Avoid allocation when creating adjacency graph

[gdalle]

Warning

Benchmark before merging.

• Add a type parameter loops::Bool to the private struct Graph that decides whether coefficients (i, i) present in the matrix should be included as edges in the graph.
• Adjust neighbors, degree, nnz accordingly. In particular, neighbors uses Iterators.filter, which slows it down by an unknown amount.
• Make bipartite_graph create two Graph{true} and adjacency_graph create a Graph{false}.
• Force star_coloring and acyclic_coloring to only work on Graph{false} (no loops).
• Add some tests.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (123889f) to head (b0a59e4).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #104   +/-   ##
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  Coverage   100.00%   100.00%           
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  Files           10        10           
  Lines          732       755   +23     
=========================================
+ Hits           732       755   +23     

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[github-actions]

Benchmark Results

	main	b0a59e4...	main/b0a59e45e3a876...
coloring/nonsymmetric/column/direct/n=1000/p=0.002	0.0992 ± 0.0048 ms	0.0984 ± 0.0049 ms	1.01
coloring/nonsymmetric/column/direct/n=1000/p=0.005	0.211 ± 0.0084 ms	0.21 ± 0.0084 ms	1.01
coloring/nonsymmetric/column/direct/n=1000/p=0.01	0.438 ± 0.015 ms	0.435 ± 0.015 ms	1.01
coloring/nonsymmetric/column/direct/n=100000/p=0.0001	0.0778 ± 0.0019 s	0.0748 ± 0.0038 s	1.04
coloring/nonsymmetric/column/direct/n=100000/p=2.0e-5	14.8 ± 0.33 ms	14.5 ± 0.66 ms	1.02
coloring/nonsymmetric/column/direct/n=100000/p=5.0e-5	0.0348 ± 0.00068 s	0.0338 ± 0.0013 s	1.03
coloring/nonsymmetric/row/direct/n=1000/p=0.002	0.112 ± 0.0054 ms	0.112 ± 0.0055 ms	1
coloring/nonsymmetric/row/direct/n=1000/p=0.005	0.236 ± 0.0095 ms	0.235 ± 0.0095 ms	1
coloring/nonsymmetric/row/direct/n=1000/p=0.01	0.482 ± 0.016 ms	0.48 ± 0.017 ms	1
coloring/nonsymmetric/row/direct/n=100000/p=0.0001	0.0893 ± 0.003 s	0.0835 ± 0.0043 s	1.07
coloring/nonsymmetric/row/direct/n=100000/p=2.0e-5	17.2 ± 0.39 ms	16.9 ± 0.4 ms	1.02
coloring/nonsymmetric/row/direct/n=100000/p=5.0e-5	0.0398 ± 0.00079 s	0.0385 ± 0.0012 s	1.03
coloring/symmetric/column/direct/n=1000/p=0.002	0.308 ± 0.015 ms	0.278 ± 0.015 ms	1.11
coloring/symmetric/column/direct/n=1000/p=0.005	0.768 ± 0.027 ms	0.746 ± 0.028 ms	1.03
coloring/symmetric/column/direct/n=1000/p=0.01	1.78 ± 0.053 ms	1.81 ± 0.059 ms	0.981
coloring/symmetric/column/direct/n=100000/p=0.0001	0.407 ± 0.073 s	0.378 ± 0.052 s	1.08
coloring/symmetric/column/direct/n=100000/p=2.0e-5	0.0409 ± 0.0017 s	0.038 ± 0.0011 s	1.07
coloring/symmetric/column/direct/n=100000/p=5.0e-5	0.131 ± 0.0056 s	0.125 ± 0.0056 s	1.04
coloring/symmetric/column/substitution/n=1000/p=0.002	0.631 ± 0.031 ms	0.619 ± 0.03 ms	1.02
coloring/symmetric/column/substitution/n=1000/p=0.005	1.61 ± 0.057 ms	1.61 ± 0.06 ms	1
coloring/symmetric/column/substitution/n=1000/p=0.01	3.44 ± 0.095 ms	3.46 ± 0.099 ms	0.995
coloring/symmetric/column/substitution/n=100000/p=0.0001	0.71 ± 0.023 s	0.75 ± 0.045 s	0.947
coloring/symmetric/column/substitution/n=100000/p=2.0e-5	0.0973 ± 0.012 s	0.0948 ± 0.0063 s	1.03
coloring/symmetric/column/substitution/n=100000/p=5.0e-5	0.305 ± 0.029 s	0.295 ± 0.022 s	1.03
decompress/nonsymmetric/column/direct/n=1000/p=0.002	4.42 ± 0.33 μs	4.29 ± 0.31 μs	1.03
decompress/nonsymmetric/column/direct/n=1000/p=0.005	9.23 ± 0.52 μs	8.97 ± 0.71 μs	1.03
decompress/nonsymmetric/column/direct/n=1000/p=0.01	20.9 ± 1.3 μs	19.6 ± 1.6 μs	1.06
decompress/nonsymmetric/column/direct/n=100000/p=0.0001	5.18 ± 0.5 ms	5.29 ± 0.46 ms	0.979
decompress/nonsymmetric/column/direct/n=100000/p=2.0e-5	1.08 ± 0.11 ms	1.08 ± 0.094 ms	1
decompress/nonsymmetric/column/direct/n=100000/p=5.0e-5	2.66 ± 0.23 ms	2.57 ± 0.22 ms	1.04
decompress/nonsymmetric/row/direct/n=1000/p=0.002	4.38 ± 0.34 μs	4.29 ± 0.38 μs	1.02
decompress/nonsymmetric/row/direct/n=1000/p=0.005	8.34 ± 0.57 μs	8.48 ± 0.72 μs	0.983
decompress/nonsymmetric/row/direct/n=1000/p=0.01	17.4 ± 1.5 μs	16.6 ± 1.5 μs	1.05
decompress/nonsymmetric/row/direct/n=100000/p=0.0001	2.14 ± 0.92 ms	2.3 ± 0.99 ms	0.929
decompress/nonsymmetric/row/direct/n=100000/p=2.0e-5	0.467 ± 0.11 ms	0.46 ± 0.054 ms	1.01
decompress/nonsymmetric/row/direct/n=100000/p=5.0e-5	1.08 ± 0.33 ms	1.02 ± 0.053 ms	1.06
decompress/symmetric/column/direct/n=1000/p=0.002	4.52 ± 0.36 μs	4.34 ± 0.34 μs	1.04
decompress/symmetric/column/direct/n=1000/p=0.005	9 ± 0.49 μs	8.86 ± 0.46 μs	1.02
decompress/symmetric/column/direct/n=1000/p=0.01	18.8 ± 1.2 μs	18.6 ± 1.1 μs	1.01
decompress/symmetric/column/direct/n=100000/p=0.0001	4.81 ± 1.3 ms	4.76 ± 0.18 ms	1.01
decompress/symmetric/column/direct/n=100000/p=2.0e-5	1.01 ± 0.2 ms	0.953 ± 0.068 ms	1.06
decompress/symmetric/column/direct/n=100000/p=5.0e-5	2.37 ± 0.13 ms	2.37 ± 0.17 ms	1
decompress/symmetric/column/substitution/n=1000/p=0.002	0.0639 ± 0.0035 ms	0.0635 ± 0.0035 ms	1.01
decompress/symmetric/column/substitution/n=1000/p=0.005	0.16 ± 0.0072 ms	0.159 ± 0.0069 ms	1.01
decompress/symmetric/column/substitution/n=1000/p=0.01	0.345 ± 0.014 ms	0.34 ± 0.014 ms	1.01
decompress/symmetric/column/substitution/n=100000/p=0.0001	0.0651 ± 0.003 s	0.0628 ± 0.0045 s	1.04
decompress/symmetric/column/substitution/n=100000/p=2.0e-5	13 ± 0.38 ms	12.7 ± 0.35 ms	1.03
decompress/symmetric/column/substitution/n=100000/p=5.0e-5	0.0317 ± 0.0014 s	29.9 ± 1.1 ms	1.06
time_to_load	0.216 ± 0.00032 s	0.217 ± 0.0014 s	0.996