🩹 Show validation problem if parameters are missing values (default: NaN)

[s-weigand]

This change fixes false positive reporting of a Model with parameters or Scheme as valid when parameters are missing values and default to np.nan.
One use case where a user would want missing parameters is in a teaching exercise where students have to fill in missing parameters.
The other use case would be that a user started editing the parameters file but didn't finish and forgot some values.

As a demo you can use this notebook.

Change summary

• 👌 Don't set default parameter value to zero
• 🧹 Improved typing and exception raising
• 🩹 Fix degraded label with nesting over 2
• ✨ Added missing_parameter_value_labels property to ParameterGroup
• ✨ Added missing parameters check to model validation
• 👌 Improved validation output

Checklist

• ✔️ Passing the tests (mandatory for all PR's)
• 🚧 Added changes to changelog (mandatory for all PR's)
• 🧪 Adds new tests for the feature (mandatory for ✨ feature and 🩹 bug fix PR's)

[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran/better-validation

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.06%.

Quality metrics	Before	After	Change
Complexity	3.48 ⭐	3.45 ⭐	-0.03 👍
Method Length	47.55 ⭐	47.86 ⭐	0.31 👎
Working memory	6.65 🙂	6.68 🙂	0.03 👎
Quality	75.06% ⭐	75.00% 🙂	-0.06% 👎

Other metrics	Before	After	Change
Lines	2851	2948	97

Changed files	Quality Before	Quality After	Quality Change
glotaran/model/model.py	68.87% 🙂	67.94% 🙂	-0.93% 👎
glotaran/model/test/test_model.py	72.80% 🙂	73.09% 🙂	0.29% 👍
glotaran/parameter/parameter.py	84.11% ⭐	84.10% ⭐	-0.01% 👎
glotaran/parameter/parameter_group.py	75.52% ⭐	75.88% ⭐	0.36% 👍
glotaran/parameter/test/test_parameter_group.py	74.07% 🙂	74.31% 🙂	0.24% 👍
glotaran/project/scheme.py	72.08% 🙂	71.96% 🙂	-0.12% 👎

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/parameter/parameter.py	Parameter.markdown	13 🙂	161 😞	13 😞	44.22% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/model/model.py	Model.markdown	13 🙂	168 😞	10 😞	48.74% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/project/scheme.py	Scheme.__post_init__	16 🙂	127 😞	11 😞	48.75% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/model/model.py	Model.from_dict	12 🙂	159 😞	10 😞	50.49% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/model/model.py	Model.generate_parameters	25 😞	106 🙂	8 🙂	51.29% 🙂	Refactor to reduce nesting

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
0 Code Smells

No Coverage information
0.7% 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]       [f9c55a55]
     <v0.5.1>                   
         63.8±1ms         67.5±4ms     1.06  BenchmarkOptimize.time_optimize(False, False, False)
         145±20ms         149±20ms     1.03  BenchmarkOptimize.time_optimize(False, False, True)
         62.2±2ms         66.8±6ms     1.07  BenchmarkOptimize.time_optimize(False, True, False)
          149±5ms         133±20ms    ~0.89  BenchmarkOptimize.time_optimize(False, True, True)
         81.1±3ms         86.1±6ms     1.06  BenchmarkOptimize.time_optimize(True, False, False)
       82.0±0.5ms        86.3±40ms     1.05  BenchmarkOptimize.time_optimize(True, False, True)
         77.9±2ms       75.8±0.9ms     0.97  BenchmarkOptimize.time_optimize(True, True, False)
        87.2±40ms         121±50ms    ~1.38  BenchmarkOptimize.time_optimize(True, True, True)
             202M             211M     1.04  IntegrationTwoDatasets.peakmem_optimize
       2.05±0.07s       1.95±0.04s     0.95  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [0da383ee]       [f9c55a55]
         63.3±2ms         67.5±4ms     1.07  BenchmarkOptimize.time_optimize(False, False, False)
         124±20ms         149±20ms    ~1.21  BenchmarkOptimize.time_optimize(False, False, True)
         63.0±1ms         66.8±6ms     1.06  BenchmarkOptimize.time_optimize(False, True, False)
          149±6ms         133±20ms    ~0.89  BenchmarkOptimize.time_optimize(False, True, True)
         78.3±1ms         86.1±6ms     1.10  BenchmarkOptimize.time_optimize(True, False, False)
         86.7±5ms        86.3±40ms     1.00  BenchmarkOptimize.time_optimize(True, False, True)
         81.3±2ms       75.8±0.9ms     0.93  BenchmarkOptimize.time_optimize(True, True, False)
         105±50ms         121±50ms    ~1.15  BenchmarkOptimize.time_optimize(True, True, True)
             206M             211M     1.02  IntegrationTwoDatasets.peakmem_optimize
       1.92±0.08s       1.95±0.04s     1.01  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Attention: Patch coverage is 83.33333% with 4 lines in your changes missing coverage. Please review.

Project coverage is 87.3%. Comparing base (0da383e) to head (f9c55a5).
Report is 209 commits behind head on main.

Files	Patch %	Lines
glotaran/model/model.py	77.7%	2 Missing ⚠️
glotaran/parameter/parameter_group.py	83.3%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##            main   #1076     +/-   ##
=======================================
+ Coverage   87.1%   87.3%   +0.1%     
=======================================
  Files        102     102             
  Lines       5381    5388      +7     
  Branches     995     997      +2     
=======================================
+ Hits        4691    4704     +13     
+ Misses       536     530      -6     
  Partials     154     154             

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[jsnel]

Nice user experience improvement!
Good tests and thanks for beautifying the code here and there.