♻️ Refactor/821 refactor model spec

[jsnel]

♻️ Refactor model specification

Change summary

• ♻️ In model spec changed relation to clp_relations
• ♻️ In model spec changed constraints to clp_constaints

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 #821

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.16%.

Quality metrics	Before	After	Change
Complexity	3.64 ⭐	3.66 ⭐	0.02 👎
Method Length	72.05 🙂	72.90 🙂	0.85 👎
Working memory	6.93 🙂	6.94 🙂	0.01 👎
Quality	71.47% 🙂	71.31% 🙂	-0.16% 👎

Other metrics	Before	After	Change
Lines	1449	1495	46

Changed files	Quality Before	Quality After	Quality Change
glotaran/analysis/util.py	66.64% 🙂	66.64% 🙂	0.00%
glotaran/analysis/test/test_constraints.py	57.15% 🙂	57.15% 🙂	0.00%
glotaran/analysis/test/test_relations.py	57.85% 🙂	57.85% 🙂	0.00%
glotaran/builtin/io/yml/test/test_model_parser.py	82.35% ⭐	82.35% ⭐	0.00%
glotaran/deprecation/modules/builtin_io_yml.py	51.78% 🙂	49.53% 😞	-2.25% 👎
glotaran/deprecation/modules/test/test_builtin_io_yml.py	64.77% 🙂	62.09% 🙂	-2.68% 👎
glotaran/model/model.py	73.24% 🙂	73.24% 🙂	0.00%
glotaran/model/test/test_model.py	71.05% 🙂	71.05% 🙂	0.00%

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/deprecation/modules/builtin_io_yml.py	model_spec_deprecations	11 🙂	243 ⛔	9 🙂	47.09% 😞	Try splitting into smaller methods
glotaran/model/model.py	Model.markdown	10 🙂	118 🙂	10 😞	56.92% 🙂	Extract out complex expressions
glotaran/analysis/test/test_constraints.py	test_constraint	6 ⭐	169 😞	9 🙂	57.15% 🙂	Try splitting into smaller methods
glotaran/model/model.py	Model._add_dict_items	10 🙂	97 🙂	11 😞	57.81% 🙂	Extract out complex expressions
glotaran/analysis/test/test_relations.py	test_relations	6 ⭐	186 😞	8 🙂	57.85% 🙂	Try splitting into smaller methods

Legend and Explanation

The emojis denote the absolute quality of the code:

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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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Help us improve this quality report!

[github-actions]

👈 Launch a binder notebook on branch jsnel/pyglotaran/refactor/821_refactor_model_spec

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[codecov]

Codecov Report

Merging #836 (dbfc200) into main (ace90c5) will increase coverage by 0.0%.
The diff coverage is 100.0%.

@@          Coverage Diff          @@
##            main    #836   +/-   ##
=====================================
  Coverage   84.8%   84.8%           
=====================================
  Files         77      77           
  Lines       4364    4366    +2     
  Branches     787     787           
=====================================
+ Hits        3703    3705    +2     
  Misses       521     521           
  Partials     140     140           

Impacted Files	Coverage Δ
glotaran/analysis/util.py	91.3% <100.0%> (ø)
glotaran/deprecation/modules/builtin_io_yml.py	100.0% <100.0%> (ø)
glotaran/model/model.py	86.3% <100.0%> (ø)

---

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[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]       [dbfc2009]
     <v0.4.1>                   
-        63.6±1ms         38.3±1ms     0.60  BenchmarkOptimize.time_optimize(False, False, False)
-         396±6ms        54.6±30ms     0.14  BenchmarkOptimize.time_optimize(False, False, True)
-        84.2±6ms         68.9±3ms     0.82  BenchmarkOptimize.time_optimize(False, True, False)
         86.5±2ms        80.0±40ms     0.92  BenchmarkOptimize.time_optimize(False, True, True)
-        63.8±2ms         53.2±2ms     0.83  BenchmarkOptimize.time_optimize(True, False, False)
-         393±7ms        78.3±30ms     0.20  BenchmarkOptimize.time_optimize(True, False, True)
         81.8±3ms         80.6±3ms     0.99  BenchmarkOptimize.time_optimize(True, True, False)
         83.1±7ms        88.0±30ms     1.06  BenchmarkOptimize.time_optimize(True, True, True)
             182M             181M     1.00  IntegrationTwoDatasets.peakmem_create_result
             198M             197M     1.00  IntegrationTwoDatasets.peakmem_optimize
-         250±3ms          198±8ms     0.79  IntegrationTwoDatasets.time_create_result
        5.38±0.2s        1.87±0.1s    ~0.35  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [ace90c59]       [dbfc2009]
       40.5±0.9ms         38.3±1ms     0.94  BenchmarkOptimize.time_optimize(False, False, False)
         51.0±3ms        54.6±30ms     1.07  BenchmarkOptimize.time_optimize(False, False, True)
         66.6±4ms         68.9±3ms     1.03  BenchmarkOptimize.time_optimize(False, True, False)
        82.2±10ms        80.0±40ms     0.97  BenchmarkOptimize.time_optimize(False, True, True)
         53.0±2ms         53.2±2ms     1.00  BenchmarkOptimize.time_optimize(True, False, False)
        85.5±20ms        78.3±30ms     0.92  BenchmarkOptimize.time_optimize(True, False, True)
         82.1±2ms         80.6±3ms     0.98  BenchmarkOptimize.time_optimize(True, True, False)
         108±50ms        88.0±30ms    ~0.82  BenchmarkOptimize.time_optimize(True, True, True)
             181M             181M     1.00  IntegrationTwoDatasets.peakmem_create_result
             197M             197M     1.00  IntegrationTwoDatasets.peakmem_optimize
          203±5ms          198±8ms     0.98  IntegrationTwoDatasets.time_create_result
        1.87±0.1s        1.87±0.1s     1.00  IntegrationTwoDatasets.time_optimize

[s-weigand]

LGTM

[jsnel]

@joernweissenborn this PR makes the changes you requested changing relations to clp_relations and constraints to clp_constraints.