- | 0.1.1 | 0.1.2 | 0.1.3 | 0.1.4 | 0.1.5 | 0.2.1 | 0.2.2 | 0.2.3 | 0.3.0 | 0.3.1 | 0.3.2 | 0.3.3 | 0.3.4 | 0.3.5 | 0.3.6 | 0.3.7 | 0.4.0 | 0.4.1 | 0.5.0 | 0.5.1 | 0.5.2 |
|---|
- | for _ in ts.trees(): pass;'{filename}' |
-| for _ in ts.trees(): pass;'bench.trees' | 30.6 m | 30.8 m (0.8%) | 30.9 m (0.2%) | 31.5 m (2.0%) | 39.5 m (25.3%) | 41.0 m (3.7%) | 40.7 m (-0.8%) | 40.2 m (-1.1%) | 39.3 m (-2.3%) | 39.5 m (0.6%) | 38.6 m (-2.2%) | 39.6 m (2.5%) | 40.3 m (1.8%) | 38.6 m (-4.2%) | 39.2 m (1.6%) | 38.4 m (-2.1%) | 41.7 m (8.5%) | 41.9 m (0.4%) | 44.6 m (6.6%) | 44.5 m (-0.3%) | 44.6 m (0.2%) |
-| for _ in ts.trees(): pass;'tiny.trees' | 1.2 µ | 1.2 µ (-0.4%) | 1.1 µ (-1.8%) | 1.2 µ (1.7%) | 2.1 µ (78.8%) | 2.1 µ (2.1%) | 2.0 µ (-3.5%) | 2.1 µ (0.8%) | 2.1 µ (2.3%) | 2.1 µ (-0.7%) | 2.1 µ (1.1%) | 2.1 µ (-1.9%) | 2.1 µ (1.7%) | 2.1 µ (1.5%) | 2.8 µ (28.6%) | 2.7 µ (-0.5%) | 2.6 µ (-3.7%) | 2.8 µ (6.2%) | 3.2 µ (14.6%) | 3.0 µ (-5.7%) | 3.0 µ (-1.0%) |
- | for row in ts.populations(): {decode_metadata} |
-| for row in ts.populations(): pass | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 669.8 µ | 686.0 µ (2.4%) | 684.6 µ (-0.2%) | 675.6 µ (-1.3%) | 662.6 µ (-1.9%) | 648.8 µ (-2.1%) | 1.2 m (78.5%) | 1.1 m (-5.9%) | 1.1 m (4.0%) | 1.1 m (-3.0%) | 1.1 m (2.9%) | 1.2 m (5.2%) | 1.1 m (-5.9%) |
-| for row in ts.populations(): row.metadata | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 2.4 m | 2.4 m (0.3%) | 2.2 m (-8.6%) | 2.2 m (0.3%) | 2.2 m (2.5%) | 2.4 m (6.0%) | 3.2 m (34.2%) | 3.1 m (-3.1%) | 3.2 m (2.2%) | 3.3 m (3.1%) | 3.3 m (0.1%) | 3.3 m (0.5%) | 3.2 m (-3.7%) |
- | for row in ts.{table}(): pass |
-| for row in ts.edges(): pass | 168.9 m | 169.9 m (0.6%) | 174.5 m (2.7%) | 168.8 m (-3.3%) | 170.4 m (1.0%) | 194.1 m (13.9%) | 186.0 m (-4.2%) | 203.7 m (9.5%) | 340.6 m (67.3%) | 331.0 m (-2.8%) | 333.4 m (0.7%) | 336.7 m (1.0%) | 339.1 m (0.7%) | 336.0 m (-0.9%) | 626.0 m (86.3%) | 572.6 m (-8.5%) | 586.1 m (2.4%) | 594.2 m (1.4%) | 378.6 m (-36.3%) | 392.8 m (3.7%) | 398.2 m (1.4%) |
-| for row in ts.individuals(): pass | 33.4 m | 34.8 m (3.9%) | 33.9 m (-2.5%) | 33.1 m (-2.1%) | 34.1 m (2.8%) | 36.2 m (6.1%) | 34.6 m (-4.4%) | 34.0 m (-1.6%) | 49.0 m (44.1%) | 51.0 m (4.1%) | 49.9 m (-2.2%) | 50.2 m (0.7%) | 50.2 m (-0.1%) | 56.6 m (12.8%) | 91.9 m (62.4%) | 88.4 m (-3.8%) | 88.9 m (0.5%) | 92.2 m (3.7%) | 128.6 m (39.5%) | 123.8 m (-3.7%) | 128.3 m (3.6%) |
-| for row in ts.migrations(): pass | 3.3 m | 3.4 m (2.2%) | 3.3 m (-4.2%) | 3.3 m (0.6%) | 3.3 m (1.1%) | 3.3 m (-1.0%) | 3.2 m (-3.1%) | 3.5 m (8.8%) | 8.7 m (152.2%) | 8.9 m (1.5%) | 8.6 m (-3.1%) | 8.7 m (1.1%) | 8.9 m (2.6%) | 8.6 m (-3.5%) | 15.9 m (85.5%) | 15.5 m (-2.9%) | 15.4 m (-0.4%) | 15.7 m (1.8%) | 15.7 m (-0.1%) | 15.1 m (-3.7%) | 15.6 m (3.3%) |
-| for row in ts.mutations(): pass | 666.9 m | 671.5 m (0.7%) | 654.8 m (-2.5%) | 659.9 m (0.8%) | 647.8 m (-1.8%) | 661.8 m (2.2%) | 670.4 m (1.3%) | 664.3 m (-0.9%) | 888.4 m (33.7%) | 923.9 m (4.0%) | 920.3 m (-0.4%) | 886.5 m (-3.7%) | 921.1 m (3.9%) | 885.4 m (-3.9%) | 1.5 (68.3%) | 1.5 (-2.3%) | 1.4 (-1.1%) | 1.5 (2.3%) | 1.5 (3.4%) | 1.6 (3.6%) | 1.6 (-0.5%) |
-| for row in ts.nodes(): pass | 142.7 m | 147.4 m (3.3%) | 140.0 m (-5.1%) | 143.9 m (2.8%) | 142.2 m (-1.2%) | 138.1 m (-2.9%) | 140.0 m (1.4%) | 144.8 m (3.5%) | 200.8 m (38.6%) | 198.9 m (-1.0%) | 201.5 m (1.3%) | 199.8 m (-0.8%) | 202.4 m (1.3%) | 201.7 m (-0.3%) | 371.0 m (83.9%) | 347.4 m (-6.3%) | 351.9 m (1.3%) | 362.8 m (3.1%) | 354.2 m (-2.4%) | 368.4 m (4.0%) | 367.3 m (-0.3%) |
-| for row in ts.populations(): pass | 1.5 µ | 1.5 µ (-2.6%) | 1.6 µ (5.4%) | 1.5 µ (-4.7%) | 1.5 µ (-0.9%) | 1.5 µ (2.8%) | 1.5 µ (-1.2%) | 1.5 µ (1.6%) | 2.5 µ (68.1%) | 2.7 µ (5.0%) | 2.7 µ (0.0%) | 2.7 µ (1.5%) | 2.6 µ (-2.8%) | 2.7 µ (1.6%) | 4.2 µ (57.5%) | 4.0 µ (-4.5%) | 4.0 µ (-0.3%) | 4.1 µ (0.9%) | 4.1 µ (0.7%) | 4.2 µ (4.0%) | 4.1 µ (-4.2%) |
-| for row in ts.provenances(): pass | 1.4 µ | 1.4 µ (-0.3%) | 1.4 µ (2.3%) | 1.4 µ (-2.4%) | 1.4 µ (2.2%) | 1.4 µ (0.0%) | 1.4 µ (-1.1%) | 1.4 µ (1.4%) | 2.0 µ (42.8%) | 2.0 µ (-1.1%) | 2.0 µ (1.1%) | 1.9 µ (-4.5%) | 2.0 µ (3.6%) | 2.1 µ (3.7%) | 2.0 µ (-6.6%) | 2.0 µ (1.9%) | 2.0 µ (-1.7%) | 2.0 µ (-0.2%) | 2.0 µ (2.0%) | 2.0 µ (-1.2%) | 2.0 µ (-0.7%) |
-| for row in ts.sites(): pass | 600.0 m | 584.9 m (-2.5%) | 586.4 m (0.3%) | 596.3 m (1.7%) | 578.4 m (-3.0%) | 585.8 m (1.3%) | 606.6 m (3.5%) | 590.1 m (-2.7%) | 789.9 m (33.9%) | 828.0 m (4.8%) | 834.7 m (0.8%) | 785.7 m (-5.9%) | 831.8 m (5.9%) | 798.6 m (-4.0%) | 1.4 (81.3%) | 1.4 (-3.0%) | 1.4 (-0.3%) | 1.5 (3.7%) | 1.5 (1.7%) | 1.5 (1.8%) | 1.5 (1.0%) |
- | for v in ts.variants(): pass;'{filename}' |
-| for v in ts.variants(): pass;'bench.trees' | 5.1 | 5.3 (4.0%) | 5.3 (-0.4%) | 5.3 (-0.2%) | 5.1 (-2.7%) | 5.5 (7.0%) | 5.5 (0.2%) | 5.4 (-2.8%) | 21.7 (304.2%) | 21.3 (-2.0%) | 21.2 (-0.2%) | 21.1 (-0.5%) | 21.4 (1.5%) | 21.5 (0.3%) | 21.8 (1.5%) | 21.8 (-0.1%) | 18.3 (-16.1%) | 18.2 (-0.3%) | 12.3 (-32.8%) | 17.5 (42.8%) | 17.6 (0.4%) |
-| for v in ts.variants(): pass;'tiny.trees' | 5.7 µ | 5.5 µ (-2.0%) | 5.5 µ (-0.3%) | 5.6 µ (1.0%) | 5.5 µ (-2.3%) | 5.8 µ (6.5%) | 5.7 µ (-1.6%) | 6.0 µ (4.4%) | 7.5 µ (25.1%) | 7.2 µ (-3.5%) | 7.3 µ (1.4%) | 7.2 µ (-1.5%) | 7.5 µ (4.2%) | 7.1 µ (-5.9%) | 11.5 µ (62.9%) | 10.9 µ (-4.7%) | 11.2 µ (2.3%) | 11.3 µ (0.7%) | 2.2 µ (-80.2%) | 54.2 µ (2325.3%) | 11.7 µ (-78.4%) |
- | tables.{table} |
-| tables.edges | 450.7 n | 463.8 n (2.9%) | 467.4 n (0.8%) | 433.3 n (-7.3%) | 457.2 n (5.5%) | 777.4 n (70.0%) | 806.2 n (3.7%) | 796.2 n (-1.2%) | 3.4 µ (324.0%) | 3.4 µ (0.1%) | 3.3 µ (-1.4%) | 3.3 µ (-0.3%) | 3.4 µ (2.6%) | 3.4 µ (-0.8%) | 2.7 µ (-21.3%) | 1.8 µ (-30.6%) | 1.9 µ (4.4%) | 1.9 µ (-3.7%) | 1.9 µ (2.6%) | 1.9 µ (-2.4%) | 51.0 n (-97.3%) |
-| tables.individuals | 450.2 n | 452.7 n (0.6%) | 447.4 n (-1.2%) | 440.1 n (-1.6%) | 444.8 n (1.1%) | 795.9 n (78.9%) | 797.8 n (0.2%) | 809.0 n (1.4%) | 3.2 µ (289.5%) | 3.2 µ (0.8%) | 3.2 µ (0.3%) | 3.1 µ (-3.2%) | 3.2 µ (4.7%) | 3.3 µ (2.3%) | 2.5 µ (-23.2%) | 1.9 µ (-25.8%) | 1.9 µ (2.9%) | 1.9 µ (-3.6%) | 1.9 µ (1.3%) | 1.9 µ (-0.0%) | 45.0 n (-97.6%) |
-| tables.migrations | 445.3 n | 440.5 n (-1.1%) | 447.9 n (1.7%) | 432.9 n (-3.4%) | 436.9 n (0.9%) | 811.8 n (85.8%) | 811.7 n (-0.0%) | 812.7 n (0.1%) | 3.5 µ (333.6%) | 3.5 µ (0.3%) | 3.6 µ (1.5%) | 3.6 µ (-0.9%) | 3.6 µ (2.0%) | 3.6 µ (-1.5%) | 2.6 µ (-27.4%) | 1.9 µ (-26.4%) | 1.9 µ (0.7%) | 1.9 µ (-0.2%) | 1.9 µ (1.4%) | 1.9 µ (-2.3%) | 54.6 n (-97.1%) |
-| tables.mutations | 486.4 n | 453.1 n (-6.9%) | 444.8 n (-1.8%) | 434.6 n (-2.3%) | 441.4 n (1.6%) | 821.8 n (86.2%) | 826.2 n (0.5%) | 855.6 n (3.6%) | 3.5 µ (314.3%) | 3.6 µ (0.5%) | 3.5 µ (-1.8%) | 3.4 µ (-1.4%) | 3.6 µ (5.1%) | 3.5 µ (-3.7%) | 2.7 µ (-21.3%) | 1.9 µ (-30.8%) | 1.9 µ (1.5%) | 1.9 µ (-0.8%) | 1.9 µ (-0.5%) | 1.9 µ (1.1%) | 49.5 n (-97.4%) |
-| tables.nodes | 455.3 n | 447.8 n (-1.7%) | 453.5 n (1.3%) | 435.7 n (-3.9%) | 438.6 n (0.7%) | 810.9 n (84.9%) | 872.6 n (7.6%) | 839.5 n (-3.8%) | 3.4 µ (303.4%) | 3.5 µ (2.0%) | 3.4 µ (-2.7%) | 3.4 µ (2.3%) | 3.3 µ (-2.9%) | 3.3 µ (-0.0%) | 2.7 µ (-19.4%) | 1.9 µ (-30.7%) | 1.9 µ (0.9%) | 1.9 µ (0.2%) | 1.9 µ (1.3%) | 1.9 µ (-2.6%) | 47.7 n (-97.4%) |
-| tables.populations | 462.2 n | 457.0 n (-1.1%) | 462.0 n (1.1%) | 434.8 n (-5.9%) | 429.8 n (-1.1%) | 756.9 n (76.1%) | 758.4 n (0.2%) | 766.0 n (1.0%) | 246.6 µ (32096.1%) | 245.6 µ (-0.4%) | 244.2 µ (-0.6%) | 242.8 µ (-0.6%) | 245.4 µ (1.1%) | 244.5 µ (-0.4%) | 431.3 µ (76.4%) | 1.8 µ (-99.6%) | 1.9 µ (1.2%) | 1.9 µ (-0.1%) | 1.9 µ (2.3%) | 1.9 µ (0.4%) | 45.2 n (-97.6%) |
-| tables.provenances | 445.6 n | 468.8 n (5.2%) | 452.8 n (-3.4%) | 436.4 n (-3.6%) | 444.4 n (1.8%) | 772.5 n (73.8%) | 792.7 n (2.6%) | 777.5 n (-1.9%) | 976.4 n (25.6%) | 997.1 n (2.1%) | 947.5 n (-5.0%) | 925.5 n (-2.3%) | 970.7 n (4.9%) | 967.0 n (-0.4%) | 981.4 n (1.5%) | 971.0 n (-1.1%) | 935.3 n (-3.7%) | 931.2 n (-0.4%) | 943.0 n (1.3%) | 1.0 µ (7.3%) | 44.5 n (-95.6%) |
-| tables.sites | 457.1 n | 471.4 n (3.1%) | 442.8 n (-6.1%) | 438.2 n (-1.0%) | 449.3 n (2.5%) | 805.5 n (79.3%) | 809.8 n (0.5%) | 851.6 n (5.2%) | 3.1 µ (269.4%) | 3.2 µ (1.5%) | 3.3 µ (2.4%) | 3.2 µ (-2.3%) | 3.4 µ (7.2%) | 3.2 µ (-6.8%) | 2.7 µ (-16.7%) | 1.8 µ (-30.7%) | 1.9 µ (3.4%) | 1.8 µ (-4.6%) | 1.8 µ (1.7%) | 1.8 µ (-2.1%) | 45.7 n (-97.5%) |
- | tree = ts.first();"{filename}" |
-| tree = ts.first();"bench.trees" | 4.4 m | 4.5 m (0.9%) | 4.4 m (-2.0%) | 4.8 m (9.0%) | 4.5 m (-5.5%) | 4.6 m (2.3%) | 4.6 m (-0.1%) | 4.6 m (-1.0%) | 4.7 m (3.0%) | 4.6 m (-1.3%) | 4.5 m (-3.4%) | 4.6 m (3.7%) | 4.7 m (1.8%) | 4.7 m (-0.4%) | 4.6 m (-2.7%) | 4.7 m (2.8%) | 5.6 m (18.9%) | 5.6 m (0.6%) | 7.0 m (23.7%) | 7.0 m (0.4%) | 7.2 m (2.5%) |
-| tree = ts.first();"tiny.trees" | 1.3 µ | 1.4 µ (3.1%) | 1.3 µ (-2.0%) | 1.4 µ (3.6%) | 1.2 µ (-15.7%) | 1.2 µ (1.8%) | 1.1 µ (-3.5%) | 1.2 µ (5.3%) | 1.2 µ (-0.1%) | 1.2 µ (-3.7%) | 1.2 µ (2.9%) | 1.2 µ (1.4%) | 1.3 µ (6.2%) | 1.2 µ (-4.4%) | 1.8 µ (44.5%) | 1.8 µ (-0.6%) | 1.6 µ (-9.3%) | 1.7 µ (7.0%) | 2.2 µ (26.2%) | 2.0 µ (-6.4%) | 2.0 µ (-2.3%) |
-| tree.seek(pos)
-pos = 0 if pos == 500_000 else 500_000
- | N/A | N/A | N/A | N/A | 13.0 m | 13.7 m (5.3%) | 13.6 m (-0.2%) | 13.3 m (-2.3%) | 13.3 m (-0.4%) | 15.0 m (12.8%) | 14.9 m (-0.3%) | 14.9 m (-0.1%) | 15.6 m (4.6%) | 15.4 m (-1.0%) | 15.1 m (-2.1%) | 15.0 m (-0.5%) | 14.7 m (-2.5%) | 14.9 m (1.4%) | 16.4 m (10.5%) | 16.7 m (1.5%) | 16.7 m (0.4%) |
- | tree.{array} |
-| tree.edge_array | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 42.5 n | 45.1 n (6.1%) | 50.8 n (12.6%) |
-| tree.left_child_array | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 43.4 n | 40.3 n (-7.0%) | 40.7 n (0.8%) | 40.5 n (-0.3%) | 49.0 n (20.7%) | 46.4 n (-5.1%) | 41.6 n (-10.3%) |
-| tree.left_sib_array | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 44.4 n | 40.4 n (-8.9%) | 47.4 n (17.3%) | 41.0 n (-13.6%) | 53.0 n (29.2%) | 47.6 n (-10.1%) | 41.2 n (-13.5%) |
-| tree.num_children_array | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 46.9 n | 47.9 n (2.1%) | 47.3 n (-1.3%) |
-| tree.parent_array | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 44.2 n | 40.8 n (-7.6%) | 40.7 n (-0.2%) | 41.0 n (0.7%) | 49.3 n (20.0%) | 45.6 n (-7.4%) | 42.6 n (-6.5%) |
-| tree.right_child_array | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 46.1 n | 44.0 n (-4.7%) | 43.4 n (-1.3%) | 45.3 n (4.4%) | 43.2 n (-4.7%) | 43.6 n (1.0%) | 43.7 n (0.2%) |
-| tree.right_sib_array | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 42.1 n | 50.4 n (19.7%) | 41.1 n (-18.5%) | 43.0 n (4.8%) | 43.6 n (1.3%) | 43.0 n (-1.5%) | 43.5 n (1.2%) |
- | tree.{array}(42); |
-| tree.edge(42); | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 99.1 n | 103.2 n (4.1%) | 105.2 n (1.9%) |
-| tree.left_child(42); | 101.8 n | 94.1 n (-7.6%) | 96.0 n (2.1%) | 106.0 n (10.4%) | 99.3 n (-6.3%) | 103.6 n (4.3%) | 99.3 n (-4.1%) | 96.8 n (-2.5%) | 97.3 n (0.5%) | 99.7 n (2.5%) | 100.0 n (0.2%) | 101.9 n (1.9%) | 105.2 n (3.3%) | 99.8 n (-5.2%) | 98.9 n (-0.9%) | 98.2 n (-0.6%) | 108.6 n (10.6%) | 96.1 n (-11.6%) | 93.2 n (-3.0%) | 107.3 n (15.1%) | 99.9 n (-6.8%) |
-| tree.left_sib(42); | 102.1 n | 106.6 n (4.4%) | 96.3 n (-9.6%) | 103.9 n (7.9%) | 98.6 n (-5.1%) | 99.0 n (0.4%) | 94.8 n (-4.2%) | 98.7 n (4.1%) | 101.1 n (2.4%) | 99.6 n (-1.5%) | 105.7 n (6.2%) | 97.1 n (-8.2%) | 102.8 n (5.9%) | 101.4 n (-1.3%) | 102.6 n (1.1%) | 96.9 n (-5.5%) | 96.9 n (0.0%) | 95.4 n (-1.6%) | 100.5 n (5.3%) | 109.5 n (9.0%) | 96.9 n (-11.5%) |
-| tree.num_children(42); | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 99.6 n | 97.4 n (-2.2%) | 101.7 n (4.4%) | 99.5 n (-2.2%) | 106.4 n (7.0%) | 102.1 n (-4.1%) | 107.4 n (5.2%) | 98.0 n (-8.7%) | 101.5 n (3.5%) | 95.3 n (-6.1%) | 98.5 n (3.3%) | 101.9 n (3.5%) | 96.1 n (-5.8%) |
-| tree.parent(42); | 105.5 n | 107.3 n (1.7%) | 105.8 n (-1.4%) | 103.6 n (-2.1%) | 108.8 n (5.0%) | 102.7 n (-5.6%) | 98.9 n (-3.7%) | 98.0 n (-0.9%) | 100.2 n (2.3%) | 105.8 n (5.6%) | 103.0 n (-2.7%) | 96.8 n (-6.0%) | 105.3 n (8.7%) | 105.4 n (0.1%) | 99.3 n (-5.7%) | 93.8 n (-5.6%) | 104.0 n (10.9%) | 96.7 n (-7.0%) | 96.3 n (-0.5%) | 108.4 n (12.6%) | 101.8 n (-6.1%) |
-| tree.right_child(42); | 101.4 n | 97.8 n (-3.6%) | 95.8 n (-2.1%) | 106.4 n (11.1%) | 98.9 n (-7.1%) | 104.6 n (5.8%) | 100.0 n (-4.5%) | 95.8 n (-4.1%) | 94.1 n (-1.8%) | 104.1 n (10.6%) | 99.0 n (-4.9%) | 97.5 n (-1.5%) | 105.5 n (8.2%) | 97.7 n (-7.4%) | 106.8 n (9.3%) | 95.3 n (-10.8%) | 97.4 n (2.2%) | 101.8 n (4.5%) | 99.1 n (-2.6%) | 118.9 n (19.9%) | 98.0 n (-17.6%) |
-| tree.right_sib(42); | 101.9 n | 103.7 n (1.8%) | 101.8 n (-1.9%) | 99.5 n (-2.3%) | 102.2 n (2.7%) | 98.3 n (-3.8%) | 102.8 n (4.6%) | 97.1 n (-5.6%) | 103.3 n (6.5%) | 104.2 n (0.8%) | 105.3 n (1.0%) | 94.6 n (-10.2%) | 103.3 n (9.3%) | 104.3 n (1.0%) | 105.8 n (1.4%) | 103.4 n (-2.2%) | 96.5 n (-6.7%) | 92.9 n (-3.7%) | 102.0 n (9.8%) | 107.5 n (5.4%) | 104.9 n (-2.4%) |
- | tree.{traversal_order}() |
-| tree.postorder() | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 1.7 m | 1.8 m (2.2%) | 1.8 m (2.4%) | 2.3 m (26.9%) | 1.7 m (-27.4%) |
-| tree.preorder() | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 1.4 m | 1.5 m (1.8%) | 1.4 m (-5.7%) | 1.4 m (0.8%) | 1.6 m (15.7%) |
-| tree.timeasc() | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 29.0 m | 29.1 m (0.4%) | 29.1 m (0.0%) | 28.7 m (-1.4%) | 15.4 m (-46.5%) |
-| tree.timedesc() | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 28.6 m | 28.9 m (0.8%) | 28.5 m (-1.1%) | 28.6 m (0.3%) | 15.4 m (-46.3%) |
- | ts = tskit.load("{filename}") |
-| ts = tskit.load("bench.trees") | 27.5 m | 27.0 m (-2.0%) | 27.9 m (3.5%) | 27.6 m (-1.2%) | 27.1 m (-1.6%) | 27.3 m (0.6%) | 27.2 m (-0.3%) | 27.1 m (-0.6%) | 44.3 m (63.5%) | 44.7 m (0.9%) | 43.8 m (-2.0%) | 46.1 m (5.4%) | 45.6 m (-1.2%) | 45.0 m (-1.4%) | 45.6 m (1.4%) | 44.2 m (-3.1%) | 53.5 m (21.2%) | 51.6 m (-3.6%) | 46.1 m (-10.7%) | 46.2 m (0.3%) | 46.5 m (0.6%) |
-| ts = tskit.load("tiny.trees") | 13.1 µ | 13.1 µ (0.0%) | 12.9 µ (-1.6%) | 11.7 µ (-9.3%) | 11.9 µ (1.9%) | 12.1 µ (1.9%) | 11.5 µ (-4.9%) | 11.5 µ (-0.0%) | 306.2 µ (2558.4%) | 305.7 µ (-0.2%) | 300.4 µ (-1.8%) | 308.7 µ (2.8%) | 314.8 µ (2.0%) | 309.8 µ (-1.6%) | 511.7 µ (65.2%) | 86.0 µ (-83.2%) | 37.2 µ (-56.8%) | 90.6 µ (143.7%) | 39.6 µ (-56.3%) | 39.4 µ (-0.3%) | 45.1 µ (14.3%) |
- | ts.dump("/dev/null");"{filename}" |
-| ts.dump("/dev/null");"bench.trees" | 3.4 m | 3.4 m (0.5%) | 3.4 m (0.1%) | 3.4 m (0.5%) | 3.4 m (-0.9%) | 3.4 m (1.2%) | 3.5 m (1.7%) | 3.4 m (-2.3%) | 4.1 m (18.5%) | 4.0 m (-1.3%) | 3.9 m (-3.5%) | 4.0 m (3.1%) | 4.1 m (2.2%) | 4.1 m (0.9%) | 4.0 m (-2.5%) | 4.1 m (1.2%) | 4.7 m (16.0%) | 4.7 m (0.5%) | 1.7 m (-64.2%) | 1.7 m (1.4%) | 1.7 m (-0.0%) |
-| ts.dump("/dev/null");"tiny.trees" | 34.7 µ | 34.2 µ (-1.4%) | 35.1 µ (2.7%) | 35.3 µ (0.5%) | 35.1 µ (-0.5%) | 35.0 µ (-0.4%) | 87.8 µ (151.0%) | 34.9 µ (-60.3%) | 41.8 µ (20.0%) | 41.1 µ (-1.8%) | 41.7 µ (1.5%) | 44.6 µ (6.8%) | 45.2 µ (1.3%) | 46.4 µ (2.8%) | 46.3 µ (-0.3%) | 45.9 µ (-1.0%) | 46.2 µ (0.7%) | 46.4 µ (0.4%) | 42.6 µ (-8.1%) | 42.8 µ (0.4%) | 43.9 µ (2.5%) |
- | ts.genotype_matrix();'{filename}' |
-| ts.genotype_matrix();'bench.trees' | 30.1 m | 30.3 m (0.7%) | 30.2 m (-0.2%) | 30.2 m (-0.2%) | 30.3 m (0.6%) | 31.3 m (3.2%) | 30.6 m (-2.2%) | 30.9 m (1.1%) | 92.5 m (198.9%) | 91.8 m (-0.8%) | 91.4 m (-0.4%) | 90.9 m (-0.5%) | 92.1 m (1.3%) | 92.1 m (-0.1%) | 91.1 m (-1.0%) | 91.3 m (0.3%) | 71.5 m (-21.8%) | 77.7 m (8.8%) | 80.8 m (3.9%) | 67.6 m (-16.3%) | 81.2 m (20.1%) |
-| ts.genotype_matrix();'tiny.trees' | 608.8 n | 609.3 n (0.1%) | 615.4 n (1.0%) | 615.2 n (-0.0%) | 620.8 n (0.9%) | 842.0 n (35.6%) | 781.7 n (-7.2%) | 812.9 n (4.0%) | 1.1 µ (40.9%) | 1.0 µ (-8.7%) | 1.0 µ (-1.6%) | 1.0 µ (0.9%) | 1.0 µ (0.2%) | 1.0 µ (0.4%) | 1.0 µ (-1.8%) | 1.0 µ (-0.4%) | 921.9 n (-9.7%) | 1.0 µ (10.8%) | 1.1 µ (6.8%) | 1.1 µ (-0.4%) | 1.0 µ (-5.3%) |
-| ts.tables | 4.7 m | 4.3 m (-7.1%) | 4.4 m (1.5%) | 4.5 m (2.3%) | 4.5 m (0.5%) | 4.6 m (1.2%) | 4.4 m (-3.3%) | 4.4 m (0.4%) | 5.1 m (14.6%) | 5.4 m (7.3%) | 5.2 m (-4.5%) | 5.4 m (4.4%) | 5.5 m (0.6%) | 5.3 m (-3.4%) | 5.3 m (1.3%) | 5.4 m (0.1%) | 6.4 m (20.4%) | 6.4 m (-1.1%) | 6.4 m (0.9%) | 6.3 m (-2.0%) | 6.4 m (0.9%) |
-| ts.write_vcf(null) | 392.0 m | 389.3 m (-0.7%) | 394.1 m (1.2%) | 391.8 m (-0.6%) | 395.7 m (1.0%) | 1.5 (266.9%) | 1.4 (-0.7%) | 1.4 (0.2%) | 1.6 (13.6%) | 1.6 (0.2%) | 1.6 (-4.9%) | 1.6 (-0.5%) | 1.6 (4.3%) | 1.6 (-0.7%) | 2.0 (22.3%) | 1.9 (-2.3%) | 1.8 (-4.0%) | 2.0 (6.9%) | 2.9 (47.3%) | 2.9 (1.4%) | 3.0 (1.4%) |
- | ts.{table}(1) |
-| ts.edge(1) | N/A | N/A | N/A | N/A | N/A | 466.3 n | 472.5 n (1.3%) | 499.9 n (5.8%) | 709.3 n (41.9%) | 695.4 n (-2.0%) | 694.2 n (-0.2%) | 718.2 n (3.5%) | 701.1 n (-2.4%) | 712.8 n (1.7%) | 1.4 µ (99.2%) | 1.3 µ (-7.6%) | 1.4 µ (3.4%) | 1.4 µ (-0.3%) | 771.5 n (-42.9%) | 806.8 n (4.6%) | 825.9 n (2.4%) |
-| ts.individual(1) | 649.8 n | 669.7 n (3.1%) | 639.3 n (-4.5%) | 631.5 n (-1.2%) | 666.8 n (5.6%) | 693.0 n (3.9%) | 682.4 n (-1.5%) | 637.6 n (-6.6%) | 814.9 n (27.8%) | 813.7 n (-0.1%) | 796.7 n (-2.1%) | 832.6 n (4.5%) | 787.8 n (-5.4%) | 939.4 n (19.2%) | 1.6 µ (67.5%) | 1.5 µ (-2.1%) | 1.5 µ (-1.1%) | 1.5 µ (1.2%) | 2.3 µ (49.4%) | 2.3 µ (-1.5%) | 2.4 µ (3.8%) |
-| ts.migration(1) | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 797.3 n | 800.2 n (0.4%) | 797.3 n (-0.4%) | 814.3 n (2.1%) | 834.0 n (2.4%) | 808.3 n (-3.1%) | 1.5 µ (90.6%) | 1.5 µ (-2.6%) | 1.5 µ (2.6%) | 1.5 µ (-0.5%) | 1.5 µ (-1.7%) | 1.5 µ (1.0%) | 1.5 µ (1.1%) |
-| ts.mutation(1) | 615.1 n | 595.9 n (-3.1%) | 621.5 n (4.3%) | 613.3 n (-1.3%) | 621.0 n (1.3%) | 624.2 n (0.5%) | 602.0 n (-3.6%) | 616.2 n (2.4%) | 774.0 n (25.6%) | 742.9 n (-4.0%) | 763.2 n (2.7%) | 750.1 n (-1.7%) | 756.4 n (0.8%) | 767.2 n (1.4%) | 1.5 µ (91.0%) | 1.4 µ (-2.6%) | 1.5 µ (3.2%) | 1.4 µ (-3.0%) | 1.5 µ (6.2%) | 1.5 µ (1.4%) | 1.6 µ (3.0%) |
-| ts.node(1) | 587.2 n | 566.7 n (-3.5%) | 564.1 n (-0.5%) | 579.9 n (2.8%) | 582.8 n (0.5%) | 560.1 n (-3.9%) | 567.6 n (1.3%) | 567.6 n (0.0%) | 696.2 n (22.7%) | 682.6 n (-2.0%) | 699.9 n (2.5%) | 702.9 n (0.4%) | 730.9 n (4.0%) | 690.4 n (-5.5%) | 1.4 µ (99.4%) | 1.3 µ (-4.6%) | 1.3 µ (2.1%) | 1.3 µ (-1.8%) | 1.3 µ (1.4%) | 1.4 µ (2.3%) | 1.4 µ (-0.2%) |
-| ts.population(1) | 401.5 n | 384.2 n (-4.3%) | 402.5 n (4.8%) | 386.0 n (-4.1%) | 389.1 n (0.8%) | 385.8 n (-0.9%) | 376.9 n (-2.3%) | 387.8 n (2.9%) | 520.5 n (34.2%) | 500.2 n (-3.9%) | 507.5 n (1.5%) | 517.1 n (1.9%) | 505.1 n (-2.3%) | 505.4 n (0.1%) | 943.7 n (86.7%) | 884.8 n (-6.2%) | 899.5 n (1.7%) | 915.3 n (1.8%) | 930.4 n (1.7%) | 922.7 n (-0.8%) | 949.7 n (2.9%) |
-| ts.provenance(1) | 515.9 n | 499.3 n (-3.2%) | 498.6 n (-0.2%) | 501.6 n (0.6%) | 511.0 n (1.9%) | 498.8 n (-2.4%) | 507.5 n (1.7%) | 510.5 n (0.6%) | 503.7 n (-1.3%) | 509.8 n (1.2%) | 506.3 n (-0.7%) | 502.5 n (-0.8%) | 496.3 n (-1.2%) | 490.6 n (-1.2%) | 482.5 n (-1.6%) | 466.7 n (-3.3%) | 471.5 n (1.0%) | 468.2 n (-0.7%) | 469.6 n (0.3%) | 461.5 n (-1.7%) | 477.8 n (3.5%) |
-| ts.site(1) | 1.4 µ | 1.3 µ (-4.8%) | 1.4 µ (1.1%) | 1.4 µ (0.6%) | 1.3 µ (-1.6%) | 1.4 µ (3.9%) | 1.4 µ (-1.5%) | 1.4 µ (-1.9%) | 1.7 µ (24.9%) | 1.7 µ (2.5%) | 1.7 µ (0.4%) | 1.7 µ (0.1%) | 1.7 µ (-2.3%) | 1.7 µ (0.1%) | 3.1 µ (82.1%) | 3.0 µ (-1.7%) | 3.1 µ (1.0%) | 3.1 µ (0.7%) | 3.2 µ (2.8%) | 3.3 µ (2.9%) | 3.3 µ (2.2%) |
- | x = {table}.{column} |
-| x = edges.child | 41.9 µ | 44.9 µ (7.4%) | 42.8 µ (-4.7%) | 44.6 µ (4.1%) | 42.4 µ (-4.9%) | 44.0 µ (3.7%) | 42.3 µ (-3.9%) | 42.2 µ (-0.1%) | 46.9 µ (11.0%) | 43.1 µ (-7.9%) | 43.1 µ (-0.0%) | 42.2 µ (-2.1%) | 44.1 µ (4.3%) | 45.5 µ (3.3%) | 42.5 µ (-6.6%) | 44.4 µ (4.6%) | 55.7 µ (25.3%) | 58.4 µ (4.9%) | 51.7 µ (-11.4%) | 51.9 µ (0.2%) | 51.3 µ (-1.1%) |
-| x = edges.left | 103.8 µ | 107.1 µ (3.1%) | 102.5 µ (-4.2%) | 108.8 µ (6.1%) | 102.2 µ (-6.0%) | 107.7 µ (5.4%) | 105.1 µ (-2.4%) | 103.7 µ (-1.3%) | 112.8 µ (8.7%) | 102.4 µ (-9.2%) | 107.7 µ (5.2%) | 103.8 µ (-3.6%) | 106.5 µ (2.6%) | 110.6 µ (3.9%) | 103.6 µ (-6.3%) | 102.0 µ (-1.6%) | 120.7 µ (18.4%) | 128.6 µ (6.6%) | 115.7 µ (-10.1%) | 112.9 µ (-2.4%) | 117.8 µ (4.3%) |
-| x = edges.metadata | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 351.4 n | 362.7 n (3.2%) | 340.6 n (-6.1%) | 336.0 n (-1.3%) | 367.5 n (9.4%) | 330.5 n (-10.1%) | 344.1 n (4.1%) | 327.8 n (-4.7%) | 332.7 n (1.5%) | 323.3 n (-2.8%) | 350.5 n (8.4%) | 372.7 n (6.3%) | 326.0 n (-12.5%) |
-| x = edges.metadata_offset | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 46.7 µ | 43.0 µ (-8.0%) | 43.6 µ (1.5%) | 42.8 µ (-1.9%) | 44.9 µ (5.0%) | 45.6 µ (1.5%) | 43.1 µ (-5.5%) | 44.7 µ (3.7%) | 123.2 µ (175.8%) | 125.8 µ (2.1%) | 115.3 µ (-8.4%) | 117.4 µ (1.9%) | 122.4 µ (4.3%) |
-| x = edges.parent | 42.9 µ | 44.0 µ (2.7%) | 42.5 µ (-3.4%) | 44.7 µ (5.2%) | 43.1 µ (-3.6%) | 45.2 µ (4.8%) | 43.7 µ (-3.3%) | 43.3 µ (-1.1%) | 47.1 µ (8.9%) | 43.7 µ (-7.2%) | 42.4 µ (-3.1%) | 43.7 µ (3.2%) | 46.2 µ (5.6%) | 45.5 µ (-1.4%) | 42.3 µ (-7.1%) | 45.7 µ (8.2%) | 56.0 µ (22.5%) | 57.7 µ (3.0%) | 51.7 µ (-10.4%) | 53.8 µ (4.1%) | 52.3 µ (-2.7%) |
-| x = edges.right | 101.4 µ | 105.7 µ (4.2%) | 106.8 µ (1.1%) | 108.7 µ (1.7%) | 104.5 µ (-3.9%) | 110.5 µ (5.8%) | 103.0 µ (-6.8%) | 102.5 µ (-0.5%) | 116.1 µ (13.2%) | 104.8 µ (-9.8%) | 103.9 µ (-0.8%) | 107.7 µ (3.6%) | 108.1 µ (0.4%) | 109.8 µ (1.5%) | 108.3 µ (-1.4%) | 112.0 µ (3.4%) | 118.7 µ (6.0%) | 122.5 µ (3.2%) | 122.3 µ (-0.1%) | 118.7 µ (-2.9%) | 116.6 µ (-1.8%) |
-| x = individuals.flags | 5.0 µ | 5.1 µ (2.8%) | 5.0 µ (-2.6%) | 4.9 µ (-1.8%) | 4.9 µ (1.0%) | 5.4 µ (10.5%) | 5.1 µ (-6.4%) | 5.2 µ (1.3%) | 5.5 µ (5.6%) | 5.5 µ (1.0%) | 5.4 µ (-1.6%) | 5.1 µ (-5.6%) | 5.5 µ (7.6%) | 5.3 µ (-3.2%) | 5.3 µ (-1.3%) | 5.5 µ (4.5%) | 7.5 µ (35.9%) | 7.1 µ (-5.6%) | 7.2 µ (1.9%) | 6.9 µ (-4.4%) | 6.8 µ (-0.4%) |
-| x = individuals.location | 127.6 n | 137.6 n (7.8%) | 128.8 n (-6.4%) | 128.8 n (-0.0%) | 130.6 n (1.4%) | 362.4 n (177.5%) | 337.0 n (-7.0%) | 350.6 n (4.0%) | 318.8 n (-9.1%) | 327.6 n (2.7%) | 310.2 n (-5.3%) | 314.2 n (1.3%) | 360.0 n (14.6%) | 314.4 n (-12.7%) | 316.3 n (0.6%) | 312.6 n (-1.2%) | 314.9 n (0.7%) | 309.2 n (-1.8%) | 331.0 n (7.0%) | 365.1 n (10.3%) | 325.9 n (-10.7%) |
-| x = individuals.location_offset | 5.0 µ | 5.2 µ (4.1%) | 4.9 µ (-5.8%) | 5.1 µ (4.7%) | 4.9 µ (-4.7%) | 5.4 µ (10.6%) | 5.3 µ (-1.1%) | 5.2 µ (-3.0%) | 5.8 µ (12.1%) | 5.6 µ (-3.4%) | 5.3 µ (-4.7%) | 5.3 µ (-1.4%) | 5.5 µ (5.4%) | 5.3 µ (-4.3%) | 5.3 µ (-0.2%) | 5.6 µ (5.3%) | 14.6 µ (161.8%) | 15.3 µ (5.3%) | 13.6 µ (-11.0%) | 14.3 µ (4.5%) | 13.9 µ (-2.5%) |
-| x = individuals.metadata | 134.7 n | 137.9 n (2.4%) | 128.3 n (-6.9%) | 134.0 n (4.4%) | 136.4 n (1.8%) | 388.5 n (184.8%) | 344.6 n (-11.3%) | 344.3 n (-0.1%) | 348.9 n (1.4%) | 348.8 n (-0.0%) | 342.7 n (-1.8%) | 338.1 n (-1.3%) | 384.6 n (13.8%) | 340.9 n (-11.4%) | 344.2 n (1.0%) | 343.3 n (-0.3%) | 344.4 n (0.3%) | 339.9 n (-1.3%) | 363.6 n (7.0%) | 387.2 n (6.5%) | 353.3 n (-8.8%) |
-| x = individuals.parents | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 329.4 n | 331.1 n (0.5%) | 327.2 n (-1.2%) | 326.4 n (-0.3%) | 323.5 n (-0.9%) | 343.8 n (6.3%) | 374.9 n (9.0%) | 338.8 n (-9.6%) |
-| x = migrations.dest | 835.8 n | 848.6 n (1.5%) | 835.4 n (-1.6%) | 843.3 n (0.9%) | 858.0 n (1.7%) | 1.1 µ (24.6%) | 1.1 µ (5.1%) | 1.1 µ (-2.9%) | 1.2 µ (8.0%) | 1.1 µ (-4.8%) | 1.1 µ (-4.3%) | 1.1 µ (-0.5%) | 1.2 µ (9.8%) | 1.1 µ (-6.3%) | 1.1 µ (-0.6%) | 1.1 µ (-3.4%) | 1.3 µ (25.8%) | 1.5 µ (12.8%) | 1.3 µ (-14.3%) | 1.3 µ (4.1%) | 1.2 µ (-7.8%) |
-| x = migrations.left | 1.4 µ | 1.5 µ (7.6%) | 1.4 µ (-3.2%) | 1.7 µ (19.0%) | 1.6 µ (-9.9%) | 1.7 µ (12.6%) | 1.8 µ (5.6%) | 1.6 µ (-14.3%) | 1.9 µ (20.9%) | 1.6 µ (-14.4%) | 1.9 µ (14.6%) | 1.6 µ (-13.1%) | 1.9 µ (15.7%) | 1.7 µ (-8.4%) | 1.7 µ (-2.7%) | 1.7 µ (-0.3%) | 2.3 µ (39.5%) | 2.3 µ (-2.3%) | 2.3 µ (1.1%) | 2.1 µ (-7.0%) | 2.1 µ (-2.8%) |
-| x = migrations.metadata | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 387.3 n | 367.9 n (-5.0%) | 356.1 n (-3.2%) | 350.8 n (-1.5%) | 401.5 n (14.4%) | 344.1 n (-14.3%) | 348.8 n (1.3%) | 348.9 n (0.0%) | 342.6 n (-1.8%) | 338.6 n (-1.2%) | 366.7 n (8.3%) | 394.3 n (7.5%) | 339.5 n (-13.9%) |
-| x = migrations.metadata_offset | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 1.1 µ | 1.1 µ (1.4%) | 1.1 µ (-5.9%) | 1.1 µ (-1.9%) | 1.3 µ (19.1%) | 1.1 µ (-11.2%) | 1.1 µ (-3.8%) | 1.1 µ (-1.5%) | 2.2 µ (102.7%) | 2.2 µ (2.3%) | 2.3 µ (3.0%) | 2.3 µ (-0.4%) | 2.1 µ (-7.8%) |
-| x = migrations.node | 927.6 n | 851.8 n (-8.2%) | 877.0 n (3.0%) | 868.9 n (-0.9%) | 845.7 n (-2.7%) | 1.0 µ (22.1%) | 1.1 µ (7.0%) | 1.2 µ (4.5%) | 1.1 µ (-4.1%) | 1.1 µ (-1.8%) | 1.2 µ (6.2%) | 1.0 µ (-9.2%) | 1.2 µ (14.6%) | 1.1 µ (-6.2%) | 1.1 µ (-3.5%) | 1.0 µ (-6.1%) | 1.3 µ (22.9%) | 1.3 µ (1.4%) | 1.2 µ (-2.7%) | 1.3 µ (2.7%) | 1.2 µ (-7.1%) |
-| x = migrations.right | 1.4 µ | 1.6 µ (9.4%) | 1.4 µ (-9.1%) | 1.6 µ (9.3%) | 1.5 µ (-1.6%) | 1.7 µ (13.6%) | 1.8 µ (5.8%) | 1.7 µ (-7.1%) | 1.9 µ (12.9%) | 1.7 µ (-10.4%) | 1.9 µ (8.4%) | 1.7 µ (-9.7%) | 2.0 µ (16.8%) | 1.7 µ (-16.4%) | 1.7 µ (0.8%) | 1.9 µ (11.3%) | 2.2 µ (15.7%) | 2.1 µ (-0.6%) | 2.3 µ (9.1%) | 2.3 µ (-2.0%) | 2.2 µ (-6.1%) |
-| x = migrations.source | 878.8 n | 838.4 n (-4.6%) | 804.5 n (-4.0%) | 827.9 n (2.9%) | 850.2 n (2.7%) | 1.0 µ (21.8%) | 1.1 µ (7.7%) | 1.1 µ (0.2%) | 1.1 µ (1.7%) | 1.1 µ (0.0%) | 1.2 µ (4.4%) | 1.0 µ (-12.1%) | 1.3 µ (22.6%) | 1.1 µ (-12.2%) | 1.1 µ (-5.9%) | 992.2 n (-6.0%) | 1.2 µ (22.7%) | 1.3 µ (3.0%) | 1.3 µ (5.3%) | 1.2 µ (-5.5%) | 1.3 µ (5.0%) |
-| x = migrations.time | 1.4 µ | 1.6 µ (17.3%) | 1.3 µ (-16.9%) | 1.5 µ (16.6%) | 1.6 µ (4.3%) | 1.9 µ (18.3%) | 1.8 µ (-3.5%) | 1.7 µ (-8.8%) | 1.9 µ (12.4%) | 1.8 µ (-5.8%) | 2.0 µ (10.1%) | 1.8 µ (-7.7%) | 1.9 µ (7.4%) | 1.9 µ (-4.2%) | 1.7 µ (-9.0%) | 1.9 µ (10.8%) | 2.3 µ (20.7%) | 2.1 µ (-7.4%) | 2.1 µ (-1.6%) | 2.2 µ (8.7%) | 2.1 µ (-4.7%) |
-| x = mutations.derived_state | 13.4 µ | 13.4 µ (-0.5%) | 12.9 µ (-3.3%) | 13.9 µ (7.7%) | 13.2 µ (-5.2%) | 14.3 µ (8.2%) | 13.5 µ (-5.5%) | 13.6 µ (0.7%) | 14.5 µ (6.6%) | 13.5 µ (-6.6%) | 13.2 µ (-2.4%) | 13.7 µ (3.8%) | 14.2 µ (3.2%) | 14.2 µ (0.4%) | 13.2 µ (-6.9%) | 13.7 µ (3.3%) | 16.7 µ (21.9%) | 17.3 µ (3.7%) | 16.0 µ (-7.5%) | 16.0 µ (0.3%) | 16.5 µ (3.0%) |
-| x = mutations.derived_state_offset | 52.3 µ | 54.6 µ (4.3%) | 51.6 µ (-5.4%) | 55.3 µ (7.0%) | 52.1 µ (-5.8%) | 55.0 µ (5.7%) | 53.7 µ (-2.4%) | 52.4 µ (-2.4%) | 56.4 µ (7.7%) | 53.2 µ (-5.8%) | 53.8 µ (1.3%) | 52.3 µ (-2.9%) | 55.0 µ (5.2%) | 56.7 µ (3.1%) | 51.5 µ (-9.1%) | 53.9 µ (4.6%) | 159.8 µ (196.4%) | 167.2 µ (4.6%) | 153.6 µ (-8.1%) | 157.6 µ (2.6%) | 165.6 µ (5.1%) |
-| x = mutations.metadata | 129.6 n | 133.5 n (3.0%) | 134.2 n (0.5%) | 132.9 n (-0.9%) | 136.8 n (2.9%) | 397.4 n (190.4%) | 364.6 n (-8.3%) | 361.9 n (-0.7%) | 367.8 n (1.6%) | 369.3 n (0.4%) | 363.5 n (-1.6%) | 352.8 n (-3.0%) | 450.4 n (27.7%) | 344.1 n (-23.6%) | 348.1 n (1.2%) | 344.1 n (-1.2%) | 340.1 n (-1.1%) | 340.7 n (0.2%) | 368.4 n (8.1%) | 390.9 n (6.1%) | 358.6 n (-8.3%) |
-| x = mutations.metadata_offset | 51.5 µ | 54.6 µ (6.1%) | 52.4 µ (-4.0%) | 54.6 µ (4.2%) | 51.1 µ (-6.5%) | 55.4 µ (8.5%) | 52.5 µ (-5.3%) | 51.2 µ (-2.4%) | 57.6 µ (12.3%) | 52.7 µ (-8.4%) | 51.5 µ (-2.3%) | 51.7 µ (0.4%) | 55.7 µ (7.8%) | 56.5 µ (1.3%) | 51.5 µ (-8.9%) | 54.7 µ (6.2%) | 162.8 µ (197.9%) | 166.6 µ (2.3%) | 173.5 µ (4.2%) | 165.9 µ (-4.4%) | 164.4 µ (-0.9%) |
-| x = mutations.node | 52.9 µ | 54.7 µ (3.4%) | 50.6 µ (-7.4%) | 55.6 µ (9.8%) | 52.3 µ (-6.0%) | 54.8 µ (4.8%) | 53.1 µ (-3.1%) | 52.6 µ (-0.9%) | 57.1 µ (8.6%) | 53.8 µ (-5.9%) | 52.9 µ (-1.5%) | 53.8 µ (1.6%) | 53.4 µ (-0.7%) | 54.1 µ (1.3%) | 54.2 µ (0.1%) | 55.8 µ (3.1%) | 67.0 µ (20.0%) | 70.7 µ (5.5%) | 63.4 µ (-10.3%) | 63.6 µ (0.4%) | 63.8 µ (0.3%) |
-| x = mutations.parent | 51.1 µ | 55.3 µ (8.2%) | 51.9 µ (-6.1%) | 55.7 µ (7.2%) | 52.0 µ (-6.6%) | 53.7 µ (3.3%) | 52.4 µ (-2.4%) | 51.8 µ (-1.1%) | 56.9 µ (9.8%) | 53.0 µ (-6.9%) | 52.7 µ (-0.5%) | 51.1 µ (-3.0%) | 54.9 µ (7.4%) | 54.4 µ (-0.9%) | 52.1 µ (-4.2%) | 55.9 µ (7.2%) | 67.3 µ (20.3%) | 69.0 µ (2.5%) | 65.1 µ (-5.7%) | 64.8 µ (-0.4%) | 63.8 µ (-1.5%) |
-| x = mutations.site | 50.7 µ | 55.2 µ (8.8%) | 52.3 µ (-5.2%) | 54.6 µ (4.4%) | 51.1 µ (-6.4%) | 54.2 µ (6.1%) | 52.4 µ (-3.4%) | 50.6 µ (-3.5%) | 56.2 µ (11.2%) | 53.5 µ (-4.8%) | 52.0 µ (-2.9%) | 50.7 µ (-2.4%) | 54.7 µ (7.8%) | 54.6 µ (-0.2%) | 53.1 µ (-2.7%) | 55.0 µ (3.6%) | 67.4 µ (22.4%) | 69.9 µ (3.8%) | 65.1 µ (-6.8%) | 64.8 µ (-0.5%) | 64.1 µ (-1.1%) |
-| x = mutations.time | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | 165.5 µ | 161.6 µ (-2.3%) | 158.3 µ (-2.1%) | 152.9 µ (-3.4%) | 154.8 µ (1.2%) | 157.8 µ (1.9%) | 165.5 µ (4.9%) | 169.9 µ (2.6%) | 168.6 µ (-0.8%) | 170.0 µ (0.9%) | 173.5 µ (2.0%) | 173.6 µ (0.1%) | 158.3 µ (-8.9%) |
-| x = nodes.flags | 26.3 µ | 28.1 µ (6.7%) | 25.5 µ (-9.0%) | 27.5 µ (7.8%) | 26.2 µ (-4.9%) | 27.8 µ (6.3%) | 25.9 µ (-6.8%) | 25.9 µ (0.0%) | 28.5 µ (10.0%) | 26.9 µ (-5.7%) | 26.6 µ (-1.1%) | 26.5 µ (-0.3%) | 27.4 µ (3.4%) | 27.5 µ (0.4%) | 26.1 µ (-5.1%) | 27.2 µ (4.2%) | 32.6 µ (19.7%) | 33.5 µ (3.0%) | 31.8 µ (-5.1%) | 32.1 µ (0.8%) | 32.9 µ (2.5%) |
-| x = nodes.individual | 26.2 µ | 27.6 µ (5.3%) | 25.5 µ (-7.5%) | 27.9 µ (9.5%) | 26.2 µ (-6.4%) | 27.9 µ (6.5%) | 26.0 µ (-6.9%) | 26.0 µ (0.1%) | 28.3 µ (8.9%) | 26.9 µ (-4.9%) | 26.7 µ (-0.7%) | 26.7 µ (0.0%) | 28.4 µ (6.1%) | 27.2 µ (-4.1%) | 26.5 µ (-2.7%) | 27.4 µ (3.6%) | 32.6 µ (18.9%) | 34.8 µ (6.7%) | 32.2 µ (-7.4%) | 31.6 µ (-1.8%) | 32.4 µ (2.5%) |
-| x = nodes.metadata | 129.4 n | 128.6 n (-0.7%) | 128.5 n (-0.0%) | 131.3 n (2.2%) | 133.9 n (1.9%) | 359.9 n (168.8%) | 361.7 n (0.5%) | 330.1 n (-8.7%) | 331.7 n (0.5%) | 330.4 n (-0.4%) | 329.1 n (-0.4%) | 335.0 n (1.8%) | 378.9 n (13.1%) | 329.4 n (-13.1%) | 328.3 n (-0.3%) | 328.7 n (0.1%) | 333.5 n (1.5%) | 322.3 n (-3.4%) | 350.9 n (8.9%) | 373.9 n (6.5%) | 325.1 n (-13.1%) |
-| x = nodes.metadata_offset | 25.6 µ | 26.9 µ (5.1%) | 26.5 µ (-1.5%) | 27.0 µ (1.8%) | 26.1 µ (-3.1%) | 27.2 µ (4.0%) | 26.8 µ (-1.6%) | 26.9 µ (0.7%) | 28.8 µ (6.8%) | 26.2 µ (-8.8%) | 26.2 µ (-0.3%) | 26.6 µ (1.6%) | 27.4 µ (3.2%) | 28.2 µ (2.7%) | 26.0 µ (-7.7%) | 27.3 µ (5.1%) | 67.5 µ (146.9%) | 69.1 µ (2.4%) | 67.6 µ (-2.2%) | 64.2 µ (-5.0%) | 64.7 µ (0.8%) |
-| x = nodes.population | 25.9 µ | 27.0 µ (4.4%) | 26.5 µ (-1.8%) | 27.1 µ (2.3%) | 25.7 µ (-5.2%) | 27.5 µ (7.2%) | 26.6 µ (-3.6%) | 26.6 µ (-0.1%) | 29.2 µ (9.9%) | 26.6 µ (-8.8%) | 25.8 µ (-2.9%) | 26.1 µ (0.9%) | 27.4 µ (5.0%) | 27.7 µ (1.3%) | 26.6 µ (-4.2%) | 27.3 µ (2.7%) | 34.3 µ (25.5%) | 35.4 µ (3.2%) | 32.1 µ (-9.2%) | 32.1 µ (0.0%) | 33.2 µ (3.3%) |
-| x = nodes.time | 51.6 µ | 53.8 µ (4.4%) | 53.1 µ (-1.4%) | 54.3 µ (2.3%) | 51.6 µ (-5.0%) | 55.2 µ (7.1%) | 53.6 µ (-3.0%) | 53.1 µ (-0.9%) | 57.9 µ (9.1%) | 52.5 µ (-9.3%) | 53.2 µ (1.3%) | 53.1 µ (-0.2%) | 56.4 µ (6.2%) | 55.6 µ (-1.5%) | 53.0 µ (-4.6%) | 54.6 µ (3.0%) | 67.0 µ (22.6%) | 69.7 µ (4.0%) | 64.1 µ (-8.0%) | 63.8 µ (-0.4%) | 64.1 µ (0.5%) |
-| x = populations.metadata | 135.8 n | 136.9 n (0.8%) | 136.6 n (-0.3%) | 137.4 n (0.6%) | 137.2 n (-0.1%) | 376.7 n (174.5%) | 322.3 n (-14.5%) | 325.9 n (1.1%) | 340.8 n (4.6%) | 353.5 n (3.7%) | 320.6 n (-9.3%) | 317.4 n (-1.0%) | 373.7 n (17.8%) | 305.5 n (-18.2%) | 303.9 n (-0.5%) | 308.0 n (1.3%) | 309.2 n (0.4%) | 303.5 n (-1.8%) | 327.5 n (7.9%) | 351.9 n (7.5%) | 302.5 n (-14.0%) |
-| x = populations.metadata_offset | 134.5 n | 135.4 n (0.7%) | 131.5 n (-2.9%) | 130.6 n (-0.6%) | 131.5 n (0.7%) | 375.7 n (185.7%) | 330.4 n (-12.0%) | 328.3 n (-0.7%) | 372.4 n (13.5%) | 337.8 n (-9.3%) | 323.3 n (-4.3%) | 332.6 n (2.9%) | 359.2 n (8.0%) | 315.9 n (-12.1%) | 319.0 n (1.0%) | 317.3 n (-0.5%) | 348.8 n (9.9%) | 310.2 n (-11.0%) | 339.5 n (9.4%) | 364.9 n (7.5%) | 307.9 n (-15.6%) |
-| x = provenances.record | 219.1 n | 211.2 n (-3.6%) | 213.4 n (1.0%) | 214.1 n (0.3%) | 196.0 n (-8.4%) | 462.3 n (135.8%) | 452.3 n (-2.2%) | 405.3 n (-10.4%) | 414.9 n (2.4%) | 429.2 n (3.4%) | 429.3 n (0.0%) | 419.3 n (-2.3%) | 481.9 n (14.9%) | 406.9 n (-15.6%) | 399.7 n (-1.8%) | 397.7 n (-0.5%) | 426.8 n (7.3%) | 435.5 n (2.1%) | 437.5 n (0.4%) | 452.3 n (3.4%) | 441.8 n (-2.3%) |
-| x = provenances.record_offset | 142.7 n | 136.8 n (-4.1%) | 130.2 n (-4.8%) | 130.9 n (0.5%) | 130.7 n (-0.2%) | 368.2 n (181.7%) | 383.2 n (4.1%) | 335.5 n (-12.5%) | 341.8 n (1.9%) | 368.4 n (7.8%) | 322.8 n (-12.4%) | 323.6 n (0.2%) | 368.3 n (13.8%) | 315.6 n (-14.3%) | 314.4 n (-0.4%) | 314.0 n (-0.1%) | 343.8 n (9.5%) | 306.4 n (-10.9%) | 373.4 n (21.9%) | 365.2 n (-2.2%) | 309.8 n (-15.2%) |
-| x = provenances.timestamp | 140.0 n | 133.3 n (-4.8%) | 132.9 n (-0.3%) | 127.0 n (-4.4%) | 128.1 n (0.9%) | 382.6 n (198.6%) | 329.6 n (-13.9%) | 333.6 n (1.2%) | 358.3 n (7.4%) | 340.7 n (-4.9%) | 334.5 n (-1.8%) | 337.5 n (0.9%) | 399.4 n (18.3%) | 320.7 n (-19.7%) | 323.1 n (0.8%) | 319.8 n (-1.0%) | 320.9 n (0.4%) | 314.4 n (-2.0%) | 342.2 n (8.8%) | 367.3 n (7.3%) | 327.7 n (-10.8%) |
-| x = provenances.timestamp_offset | 131.7 n | 138.2 n (4.9%) | 134.9 n (-2.4%) | 131.5 n (-2.5%) | 135.2 n (2.8%) | 383.2 n (183.4%) | 350.0 n (-8.7%) | 343.9 n (-1.7%) | 376.3 n (9.4%) | 343.4 n (-8.7%) | 335.4 n (-2.3%) | 336.9 n (0.4%) | 384.5 n (14.1%) | 327.5 n (-14.8%) | 333.9 n (2.0%) | 327.3 n (-2.0%) | 361.2 n (10.4%) | 322.2 n (-10.8%) | 345.1 n (7.1%) | 377.1 n (9.3%) | 324.5 n (-14.0%) |
-| x = sites.ancestral_state | 10.2 µ | 10.9 µ (7.0%) | 10.5 µ (-4.1%) | 10.5 µ (0.6%) | 10.2 µ (-3.2%) | 11.1 µ (8.5%) | 10.7 µ (-2.9%) | 10.4 µ (-3.0%) | 11.7 µ (12.1%) | 10.8 µ (-7.4%) | 10.7 µ (-1.3%) | 10.6 µ (-0.7%) | 11.3 µ (6.4%) | 10.8 µ (-4.0%) | 10.5 µ (-2.6%) | 11.3 µ (6.9%) | 14.0 µ (24.0%) | 14.0 µ (0.3%) | 13.0 µ (-7.4%) | 13.0 µ (0.2%) | 12.8 µ (-1.4%) |
-| x = sites.ancestral_state_offset | 40.4 µ | 43.7 µ (8.1%) | 41.5 µ (-5.0%) | 42.6 µ (2.5%) | 40.4 µ (-5.2%) | 43.2 µ (6.9%) | 42.0 µ (-2.6%) | 40.8 µ (-3.0%) | 45.5 µ (11.5%) | 42.4 µ (-6.8%) | 42.2 µ (-0.4%) | 41.2 µ (-2.3%) | 44.7 µ (8.4%) | 42.8 µ (-4.3%) | 41.5 µ (-3.1%) | 43.1 µ (4.1%) | 115.2 µ (167.0%) | 118.9 µ (3.2%) | 111.8 µ (-5.9%) | 113.9 µ (1.9%) | 110.1 µ (-3.3%) |
-| x = sites.metadata | 132.1 n | 138.3 n (4.7%) | 132.2 n (-4.4%) | 135.7 n (2.6%) | 131.6 n (-3.0%) | 378.1 n (187.4%) | 339.4 n (-10.2%) | 337.8 n (-0.5%) | 338.4 n (0.2%) | 378.4 n (11.8%) | 338.9 n (-10.4%) | 336.6 n (-0.7%) | 386.4 n (14.8%) | 330.1 n (-14.6%) | 328.7 n (-0.4%) | 325.4 n (-1.0%) | 323.5 n (-0.6%) | 321.5 n (-0.6%) | 350.5 n (9.0%) | 374.8 n (6.9%) | 320.1 n (-14.6%) |
-| x = sites.metadata_offset | 41.8 µ | 43.0 µ (2.9%) | 40.6 µ (-5.7%) | 43.7 µ (7.7%) | 41.7 µ (-4.6%) | 44.8 µ (7.5%) | 41.9 µ (-6.5%) | 42.0 µ (0.3%) | 46.4 µ (10.3%) | 40.9 µ (-11.7%) | 41.5 µ (1.3%) | 42.1 µ (1.4%) | 43.9 µ (4.5%) | 44.6 µ (1.5%) | 41.8 µ (-6.3%) | 42.7 µ (2.3%) | 117.3 µ (174.5%) | 119.1 µ (1.5%) | 115.1 µ (-3.3%) | 111.0 µ (-3.6%) | 112.4 µ (1.3%) |
-| x = sites.position | 101.2 µ | 103.8 µ (2.6%) | 99.2 µ (-4.5%) | 106.0 µ (6.9%) | 99.2 µ (-6.4%) | 100.9 µ (1.8%) | 100.9 µ (-0.0%) | 102.4 µ (1.4%) | 110.4 µ (7.8%) | 99.6 µ (-9.7%) | 100.1 µ (0.5%) | 100.7 µ (0.6%) | 100.0 µ (-0.7%) | 105.1 µ (5.1%) | 99.0 µ (-5.8%) | 102.2 µ (3.2%) | 114.5 µ (12.0%) | 120.9 µ (5.7%) | 116.3 µ (-3.9%) | 114.1 µ (-1.8%) | 110.0 µ (-3.6%) |
-
diff --git a/python/benchmark/bench-results.json b/python/benchmark/bench-results.json
deleted file mode 100644
index 5390ad60d7..0000000000
--- a/python/benchmark/bench-results.json
+++ /dev/null
@@ -1,10646 +0,0 @@
-{
- "0.2.1": {
- "system": {
- "system": "Linux",
- "node": "treebeard",
- "release": "5.4.0-109-generic",
- "version": "#123-Ubuntu SMP Fri Apr 8 09:10:54 UTC 2022",
- "machine": "x86_64",
- "processor": "x86_64",
- "python_version": "3.10.4 (main, Apr 8 2022, 17:35:13) [GCC 9.4.0]",
- "physical_cores": 8,
- "total_cores": 8,
- "max_frequency": 4700.0,
- "min_frequency": 800.0,
- "current_frequency": 4628.1085,
- "cpu_usage_per_core": [
- 0.0,
- 0.0,
- 0.0,
- 1.0,
- 0.0,
- 1.0,
- 1.0,
- 0.0
- ],
- "total_cpu_usage": 9.0
- },
- "tskit_benchmarks": {
- "ts = tskit.load(\"{filename}\")": {
- "ts = tskit.load(\"tiny.trees\")": {
- "one_run": 7.169899981818162e-05,
- "num_trials": 27894,
- "avg": 1.21104739011197e-05
- },
- "ts = tskit.load(\"bench.trees\")": {
- "one_run": 0.04981149299783283,
- "num_trials": 40,
- "avg": 0.027300330100024438
- }
- },
- "ts.dump(\"/dev/null\");\"{filename}\"": {
- "ts.dump(\"/dev/null\");\"tiny.trees\"": {
- "one_run": 5.626499842037447e-05,
- "num_trials": 35546,
- "avg": 3.498602183084326e-05
- },
- "ts.dump(\"/dev/null\");\"bench.trees\"": {
- "one_run": 0.009305341998697259,
- "num_trials": 214,
- "avg": 0.003444172775701437
- }
- },
- "ts.write_vcf(null)": {
- "ts.write_vcf(null)": {
- "one_run": 1.4667132159993344,
- "num_trials": 1,
- "avg": 1.4518820960001904
- }
- },
- "tree = ts.first();\"{filename}\"": {
- "tree = ts.first();\"tiny.trees\"": {
- "one_run": 1.0121999366674572e-05,
- "num_trials": 197589,
- "avg": 1.1891507978683357e-06
- },
- "tree = ts.first();\"bench.trees\"": {
- "one_run": 0.004617866001353832,
- "num_trials": 433,
- "avg": 0.0046029724295635
- }
- },
- "tree.seek()": {
- "tree.seek(pos)\npos = 0 if pos == 500_000 else 500_000\n": {
- "one_run": 0.023492426000302657,
- "num_trials": 85,
- "avg": 0.01366620522351107
- }
- },
- "for _ in ts.trees(): pass;'{filename}'": {
- "for _ in ts.trees(): pass;'tiny.trees'": {
- "one_run": 1.4365999959409237e-05,
- "num_trials": 139217,
- "avg": 2.1159993678925433e-06
- },
- "for _ in ts.trees(): pass;'bench.trees'": {
- "one_run": 0.039966147000086494,
- "num_trials": 50,
- "avg": 0.04097217046000878
- }
- },
- "tree.{array}(42);": {
- "tree.parent(42);": {
- "one_run": 2.4601999029982835e-05,
- "num_trials": 81294,
- "avg": 1.02698194210241e-07
- },
- "tree.left_child(42);": {
- "one_run": 5.1220013119746e-06,
- "num_trials": 390472,
- "avg": 1.035947084537188e-07
- },
- "tree.right_child(42);": {
- "one_run": 4.68900179839693e-06,
- "num_trials": 426530,
- "avg": 1.0461982041555553e-07
- },
- "tree.left_sib(42);": {
- "one_run": 4.522000381257385e-06,
- "num_trials": 442282,
- "avg": 9.898750119202633e-08
- },
- "tree.right_sib(42);": {
- "one_run": 5.664998752763495e-06,
- "num_trials": 353045,
- "avg": 9.829951705971764e-08
- }
- },
- "for v in ts.variants(): pass;'{filename}'": {
- "for v in ts.variants(): pass;'tiny.trees'": {
- "one_run": 2.3300999600905925e-05,
- "num_trials": 85833,
- "avg": 5.808918248259744e-06
- },
- "for v in ts.variants(): pass;'bench.trees'": {
- "one_run": 5.51277134799966,
- "num_trials": 1,
- "avg": 5.504353054999228
- }
- },
- "ts.genotype_matrix();'{filename}'": {
- "ts.genotype_matrix();'tiny.trees'": {
- "one_run": 5.788002454210073e-06,
- "num_trials": 345542,
- "avg": 8.420319121846837e-07
- },
- "ts.genotype_matrix();'bench.trees'": {
- "one_run": 0.03133426700151176,
- "num_trials": 63,
- "avg": 0.03129004395241426
- }
- },
- "for row in ts.{table}(): pass": {
- "for row in ts.nodes(): pass": {
- "one_run": 0.13981123899793602,
- "num_trials": 14,
- "avg": 0.13809905764277833
- },
- "for row in ts.edges(): pass": {
- "one_run": 0.19558949200290954,
- "num_trials": 10,
- "avg": 0.1940532548000192
- },
- "for row in ts.sites(): pass": {
- "one_run": 0.5893821320023562,
- "num_trials": 3,
- "avg": 0.585843709333858
- },
- "for row in ts.mutations(): pass": {
- "one_run": 0.6516343490002328,
- "num_trials": 3,
- "avg": 0.6617704256665699
- },
- "for row in ts.populations(): pass": {
- "one_run": 1.9019000319531187e-05,
- "num_trials": 105157,
- "avg": 1.50845380716983e-06
- },
- "for row in ts.individuals(): pass": {
- "one_run": 0.036903902000631206,
- "num_trials": 54,
- "avg": 0.036153033481510916
- },
- "for row in ts.migrations(): pass": {
- "one_run": 0.0033332229977531824,
- "num_trials": 600,
- "avg": 0.003281316793333341
- },
- "for row in ts.provenances(): pass": {
- "one_run": 2.7283997042104602e-05,
- "num_trials": 73303,
- "avg": 1.4253826719090917e-06
- }
- },
- "ts.{table}(1)": {
- "ts.node(1)": {
- "one_run": 1.0314000974176452e-05,
- "num_trials": 193911,
- "avg": 5.601309312061469e-07
- },
- "ts.edge(1)": {
- "one_run": 9.16299904929474e-06,
- "num_trials": 218269,
- "avg": 4.6631904668996587e-07
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- "0.3.1": {
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- "version": "#123-Ubuntu SMP Fri Apr 8 09:10:54 UTC 2022",
- "machine": "x86_64",
- "processor": "x86_64",
- "python_version": "3.10.4 (main, Apr 8 2022, 17:35:13) [GCC 9.4.0]",
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- "ts = tskit.load(\"{filename}\")": {
- "ts = tskit.load(\"tiny.trees\")": {
- "one_run": 0.0008191369997803122,
- "num_trials": 2441,
- "avg": 3.718517574810548e-05
- },
- "ts = tskit.load(\"bench.trees\")": {
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- "num_trials": 23,
- "avg": 0.05351028813042238
- }
- },
- "ts.dump(\"/dev/null\");\"{filename}\"": {
- "ts.dump(\"/dev/null\");\"tiny.trees\"": {
- "one_run": 7.808200098224916e-05,
- "num_trials": 25614,
- "avg": 4.617731900521702e-05
- },
- "ts.dump(\"/dev/null\");\"bench.trees\"": {
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- "num_trials": 407,
- "avg": 0.004702381793608307
- }
- },
- "ts.write_vcf(null)": {
- "ts.write_vcf(null)": {
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- "num_trials": 1,
- "avg": 1.845550527999876
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- },
- "tree = ts.first();\"{filename}\"": {
- "tree = ts.first();\"tiny.trees\"": {
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- "num_trials": 139635,
- "avg": 1.6059128299004547e-06
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- "tree = ts.first();\"bench.trees\"": {
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- "avg": 0.0055895308159361464
- }
- },
- "tree.seek()": {
- "tree.seek(pos)\npos = 0 if pos == 500_000 else 500_000\n": {
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- "avg": 0.014654612303227975
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- },
- "for _ in ts.trees(): pass;'{filename}'": {
- "for _ in ts.trees(): pass;'tiny.trees'": {
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- "num_trials": 94232,
- "avg": 2.6364728542422566e-06
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- "for _ in ts.trees(): pass;'bench.trees'": {
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- "avg": 0.041702174749995415
- }
- },
- "tree.{array}": {
- "tree.parent_array": {
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- "avg": 4.074379028023068e-08
- },
- "tree.left_child_array": {
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- "num_trials": 728331,
- "avg": 4.065955863473535e-08
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- "tree.right_child_array": {
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- "avg": 4.340606848557833e-08
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- "tree.left_sib_array": {
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- "avg": 4.740513497874988e-08
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- "tree.right_sib_array": {
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- "avg": 4.1063308842994394e-08
- }
- },
- "tree.{array}(42);": {
- "tree.parent(42);": {
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- "num_trials": 426257,
- "avg": 1.0395588108475443e-07
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- "tree.left_child(42);": {
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- "num_trials": 399360,
- "avg": 1.0863944561051015e-07
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- "tree.right_child(42);": {
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- "num_trials": 421851,
- "avg": 9.74248988386127e-08
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- "tree.left_sib(42);": {
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- "num_trials": 438500,
- "avg": 9.692546636030235e-08
- },
- "tree.right_sib(42);": {
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- "avg": 9.64835913087797e-08
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- "tree.num_children(42);": {
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- "num_trials": 420256,
- "avg": 1.0146763401124667e-07
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- },
- "tree.{traversal_order}()": {
- "tree.postorder()": {
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- "num_trials": 1130,
- "avg": 0.0017244870716819757
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- "tree.preorder()": {
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- "avg": 0.0014258514345936969
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- "tree.timeasc()": {
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- "tree.timedesc()": {
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- "for v in ts.variants(): pass;'{filename}'": {
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- "num_trials": 58920,
- "avg": 1.1203675169670968e-05
- },
- "for v in ts.variants(): pass;'bench.trees'": {
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- "ts.genotype_matrix();'{filename}'": {
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- "num_trials": 250658,
- "avg": 9.21866172230662e-07
- },
- "ts.genotype_matrix();'bench.trees'": {
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- "num_trials": 27,
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- }
- },
- "for row in ts.{table}(): pass": {
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- "for row in ts.edges(): pass": {
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- "for row in ts.sites(): pass": {
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- "for row in ts.mutations(): pass": {
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- "for row in ts.populations(): pass": {
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- "avg": 4.014103440106233e-06
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- "for row in ts.individuals(): pass": {
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- "avg": 0.08889306990915263
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- "for row in ts.migrations(): pass": {
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- "for row in ts.provenances(): pass": {
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- "avg": 1.957072887597077e-06
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- },
- "for row in ts.populations(): {decode_metadata}": {
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- "for row in ts.populations(): row.metadata": {
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- "avg": 3.427413685166084e-05
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- "avg": 3.258979960420893e-05
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- "x = individuals.flags": {
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- "avg": 3.2639943822073905e-07
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- "x = migrations.dest": {
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- "x = migrations.time": {
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- "x = migrations.metadata": {
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- "x = migrations.metadata_offset": {
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- "x = populations.metadata_offset": {
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- "x = provenances.timestamp": {
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- "x = provenances.timestamp_offset": {
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- "x = provenances.record": {
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- "avg": 4.267602340919547e-07
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- "x = provenances.record_offset": {
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- "avg": 3.438170464907622e-07
- }
- }
- }
- },
- "0.4.1": {
- "system": {
- "system": "Linux",
- "node": "treebeard",
- "release": "5.4.0-109-generic",
- "version": "#123-Ubuntu SMP Fri Apr 8 09:10:54 UTC 2022",
- "machine": "x86_64",
- "processor": "x86_64",
- "python_version": "3.10.4 (main, Apr 8 2022, 17:35:13) [GCC 9.4.0]",
- "physical_cores": 8,
- "total_cores": 8,
- "max_frequency": 4700.0,
- "min_frequency": 800.0,
- "current_frequency": 4670.509375000001,
- "cpu_usage_per_core": [
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- 1.0,
- 1.0,
- 3.9,
- 2.0,
- 0.0,
- 2.0,
- 2.0
- ],
- "total_cpu_usage": 9.5
- },
- "tskit_benchmarks": {
- "ts = tskit.load(\"{filename}\")": {
- "ts = tskit.load(\"tiny.trees\")": {
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- "num_trials": 621,
- "avg": 9.060590498894753e-05
- },
- "ts = tskit.load(\"bench.trees\")": {
- "one_run": 0.08641747499859775,
- "num_trials": 23,
- "avg": 0.051589642652169976
- }
- },
- "ts.dump(\"/dev/null\");\"{filename}\"": {
- "ts.dump(\"/dev/null\");\"tiny.trees\"": {
- "one_run": 8.03379989520181e-05,
- "num_trials": 24894,
- "avg": 4.635881694389002e-05
- },
- "ts.dump(\"/dev/null\");\"bench.trees\"": {
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- "num_trials": 396,
- "avg": 0.004725208121216741
- }
- },
- "ts.write_vcf(null)": {
- "ts.write_vcf(null)": {
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- "num_trials": 1,
- "avg": 1.97289988799821
- }
- },
- "tree = ts.first();\"{filename}\"": {
- "tree = ts.first();\"tiny.trees\"": {
- "one_run": 1.4455999917117879e-05,
- "num_trials": 138350,
- "avg": 1.7191142031156286e-06
- },
- "tree = ts.first();\"bench.trees\"": {
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- "avg": 0.005625240661204577
- }
- },
- "tree.seek()": {
- "tree.seek(pos)\npos = 0 if pos == 500_000 else 500_000\n": {
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- "num_trials": 153,
- "avg": 0.014864424986929711
- }
- },
- "for _ in ts.trees(): pass;'{filename}'": {
- "for _ in ts.trees(): pass;'tiny.trees'": {
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- "num_trials": 93023,
- "avg": 2.7996299517232134e-06
- },
- "for _ in ts.trees(): pass;'bench.trees'": {
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- "avg": 0.04186555439582662
- }
- },
- "tree.{array}": {
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- "num_trials": 717617,
- "avg": 4.1033774280073015e-08
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\ No newline at end of file