✨ Use xarray internally and move relations/constraints/penaltys to glotaran.model

[s-weigand]

Same as #715 but with the targe branch being staging.
Author @joernweissenborn

Change summary

• moved relations, contraints and penalties to glotaran.model
• megacomplex.calculate_matrix now returns xarray.DataArray

DEPRECATION FOR MODELDICTS STILL NEEDED

Checklist

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

closes #715

[github-actions]

👈 Launch a binder notebook on branch joernweissenborn/pyglotaran/feature/moverelationsandconstraints

[sourcery-ai]

Sourcery Code Quality Report

✅  Merging this PR will increase code quality in the affected files by 0.97%.

Quality metrics	Before	After	Change
Complexity	5.71 ⭐	5.34 ⭐	-0.37 👍
Method Length	80.98 🙂	77.81 🙂	-3.17 👍
Working memory	10.05 😞	10.02 😞	-0.03 👍
Quality	60.42% 🙂	61.39% 🙂	0.97% 👍

Other metrics	Before	After	Change
Lines	3707	3394	-313

Changed files	Quality Before	Quality After	Quality Change
glotaran/analysis/problem.py	82.00% ⭐	82.09% ⭐	0.09% 👍
glotaran/analysis/problem_grouped.py	53.35% 🙂	54.85% 🙂	1.50% 👍
glotaran/analysis/problem_ungrouped.py	68.72% 🙂	62.99% 🙂	-5.73% 👎
glotaran/analysis/simulation.py	17.43% ⛔	21.92% ⛔	4.49% 👍
glotaran/analysis/util.py	57.57% 🙂	64.34% 🙂	6.77% 👍
glotaran/analysis/test/models.py	66.85% 🙂	66.48% 🙂	-0.37% 👎
glotaran/analysis/test/test_optimization.py	24.77% ⛔	26.31% 😞	1.54% 👍
glotaran/analysis/test/test_problem.py	59.95% 🙂	61.49% 🙂	1.54% 👍
glotaran/builtin/models/kinetic_image/kinetic_baseline_megacomplex.py	90.73% ⭐	86.85% ⭐	-3.88% 👎
glotaran/builtin/models/kinetic_image/kinetic_decay_megacomplex.py	65.10% 🙂	64.36% 🙂	-0.74% 👎
glotaran/builtin/models/kinetic_image/test/test_baseline.py	70.07% 🙂	65.39% 🙂	-4.68% 👎
glotaran/builtin/models/kinetic_spectrum/coherent_artifact_megacomplex.py	69.27% 🙂	68.38% 🙂	-0.89% 👎
glotaran/builtin/models/kinetic_spectrum/test/test_coherent_artifact.py	52.26% 🙂	51.69% 🙂	-0.57% 👎
glotaran/builtin/models/kinetic_spectrum/test/test_spectral_penalties.py	45.86% 😞	43.41% 😞	-2.45% 👎
glotaran/builtin/models/spectral/spectral_megacomplex.py	73.47% 🙂	71.44% 🙂	-2.03% 👎
glotaran/builtin/models/spectral/test/test_spectral_model.py	56.65% 🙂	56.65% 🙂	0.00%
glotaran/model/init.py	%	%	%
glotaran/model/dataset_descriptor.py	83.20% ⭐	86.28% ⭐	3.08% 👍
glotaran/model/decorator.py	63.07% 🙂	62.16% 🙂	-0.91% 👎
glotaran/model/megacomplex.py	93.31% ⭐	94.50% ⭐	1.19% 👍

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/analysis/simulation.py	simulate	24 😞	318 ⛔	20 ⛔	19.82% ⛔	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/test/test_optimization.py	test_optimization	19 😞	529 ⛔	14 😞	26.31% 😞	Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/problem_ungrouped.py	UngroupedProblem._calculate_residual_for_problem	16 🙂	355 ⛔	16 ⛔	27.91% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/model/decorator.py	model	14 🙂	282 ⛔	19 ⛔	29.01% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/problem_grouped.py	GroupedProblem._append_to_grouped_bag	8 ⭐	286 ⛔	22 ⛔	32.50% 😞	Try splitting into smaller methods. Extract out complex expressions

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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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[sonarcloud]

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
No Duplication information

[codecov]

Codecov Report

Merging #734 (0d301cd) into staging (2e7421b) will decrease coverage by 2.4%.
The diff coverage is 85.0%.

@@            Coverage Diff            @@
##           staging    #734     +/-   ##
=========================================
- Coverage     81.7%   79.3%   -2.5%     
=========================================
  Files           79      83      +4     
  Lines         4024    4127    +103     
  Branches       706     720     +14     
=========================================
- Hits          3291    3274     -17     
- Misses         606     728    +122     
+ Partials       127     125      -2     

Impacted Files	Coverage Δ
glotaran/model/clp_penalties.py	31.9% <31.9%> (ø)
glotaran/model/interval_property.py	60.0% <60.0%> (ø)
glotaran/analysis/util.py	89.1% <88.1%> (-7.2%)	⬇️
glotaran/model/constraint.py	92.3% <92.3%> (ø)
glotaran/analysis/problem_grouped.py	96.2% <97.7%> (-0.2%)	⬇️
glotaran/analysis/problem.py	93.2% <100.0%> (+2.3%)	⬆️
glotaran/analysis/problem_ungrouped.py	98.3% <100.0%> (+0.2%)	⬆️
glotaran/analysis/simulation.py	61.9% <100.0%> (-7.9%)	⬇️
...dels/kinetic_image/kinetic_baseline_megacomplex.py	93.7% <100.0%> (+0.8%)	⬆️
.../models/kinetic_image/kinetic_decay_megacomplex.py	62.9% <100.0%> (+0.4%)	⬆️
... and 21 more

---

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[jsnel]

Extensively reviewed in PR #715 but agreed to re-create against a staging branch instead of main to address performance regressions before merging the feature(s) into main.

[github-actions]

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

Benchmark diff

All benchmarks:

       before           after         ratio
     [dc00e6da]       [0d301cd4]
     <v0.4.0>                   
             178M             183M     1.02  IntegrationTwoDatasets.peakmem_create_result
             199M             204M     1.02  IntegrationTwoDatasets.peakmem_optimize
+         293±5ms       1.01±0.02s     3.44  IntegrationTwoDatasets.time_create_result
+      6.19±0.03s          1.15±0m    11.16  IntegrationTwoDatasets.time_optimize