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Store edge index in AdjacencyGraph & get rid of dicts#216

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gdalle wants to merge 3 commits intomainfrom
gd/edgeindex
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Store edge index in AdjacencyGraph & get rid of dicts#216
gdalle wants to merge 3 commits intomainfrom
gd/edgeindex

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@gdalle gdalle commented Mar 31, 2025

Alternative take on #214

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amontoison commented Mar 31, 2025

I think we also need to modify the functions for ordering if we modify neighbors.

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gdalle commented Mar 31, 2025

Yeah this is still very much a work in progress

@gdalle gdalle added the benchmark Run benchmarks on PR label Mar 31, 2025
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codecov Bot commented Mar 31, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (b33d436) to head (0efc816).
Report is 3 commits behind head on main.

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@@            Coverage Diff            @@
##              main      #216   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           15        15           
  Lines         1661      1706   +45     
=========================================
+ Hits          1661      1706   +45

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@gdalle gdalle removed the benchmark Run benchmarks on PR label Mar 31, 2025
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github-actions Bot commented Mar 31, 2025

Benchmark Results

main 0efc816... main/0efc816cf71210...
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.002 2.97 ± 0.17 ms 2.34 ± 0.019 ms 1.27
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.005 7.89 ± 0.37 ms 5.14 ± 0.04 ms 1.53
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.01 19.7 ± 0.56 ms 11.4 ± 0.13 ms 1.73
coloring/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 5.63 s 2.59 ± 0.0099 s 2.17
coloring/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 0.503 ± 0.023 s 0.352 ± 0.011 s 1.43
coloring/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 1.82 ± 0.03 s 0.953 ± 0.073 s 1.91
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 7.28 ± 0.14 ms 7.21 ± 0.22 ms 1.01
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 17.8 ± 0.26 ms 17.6 ± 0.31 ms 1.01
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.0396 ± 0.00071 s 0.0391 ± 0.00061 s 1.01
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 9.01 s 8.95 s 1.01
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 1.2 ± 0.083 s 1.14 ± 0.054 s 1.06
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 3.72 ± 0.13 s 3.57 ± 0.12 s 1.04
coloring/nonsymmetric/column/direct/n=1000/p=0.002 0.492 ± 0.013 ms 0.487 ± 0.0097 ms 1.01
coloring/nonsymmetric/column/direct/n=1000/p=0.005 1.22 ± 0.2 ms 1.2 ± 0.0091 ms 1.02
coloring/nonsymmetric/column/direct/n=1000/p=0.01 3.07 ± 0.035 ms 2.99 ± 0.014 ms 1.03
coloring/nonsymmetric/column/direct/n=100000/p=0.0001 0.532 ± 0.013 s 0.513 ± 0.0086 s 1.04
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5 0.0817 ± 0.013 s 0.0808 ± 0.00095 s 1.01
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5 0.215 ± 0.015 s 0.212 ± 0.0055 s 1.01
coloring/nonsymmetric/row/direct/n=1000/p=0.002 0.482 ± 0.014 ms 0.481 ± 0.0098 ms 1
coloring/nonsymmetric/row/direct/n=1000/p=0.005 1.22 ± 0.2 ms 1.21 ± 0.0093 ms 1.01
coloring/nonsymmetric/row/direct/n=1000/p=0.01 3.06 ± 0.033 ms 3.01 ± 0.014 ms 1.02
coloring/nonsymmetric/row/direct/n=100000/p=0.0001 0.531 ± 0.009 s 0.508 ± 0.0096 s 1.05
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5 0.0805 ± 0.012 s 0.0818 ± 0.00042 s 0.984
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5 0.208 ± 0.009 s 0.208 ± 0.0021 s 1
coloring/symmetric/column/direct/n=1000/p=0.002 1.55 ± 0.032 ms 1.14 ± 0.017 ms 1.36
coloring/symmetric/column/direct/n=1000/p=0.005 4 ± 0.034 ms 2.55 ± 0.016 ms 1.57
coloring/symmetric/column/direct/n=1000/p=0.01 9.77 ± 0.11 ms 5.6 ± 0.92 ms 1.74
coloring/symmetric/column/direct/n=100000/p=0.0001 2.14 ± 0.0045 s 0.936 ± 0.013 s 2.29
coloring/symmetric/column/direct/n=100000/p=2.0e-5 0.218 ± 0.0086 s 0.169 ± 0.0027 s 1.29
coloring/symmetric/column/direct/n=100000/p=5.0e-5 0.666 ± 0.0066 s 0.393 ± 0.0066 s 1.7
coloring/symmetric/column/substitution/n=1000/p=0.002 3.66 ± 0.12 ms 3.57 ± 0.055 ms 1.03
coloring/symmetric/column/substitution/n=1000/p=0.005 8.76 ± 0.074 ms 8.53 ± 0.1 ms 1.03
coloring/symmetric/column/substitution/n=1000/p=0.01 19.8 ± 0.15 ms 18.9 ± 0.26 ms 1.05
coloring/symmetric/column/substitution/n=100000/p=0.0001 3.86 ± 0.1 s 3.7 ± 0.13 s 1.04
coloring/symmetric/column/substitution/n=100000/p=2.0e-5 0.497 ± 0.0066 s 0.499 ± 0.028 s 0.998
coloring/symmetric/column/substitution/n=100000/p=5.0e-5 1.47 ± 0.066 s 1.44 ± 0.058 s 1.02
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.002 0.141 ± 0.0053 ms 0.15 ± 0.0061 ms 0.942
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.005 0.225 ± 0.0084 ms 0.237 ± 0.0082 ms 0.95
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.364 ± 0.011 ms 0.383 ± 0.011 ms 0.951
decompress/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 0.0863 ± 0.0031 s 0.0903 ± 0.0016 s 0.956
decompress/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 29.3 ± 1.1 ms 30.9 ± 0.7 ms 0.948
decompress/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 0.0554 ± 0.00099 s 0.0579 ± 0.00084 s 0.958
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.16 ± 0.011 ms 0.161 ± 0.0063 ms 0.996
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.312 ± 0.0098 ms 0.312 ± 0.0097 ms 1
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.619 ± 0.012 ms 0.609 ± 0.014 ms 1.02
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 0.205 ± 0.009 s 0.192 ± 0.0084 s 1.07
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 0.0373 ± 0.0014 s 0.037 ± 0.0012 s 1.01
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 0.0869 ± 0.0075 s 0.0807 ± 0.002 s 1.08
decompress/nonsymmetric/column/direct/n=1000/p=0.002 24.9 ± 1.2 μs 25.5 ± 1 μs 0.976
decompress/nonsymmetric/column/direct/n=1000/p=0.005 0.048 ± 0.0017 ms 0.048 ± 0.0018 ms 1
decompress/nonsymmetric/column/direct/n=1000/p=0.01 0.0861 ± 0.0041 ms 0.0862 ± 0.0038 ms 1
decompress/nonsymmetric/column/direct/n=100000/p=0.0001 23.2 ± 0.83 ms 26 ± 1.4 ms 0.893
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5 4.08 ± 0.29 ms 4.49 ± 0.28 ms 0.909
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5 11.1 ± 0.3 ms 12.4 ± 0.36 ms 0.898
decompress/nonsymmetric/row/direct/n=1000/p=0.002 24.1 ± 1.4 μs 25.2 ± 1.2 μs 0.958
decompress/nonsymmetric/row/direct/n=1000/p=0.005 0.0431 ± 0.0024 ms 0.0437 ± 0.0015 ms 0.987
decompress/nonsymmetric/row/direct/n=1000/p=0.01 0.0753 ± 0.0062 ms 0.0793 ± 0.0033 ms 0.95
decompress/nonsymmetric/row/direct/n=100000/p=0.0001 11.3 ± 0.5 ms 11.5 ± 0.91 ms 0.975
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5 2.82 ± 0.11 ms 3.14 ± 0.23 ms 0.898
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5 5.49 ± 0.18 ms 5.78 ± 0.23 ms 0.95
decompress/symmetric/column/direct/n=1000/p=0.002 25 ± 1.9 μs 24.5 ± 1.1 μs 1.02
decompress/symmetric/column/direct/n=1000/p=0.005 0.0472 ± 0.0017 ms 0.0449 ± 0.002 ms 1.05
decompress/symmetric/column/direct/n=1000/p=0.01 0.0852 ± 0.0036 ms 0.0793 ± 0.0037 ms 1.07
decompress/symmetric/column/direct/n=100000/p=0.0001 22.6 ± 0.99 ms 20.6 ± 1.8 ms 1.1
decompress/symmetric/column/direct/n=100000/p=2.0e-5 4.18 ± 0.74 ms 3.47 ± 0.34 ms 1.2
decompress/symmetric/column/direct/n=100000/p=5.0e-5 11 ± 0.26 ms 10 ± 0.32 ms 1.1
decompress/symmetric/column/substitution/n=1000/p=0.002 0.0877 ± 0.0026 ms 0.0872 ± 0.002 ms 1.01
decompress/symmetric/column/substitution/n=1000/p=0.005 0.187 ± 0.0076 ms 0.17 ± 0.0067 ms 1.1
decompress/symmetric/column/substitution/n=1000/p=0.01 0.332 ± 0.01 ms 0.334 ± 0.011 ms 0.995
decompress/symmetric/column/substitution/n=100000/p=0.0001 0.0924 ± 0.0042 s 0.0934 ± 0.0027 s 0.989
decompress/symmetric/column/substitution/n=100000/p=2.0e-5 24.1 ± 0.43 ms 26.5 ± 0.27 ms 0.91
decompress/symmetric/column/substitution/n=100000/p=5.0e-5 0.0485 ± 0.00091 s 0.0455 ± 0.00077 s 1.06
time_to_load 0.216 ± 0.0025 s 0.216 ± 0.00051 s 0.997
main 0efc816... main/0efc816cf71210...
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.002 12.7 k allocs: 3.1 MB 0.56 k allocs: 2.84 MB 1.09
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.005 29.4 k allocs: 5.67 MB 0.58 k allocs: 5.04 MB 1.12
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.0612 M allocs: 10.6 MB 0.6 k allocs: 9.2 MB 1.16
coloring/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 6.05 M allocs: 1.15 GB 0.72 k allocs: 0.954 GB 1.2
coloring/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 1.18 M allocs: 0.324 GB 0.66 k allocs: 0.286 GB 1.14
coloring/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 2.87 M allocs: 0.635 GB 0.7 k allocs: 0.547 GB 1.16
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.0513 M allocs: 6.61 MB 0.0513 M allocs: 6.85 MB 0.966
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.0978 M allocs: 12 MB 0.0978 M allocs: 12.4 MB 0.963
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.187 M allocs: 22.8 MB 0.187 M allocs: 23.7 MB 0.965
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 17.9 M allocs: 2.2 GB 17.9 M allocs: 2.28 GB 0.964
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 4.93 M allocs: 0.623 GB 4.93 M allocs: 0.646 GB 0.965
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 9.54 M allocs: 1.21 GB 9.54 M allocs: 1.25 GB 0.964
coloring/nonsymmetric/column/direct/n=1000/p=0.002 0.135 k allocs: 0.354 MB 0.135 k allocs: 0.354 MB 1
coloring/nonsymmetric/column/direct/n=1000/p=0.005 0.135 k allocs: 0.578 MB 0.135 k allocs: 0.578 MB 1
coloring/nonsymmetric/column/direct/n=1000/p=0.01 0.135 k allocs: 0.967 MB 0.135 k allocs: 0.967 MB 1
coloring/nonsymmetric/column/direct/n=100000/p=0.0001 0.135 k allocs: 0.0931 GB 0.135 k allocs: 0.0931 GB 1
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5 0.135 k allocs: 0.0335 GB 0.135 k allocs: 0.0335 GB 1
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5 0.135 k allocs: 0.0558 GB 0.135 k allocs: 0.0558 GB 1
coloring/nonsymmetric/row/direct/n=1000/p=0.002 0.135 k allocs: 0.354 MB 0.135 k allocs: 0.354 MB 1
coloring/nonsymmetric/row/direct/n=1000/p=0.005 0.135 k allocs: 0.578 MB 0.135 k allocs: 0.578 MB 1
coloring/nonsymmetric/row/direct/n=1000/p=0.01 0.135 k allocs: 0.967 MB 0.135 k allocs: 0.967 MB 1
coloring/nonsymmetric/row/direct/n=100000/p=0.0001 0.135 k allocs: 0.0931 GB 0.135 k allocs: 0.0931 GB 1
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5 0.135 k allocs: 0.0335 GB 0.135 k allocs: 0.0335 GB 1
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5 0.135 k allocs: 0.0558 GB 0.135 k allocs: 0.0558 GB 1
coloring/symmetric/column/direct/n=1000/p=0.002 6.26 k allocs: 0.902 MB 0.28 k allocs: 0.775 MB 1.16
coloring/symmetric/column/direct/n=1000/p=0.005 14.5 k allocs: 1.72 MB 0.3 k allocs: 1.41 MB 1.22
coloring/symmetric/column/direct/n=1000/p=0.01 30.6 k allocs: 3.32 MB 0.32 k allocs: 2.6 MB 1.27
coloring/symmetric/column/direct/n=100000/p=0.0001 3.02 M allocs: 0.38 GB 0.44 k allocs: 0.284 GB 1.34
coloring/symmetric/column/direct/n=100000/p=2.0e-5 0.589 M allocs: 0.0939 GB 0.38 k allocs: 0.0746 GB 1.26
coloring/symmetric/column/direct/n=100000/p=5.0e-5 1.44 M allocs: 0.199 GB 0.42 k allocs: 0.155 GB 1.28
coloring/symmetric/column/substitution/n=1000/p=0.002 25.6 k allocs: 2.84 MB 25.6 k allocs: 2.95 MB 0.96
coloring/symmetric/column/substitution/n=1000/p=0.005 0.0492 M allocs: 5.17 MB 0.0492 M allocs: 5.4 MB 0.958
coloring/symmetric/column/substitution/n=1000/p=0.01 0.0937 M allocs: 10.3 MB 0.0937 M allocs: 10.7 MB 0.961
coloring/symmetric/column/substitution/n=100000/p=0.0001 8.95 M allocs: 0.965 GB 8.95 M allocs: 1.01 GB 0.959
coloring/symmetric/column/substitution/n=100000/p=2.0e-5 2.47 M allocs: 0.262 GB 2.47 M allocs: 0.273 GB 0.959
coloring/symmetric/column/substitution/n=100000/p=5.0e-5 4.77 M allocs: 0.525 GB 4.77 M allocs: 0.547 GB 0.959
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/nonsymmetric/column/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/column/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/column/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/column/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/nonsymmetric/row/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/nonsymmetric/row/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/nonsymmetric/row/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/nonsymmetric/row/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/symmetric/column/direct/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/symmetric/column/direct/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/symmetric/column/direct/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/symmetric/column/direct/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/symmetric/column/direct/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/symmetric/column/direct/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
decompress/symmetric/column/substitution/n=1000/p=0.002 0.045 k allocs: 0.197 MB 0.045 k allocs: 0.197 MB 1
decompress/symmetric/column/substitution/n=1000/p=0.005 0.045 k allocs: 0.419 MB 0.045 k allocs: 0.419 MB 1
decompress/symmetric/column/substitution/n=1000/p=0.01 0.045 k allocs: 0.802 MB 0.045 k allocs: 0.802 MB 1
decompress/symmetric/column/substitution/n=100000/p=0.0001 0.045 k allocs: 0.0782 GB 0.045 k allocs: 0.0782 GB 1
decompress/symmetric/column/substitution/n=100000/p=2.0e-5 0.045 k allocs: 19.1 MB 0.045 k allocs: 19.1 MB 1
decompress/symmetric/column/substitution/n=100000/p=5.0e-5 0.045 k allocs: 0.0409 GB 0.045 k allocs: 0.0409 GB 1
time_to_load 0.159 k allocs: 11.2 kB 0.159 k allocs: 11.2 kB 1

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gdalle commented Mar 31, 2025

Closing in favor of #214

@gdalle gdalle closed this Mar 31, 2025
@amontoison amontoison mentioned this pull request Apr 1, 2025
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@gdalle gdalle deleted the gd/edgeindex branch April 1, 2025 14:03
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@gdalle @amontoison