👌 Make PreProcessingPipeline methods return a new instance

[s-weigand]

This changes the behavior of methods on PreProcessingPipeline to be closer to how pandas or xarray work (object creation instead of in place mutation), which makes it more intuitive and prevents accidental state changes in the pipeline (e.g. executing a cell in a notebook that does not include the instantiation multiple times).

Change summary

• 👌 Make PreProcessingPipeline methods return a new instance

Checklist

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

[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	0.12 ⭐	0.16 ⭐	0.04 👎
Method Length	39.60 ⭐	41.56 ⭐	1.96 👎
Working memory	4.35 ⭐	4.39 ⭐	0.04 👎
Quality	90.45% ⭐	90.29% ⭐	-0.16% 👎

Other metrics	Before	After	Change
Lines	114	106	-8

Changed files	Quality Before	Quality After	Quality Change
glotaran/io/preprocessor/pipeline.py	93.92% ⭐	92.60% ⭐	-1.32% 👎
glotaran/io/preprocessor/test/test_preprocessor.py	88.58% ⭐	89.18% ⭐	0.60% 👍

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation

Legend and Explanation

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[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran/better-pre-process-pipeline

[github-actions]

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

Benchmark diff v0.6.0 vs. main

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [6c3c390e]       [a1290e7c]
     <v0.6.0>                   
!      41.3±0.1ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
!      43.8±0.3ms           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
!      41.3±0.1ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
!      44.0±0.2ms           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
!      51.4±0.4ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
!       92.1±40ms           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
!      50.9±0.4ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
!       96.1±20ms           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             205M             211M     1.03  IntegrationTwoDatasets.peakmem_optimize
-      1.83±0.02s       1.02±0.02s     0.56  IntegrationTwoDatasets.time_optimize

Benchmark diff main vs. PR

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [a1290e7c]       [73b9dde7]
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, False, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, False, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, True, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(False, True, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, False, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, False, True)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, True, False)
           failed           failed      n/a  BenchmarkOptimize.time_optimize(True, True, True)
             211M             210M     1.00  IntegrationTwoDatasets.peakmem_optimize
       1.02±0.02s         987±30ms     0.97  IntegrationTwoDatasets.time_optimize

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[codecov]

Codecov Report

Patch coverage: 100.0% and project coverage change: -0.1 ⚠️

Comparison is base (a1290e7) 88.4% compared to head (73b9dde) 88.4%.

Additional details and impacted files

@@           Coverage Diff           @@
##            main   #1263     +/-   ##
=======================================
- Coverage   88.4%   88.4%   -0.1%     
=======================================
  Files        107     107             
  Lines       5151    5147      -4     
  Branches     854     854             
=======================================
- Hits        4554    4550      -4     
  Misses       479     479             
  Partials     118     118             

Impacted Files	Coverage Δ
glotaran/io/preprocessor/pipeline.py	100.0% <100.0%> (ø)

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[jsnel]

Looks good to me.