INFO: squashfs image was compressed with lz4, if it failed to run, please contact image's author
INFO: squashfs image was compressed with lz4, if it failed to run, please contact image's author
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---------- coverage: platform linux, python 3.11.0-final-0 -----------
Name Stmts Miss Cover Missing
-------------------------------------------------------------------------
Attention_module.py 279 279 0% 1-403
AuxiliaryPredictor.py 62 62 0% 1-89
Embeddings.py 220 220 0% 1-410
RoseTTAFoldModel.py 61 61 0% 1-151
SE3_network.py 45 45 0% 1-82
Track_module.py 269 269 0% 1-486
__init__.py 25 0 100%
aa_model.py 1722 799 54% 78-83, 86-104, 156-171, 197, 239-240, 257-262, 265-268, 280, 292-302, 324-327, 333, 336, 339-340, 343-345, 352, 358, 361-362, 365, 373-379, 382-383, 420-431, 434-443, 526-527, 531-543, 547-551, 557, 560, 563, 570-576, 579-583, 586-588, 591-598, 601, 608-632, 645-667, 674-699, 702-712, 715-721, 728-735, 741-758, 761-762, 774-800, 805-810, 826-996, 1025-1038, 1052-1054, 1066-1219, 1323, 1400, 1496-1504, 1508-1516, 1520-1523, 1539-1551, 1554-1559, 1758-1765, 1894-1896, 1952-1955, 1980-1982, 1985-1999, 2006-2026, 2030-2031, 2039-2050, 2053-2066, 2070-2073, 2105-2127, 2181-2305, 2318-2325, 2354, 2388-2389, 2392-2393, 2397-2398, 2420-2428, 2545-2568, 2630, 2636-2643, 2649-2657, 2767-2768, 2956-2964, 2968-2971, 2987-3016, 3019-3025, 3029-3038, 3042-3048, 3051-3053, 3073, 3076-3079
apply_masks.py 189 189 0% 1-529
arguments.py 216 216 0% 1-466
atomization_primitives.py 9 0 100%
atomize.py 134 34 75% 12-17, 35-36, 107-108, 119-135, 238-257, 297
benchmark/compile_metrics.py 215 199 7% 16-23, 26, 29, 35-36, 39-43, 46-272, 276-293, 296
blosum62.py 24 24 0% 2-105
bond_geometry.py 108 108 0% 1-196
build_coords.py 77 48 38% 29, 54-62, 115-134, 153-165, 223-244, 259-273
calc_hbonds.py 434 76 82% 295-299, 502, 542, 568-578, 597, 637-656, 675-682, 880-883, 978, 1002-1045
chemical.py 45 1 98% 29
conditioning.py 317 126 60% 8, 82, 177, 192-195, 220-223, 226-282, 328, 363-367, 371-425, 441-443, 446-454, 563-569, 580, 733, 752, 764-787, 793-794, 821, 831-840
conditions/__init__.py 0 0 100%
conditions/hbond_satisfaction.py 271 83 69% 25, 34, 68, 80, 83-85, 127-164, 176-191, 202-210, 226-252, 266-277, 500-501, 513, 623, 645, 650
conditions/ideal_ss.py 396 121 69% 166-171, 209, 227, 232-233, 242-243, 347-350, 354-357, 370, 402, 434, 451-468, 499, 514-518, 551-557, 691-695, 722-724, 758, 763-878, 890, 912, 917, 919, 921, 923
conditions/ss_adj/sec_struct_adjacency.py 550 351 36% 57-65, 69, 79, 88, 97, 161-173, 205-211, 342-352, 379, 383-392, 429-442, 498-499, 518-528, 543-555, 575-630, 655-675, 686, 705, 768-769, 776, 778, 804, 821-828, 838-858, 874-908, 925-936, 951-966, 1002-1032, 1036-1099, 1114-1126, 1131-1265
conditions/util.py 30 9 70% 86-107
conditions/v2.py 74 31 58% 72-85, 101-119, 135-141
config/config_format.py 56 46 18% 28-39, 54-58, 72-77, 92-97, 112-118, 131-152
conftest.py 24 0 100%
contig_shuffler.py 85 74 13% 18-30, 35-43, 46, 49-62, 65-72, 75-87, 100-133
contigs.py 273 252 8% 17-21, 53-151, 158-205, 208-209, 212-214, 217-250, 256-267, 270-285, 288, 316-361, 381-434
coords6d.py 45 45 0% 1-80
data_loader.py 1223 832 32% 59-64, 66-138, 145-154, 157-158, 175-296, 313-356, 359-414, 426-437, 441-662, 672-675, 688-713, 717-735, 739-774, 782-805, 811-831, 835-847, 851-888, 894-926, 933-1002, 1008-1018, 1021-1022, 1027-1046, 1050-1079, 1090-1134, 1141-1149, 1152-1155, 1158-1261, 1267-1338, 1389-1394, 1588-1597, 1601, 1610, 1661, 1686, 1691, 1705-1706, 1718-1722, 1736, 1745, 1760, 1768-1773, 1798-1823, 1826-1835, 1852, 1892, 1930, 1958-1959, 2015, 2048-2049, 2052, 2072-2086, 2098-2103, 2105-2110, 2122, 2173, 2176, 2184-2187
datahub_dataset_interface.py 44 44 0% 1-94
dev/analyze.py 1127 973 14% 33-37, 40-41, 44-46, 49-59, 66-67, 72-81, 84-87, 90, 93-99, 102-104, 108-145, 148-160, 163-181, 220-221, 225-281, 285-288, 291-294, 297-330, 333-334, 337-347, 350-354, 358-383, 386-391, 395-400, 403-406, 409-412, 416-418, 431-447, 450-451, 455, 458-460, 463-470, 473-489, 493-501, 505-507, 510-511, 515-517, 520-522, 527-530, 539, 550-566, 569-606, 612-693, 698-699, 703-709, 712-717, 722-724, 729-730, 733-751, 755-763, 766, 772-800, 803-810, 817-839, 856-869, 873-897, 902-903, 906-925, 928-930, 933-946, 950-953, 956-958, 961-964, 967-971, 974-977, 981-985, 989-993, 999-1019, 1022-1030, 1033-1035, 1038, 1041, 1044-1046, 1049-1051, 1062-1074, 1078-1089, 1092-1108, 1113-1161, 1165-1220, 1224-1313, 1317-1338, 1343-1383, 1387-1390, 1393-1398, 1403-1405, 1408-1415, 1420-1449, 1452-1454, 1457-1460, 1471-1538, 1542-1551, 1555-1561, 1564-1565, 1568-1569, 1572-1573, 1577-1578, 1581-1583, 1586, 1590-1593, 1597-1600, 1604-1620, 1627, 1639, 1642-1694, 1697-1700, 1704-1714, 1717, 1720, 1723, 1727-1732, 1735-1737, 1740, 1743-1744, 1747-1756
dev/draw_with_atoms.py 19 13 32% 47, 61-63, 75, 89-100
dev/idealize_backbone.py 62 46 26% 27-31, 34-38, 52-80, 96-119, 122-126, 129
dev/pymol.py 43 21 51% 17-24, 29, 39-40, 45-56
dev/show_tip_row.py 147 121 18% 13-22, 25-27, 35-38, 41, 44, 47, 50, 53-61, 64-71, 74-94, 97-104, 108-152, 155-158, 161-162, 166, 169-188, 191-202, 205-214
diff_util.py 40 40 0% 1-92
diffusion_ve.py 91 91 0% 2-245
distributions.py 51 19 63% 10, 12, 16-19, 22-25, 28-31, 36-39, 49
error.py 16 10 38% 8-12, 16-21
estimate_likelihood.py 198 154 22% 22-31, 34-39, 42-44, 47-48, 51-55, 58-61, 64-79, 86-163, 176-183, 186-193, 198-212, 216, 220-221, 225-234, 240-249, 253-303
features.py 277 205 26% 17, 27-33, 36-44, 47-52, 68, 75-77, 87-90, 100, 114-116, 119-134, 137-141, 144, 147, 169-182, 185-188, 235-248, 264-267, 285-288, 305-338, 359-386, 409-429, 454-472, 482, 497-546
frame_diffusion/data/all_atom.py 36 0 100%
frame_diffusion/data/r3_diffuser.py 85 47 45% 26-28, 32, 36, 39, 45-49, 62-68, 71-78, 92, 128-145, 154, 159, 163-164
frame_diffusion/data/residue_constants.py 219 92 58% 406-476, 568-586, 858-894
frame_diffusion/data/se3_diffuser.py 117 61 48% 65, 76, 103, 113, 116, 120-125, 131, 139-153, 156-158, 186-215, 231-269
frame_diffusion/data/so3_diffuser.py 146 44 70% 36-38, 44, 49, 63-68, 103, 105, 116, 146, 157-176, 197, 201, 204, 208-214, 234, 256, 275, 300-306, 359-373
frame_diffusion/data/utils.py 57 27 53% 48-50, 66-79, 200, 588-603
frame_diffusion/rf_score/model.py 182 140 23% 32-55, 77-98, 102-121, 125-172, 176-229, 232, 237-241, 244-246, 251-257, 260-295, 298-317, 320-338
guide_posts.py 331 299 10% 52-65, 82-106, 131-163, 168-169, 180-189, 195-202, 210-213, 235-281, 290-298, 309-324, 335-342, 363-400, 416-432, 440-444, 458-469, 475-486, 494-540, 543, 567-590, 603-641, 648-659, 666-691, 695-705, 709-718
idealize.py 43 37 14% 23-47, 67-107
igso3.py 45 45 0% 2-165
import_pyrosetta.py 16 11 31% 18-21, 29-37, 43
inference/__init__.py 2 0 100%
inference/centering.py 34 26 24% 19-44, 59-64, 79-83
inference/data_loader.py 105 71 32% 34-37, 45-48, 51-77, 80, 93-95, 98-102, 105, 108, 122-131, 142-150, 166-171, 184-276, 279, 282
inference/model_runners.py 317 258 19% 46-47, 57-103, 106-175, 192-194, 200-203, 230-322, 325-330, 333-335, 347-367, 370-381, 385-393, 396-397, 415-422, 428-434, 439-465, 470-488, 509-538, 543-544, 549-550, 555-556, 559-567, 573-574, 578-586, 589-628
inference/old_symmetry.py 191 170 11% 10, 23-81, 87-93, 96-106, 109-122, 128-151, 154-188, 194-203, 209-211, 214-233, 247-269, 280-286
inference/scaffold.py 202 175 13% 21, 32, 35, 38, 61, 64, 76-166, 170-176, 204-298, 302, 319-351, 365-373, 386-399, 416-431, 449-468, 474-480
inference/utils.py 425 375 12% 36-52, 76-114, 122-133, 158-178, 188-203, 217-233, 240-267, 272, 288-358, 361-366, 370-371, 375-439, 446-472, 483-496, 528-573, 579-582, 588-611, 617-630, 636-652, 659-670, 676-703, 718-736, 742-750, 762-783, 786, 789-790, 794, 797, 814, 830-876, 896-916
kinematics.py 159 142 11% 26-27, 43-49, 65-77, 81-87, 104-129, 145-157, 172-183, 187-203, 207-212, 218-234, 242-248, 256-279, 288-320
loss.py 452 452 0% 1-858
loss_aa.py 3 3 0% 1-4
manual_test_mpnn.py 33 33 0% 1-59
mask_generator.py 1121 456 59% 64-77, 89-96, 111-123, 126-128, 131-140, 143-151, 155-162, 165-175, 184-222, 225, 252-253, 347-350, 378, 431-434, 444, 468-475, 478-501, 504-511, 527, 531-533, 543-599, 607-656, 680-684, 704, 708, 739, 779-780, 786-791, 802, 804, 823, 827, 861, 870-880, 892, 897, 907-920, 933, 943-956, 980-995, 1023-1044, 1072-1093, 1129, 1140, 1143, 1195-1228, 1235-1245, 1284-1287, 1294-1302, 1326, 1343-1348, 1387, 1403, 1414, 1425, 1610, 1639, 1644-1674, 1692-1712, 1728-1737, 1749-1753, 1764, 1779-1784, 1797-1802, 1821-1826, 1840-1858, 1914, 1945-1956, 1989-1996
master_addr.py 9 9 0% 1-11
metrics.py 224 224 0% 1-488
model_input_logger.py 63 63 0% 1-109
motif/__init__.py 0 0 100%
motif/rfd_motif_manager.py 10 10 0% 1-13
noisers.py 112 61 46% 19, 30-34, 57-65, 93-94, 99, 110-119, 129-142, 145-152, 156-157, 164-174, 185-199, 203
nucleic_compatibility_utils.py 914 657 28% 13-14, 96-123, 149-179, 210-213, 223, 233, 237, 246-279, 283-300, 319-331, 409-431, 445-456, 474-482, 499-540, 545-570, 574-579, 582-608, 612-628, 635-663, 667-702, 705-727, 730-744, 782-816, 820-827, 831-833, 837-898, 902-928, 936-944, 947-961, 964-983, 1009, 1030-1031, 1056-1062, 1064-1076, 1098-1105, 1177-1229, 1238-1319, 1463, 1523, 1543-1547, 1552-1573, 1581-1599, 1603-1608, 1618-1664, 1676-1790, 1794-1799
observer/__init__.py 1 0 100%
observer/pymol_observer.py 62 43 31% 28-38, 41-43, 46-48, 52-57, 61-86
parsers.py 131 79 40% 22-86, 93-94, 153-167, 204-225, 229-253
partials_from_training.py 86 86 0% 1-120
perturbations.py 6 6 0% 1-8
ppi.py 559 177 68% 27-28, 148-149, 195-196, 227-228, 236, 261, 275, 325, 346, 422, 427-428, 436, 444, 478, 507, 579, 584-585, 598, 608, 639, 643-644, 648, 656, 664, 713-730, 761-803, 844-852, 920, 923, 940, 946, 970-1000, 1036, 1080, 1091-1092, 1109, 1123, 1144, 1146, 1148, 1179-1181, 1186-1262, 1270-1292, 1310-1334
reshape_weights.py 64 64 0% 2-105
restart_training.py 26 26 0% 1-43
rotation_conversions.py 157 130 17% 50-68, 85-86, 94-97, 110-157, 175-189, 204-218, 243-251, 255-261, 275-303, 322-328, 346-347, 364, 379, 394-400, 416-417, 433-434, 449-457, 473, 489, 505-521, 538-552, 571-576, 594-595
run_inference.py 394 338 14% 64-65, 73, 81-86, 89-107, 110-119, 133-135, 149-152, 164-189, 199-201, 204-235, 239-398, 415-434, 444-468, 489-526, 529-725, 729
sasa.py 142 20 86% 89-98, 134-135, 201-209
save_forward_diffusion.py 54 54 0% 1-63
scheduler.py 64 64 0% 1-180
scoring.py 94 0 100%
seq_diffusion.py 260 260 0% 2-818
show.py 52 37 29% 15-16, 20-23, 27-41, 44, 47, 50-55, 59-67, 70-72
show_dataset.py 119 119 0% 6-246
silent_files.py 60 45 25% 23-24, 41-50, 65-74, 85-90, 105-115, 126-128, 147-156
slurm.py 21 21 0% 1-29
structure.py 232 53 77% 15, 123, 168, 281, 333-360, 394, 400-401, 415-431, 475, 506-507
sym/__init__.py 3 3 0% 1-3
sym/rfd_highT_sym_manager.py 82 82 0% 1-123
sym/rfd_sym_manager.py 65 65 0% 1-103
sym/sym_indep.py 50 50 0% 5-93
test_aa_model.py 190 190 0% 1-261
test_apptainer.py 43 43 0% 1-78
test_atomize.py 69 69 0% 1-129
test_build_coords.py 52 52 0% 1-94
test_chai.py 41 41 0% 7-83
test_contigs.py 71 71 0% 1-145
test_dataset.py 530 67 87% 338-344, 382-383, 417-418, 437-438, 458-459, 479, 497-499, 519-521, 542-544, 565-567, 585-587, 627-634, 688-690, 720-722, 748-750, 772, 792-794, 815-817, 845-847, 890, 896-902, 908, 991-994, 1177
test_diffusion.py 0 0 100%
test_features.py 119 119 0% 1-235
test_geometry.py 102 102 0% 4-163
test_guidepost.py 32 32 0% 1-60
test_idealize.py 30 30 0% 1-57
test_inference.py 763 763 0% 1-1883
test_inference_mini.py 134 134 0% 14-250
test_inference_open_source.py 87 87 0% 1-180
test_loss.py 60 60 0% 2-91
test_metrics_regression.py 46 46 0% 1-97
test_pipeline.py 64 64 0% 1-244
test_pyrosetta.py 177 177 0% 1-266
test_seq_diff/__init__.py 0 0 100%
test_seq_diff/inference.py 15 15 0% 1-24
test_seq_diff/network.py 23 23 0% 1-45
test_seq_diff/seq_diff_util.py 17 17 0% 1-23
test_seq_diff/train.py 87 87 0% 1-177
test_train_open_source.py 90 90 0% 1-135
test_training_regression.py 172 172 0% 1-249
test_transform.py 136 136 0% 1-228
test_utils.py 339 175 48% 38, 42-45, 49-50, 59-62, 64, 89-98, 112-134, 137-147, 151-156, 165-268, 271-280, 283-285, 288-290, 293-295, 300-306, 314, 367-372, 392-397, 470-472, 476-482, 517
tip_atoms.py 27 0 100%
train_data/exceptions.py 8 1 88% 27
train_data/fast_filters.py 13 5 62% 22-28
train_multi_deep.py 784 784 0% 3-1374
util.py 215 186 13% 14-21, 24-32, 35-49, 52, 59-84, 87-113, 116-188, 191-208, 212-218, 221-229, 233-285, 318-329
util_module.py 175 175 0% 1-308
viz/__init__.py 1 1 0% 1
viz/viz_indep_pymol.py 57 57 0% 1-119
write_file.py 140 39 72% 11-14, 29-33, 50, 59, 64-67, 71-72, 75, 81, 99-103, 119, 125, 143, 185, 187, 189, 206, 220-221, 227-239
-------------------------------------------------------------------------
TOTAL 22939 16257 29%
33 passed, 136 warnings in 293.66s (0:04:53)