♻️ Move simulation to own module

[joernweissenborn]

This PR moves all simulation code into a new simulation module.

Change summary

• created glotaran.simulation
• deprecated glotaran.analysis.simulation
• fix doc strings in sumaltion
• added mypy checks for simulation

Checklist

• ✔️ Passing the tests (mandatory for all PR's)
• 🚧 Added changes to changelog (mandatory for all PR's)

[github-actions]

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

[joernweissenborn]

@s-weigand I tried to create a deprecation test like analysis.Scheme, but it does not work. Can you please have look?

[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]       [1eecdb03]
     <v0.5.1>                   
         78.6±2ms         81.9±1ms     1.04  BenchmarkOptimize.time_optimize(False, False, False)
         166±40ms         171±20ms     1.03  BenchmarkOptimize.time_optimize(False, False, True)
       80.5±0.8ms         80.4±3ms     1.00  BenchmarkOptimize.time_optimize(False, True, False)
         165±40ms         162±30ms     0.99  BenchmarkOptimize.time_optimize(False, True, True)
         99.1±2ms         98.7±4ms     1.00  BenchmarkOptimize.time_optimize(True, False, False)
         106±30ms         106±20ms     1.01  BenchmarkOptimize.time_optimize(True, False, True)
          102±5ms         98.2±1ms     0.96  BenchmarkOptimize.time_optimize(True, True, False)
         108±30ms         106±20ms     0.98  BenchmarkOptimize.time_optimize(True, True, True)
             206M             207M     1.00  IntegrationTwoDatasets.peakmem_optimize
       2.58±0.07s       2.44±0.07s     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
     [d1a96374]       [1eecdb03]
         80.4±3ms         81.9±1ms     1.02  BenchmarkOptimize.time_optimize(False, False, False)
          181±9ms         171±20ms     0.95  BenchmarkOptimize.time_optimize(False, False, True)
         81.2±2ms         80.4±3ms     0.99  BenchmarkOptimize.time_optimize(False, True, False)
         162±30ms         162±30ms     1.00  BenchmarkOptimize.time_optimize(False, True, True)
         98.7±2ms         98.7±4ms     1.00  BenchmarkOptimize.time_optimize(True, False, False)
          106±2ms         106±20ms     1.00  BenchmarkOptimize.time_optimize(True, False, True)
         99.8±2ms         98.2±1ms     0.98  BenchmarkOptimize.time_optimize(True, True, False)
         109±30ms         106±20ms     0.98  BenchmarkOptimize.time_optimize(True, True, True)
             209M             207M     0.99  IntegrationTwoDatasets.peakmem_optimize
       2.33±0.07s       2.44±0.07s     1.05  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Attention: Patch coverage is 91.66667% with 1 line in your changes missing coverage. Please review.

Project coverage is 87.1%. Comparing base (d1a9637) to head (1eecdb0).
Report is 238 commits behind head on main.

Files	Patch %	Lines
glotaran/simulation/simulation.py	85.7%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@          Coverage Diff          @@
##            main   #1041   +/-   ##
=====================================
  Coverage   87.1%   87.1%           
=====================================
  Files        101     102    +1     
  Lines       5379    5381    +2     
  Branches     995     995           
=====================================
+ Hits        4689    4691    +2     
  Misses       536     536           
  Partials     154     154           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[s-weigand]

@joernweissenborn the problem with the test was that we don't warn when you import the module (this would be to spammy) but when you use something of it (see a9919c2)

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[s-weigand]

LGTM 👍