👌 Improve ParameterGroup markdown rendering

[s-weigand]

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Change summary

• Table headers in markdown don't use a mix of abbreviations and spelled out names but only spelled out names
• Expression column doesn't evidently render as latex when 2 or more parameters are present
• Numbers get formatted as .3e by default
• User can decide on the float precision of the markdown table by passing float_format

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)

Closes issues

closes #916

[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran/improve-parametergroup-markdown

[github-actions]

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

Benchmark diff v0.5.0rc1 vs. main

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [d05c042a]       [db9d46d6]
     <v0.5.0rc1>                 
         75.8±1ms       82.3±0.9ms     1.09  BenchmarkOptimize.time_optimize(False, False, False)
         135±40ms         162±20ms    ~1.20  BenchmarkOptimize.time_optimize(False, False, True)
         77.8±1ms         82.6±1ms     1.06  BenchmarkOptimize.time_optimize(False, True, False)
         158±20ms         176±30ms    ~1.11  BenchmarkOptimize.time_optimize(False, True, True)
         96.6±2ms         99.9±2ms     1.03  BenchmarkOptimize.time_optimize(True, False, False)
         111±30ms         109±20ms     0.98  BenchmarkOptimize.time_optimize(True, False, True)
         96.0±2ms          102±2ms     1.06  BenchmarkOptimize.time_optimize(True, True, False)
       100.0±20ms         110±20ms     1.10  BenchmarkOptimize.time_optimize(True, True, True)
             191M             199M     1.04  IntegrationTwoDatasets.peakmem_optimize
+      2.01±0.04s       2.46±0.09s     1.22  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [88111bb1]       [db9d46d6]
         84.8±2ms       82.3±0.9ms     0.97  BenchmarkOptimize.time_optimize(False, False, False)
         160±20ms         162±20ms     1.02  BenchmarkOptimize.time_optimize(False, False, True)
         85.1±2ms         82.6±1ms     0.97  BenchmarkOptimize.time_optimize(False, True, False)
          179±5ms         176±30ms     0.98  BenchmarkOptimize.time_optimize(False, True, True)
          103±1ms         99.9±2ms     0.97  BenchmarkOptimize.time_optimize(True, False, False)
          111±1ms         109±20ms     0.98  BenchmarkOptimize.time_optimize(True, False, True)
        104±0.9ms          102±2ms     0.98  BenchmarkOptimize.time_optimize(True, True, False)
         143±50ms         110±20ms    ~0.77  BenchmarkOptimize.time_optimize(True, True, True)
             193M             199M     1.03  IntegrationTwoDatasets.peakmem_optimize
        2.50±0.1s       2.46±0.09s     0.98  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Merging #918 (db9d46d) into main (88111bb) will increase coverage by 0.0%.
The diff coverage is 100.0%.

@@          Coverage Diff          @@
##            main    #918   +/-   ##
=====================================
  Coverage   85.1%   85.1%           
=====================================
  Files         85      85           
  Lines       4793    4796    +3     
  Branches     920     921    +1     
=====================================
+ Hits        4079    4082    +3     
  Misses       562     562           
  Partials     152     152           

Impacted Files	Coverage Δ
glotaran/parameter/parameter.py	95.5% <100.0%> (+<0.1%)	⬆️
glotaran/parameter/parameter_group.py	88.1% <100.0%> (ø)

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[jsnel]

Reviewed ok!

[s-weigand]

Using the kinetic parameters

kinetic: 
    - 0.5
    - 0.3
    - ["3", {expr: "$kinetic.expression_parameter+2*$input.1"}]
    - ["expression_parameter", 0.1]

Old render

New render

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.24%.

Quality metrics	Before	After	Change
Complexity	3.21 ⭐	3.22 ⭐	0.01 👎
Method Length	31.75 ⭐	32.33 ⭐	0.58 👎
Working memory	6.43 🙂	6.44 🙂	0.01 👎
Quality	81.20% ⭐	80.96% ⭐	-0.24% 👎

Other metrics	Before	After	Change
Lines	1370	1397	27

Changed files	Quality Before	Quality After	Quality Change
glotaran/parameter/parameter.py	84.83% ⭐	84.60% ⭐	-0.23% 👎
glotaran/parameter/parameter_group.py	75.69% ⭐	75.47% ⭐	-0.22% 👎
glotaran/parameter/test/test_parameter_group_rendering.py	87.06% ⭐	85.79% ⭐	-1.27% 👎

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 🙂	148 😞	11 😞	48.86% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/parameter/parameter_group.py	ParameterGroup.from_dataframe	14 🙂	134 😞	10 😞	51.47% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/parameter/parameter_group.py	ParameterGroup.markdown	3 ⭐	128 😞	11 😞	60.51% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/parameter/parameter.py	Parameter.__init__	1 ⭐	70 🙂	16 ⛔	63.36% 🙂	Extract out complex expressions
glotaran/parameter/parameter_group.py	ParameterGroup.__repr__	6 ⭐	72 🙂	12 😞	63.49% 🙂	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!

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
1.5% Duplication

[jsnel]

👍