05 👎
Method Length	36.66 ⭐	37.50 ⭐	0.84 👎
Working memory	5.80 ⭐	5.91 ⭐	0.11 👎
Quality	83.50% ⭐	82.98% ⭐	-0.52% 👎

Other metrics	Before	After	Change
Lines	2646	2842	196

Changed files	Quality Before	Quality After	Quality Change
glotaran/builtin/io/ascii/wavelength_time_explicit_file.py	78.10% ⭐	78.01% ⭐	-0.09% 👎
glotaran/builtin/io/folder/folder_plugin.py	59.69% 🙂	62.16% 🙂	2.47% 👍
glotaran/builtin/io/folder/test/test_folder_plugin.py	87.00% ⭐	86.36% ⭐	-0.64% 👎
glotaran/builtin/io/yml/yml.py	77.86% ⭐	77.36% ⭐	-0.50% 👎
glotaran/builtin/io/yml/test/test_save_result.py	87.74% ⭐	81.46% ⭐	-6.28% 👎
glotaran/io/init.py	87.99% ⭐	87.99% ⭐	0.00%
glotaran/io/interface.py	97.71% ⭐	92.06% ⭐	-5.65% 👎
glotaran/plugin_system/data_io_registration.py	84.42% ⭐	84.36% ⭐	-0.06% 👎
glotaran/plugin_system/project_io_registration.py	83.86% ⭐	84.70% ⭐	0.84% 👍
glotaran/plugin_system/test/test_data_io_registration.py	90.24% ⭐	90.13% ⭐	-0.11% 👎
glotaran/plugin_system/test/test_project_io_registration.py	90.24% ⭐	90.16% ⭐	-0.08% 👎
glotaran/project/result.py	77.52% ⭐	77.38% ⭐	-0.14% 👎
glotaran/project/test/test_result.py	93.62% ⭐	82.73% ⭐	-10.89% 👎

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/builtin/io/yml/yml.py	YmlProjectIo.save_model	15 🙂	106 🙂	13 😞	48.93% 😞	Extract out complex expressions
glotaran/project/result.py	Result.markdown	6 ⭐	173 😞	13 😞	49.52% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/io/ascii/wavelength_time_explicit_file.py	ExplicitFile.write	5 ⭐	170 😞	13 😞	50.77% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/io/ascii/wavelength_time_explicit_file.py	ExplicitFile.read	4 ⭐	138 😞	12 😞	56.63% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/io/folder/folder_plugin.py	save_result_to_folder	3 ⭐	218 ⛔	8 🙂	58.41% 🙂	Try splitting into smaller methods

Legend and Explanation

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• 🙂 good
• 😞 poor
• ⛔ very poor

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

---

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[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication