🩹Fix bug in create_index_independent_result_dataset

[jsnel]

Change summary

• Indexing did not match content of _group.matrices (list of CalculatedMatrix objects)
• Dimension did not match (for guidance spectra) (global_dimension_index appeared to be missing

Checklist

• ✔️ Passing the tests (mandatory for all PR's)
• 🚧 Added changes to changelog (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 #950

[github-actions]

👈 Launch a binder notebook on branch jsnel/pyglotaran/fix-create-index-independent-result-dataset

[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]       [ba7f8bff]
     <v0.5.1>                   
       52.4±0.7ms       52.7±0.5ms     1.01  BenchmarkOptimize.time_optimize(False, False, False)
       56.1±0.7ms       55.3±0.3ms     0.98  BenchmarkOptimize.time_optimize(False, False, True)
       52.1±0.3ms       52.6±0.4ms     1.01  BenchmarkOptimize.time_optimize(False, True, False)
         56.8±1ms         57.4±9ms     1.01  BenchmarkOptimize.time_optimize(False, True, True)
       63.3±0.6ms       63.3±0.3ms     1.00  BenchmarkOptimize.time_optimize(True, False, False)
        71.8±30ms        67.8±40ms     0.94  BenchmarkOptimize.time_optimize(True, False, True)
       63.4±0.5ms       63.3±0.4ms     1.00  BenchmarkOptimize.time_optimize(True, True, False)
       66.6±0.5ms        68.0±30ms     1.02  BenchmarkOptimize.time_optimize(True, True, True)
             191M             194M     1.01  IntegrationTwoDatasets.peakmem_optimize
       1.86±0.09s       1.78±0.06s     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
     [b1f678a4]       [ba7f8bff]
       52.7±0.2ms       52.7±0.5ms     1.00  BenchmarkOptimize.time_optimize(False, False, False)
        57.9±20ms       55.3±0.3ms     0.96  BenchmarkOptimize.time_optimize(False, False, True)
       52.3±0.4ms       52.6±0.4ms     1.01  BenchmarkOptimize.time_optimize(False, True, False)
       56.3±0.6ms         57.4±9ms     1.02  BenchmarkOptimize.time_optimize(False, True, True)
       63.8±0.2ms       63.3±0.3ms     0.99  BenchmarkOptimize.time_optimize(True, False, False)
        85.5±30ms        67.8±40ms    ~0.79  BenchmarkOptimize.time_optimize(True, False, True)
       63.6±0.3ms       63.3±0.4ms     0.99  BenchmarkOptimize.time_optimize(True, True, False)
        68.0±20ms        68.0±30ms     1.00  BenchmarkOptimize.time_optimize(True, True, True)
             201M             194M     0.96  IntegrationTwoDatasets.peakmem_optimize
       1.74±0.07s       1.78±0.06s     1.02  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Merging #948 (ba7f8bf) into main (b1f678a) will decrease coverage by 0.0%.
The diff coverage is 60.0%.

@@           Coverage Diff           @@
##            main    #948     +/-   ##
=======================================
- Coverage   85.1%   85.0%   -0.1%     
=======================================
  Files         85      85             
  Lines       4799    4802      +3     
  Branches     921     923      +2     
=======================================
+ Hits        4085    4086      +1     
- Misses       562     563      +1     
- Partials     152     153      +1     

Impacted Files	Coverage Δ
...n/analysis/optimization_group_calculator_linked.py	95.7% <60.0%> (-0.8%)	⬇️

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[jsnel]

In lieu of review by another code owner (@joernweissenborn), considering all unit tests are passing I will use my administrator privileges to merge in the patch so @ism200 can proceed with his case study. If a more elegant solution is available that can be addressed in a future PR.

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.31%.

Quality metrics	Before	After	Change
Complexity	6.00 ⭐	6.07 ⭐	0.07 👎
Method Length	104.20 🙂	105.95 🙂	1.75 👎
Working memory	10.75 😞	10.75 😞	0.00
Quality	60.83% 🙂	60.52% 🙂	-0.31% 👎

Other metrics	Before	After	Change
Lines	560	571	11

Changed files	Quality Before	Quality After	Quality Change
glotaran/analysis/optimization_group_calculator_linked.py	60.83% 🙂	60.52% 🙂	-0.31% 👎

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

            | File | Function | Complexity | Length | Working Memory | Quality | Recommendation |
            | --- | --- | :---: | :---: | :---: | :---: | --- |
            | glotaran/analysis/optimization_group_calculator_linked.py | OptimizationGroupCalculatorLinked.\_append\_to\_grouped\_bag | 12 🙂 | 269 ⛔ | 23 ⛔ | 29.09% 😞 | Try splitting into smaller methods. Extract out complex expressions |

| glotaran/analysis/optimization_group_calculator_linked.py | OptimizationGroupCalculatorLinked.init_bag | 10 🙂 | 175 😞 | 16 ⛔ | 41.77% 😞 | Try splitting into smaller methods. Extract out complex expressions |
| glotaran/analysis/optimization_group_calculator_linked.py | combine_matrices | 12 🙂 | 141 😞 | 11 😞 | 50.50% 🙂 | Try splitting into smaller methods. Extract out complex expressions |
| glotaran/analysis/optimization_group_calculator_linked.py | OptimizationGroupCalculatorLinked.calculate_index_independent_matrices | 16 🙂 | 137 😞 | 9 🙂 | 51.53% 🙂 | Try splitting into smaller methods |
| glotaran/analysis/optimization_group_calculator_linked.py | OptimizationGroupCalculatorLinked.calculate_index_dependent_matrices | 6 ⭐ | 189 😞 | 10 😞 | 53.34% 🙂 | Try splitting into smaller methods. 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.

            ***

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            We are actively working on this report - lots more documentation and extra metrics to come!

            Help us [improve](https://research.typeform.com/to/j06Spdfr?type=quality_report&github_login=jsnel&base_repo=https%3A%2F%2Fgithub.com%2Fglotaran%2Fpyglotaran.git&base_remote_ref=refs%2Fpull%2F948%2Fhead&base_ref=main&base_sha=ba7f8bff26b6e5e0fc98d51caff8ee3efc547c54&head_repo=https%3A%2F%2Fgithub.com%2Fglotaran%2Fpyglotaran.git&head_ref=sourcery%2Fpull-948&base_pr_number=948&base_pr_state=open) this quality report!

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication