Fix compartment ordering randomization due to use of set

[jsnel]

Get rid of all things set()

Checklist

• ✔️ Passing the tests (mandatory for all PR's)
• 👌 Closes issue (mandatory for ✨ feature and 🩹 bug fix PR's)

Closes issues

closes #787

[github-actions]

👈 Launch a binder notebook on branch jsnel/pyglotaran/fix/787_compartment_ordering

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
9 Code Smells

No Coverage information
0.0% Duplication

[sourcery-ai]

Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.86%.

Quality metrics	Before	After	Change
Complexity	6.20 ⭐	7.06 ⭐	0.86 👎
Method Length	106.00 🙂	106.32 🙂	0.32 👎
Working memory	11.79 😞	11.79 😞	0.00
Quality	58.06% 🙂	57.20% 🙂	-0.86% 👎

Other metrics	Before	After	Change
Lines	518	521	3

Changed files	Quality Before	Quality After	Quality Change
glotaran/analysis/problem_grouped.py	58.06% 🙂	57.20% 🙂	-0.86% 👎

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

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/analysis/problem_grouped.py	GroupedProblem._append_to_grouped_bag	12 🙂	269 ⛔	23 ⛔	29.09% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/problem_grouped.py	GroupedProblem.init_bag	10 🙂	174 😞	16 ⛔	41.86% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/problem_grouped.py	GroupedProblem._index_independent_residual	8 ⭐	137 😞	14 😞	49.89% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/problem_grouped.py	GroupedProblem._index_dependent_residual	8 ⭐	123 😞	15 😞	50.28% 🙂	Try splitting into smaller methods. Extract out complex expressions
glotaran/analysis/problem_grouped.py	combine_matrices	12 🙂	141 😞	11 😞	50.50% 🙂	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.

---

Please see our documentation here for details on how these metrics are calculated.

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

Help us improve this quality report!

[github-actions]

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

Benchmark diff

Parametrized benchmark signatures:

BenchmarkOptimize.time_optimize(index_dependent, grouped, weight)

All benchmarks:

       before           after         ratio
     [dc00e6da]       [0ff7b044]
     <v0.4.0>                   
-        42.1±1ms         32.0±2ms     0.76  BenchmarkOptimize.time_optimize(False, False, False)
-         235±7ms         35.6±1ms     0.15  BenchmarkOptimize.time_optimize(False, False, True)
-        61.8±2ms         51.7±1ms     0.84  BenchmarkOptimize.time_optimize(False, True, False)
         63.7±1ms         52.4±2ms    ~0.82  BenchmarkOptimize.time_optimize(False, True, True)
         42.6±2ms         39.6±1ms     0.93  BenchmarkOptimize.time_optimize(True, False, False)
-         236±3ms        81.6±40ms     0.35  BenchmarkOptimize.time_optimize(True, False, True)
       60.6±0.9ms         66.5±4ms     1.10  BenchmarkOptimize.time_optimize(True, True, False)
         62.7±1ms        84.9±20ms    ~1.35  BenchmarkOptimize.time_optimize(True, True, True)
             181M             179M     0.99  IntegrationTwoDatasets.peakmem_create_result
             199M             196M     0.99  IntegrationTwoDatasets.peakmem_optimize
-         206±2ms          163±6ms     0.79  IntegrationTwoDatasets.time_create_result
-      4.21±0.03s       1.20±0.06s     0.29  IntegrationTwoDatasets.time_optimize

[codecov]

Codecov Report

Merging #799 (0ff7b04) into staging (9dc64af) will increase coverage by 0.0%.
The diff coverage is 100.0%.

@@           Coverage Diff           @@
##           staging    #799   +/-   ##
=======================================
  Coverage     84.3%   84.4%           
=======================================
  Files           75      75           
  Lines         4191    4196    +5     
  Branches       756     758    +2     
=======================================
+ Hits          3537    3542    +5     
  Misses         520     520           
  Partials       134     134           

Impacted Files	Coverage Δ
glotaran/analysis/problem_grouped.py	96.0% <100.0%> (+<0.1%)	⬆️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 9dc64af...0ff7b04. Read the comment docs.