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Implement our own structure Forest#190

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gdalle merged 9 commits intomainfrom
forest
Mar 25, 2025
Merged

Implement our own structure Forest#190
gdalle merged 9 commits intomainfrom
forest

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@amontoison
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@amontoison amontoison commented Feb 14, 2025 •
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#143

  • Implement our own structure Forest with only the routines and attributes that we need for SMC.jl. We don't need anymore a vector with all edges stored (revmap), so it will be great for storage.
  • root_union! returns the index of the root edge now. It was the root edge previously and we needed to recover the index with a dictionary. It's more efficient now.
  • Drop the dependency on DataStructures.jl.
  • Don't compress the forest independently; this is already handled during the creation of the TreeSet now. (see feat: allow neutral colors and postprocessing #166).

@amontoison amontoison added performance Speeding things up benchmark Run benchmarks on PR labels Feb 14, 2025
@amontoison amontoison requested a review from gdalle February 14, 2025 22:24
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (a113eea) to head (67ad288).
Report is 3 commits behind head on main.

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@@            Coverage Diff            @@
##              main      #190   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           14        15    +1     
  Lines         1647      1671   +24     
=========================================
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github-actions Bot commented Feb 14, 2025 •
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Benchmark Results

main 67ad288... main/67ad288da8d644...
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.002 2.97 ± 0.18 ms 2.98 ± 0.19 ms 0.996
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.005 7.89 ± 0.39 ms 7.97 ± 0.39 ms 0.99
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.01 19.5 ± 0.53 ms 19.8 ± 0.44 ms 0.987
coloring/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 5.52 s 5.62 s 0.982
coloring/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 0.484 ± 0.017 s 0.493 ± 0.029 s 0.983
coloring/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 1.74 ± 0.061 s 1.82 ± 0.068 s 0.958
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 8.03 ± 0.19 ms 7.33 ± 0.16 ms 1.1
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 19.8 ± 0.37 ms 17.8 ± 0.19 ms 1.11
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.0443 ± 0.0009 s 0.0396 ± 0.00024 s 1.12
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 9.45 s 8.96 s 1.05
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 1.29 ± 0.1 s 1.2 ± 0.051 s 1.08
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 3.95 ± 0.12 s 3.77 ± 0.17 s 1.05
coloring/nonsymmetric/column/direct/n=1000/p=0.002 0.489 ± 0.014 ms 0.496 ± 0.014 ms 0.987
coloring/nonsymmetric/column/direct/n=1000/p=0.005 1.22 ± 0.2 ms 1.23 ± 0.21 ms 0.994
coloring/nonsymmetric/column/direct/n=1000/p=0.01 3.08 ± 0.031 ms 3.03 ± 0.027 ms 1.02
coloring/nonsymmetric/column/direct/n=100000/p=0.0001 0.517 ± 0.0077 s 0.533 ± 0.01 s 0.97
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5 0.0823 ± 0.013 s 0.082 ± 0.013 s 1
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5 0.207 ± 0.0046 s 0.209 ± 0.0067 s 0.991
coloring/nonsymmetric/row/direct/n=1000/p=0.002 0.476 ± 0.016 ms 0.478 ± 0.014 ms 0.997
coloring/nonsymmetric/row/direct/n=1000/p=0.005 1.19 ± 0.2 ms 1.19 ± 0.21 ms 0.997
coloring/nonsymmetric/row/direct/n=1000/p=0.01 2.97 ± 0.035 ms 2.97 ± 0.039 ms 1
coloring/nonsymmetric/row/direct/n=100000/p=0.0001 0.48 ± 0.0092 s 0.5 ± 0.016 s 0.96
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5 0.0792 ± 0.013 s 0.0821 ± 0.013 s 0.964
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5 0.196 ± 0.01 s 0.209 ± 0.0071 s 0.934
coloring/symmetric/column/direct/n=1000/p=0.002 1.55 ± 0.029 ms 1.55 ± 0.027 ms 0.999
coloring/symmetric/column/direct/n=1000/p=0.005 3.99 ± 0.033 ms 4.01 ± 0.035 ms 0.996
coloring/symmetric/column/direct/n=1000/p=0.01 9.68 ± 0.084 ms 9.82 ± 0.08 ms 0.986
coloring/symmetric/column/direct/n=100000/p=0.0001 2.08 ± 0.027 s 2.14 ± 0.016 s 0.973
coloring/symmetric/column/direct/n=100000/p=2.0e-5 0.214 ± 0.0074 s 0.217 ± 0.0052 s 0.99
coloring/symmetric/column/direct/n=100000/p=5.0e-5 0.651 ± 0.035 s 0.67 ± 0.012 s 0.971
coloring/symmetric/column/substitution/n=1000/p=0.002 4 ± 0.077 ms 3.69 ± 0.056 ms 1.09
coloring/symmetric/column/substitution/n=1000/p=0.005 9.82 ± 0.19 ms 8.86 ± 0.13 ms 1.11
coloring/symmetric/column/substitution/n=1000/p=0.01 21.7 ± 0.19 ms 19.7 ± 0.15 ms 1.1
coloring/symmetric/column/substitution/n=100000/p=0.0001 4.02 ± 0.047 s 3.99 ± 0.0084 s 1.01
coloring/symmetric/column/substitution/n=100000/p=2.0e-5 0.55 ± 0.011 s 0.505 ± 0.0086 s 1.09
coloring/symmetric/column/substitution/n=100000/p=5.0e-5 1.6 ± 0.12 s 1.48 ± 0.059 s 1.08
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.002 0.152 ± 0.0072 ms 0.14 ± 0.0094 ms 1.08
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.005 0.241 ± 0.0081 ms 0.232 ± 0.0091 ms 1.04
decompress/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.377 ± 0.013 ms 0.372 ± 0.011 ms 1.01
decompress/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 0.0893 ± 0.0028 s 0.0886 ± 0.0048 s 1.01
decompress/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 30.2 ± 1 ms 30.3 ± 1.4 ms 0.998
decompress/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 0.058 ± 0.0019 s 0.0565 ± 0.0026 s 1.03
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.16 ± 0.0077 ms 0.156 ± 0.0066 ms 1.02
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.311 ± 0.01 ms 0.313 ± 0.01 ms 0.993
decompress/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.612 ± 0.014 ms 0.612 ± 0.013 ms 1
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 0.18 ± 0.0078 s 0.203 ± 0.0084 s 0.886
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 0.0356 ± 0.0017 s 0.038 ± 0.002 s 0.936
decompress/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 0.0768 ± 0.0039 s 0.0803 ± 0.0054 s 0.957
decompress/nonsymmetric/column/direct/n=1000/p=0.002 25.9 ± 1.3 μs 25.6 ± 1.4 μs 1.01
decompress/nonsymmetric/column/direct/n=1000/p=0.005 0.048 ± 0.0024 ms 0.0475 ± 0.0018 ms 1.01
decompress/nonsymmetric/column/direct/n=1000/p=0.01 0.09 ± 0.0045 ms 0.088 ± 0.004 ms 1.02
decompress/nonsymmetric/column/direct/n=100000/p=0.0001 25.6 ± 1.6 ms 24.5 ± 1.5 ms 1.04
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5 4.49 ± 0.48 ms 4.08 ± 0.27 ms 1.1
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5 12.2 ± 0.58 ms 11.7 ± 0.42 ms 1.04
decompress/nonsymmetric/row/direct/n=1000/p=0.002 23.8 ± 1.6 μs 24.3 ± 1.5 μs 0.981
decompress/nonsymmetric/row/direct/n=1000/p=0.005 0.0419 ± 0.0016 ms 0.0422 ± 0.0026 ms 0.991
decompress/nonsymmetric/row/direct/n=1000/p=0.01 0.0724 ± 0.0034 ms 0.0744 ± 0.0036 ms 0.972
decompress/nonsymmetric/row/direct/n=100000/p=0.0001 11 ± 0.62 ms 11.6 ± 0.55 ms 0.951
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5 2.95 ± 0.15 ms 2.98 ± 0.14 ms 0.988
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5 5.64 ± 0.31 ms 5.81 ± 0.22 ms 0.972
decompress/symmetric/column/direct/n=1000/p=0.002 26.1 ± 2.7 μs 24.8 ± 2.1 μs 1.05
decompress/symmetric/column/direct/n=1000/p=0.005 0.0479 ± 0.0023 ms 0.0456 ± 0.0019 ms 1.05
decompress/symmetric/column/direct/n=1000/p=0.01 0.0862 ± 0.0043 ms 0.0816 ± 0.0048 ms 1.06
decompress/symmetric/column/direct/n=100000/p=0.0001 22.8 ± 1.6 ms 20.8 ± 1 ms 1.1
decompress/symmetric/column/direct/n=100000/p=2.0e-5 3.83 ± 0.58 ms 3.48 ± 0.38 ms 1.1
decompress/symmetric/column/direct/n=100000/p=5.0e-5 10.8 ± 0.37 ms 10.1 ± 0.33 ms 1.07
decompress/symmetric/column/substitution/n=1000/p=0.002 0.103 ± 0.0028 ms 0.105 ± 0.0027 ms 0.979
decompress/symmetric/column/substitution/n=1000/p=0.005 0.197 ± 0.0078 ms 0.189 ± 0.0079 ms 1.05
decompress/symmetric/column/substitution/n=1000/p=0.01 0.327 ± 0.011 ms 0.343 ± 0.012 ms 0.954
decompress/symmetric/column/substitution/n=100000/p=0.0001 0.0899 ± 0.0049 s 0.0925 ± 0.0044 s 0.972
decompress/symmetric/column/substitution/n=100000/p=2.0e-5 26 ± 0.58 ms 26.4 ± 0.59 ms 0.985
decompress/symmetric/column/substitution/n=100000/p=5.0e-5 0.047 ± 0.0009 s 0.0475 ± 0.0011 s 0.99
time_to_load 0.287 ± 0.0017 s 0.238 ± 0.00026 s 1.21
main 67ad288... main/67ad288da8d644...
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.002 12.7 k allocs: 3.1 MB 12.7 k allocs: 3.1 MB 1
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.005 29.4 k allocs: 5.67 MB 29.4 k allocs: 5.67 MB 1
coloring/nonsymmetric/bidirectional/direct/n=1000/p=0.01 0.0612 M allocs: 10.6 MB 0.0612 M allocs: 10.6 MB 1
coloring/nonsymmetric/bidirectional/direct/n=100000/p=0.0001 6.05 M allocs: 1.15 GB 6.05 M allocs: 1.15 GB 1
coloring/nonsymmetric/bidirectional/direct/n=100000/p=2.0e-5 1.18 M allocs: 0.324 GB 1.18 M allocs: 0.324 GB 1
coloring/nonsymmetric/bidirectional/direct/n=100000/p=5.0e-5 2.87 M allocs: 0.635 GB 2.87 M allocs: 0.635 GB 1
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.002 0.0513 M allocs: 6.71 MB 0.0513 M allocs: 6.61 MB 1.01
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.005 0.0978 M allocs: 12.4 MB 0.0978 M allocs: 12 MB 1.03
coloring/nonsymmetric/bidirectional/substitution/n=1000/p=0.01 0.187 M allocs: 23.7 MB 0.187 M allocs: 22.8 MB 1.04
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=0.0001 17.9 M allocs: 2.27 GB 17.9 M allocs: 2.2 GB 1.03
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=2.0e-5 4.93 M allocs: 0.638 GB 4.93 M allocs: 0.623 GB 1.02
coloring/nonsymmetric/bidirectional/substitution/n=100000/p=5.0e-5 9.54 M allocs: 1.24 GB 9.54 M allocs: 1.21 GB 1.03
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 6.26 k allocs: 0.902 MB 1
coloring/symmetric/column/direct/n=1000/p=0.005 14.5 k allocs: 1.72 MB 14.5 k allocs: 1.72 MB 1
coloring/symmetric/column/direct/n=1000/p=0.01 30.6 k allocs: 3.32 MB 30.6 k allocs: 3.32 MB 1
coloring/symmetric/column/direct/n=100000/p=0.0001 3.02 M allocs: 0.38 GB 3.02 M allocs: 0.38 GB 1
coloring/symmetric/column/direct/n=100000/p=2.0e-5 0.589 M allocs: 0.0939 GB 0.589 M allocs: 0.0939 GB 1
coloring/symmetric/column/direct/n=100000/p=5.0e-5 1.44 M allocs: 0.199 GB 1.44 M allocs: 0.199 GB 1
coloring/symmetric/column/substitution/n=1000/p=0.002 25.6 k allocs: 2.92 MB 25.6 k allocs: 2.84 MB 1.03
coloring/symmetric/column/substitution/n=1000/p=0.005 0.0492 M allocs: 5.36 MB 0.0492 M allocs: 5.17 MB 1.04
coloring/symmetric/column/substitution/n=1000/p=0.01 0.0937 M allocs: 10.6 MB 0.0937 M allocs: 10.3 MB 1.03
coloring/symmetric/column/substitution/n=100000/p=0.0001 8.95 M allocs: 1 GB 8.95 M allocs: 0.965 GB 1.04
coloring/symmetric/column/substitution/n=100000/p=2.0e-5 2.47 M allocs: 0.269 GB 2.47 M allocs: 0.262 GB 1.03
coloring/symmetric/column/substitution/n=100000/p=5.0e-5 4.77 M allocs: 0.543 GB 4.77 M allocs: 0.525 GB 1.04
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

amontoison
amontoison commented Feb 14, 2025
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gdalle
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This looks really promising! In addition to the remarks below, would it be possible to add tests that specifically target the Forest structure, regardless from coloring?

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amontoison
amontoison commented Feb 19, 2025
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amontoison commented Mar 24, 2025

@gdalle
I added some unit tests for the structure Forest as you requested last week.

@gdalle gdalle merged commit 1e8127c into main Mar 25, 2025
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@gdalle gdalle deleted the forest branch March 25, 2025 20:13
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