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  1. INVENTORY.md +215 -0
  2. configs/014_energy_backdoor_defense_test/editable.txt +0 -0
  3. configs/014_energy_backdoor_defense_test/env.yml +57 -0
  4. configs/014_energy_backdoor_defense_test/explicit.txt +31 -0
  5. configs/014_energy_backdoor_defense_test/meta.json +8 -0
  6. configs/014_energy_backdoor_defense_test/pip-clean.txt +454 -0
  7. configs/014_energy_backdoor_defense_test/pip-freeze.txt +454 -0
  8. configs/021_test/editable.txt +0 -0
  9. configs/021_test/env.yml +46 -0
  10. configs/021_test/explicit.txt +31 -0
  11. configs/021_test/meta.json +8 -0
  12. configs/021_test/pip-clean.txt +448 -0
  13. configs/021_test/pip-freeze.txt +448 -0
  14. configs/069_test/editable.txt +0 -0
  15. configs/069_test/env.yml +62 -0
  16. configs/069_test/explicit.txt +31 -0
  17. configs/069_test/meta.json +8 -0
  18. configs/069_test/pip-clean.txt +463 -0
  19. configs/069_test/pip-freeze.txt +463 -0
  20. configs/s41467_024_44930_y_test/editable.txt +0 -0
  21. configs/s41467_024_44930_y_test/env.yml +63 -0
  22. configs/s41467_024_44930_y_test/explicit.txt +31 -0
  23. configs/s41467_024_44930_y_test/meta.json +8 -0
  24. configs/s41467_024_44930_y_test/pip-clean.txt +463 -0
  25. configs/s41467_024_44930_y_test/pip-freeze.txt +463 -0
  26. configs/s41467_024_46879_4_test/editable.txt +0 -0
  27. configs/s41467_024_46879_4_test/env.yml +71 -0
  28. configs/s41467_024_46879_4_test/explicit.txt +31 -0
  29. configs/s41467_024_46879_4_test/meta.json +8 -0
  30. configs/s41467_024_46879_4_test/pip-clean.txt +472 -0
  31. configs/s41467_024_46879_4_test/pip-freeze.txt +472 -0
  32. configs/s41467_024_47677_8_test/editable.txt +0 -0
  33. configs/s41467_024_47677_8_test/env.yml +46 -0
  34. configs/s41467_024_47677_8_test/explicit.txt +31 -0
  35. configs/s41467_024_47677_8_test/meta.json +8 -0
  36. configs/s41467_024_47677_8_test/pip-clean.txt +451 -0
  37. configs/s41467_024_47677_8_test/pip-freeze.txt +451 -0
  38. configs/s41467_024_52614_w_test/editable.txt +0 -0
  39. configs/s41467_024_52614_w_test/env.yml +39 -0
  40. configs/s41467_024_52614_w_test/explicit.txt +31 -0
  41. configs/s41467_024_52614_w_test/meta.json +8 -0
  42. configs/s41467_024_52614_w_test/pip-clean.txt +444 -0
  43. configs/s41467_024_52614_w_test/pip-freeze.txt +444 -0
  44. configs/s41467_024_53672_w_test/editable.txt +0 -0
  45. configs/s41467_024_53672_w_test/env.yml +38 -0
  46. configs/s41467_024_53672_w_test/explicit.txt +31 -0
  47. configs/s41467_024_53672_w_test/meta.json +8 -0
  48. configs/s41467_024_53672_w_test/pip-clean.txt +443 -0
  49. configs/s41467_024_53672_w_test/pip-freeze.txt +443 -0
  50. editable_manifest.tsv +5 -0
INVENTORY.md ADDED
@@ -0,0 +1,215 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # MMSciCode env configs inventory
2
+
3
+ - Total envs: **204**
4
+ - Total config size: **2.71 MB**
5
+ - Envs with editable installs: **4**
6
+ - Envs with CUDA hint: **0**
7
+
8
+ ## Per-env summary
9
+
10
+ | env | python | cuda | editable | env.yml | explicit | pip-clean |
11
+ |---|---|---|---|---|---|---|
12
+ | 001_rm_bench_test | 3.8.20 | - | 0 | 2271 | 10504 | 8379 |
13
+ | 002_topolm_test | 3.8.20 | - | 0 | 1984 | 10503 | 8362 |
14
+ | 003_knowledge_entropy_test | 3.8.20 | - | 0 | 1974 | 10503 | 8362 |
15
+ | 005_trust_align_test | 3.8.20 | - | 0 | 1939 | 10503 | 8345 |
16
+ | 006_map_alignment_test | 3.8.20 | - | 1 | 2193 | 10503 | 8460 |
17
+ | 007_spa_test | 3.8.20 | - | 0 | 1946 | 10503 | 8362 |
18
+ | 009_brain_bandit_test | 3.8.20 | - | 0 | 2492 | 9695 | 8813 |
19
+ | 011_gp_hdbo_test | 3.8.20 | - | 0 | 831 | 3210 | 8425 |
20
+ | 012_oscillatory_state_space_models_test | 3.8.20 | - | 0 | 768 | 3210 | 8346 |
21
+ | 013_attention_as_hypernetwork_test | 3.8.20 | - | 0 | 1014 | 3210 | 8480 |
22
+ | 014_energy_backdoor_defense_test | 3.8.20 | - | 0 | 1205 | 3210 | 8512 |
23
+ | 015_guidance_free_ar_generation_test | 3.8.20 | - | 0 | 982 | 3210 | 8458 |
24
+ | 016_rmp_sam_test | 3.8.20 | - | 0 | 1441 | 3210 | 8688 |
25
+ | 017_test | 3.8.20 | - | 0 | 1011 | 3210 | 8562 |
26
+ | 018_test | 3.8.20 | - | 0 | 1643 | 3210 | 8957 |
27
+ | 019_test | 3.10.20 | - | 0 | 4187 | 2976 | 2790 |
28
+ | 020_test | 3.9.23 | - | 0 | 3810 | 19935 | 187 |
29
+ | 021_test | 3.8.20 | - | 0 | 911 | 3210 | 8422 |
30
+ | 022_test | 3.8.20 | - | 0 | 973 | 3210 | 8452 |
31
+ | 023_test | 3.8.20 | - | 0 | 957 | 3210 | 8456 |
32
+ | 024_test | 3.8.20 | - | 0 | 911 | 3210 | 8422 |
33
+ | 026_test | 3.8.20 | - | 0 | 928 | 3210 | 8433 |
34
+ | 027_test | 3.8.20 | - | 0 | 928 | 3210 | 8433 |
35
+ | 029_test | 3.8.20 | - | 0 | 1368 | 3210 | 8687 |
36
+ | 030_test | 3.8.20 | - | 0 | 1127 | 3210 | 8553 |
37
+ | 031_test | 3.8.20 | - | 0 | 933 | 3210 | 8422 |
38
+ | 032_test | 3.8.20 | - | 0 | 706 | 3210 | 8346 |
39
+ | 033_test | 3.8.20 | - | 0 | 1064 | 3210 | 8484 |
40
+ | 036_test | 3.8.20 | - | 0 | 947 | 3210 | 8446 |
41
+ | 037_test | 3.8.20 | - | 0 | 726 | 3210 | 8360 |
42
+ | 039_test | 3.8.20 | - | 0 | 1120 | 3210 | 8617 |
43
+ | 040_test | 3.8.20 | - | 0 | 1101 | 3210 | 8576 |
44
+ | 041_test | 3.8.20 | - | 0 | 1700 | 3210 | 9005 |
45
+ | 042_test | 3.8.20 | - | 0 | 1719 | 3210 | 8998 |
46
+ | 043_test | 3.8.20 | - | 0 | 1774 | 3210 | 9080 |
47
+ | 044_test | 3.8.20 | - | 0 | 2464 | 9682 | 8750 |
48
+ | 046_test | 3.8.20 | - | 0 | 1566 | 3210 | 8914 |
49
+ | 047_test | 3.8.20 | - | 0 | 1696 | 3210 | 8952 |
50
+ | 048_test | 3.8.20 | - | 0 | 1449 | 3210 | 8835 |
51
+ | 049_test | 3.8.20 | - | 0 | 1343 | 3210 | 8776 |
52
+ | 050_test | 3.8.20 | - | 0 | 1323 | 3210 | 8762 |
53
+ | 051_test | 3.8.20 | - | 0 | 1343 | 3210 | 8776 |
54
+ | 053_test | 3.8.20 | - | 0 | 1484 | 3210 | 8821 |
55
+ | 055_test | 3.8.20 | - | 0 | 1478 | 3210 | 8844 |
56
+ | 056_test | 3.8.20 | - | 0 | 1403 | 3210 | 8795 |
57
+ | 057_test | 3.8.20 | - | 0 | 1671 | 3210 | 8962 |
58
+ | 059_test | 3.8.20 | - | 0 | 1399 | 3210 | 8807 |
59
+ | 060_test | 3.8.20 | - | 0 | 1486 | 3210 | 8912 |
60
+ | 061_test | 3.8.20 | - | 0 | 1017 | 3210 | 8467 |
61
+ | 062_test | 3.8.20 | - | 0 | 1043 | 3210 | 8487 |
62
+ | 064_test | 3.8.20 | - | 0 | 1291 | 3210 | 8762 |
63
+ | 065_test | 3.8.20 | - | 0 | 1264 | 3210 | 8700 |
64
+ | 067_test | 3.10.18 | - | 0 | 3589 | 17161 | 328 |
65
+ | 068_test | 3.8.20 | - | 0 | 1550 | 3210 | 8941 |
66
+ | 069_test | 3.8.20 | - | 0 | 1397 | 3210 | 8807 |
67
+ | 070_test | 3.8.20 | - | 0 | 818 | 3210 | 8414 |
68
+ | 071_test | 3.8.20 | - | 0 | 1452 | 3210 | 8821 |
69
+ | 073_test | 3.8.20 | - | 0 | 1487 | 3210 | 8879 |
70
+ | 075_test | 3.8.20 | - | 0 | 1561 | 3210 | 8877 |
71
+ | 076_test | 3.8.20 | - | 0 | 1485 | 3210 | 8867 |
72
+ | cpp_test_env | 3.13.7 | - | 0 | 4148 | 21880 | 101 |
73
+ | r_test_env | 3.13.5 | - | 0 | 7633 | 42840 | 245 |
74
+ | s41467_024_44757_7_test | 3.8.20 | - | 1 | 3164 | 10574 | 8982 |
75
+ | s41467_024_44803_4_test | 3.8.20 | - | 0 | 1999 | 3210 | 8876 |
76
+ | s41467_024_44864_5_test | 3.8.20 | - | 0 | 1838 | 8882 | 8363 |
77
+ | s41467_024_44900_4_test | 3.8.20 | - | 0 | 1289 | 5095 | 8427 |
78
+ | s41467_024_44907_x_test | 3.8.20 | - | 0 | 838 | 3210 | 8360 |
79
+ | s41467_024_44930_y_test | 3.8.20 | - | 0 | 1407 | 3210 | 8729 |
80
+ | s41467_024_45059_8_test | 3.8.20 | - | 0 | 2466 | 8883 | 8809 |
81
+ | s41467_024_45514_6_test | 3.8.20 | - | 0 | 838 | 3210 | 8360 |
82
+ | s41467_024_45598_0_test | 3.8.20 | - | 0 | 985 | 3438 | 8405 |
83
+ | s41467_024_45599_z_test | 3.8.20 | - | 0 | 1517 | 3210 | 8777 |
84
+ | s41467_024_45642_z_test | 3.8.20 | - | 0 | 1835 | 8882 | 8377 |
85
+ | s41467_024_45674_5_test | 3.13.7 | - | 0 | 3825 | 20198 | 85 |
86
+ | s41467_024_45733_x_test | 3.8.20 | - | 0 | 1769 | 4515 | 8773 |
87
+ | s41467_024_45772_4_test | 3.8.20 | - | 0 | 1815 | 8882 | 8363 |
88
+ | s41467_024_46000_9_test | 3.8.20 | - | 0 | 2336 | 5096 | 9065 |
89
+ | s41467_024_46027_y_test | 3.8.20 | - | 0 | 736 | 3210 | 8346 |
90
+ | s41467_024_46089_y_test | 3.8.20 | - | 0 | 1533 | 3210 | 8769 |
91
+ | s41467_024_46107_z_test | 3.8.20 | - | 0 | 967 | 3210 | 8387 |
92
+ | s41467_024_46399_1_test | 3.8.20 | - | 0 | 1102 | 3210 | 8416 |
93
+ | s41467_024_46413_6_test | 3.8.20 | - | 0 | 1630 | 3210 | 8967 |
94
+ | s41467_024_46506_2_test | 3.8.20 | - | 0 | 776 | 3210 | 8374 |
95
+ | s41467_024_46523_1_test | 3.8.20 | - | 0 | 1081 | 5555 | 8332 |
96
+ | s41467_024_46614_z_test | 3.8.20 | - | 0 | 964 | 3210 | 8464 |
97
+ | s41467_024_46700_2_test | 3.8.20 | - | 0 | 1456 | 3210 | 8833 |
98
+ | s41467_024_46773_z_test | 3.8.20 | - | 0 | 992 | 3210 | 8443 |
99
+ | s41467_024_46879_4_test | 3.8.20 | - | 0 | 1646 | 3210 | 8950 |
100
+ | s41467_024_46945_x_test | 3.8.20 | - | 0 | 736 | 3210 | 8346 |
101
+ | s41467_024_46946_w_test | 3.8.20 | - | 0 | 1390 | 3210 | 8787 |
102
+ | s41467_024_46976_4_test | 3.8.20 | - | 0 | 1322 | 3210 | 8737 |
103
+ | s41467_024_47120_y_test | 3.8.20 | - | 0 | 938 | 3435 | 8422 |
104
+ | s41467_024_47447_6_test | 3.8.20 | - | 0 | 979 | 3210 | 8502 |
105
+ | s41467_024_47459_2_test | 3.8.20 | - | 0 | 736 | 3210 | 8346 |
106
+ | s41467_024_47569_x_test | 3.8.20 | - | 0 | 736 | 3210 | 8346 |
107
+ | s41467_024_47659_w_test | 3.8.20 | - | 0 | 1016 | 3210 | 8527 |
108
+ | s41467_024_47661_2_test | 3.8.20 | - | 0 | 1368 | 3210 | 8771 |
109
+ | s41467_024_47677_8_test | 3.8.20 | - | 0 | 949 | 3210 | 8478 |
110
+ | s41467_024_47831_2_test | 3.8.20 | - | 0 | 1096 | 3210 | 8504 |
111
+ | s41467_024_48107_5_test | 3.8.20 | - | 0 | 1053 | 3210 | 8558 |
112
+ | s41467_024_48446_3_test | 3.8.20 | - | 0 | 1361 | 3210 | 8764 |
113
+ | s41467_024_48567_9_test | 3.8.20 | - | 1 | 1443 | 3210 | 8825 |
114
+ | s41467_024_48578_6_test | 3.10.18 | - | 1 | 3576 | 16810 | 429 |
115
+ | s41467_024_48673_8_test | 3.8.20 | - | 0 | 1306 | 3210 | 8627 |
116
+ | s41467_024_49163_7_test | 3.8.20 | - | 0 | 842 | 3210 | 8399 |
117
+ | s41467_024_49261_6_test | 3.8.20 | - | 0 | 984 | 3210 | 8478 |
118
+ | s41467_024_49339_1_test | 3.8.20 | - | 0 | 984 | 3210 | 8478 |
119
+ | s41467_024_49516_2_test | 3.8.20 | - | 0 | 1097 | 3210 | 8519 |
120
+ | s41467_024_49957_9_test | 3.8.20 | - | 0 | 1247 | 6351 | 8332 |
121
+ | s41467_024_50043_3_test | 3.8.20 | - | 0 | 1313 | 3210 | 8631 |
122
+ | s41467_024_50114_5_test | 3.8.20 | - | 0 | 1386 | 3210 | 8775 |
123
+ | s41467_024_50317_w_test | 3.8.20 | - | 0 | 1026 | 3210 | 8460 |
124
+ | s41467_024_50381_2_test | 3.8.20 | - | 0 | 1167 | 3210 | 8565 |
125
+ | s41467_024_50505_8_test | 3.8.20 | - | 0 | 984 | 3210 | 8478 |
126
+ | s41467_024_50605_5_test | 3.8.20 | - | 0 | 1360 | 3435 | 8683 |
127
+ | s41467_024_50903_y_test | 3.8.20 | - | 0 | 1514 | 3210 | 8782 |
128
+ | s41467_024_51026_0_test | 3.8.20 | - | 0 | 989 | 3210 | 8456 |
129
+ | s41467_024_51477_5_test | 3.8.20 | - | 0 | 1033 | 3210 | 8519 |
130
+ | s41467_024_51491_7_test | 3.8.20 | - | 0 | 1366 | 3210 | 8744 |
131
+ | s41467_024_51555_8_test | 3.8.20 | - | 0 | 834 | 3210 | 8377 |
132
+ | s41467_024_51560_x_test | 3.8.20 | - | 0 | 1005 | 3210 | 8493 |
133
+ | s41467_024_51563_8_test | 3.8.20 | - | 0 | 1470 | 3094 | 8735 |
134
+ | s41467_024_51639_5_test | 3.8.20 | - | 0 | 1322 | 3210 | 8737 |
135
+ | s41467_024_51864_y_test | 3.8.20 | - | 0 | 736 | 3210 | 8346 |
136
+ | s41467_024_51933_2_test | 3.8.20 | - | 0 | 1322 | 3210 | 8737 |
137
+ | s41467_024_52003_3_test | 3.8.20 | - | 0 | 1226 | 3210 | 8584 |
138
+ | s41467_024_52081_3_test | 3.8.20 | - | 0 | 984 | 3210 | 8478 |
139
+ | s41467_024_52414_2_test | 3.8.20 | - | 0 | 1134 | 3210 | 8530 |
140
+ | s41467_024_52580_3_test | 3.8.20 | - | 0 | 883 | 3210 | 8380 |
141
+ | s41467_024_52614_w_test | 3.8.20 | - | 0 | 791 | 3210 | 8360 |
142
+ | s41467_024_53146_z_test | 3.8.20 | - | 0 | 1003 | 3210 | 8478 |
143
+ | s41467_024_53200_w_test | 3.8.20 | - | 0 | 736 | 3210 | 8346 |
144
+ | s41467_024_53455_3_test | 3.8.20 | - | 0 | 797 | 3210 | 8376 |
145
+ | s41467_024_53672_w_test | 3.8.20 | - | 0 | 755 | 3210 | 8346 |
146
+ | s41467_024_53818_w_test | 3.8.20 | - | 0 | 791 | 3210 | 8360 |
147
+ | s41467_024_54067_7_test | 3.8.20 | - | 0 | 894 | 3210 | 8392 |
148
+ | s41467_024_54375_y_test | 3.8.20 | - | 0 | 1727 | 5554 | 8747 |
149
+ | s41467_024_54639_7_test | 3.8.20 | - | 0 | 1352 | 3210 | 8761 |
150
+ | s41467_024_54696_y_test | 3.8.20 | - | 0 | 861 | 3210 | 8399 |
151
+ | s41467_024_54738_5_test | 3.8.20 | - | 0 | 971 | 3210 | 8446 |
152
+ | s41467_024_54846_2_test | 3.7.12 | - | 0 | 799 | 3337 | 2909 |
153
+ | s41467_024_55291_x_test | 3.8.20 | - | 0 | 1509 | 3210 | 9113 |
154
+ | s41467_024_55419_z_test | 3.8.20 | - | 0 | 1352 | 3210 | 8761 |
155
+ | s41467_024_55462_w_test | 3.8.20 | - | 0 | 1205 | 5998 | 8353 |
156
+ | s41467_024_55594_z_test | 3.8.20 | - | 0 | 860 | 3210 | 8414 |
157
+ | s41467_025_55825_x_test | 3.8.20 | - | 0 | 1535 | 3210 | 8781 |
158
+ | s41467_025_56036_0_test | 3.8.20 | - | 0 | 1056 | 3210 | 8526 |
159
+ | s41467_025_56078_4_test | 3.8.20 | - | 0 | 1770 | 3210 | 9049 |
160
+ | s41467_025_56140_1_test | 3.8.20 | - | 0 | 796 | 3210 | 8388 |
161
+ | s41467_025_56162_9_test | 3.8.20 | - | 0 | 1206 | 3210 | 8574 |
162
+ | s41467_025_56173_6_test | 3.8.20 | - | 0 | 885 | 3210 | 8398 |
163
+ | s41467_025_56348_1_test | 3.8.20 | - | 0 | 1244 | 4856 | 8447 |
164
+ | s41467_025_56378_9_test | 3.8.20 | - | 0 | 2495 | 3210 | 9401 |
165
+ | s41467_025_56424_6_test | 3.8.20 | - | 0 | 1322 | 3210 | 8737 |
166
+ | s41467_025_56622_2_test | 3.8.20 | - | 0 | 1270 | 3210 | 8603 |
167
+ | s41467_025_56623_1_test | 3.8.20 | - | 0 | 1051 | 3210 | 8478 |
168
+ | s41467_025_56749_2_test | 3.8.20 | - | 0 | 1672 | 3210 | 8900 |
169
+ | s41467_025_57007_1_test | 3.8.20 | - | 0 | 776 | 3210 | 8374 |
170
+ | s41467_025_57031_1_test | 3.8.20 | - | 0 | 1558 | 3210 | 8822 |
171
+ | s41467_025_57183_0_test | 3.8.20 | - | 0 | 971 | 3210 | 8446 |
172
+ | s41467_025_57505_2_test | 3.8.20 | - | 0 | 984 | 3210 | 8478 |
173
+ | s41467_025_57717_6_test | 3.8.20 | - | 0 | 971 | 3210 | 8446 |
174
+ | s41467_025_57867_7_test | 3.8.20 | - | 0 | 1116 | 3210 | 8466 |
175
+ | s41467_025_58011_1_test | 3.8.20 | - | 0 | 1986 | 3210 | 9113 |
176
+ | s41467_025_58055_3_test | 3.8.20 | - | 0 | 1429 | 3435 | 8790 |
177
+ | s41467_025_58227_1_test | 3.8.20 | - | 0 | 1177 | 3435 | 8567 |
178
+ | s41467_025_58231_5_test | 3.8.20 | - | 0 | 733 | 3435 | 8346 |
179
+ | s41467_025_58356_7_test | 3.8.20 | - | 0 | 753 | 3435 | 8360 |
180
+ | s41467_025_58439_5_test | 3.8.20 | - | 0 | 1057 | 3210 | 8498 |
181
+ | s41467_025_58586_9_test | 3.8.20 | - | 0 | 796 | 3210 | 8365 |
182
+ | s41467_025_58620_w_test | 3.8.20 | - | 0 | 831 | 3210 | 8360 |
183
+ | s41467_025_58741_2_test | 3.8.20 | - | 0 | 1208 | 4510 | 8464 |
184
+ | s41467_025_58854_8_test | 3.8.20 | - | 0 | 941 | 3210 | 8422 |
185
+ | s41467_025_58866_4_test | 3.8.20 | - | 0 | 941 | 3210 | 8422 |
186
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configs/014_energy_backdoor_defense_test/editable.txt ADDED
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configs/014_energy_backdoor_defense_test/env.yml ADDED
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+ name: 014_energy_backdoor_defense_test
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224
+ numpydoc==1.1.0
225
+ nvidia-ml-py==12.535.133
226
+ nvitop==1.3.2
227
+ oauthlib==3.2.2
228
+ onnx==1.16.0
229
+ onnxruntime==1.15.1
230
+ openai==1.101.0
231
+ openpyxl==3.0.9
232
+ opentelemetry-api==1.24.0
233
+ opentelemetry-exporter-otlp-proto-common==1.24.0
234
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
235
+ opentelemetry-proto==1.24.0
236
+ opentelemetry-sdk==1.24.0
237
+ opentelemetry-semantic-conventions==0.45b0
238
+ opt-einsum==3.3.0
239
+ optax==0.1.5
240
+ ordered-set==4.1.0
241
+ orjson==3.10.1
242
+ overrides==7.7.0
243
+ packaging==26.2
244
+ pandas==2.0.3
245
+ pandas-stubs==1.2.0.45
246
+ parsimonious==0.8.1
247
+ pathlib==1.0.1
248
+ patsy==1.0.1
249
+ pdf2image==1.17.0
250
+ pfzy==0.3.4
251
+ PICOS==2.6.1
252
+ pikepdf==8.4.1
253
+ pip-search==0.0.12
254
+ pkgutil_resolve_name==1.3.10
255
+ plac==0.9.6
256
+ plotly==6.3.0
257
+ pluggy==1.5.0
258
+ ply==3.11
259
+ pondpond==1.4.1
260
+ pooch==1.8.2
261
+ portalocker==2.4.0
262
+ posthog==3.5.0
263
+ preshed==3.0.9
264
+ prettytable==3.11.0
265
+ primer3-py==2.2.0
266
+ prompt-toolkit==3.0.43
267
+ propcache==0.2.0
268
+ protobuf==5.29.5
269
+ psutil==7.2.2
270
+ PuLP==3.1.1
271
+ pulsar-client==3.5.0
272
+ pyarrow==17.0.0
273
+ pyarrow-hotfix==0.6
274
+ pyclipper==1.3.0.post5
275
+ pycocotools==2.0.7
276
+ pycparser==2.21
277
+ pydantic==2.10.6
278
+ pydantic_core==2.27.2
279
+ pydeck==0.9.0b1
280
+ pyDOE2==1.3.0
281
+ pydub==0.25.1
282
+ pyfaidx==0.9.0.1
283
+ Pygments==2.19.2
284
+ PyJWT==2.8.0
285
+ pymodbus==3.6.9
286
+ PyMuPDF==1.23.16
287
+ PyMuPDFb==1.23.9
288
+ PyNaCl==1.6.2
289
+ pynndescent==0.5.13
290
+ Pyomo==6.8.2
291
+ pyOpenSSL==24.1.0
292
+ pypandoc==1.13
293
+ pyparsing==3.1.4
294
+ pypdf==4.2.0
295
+ pypdfium2==4.29.0
296
+ PyPika==0.48.9
297
+ PyQt5==5.15.7
298
+ PyQt5-Qt5==5.15.17
299
+ PyQt5_sip==12.15.0
300
+ pyro-api==0.1.2
301
+ pyro-ppl==1.9.1
302
+ pysam==0.23.3
303
+ PySocks==1.7.1
304
+ pysqlite3-binary==0.5.2.post3
305
+ pystan==2.19.1.1
306
+ pytesseract==0.3.10
307
+ pytest-cov==5.0.0
308
+ python-dateutil==2.9.0.post0
309
+ python-decouple==3.8
310
+ python-docx==1.1.0
311
+ python-dotenv==1.0.1
312
+ python-iso639==2024.4.27
313
+ python-Levenshtein==0.25.1
314
+ python-multipart==0.0.18
315
+ python-pptx==0.6.23
316
+ python-slugify==8.0.4
317
+ pytorch-pretrained-bert==0.6.2
318
+ pytz==2025.2
319
+ pyvista==0.44.2
320
+ PyWavelets==1.4.1
321
+ PyYAML==6.0.3
322
+ quantile-python==1.1
323
+ rapidfuzz==3.8.1
324
+ rapidocr-onnxruntime==1.3.8
325
+ ray==2.10.0
326
+ rdkit==2024.3.5
327
+ redis==6.1.1
328
+ referencing==0.35.1
329
+ regex==2022.4.24
330
+ requests==2.32.4
331
+ requests-oauthlib==1.3.0
332
+ responses==0.16.0
333
+ rich==13.7.1
334
+ rouge-score==0.1.2
335
+ rpds-py==0.20.1
336
+ rq==2.3.3
337
+ rsa==4.7.2
338
+ ruff==0.4.2
339
+ rustworkx==0.15.1
340
+ s3transfer==0.11.3
341
+ sacrebleu==2.1.0
342
+ sacremoses==0.0.46
343
+ safetensors==0.4.3
344
+ scipy==1.10.1
345
+ scooby==0.10.1
346
+ seaborn==0.13.2
347
+ semantic-version==2.10.0
348
+ sentence-transformers==2.2.2
349
+ sentencepiece==0.1.91
350
+ sentry-sdk==2.39.0
351
+ session_info==1.0.1
352
+ sgmllib3k==1.0.0
353
+ shapely==2.0.4
354
+ shellingham==1.5.4
355
+ shortuuid==1.0.13
356
+ six==1.17.0
357
+ smart-open==6.4.0
358
+ smmap==5.0.1
359
+ sniffio==1.3.1
360
+ snowballstemmer==2.2.0
361
+ sobol-seq==0.2.0
362
+ socksio==1.0.0
363
+ soupsieve==2.5
364
+ spacy-legacy==3.0.12
365
+ spacy-loggers==1.0.5
366
+ Sphinx==4.3.1
367
+ sphinxcontrib-applehelp==1.0.2
368
+ sphinxcontrib-devhelp==1.0.2
369
+ sphinxcontrib-htmlhelp==2.0.0
370
+ sphinxcontrib-jsmath==1.0.1
371
+ sphinxcontrib-qthelp==1.0.3
372
+ sphinxcontrib-serializinghtml==1.1.5
373
+ SQLAlchemy==2.0.19
374
+ sqlparse==0.4.2
375
+ sse-starlette==1.8.2
376
+ starlette==0.44.0
377
+ statsmodels==0.14.1
378
+ stdlib-list==0.10.0
379
+ streamlit==1.30.0
380
+ streamlit-aggrid==0.3.4.post3
381
+ streamlit-antd-components==0.3.1
382
+ streamlit-chatbox==1.1.11
383
+ streamlit-feedback==0.1.3
384
+ streamlit-modal==0.1.0
385
+ streamlit-option-menu==0.3.12
386
+ strsimpy==0.2.1
387
+ svgwrite==1.4.3
388
+ sympy==1.13.3
389
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
390
+ tabulate==0.8.9
391
+ tenacity==8.2.3
392
+ tensorboard-plugin-wit==1.8.0
393
+ tensorboardX==2.4.1
394
+ text-unidecode==1.3
395
+ texttable==1.7.0
396
+ thefuzz==0.22.1
397
+ threadpoolctl==3.5.0
398
+ tifffile==2023.7.10
399
+ tiktoken==0.7.0
400
+ timm==0.9.16
401
+ tk==0.1.0
402
+ tokenizers==0.20.3
403
+ toml==0.10.2
404
+ tomlkit==0.12.0
405
+ toolz==0.12.1
406
+ torch==2.4.1+cpu
407
+ torch-geometric==2.6.1
408
+ torchaudio==2.1.2+cu118
409
+ torchtext==0.4.0
410
+ tornado==6.4
411
+ tqdm==4.67.1
412
+ transformer-lens==2.16.1
413
+ transformers==4.46.3
414
+ transformers-stream-generator==0.0.5
415
+ typed-argument-parser==1.10.1
416
+ typeguard==4.4.0
417
+ typer==0.9.4
418
+ types-requests==2.31.0.20240406
419
+ typing-inspect==0.9.0
420
+ typing-utils==0.1.0
421
+ typing_extensions==4.13.2
422
+ tzdata==2024.1
423
+ tzlocal==5.2
424
+ umap-learn==0.5.7
425
+ Unidecode==1.3.2
426
+ unittest-xml-reporting==3.2.0
427
+ unstructured==0.11.0
428
+ unstructured-client==0.22.0
429
+ unstructured-inference==0.7.15
430
+ unstructured.pytesseract==0.3.12
431
+ urllib3==2.2.3
432
+ uvicorn==0.29.0
433
+ uvloop==0.21.0
434
+ validators==0.28.1
435
+ vllm==0.2.7
436
+ vtk==9.3.1
437
+ wandb==0.22.0
438
+ watchdog==3.0.0
439
+ watchfiles==0.21.0
440
+ wavedrom==2.0.3.post3
441
+ weasel==0.3.4
442
+ websocket-client==1.8.0
443
+ websockets==13.1
444
+ Werkzeug==2.0.2
445
+ word2number==1.1
446
+ xlrd==2.0.1
447
+ XlsxWriter==3.0.2
448
+ xxhash==2.0.2
449
+ Yapsy==1.12.2
450
+ yarl==1.15.2
451
+ youtube-search==2.1.2
452
+ zipp==3.20.2
453
+ zope.event==4.5.0
454
+ zstandard==0.23.0
configs/014_energy_backdoor_defense_test/pip-freeze.txt ADDED
@@ -0,0 +1,454 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ certifi==2026.4.22
43
+ cffi==1.15.0
44
+ cftime==1.6.4.post1
45
+ chaospy==3.3.9
46
+ charset-normalizer==3.4.7
47
+ chex==0.1.7
48
+ chroma-hnswlib==0.7.3
49
+ chromadb==0.4.15
50
+ click==8.1.7
51
+ cloudpathlib==0.16.0
52
+ cobra==0.29.1
53
+ cohere==5.3.3
54
+ coloredlogs==15.0.1
55
+ confection==0.1.4
56
+ ConfigArgParse==1.5.3
57
+ conllu==0.11
58
+ coverage==7.6.1
59
+ cpm-kernels==1.0.11
60
+ cryptography==42.0.5
61
+ cvxopt==1.3.2
62
+ cymem==2.0.8
63
+ Cython==0.29.30
64
+ dataclasses==0.6
65
+ dataclasses-json==0.6.4
66
+ datasets==2.19.0
67
+ deepdiff==7.0.1
68
+ Deprecated==1.2.14
69
+ deprecation==2.1.0
70
+ dill==0.3.8
71
+ distro==1.9.0
72
+ dm-tree==0.1.8
73
+ dnspython==2.6.1
74
+ docstring_parser==0.17.0
75
+ docutils==0.15.2
76
+ dotenv==0.9.9
77
+ duckduckgo-search==3.9.9
78
+ editdistance==0.6.0
79
+ effdet==0.4.1
80
+ einops==0.7.0
81
+ email-validator==2.3.0
82
+ emoji==2.11.1
83
+ equinox==0.10.4
84
+ et-xmlfile==1.1.0
85
+ eval_type_backport==0.2.2
86
+ exceptiongroup==1.2.1
87
+ fairseq==0.10.2
88
+ faiss-cpu==1.7.4
89
+ faiss-gpu==1.7.2
90
+ fancy-einsum==0.0.3
91
+ fastapi==0.115.14
92
+ fastapi-sso==0.16.0
93
+ fastavro==1.9.4
94
+ fastuuid==0.13.5
95
+ fbpca==1.0
96
+ feedparser==6.0.10
97
+ ffmpy==0.3.2
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gdown==5.2.0
109
+ geosketch==1.3
110
+ geotorch==0.3.0
111
+ get-annotations==0.1.2
112
+ gevent==21.12.0
113
+ gitdb==4.0.11
114
+ GitPython==3.1.43
115
+ google-pasta==0.2.0
116
+ googleapis-common-protos==1.63.0
117
+ gpustat==1.1.1
118
+ gpytorch==1.10
119
+ gradio_client==0.16.0
120
+ graphlib_backport==1.1.0
121
+ greenlet==1.1.2
122
+ gunicorn==23.0.0
123
+ h11==0.14.0
124
+ h2==4.1.0
125
+ hf-xet==1.2.0
126
+ hf_transfer==0.1.9
127
+ hpack==4.0.0
128
+ httpcore==1.0.5
129
+ httptools==0.6.1
130
+ httpx==0.28.1
131
+ httpx-sse==0.4.0
132
+ huggingface_hub==0.36.1
133
+ humanfriendly==10.0
134
+ hyperframe==6.0.1
135
+ icetk==0.0.4
136
+ idna==3.10
137
+ igraph==0.11.8
138
+ imageio==2.35.1
139
+ imagesize==1.3.0
140
+ imgaug==0.4.0
141
+ importlib-metadata==7.0.0
142
+ importlib_resources==6.4.5
143
+ inequalipy==1.0.5
144
+ iniconfig==1.1.1
145
+ inquirerpy==0.3.4
146
+ iopath==0.1.10
147
+ isodate==0.7.2
148
+ itsdangerous==2.0.1
149
+ jax==0.4.13
150
+ jaxlib==0.4.13
151
+ jaxtyping==0.2.19
152
+ Jinja2==3.1.6
153
+ jiter==0.9.1
154
+ jmespath==0.10.0
155
+ joblib==1.4.2
156
+ jsonnet==0.17.0
157
+ jsonpatch==1.33
158
+ jsonpath-python==1.0.6
159
+ jsonpickle==2.0.0
160
+ jsonschema==4.23.0
161
+ jsonschema-specifications==2023.12.1
162
+ kaggle==1.7.4.5
163
+ Keras-Preprocessing==1.1.2
164
+ kubernetes==29.0.0
165
+ langchain==0.1.16
166
+ langchain-community==0.0.34
167
+ langchain-core==0.1.46
168
+ langchain-experimental==0.0.57
169
+ langchain-text-splitters==0.0.1
170
+ langcodes==3.4.0
171
+ langdetect==1.0.9
172
+ langsmith==0.1.51
173
+ language_data==1.2.0
174
+ layoutparser==0.3.4
175
+ lazy_loader==0.4
176
+ leidenalg==0.10.2
177
+ Levenshtein==0.25.1
178
+ linear-operator==0.4.0
179
+ litellm==1.77.4
180
+ litellm-enterprise==0.1.20
181
+ litellm-proxy-extras==0.2.19
182
+ llama-index==0.9.35
183
+ llvmlite==0.41.1
184
+ lmdb==1.7.3
185
+ lxml==5.2.1
186
+ madoka==0.7.1
187
+ marisa-trie==1.1.0
188
+ Markdown==3.3.6
189
+ markdown-it-py==3.0.0
190
+ markdown2==2.4.13
191
+ markdownify==0.11.6
192
+ MarkupSafe==2.1.5
193
+ marshmallow==3.21.1
194
+ mdtex2html==1.3.0
195
+ mdurl==0.1.2
196
+ metaphor-python==0.1.23
197
+ ml-dtypes==0.2.0
198
+ monotonic==1.6
199
+ mpmath==1.3.0
200
+ mrcfile==1.5.4
201
+ msal==1.36.0
202
+ msal-extensions==1.3.0
203
+ msg-parser==1.2.0
204
+ msgpack==1.0.8
205
+ msgpack-numpy==0.4.3.2
206
+ multidict==6.0.5
207
+ multipledispatch==1.0.0
208
+ multiprocess==0.70.16
209
+ murmurhash==1.0.10
210
+ mypy-extensions==1.0.0
211
+ narwhals==1.42.1
212
+ natsort==8.4.0
213
+ nest-asyncio==1.6.0
214
+ netCDF4==1.7.2
215
+ networkx==3.1
216
+ neuroHarmonize==2.4.5
217
+ nh3==0.2.17
218
+ ninja==1.11.1.1
219
+ nltk==3.8.1
220
+ numba==0.58.1
221
+ numexpr==2.8.6
222
+ numpoly==1.0.6
223
+ numpy==1.24.4
224
+ numpydoc==1.1.0
225
+ nvidia-ml-py==12.535.133
226
+ nvitop==1.3.2
227
+ oauthlib==3.2.2
228
+ onnx==1.16.0
229
+ onnxruntime==1.15.1
230
+ openai==1.101.0
231
+ openpyxl==3.0.9
232
+ opentelemetry-api==1.24.0
233
+ opentelemetry-exporter-otlp-proto-common==1.24.0
234
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
235
+ opentelemetry-proto==1.24.0
236
+ opentelemetry-sdk==1.24.0
237
+ opentelemetry-semantic-conventions==0.45b0
238
+ opt-einsum==3.3.0
239
+ optax==0.1.5
240
+ ordered-set==4.1.0
241
+ orjson==3.10.1
242
+ overrides==7.7.0
243
+ packaging==26.2
244
+ pandas==2.0.3
245
+ pandas-stubs==1.2.0.45
246
+ parsimonious==0.8.1
247
+ pathlib==1.0.1
248
+ patsy==1.0.1
249
+ pdf2image==1.17.0
250
+ pfzy==0.3.4
251
+ PICOS==2.6.1
252
+ pikepdf==8.4.1
253
+ pip-search==0.0.12
254
+ pkgutil_resolve_name==1.3.10
255
+ plac==0.9.6
256
+ plotly==6.3.0
257
+ pluggy==1.5.0
258
+ ply==3.11
259
+ pondpond==1.4.1
260
+ pooch==1.8.2
261
+ portalocker==2.4.0
262
+ posthog==3.5.0
263
+ preshed==3.0.9
264
+ prettytable==3.11.0
265
+ primer3-py==2.2.0
266
+ prompt-toolkit==3.0.43
267
+ propcache==0.2.0
268
+ protobuf==5.29.5
269
+ psutil==7.2.2
270
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271
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272
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273
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274
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275
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276
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277
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278
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279
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280
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281
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282
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283
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284
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285
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286
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287
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288
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289
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290
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291
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292
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293
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294
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295
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296
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297
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298
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299
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300
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301
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302
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303
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304
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305
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306
+ pytesseract==0.3.10
307
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308
+ python-dateutil==2.9.0.post0
309
+ python-decouple==3.8
310
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311
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312
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313
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
+ referencing==0.35.1
329
+ regex==2022.4.24
330
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331
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332
+ responses==0.16.0
333
+ rich==13.7.1
334
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335
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336
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337
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339
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340
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342
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344
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
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359
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361
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362
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363
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364
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365
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366
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367
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368
+ sphinxcontrib-devhelp==1.0.2
369
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370
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371
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372
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373
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374
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375
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376
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377
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378
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379
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380
+ streamlit-aggrid==0.3.4.post3
381
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382
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383
+ streamlit-feedback==0.1.3
384
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385
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386
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387
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388
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389
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
390
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391
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392
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393
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394
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395
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396
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397
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398
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399
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400
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401
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402
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403
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404
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405
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406
+ torch==2.4.1+cpu
407
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408
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409
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410
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411
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412
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413
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414
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415
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416
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417
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418
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419
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420
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421
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422
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423
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424
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425
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426
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427
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428
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429
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430
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431
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432
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433
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434
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435
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436
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437
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438
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441
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446
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447
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449
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450
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451
+ youtube-search==2.1.2
452
+ zipp==3.20.2
453
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454
+ zstandard==0.23.0
configs/021_test/editable.txt ADDED
File without changes
configs/021_test/env.yml ADDED
@@ -0,0 +1,46 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: 021_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
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9
+ - ca-certificates=2025.8.3
10
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11
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12
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13
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14
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15
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16
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17
+ - libnsl=2.0.1
18
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19
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20
+ - libxcrypt=4.4.36
21
+ - libzlib=1.3.1
22
+ - ncurses=6.5
23
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24
+ - pip=22.1.2
25
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26
+ - readline=8.2
27
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28
+ - tk=8.6.13
29
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30
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32
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33
+ - pip:
34
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35
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36
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37
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38
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39
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40
+ - numpy==1.24.4
41
+ - packaging==25.0
42
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43
+ - sympy==1.13.3
44
+ - torch==2.4.1+cpu
45
+ - typing-extensions==4.12.2
46
+ prefix: /home/lily/yz979/anaconda3/envs/021_test
configs/021_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
+ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
9
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
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12
+ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
13
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14
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15
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16
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17
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18
+ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
19
+ https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
20
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21
+ https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
22
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23
+ https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
24
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25
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26
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+ https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
configs/021_test/meta.json ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "env": "021_test",
3
+ "python_version": "3.8.20",
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+ "has_cuda_hint": false,
5
+ "editable_count": 0,
6
+ "source_prefix": "/home/lily/yz979/anaconda3/envs/021_test",
7
+ "exported_at": "2026-05-17T04:03:27Z"
8
+ }
configs/021_test/pip-clean.txt ADDED
@@ -0,0 +1,448 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
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4
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5
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6
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7
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8
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9
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10
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11
+ annotated-types==0.6.0
12
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13
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14
+ arxiv==2.1.0
15
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16
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17
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18
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19
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22
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23
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24
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25
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26
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27
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28
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29
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30
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31
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32
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33
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34
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35
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36
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37
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39
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40
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41
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42
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43
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45
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47
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48
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49
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50
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51
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53
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54
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56
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57
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58
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63
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+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
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68
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69
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70
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84
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85
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86
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87
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88
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89
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90
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91
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92
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93
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94
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95
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96
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97
+ filelock==3.13.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
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101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
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128
+ httpcore==1.0.5
129
+ httptools==0.6.1
130
+ httpx==0.28.1
131
+ httpx-sse==0.4.0
132
+ huggingface_hub==0.36.1
133
+ humanfriendly==10.0
134
+ hyperframe==6.0.1
135
+ icetk==0.0.4
136
+ igraph==0.11.8
137
+ imageio==2.35.1
138
+ imagesize==1.3.0
139
+ imgaug==0.4.0
140
+ importlib-metadata==7.0.0
141
+ importlib_resources==6.4.5
142
+ inequalipy==1.0.5
143
+ iniconfig==1.1.1
144
+ inquirerpy==0.3.4
145
+ iopath==0.1.10
146
+ isodate==0.7.2
147
+ itsdangerous==2.0.1
148
+ jax==0.4.13
149
+ jaxlib==0.4.13
150
+ jaxtyping==0.2.19
151
+ Jinja2==3.1.6
152
+ jiter==0.9.1
153
+ jmespath==0.10.0
154
+ joblib==1.4.2
155
+ jsonnet==0.17.0
156
+ jsonpatch==1.33
157
+ jsonpath-python==1.0.6
158
+ jsonpickle==2.0.0
159
+ jsonschema==4.23.0
160
+ jsonschema-specifications==2023.12.1
161
+ kaggle==1.7.4.5
162
+ Keras-Preprocessing==1.1.2
163
+ kubernetes==29.0.0
164
+ langchain==0.1.16
165
+ langchain-community==0.0.34
166
+ langchain-core==0.1.46
167
+ langchain-experimental==0.0.57
168
+ langchain-text-splitters==0.0.1
169
+ langcodes==3.4.0
170
+ langdetect==1.0.9
171
+ langsmith==0.1.51
172
+ language_data==1.2.0
173
+ layoutparser==0.3.4
174
+ lazy_loader==0.4
175
+ leidenalg==0.10.2
176
+ Levenshtein==0.25.1
177
+ linear-operator==0.4.0
178
+ litellm==1.77.4
179
+ litellm-enterprise==0.1.20
180
+ litellm-proxy-extras==0.2.19
181
+ llama-index==0.9.35
182
+ llvmlite==0.41.1
183
+ lmdb==1.7.3
184
+ lxml==5.2.1
185
+ madoka==0.7.1
186
+ marisa-trie==1.1.0
187
+ Markdown==3.3.6
188
+ markdown-it-py==3.0.0
189
+ markdown2==2.4.13
190
+ markdownify==0.11.6
191
+ MarkupSafe==2.1.5
192
+ marshmallow==3.21.1
193
+ mdtex2html==1.3.0
194
+ mdurl==0.1.2
195
+ metaphor-python==0.1.23
196
+ ml-dtypes==0.2.0
197
+ monotonic==1.6
198
+ mpmath==1.3.0
199
+ mrcfile==1.5.4
200
+ msal==1.36.0
201
+ msal-extensions==1.3.0
202
+ msg-parser==1.2.0
203
+ msgpack==1.0.8
204
+ msgpack-numpy==0.4.3.2
205
+ multidict==6.0.5
206
+ multipledispatch==1.0.0
207
+ multiprocess==0.70.16
208
+ murmurhash==1.0.10
209
+ mypy-extensions==1.0.0
210
+ narwhals==1.42.1
211
+ natsort==8.4.0
212
+ nest-asyncio==1.6.0
213
+ netCDF4==1.7.2
214
+ networkx==3.0
215
+ neuroHarmonize==2.4.5
216
+ nh3==0.2.17
217
+ ninja==1.11.1.1
218
+ nltk==3.8.1
219
+ numba==0.58.1
220
+ numexpr==2.8.6
221
+ numpoly==1.0.6
222
+ numpy==1.24.4
223
+ numpydoc==1.1.0
224
+ nvidia-ml-py==12.535.133
225
+ nvitop==1.3.2
226
+ oauthlib==3.2.2
227
+ onnx==1.16.0
228
+ onnxruntime==1.15.1
229
+ openai==1.101.0
230
+ openpyxl==3.0.9
231
+ opentelemetry-api==1.24.0
232
+ opentelemetry-exporter-otlp-proto-common==1.24.0
233
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
234
+ opentelemetry-proto==1.24.0
235
+ opentelemetry-sdk==1.24.0
236
+ opentelemetry-semantic-conventions==0.45b0
237
+ opt-einsum==3.3.0
238
+ optax==0.1.5
239
+ ordered-set==4.1.0
240
+ orjson==3.10.1
241
+ overrides==7.7.0
242
+ packaging==26.2
243
+ pandas==2.0.3
244
+ pandas-stubs==1.2.0.45
245
+ parsimonious==0.8.1
246
+ pathlib==1.0.1
247
+ patsy==1.0.1
248
+ pdf2image==1.17.0
249
+ pfzy==0.3.4
250
+ PICOS==2.6.1
251
+ pikepdf==8.4.1
252
+ pip-search==0.0.12
253
+ pkgutil_resolve_name==1.3.10
254
+ plac==0.9.6
255
+ plotly==6.3.0
256
+ pluggy==1.5.0
257
+ ply==3.11
258
+ pondpond==1.4.1
259
+ pooch==1.8.2
260
+ portalocker==2.4.0
261
+ posthog==3.5.0
262
+ preshed==3.0.9
263
+ prettytable==3.11.0
264
+ primer3-py==2.2.0
265
+ prompt-toolkit==3.0.43
266
+ propcache==0.2.0
267
+ PuLP==3.1.1
268
+ pulsar-client==3.5.0
269
+ pyarrow==17.0.0
270
+ pyarrow-hotfix==0.6
271
+ pyclipper==1.3.0.post5
272
+ pycocotools==2.0.7
273
+ pycparser==2.21
274
+ pydantic==2.10.6
275
+ pydantic_core==2.27.2
276
+ pydeck==0.9.0b1
277
+ pyDOE2==1.3.0
278
+ pydub==0.25.1
279
+ pyfaidx==0.9.0.1
280
+ Pygments==2.19.2
281
+ PyJWT==2.8.0
282
+ pymodbus==3.6.9
283
+ PyMuPDF==1.23.16
284
+ PyMuPDFb==1.23.9
285
+ PyNaCl==1.6.2
286
+ pynndescent==0.5.13
287
+ Pyomo==6.8.2
288
+ pyOpenSSL==24.1.0
289
+ pypandoc==1.13
290
+ pypdf==4.2.0
291
+ pypdfium2==4.29.0
292
+ PyPika==0.48.9
293
+ PyQt5==5.15.7
294
+ PyQt5-Qt5==5.15.17
295
+ PyQt5_sip==12.15.0
296
+ pyro-api==0.1.2
297
+ pyro-ppl==1.9.1
298
+ pysam==0.23.3
299
+ PySocks==1.7.1
300
+ pysqlite3-binary==0.5.2.post3
301
+ pystan==2.19.1.1
302
+ pytesseract==0.3.10
303
+ pytest-cov==5.0.0
304
+ python-dateutil==2.9.0.post0
305
+ python-decouple==3.8
306
+ python-docx==1.1.0
307
+ python-dotenv==1.0.1
308
+ python-iso639==2024.4.27
309
+ python-Levenshtein==0.25.1
310
+ python-multipart==0.0.18
311
+ python-pptx==0.6.23
312
+ python-slugify==8.0.4
313
+ pytorch-pretrained-bert==0.6.2
314
+ pytz==2025.2
315
+ pyvista==0.44.2
316
+ PyWavelets==1.4.1
317
+ PyYAML==6.0.3
318
+ quantile-python==1.1
319
+ rapidfuzz==3.8.1
320
+ rapidocr-onnxruntime==1.3.8
321
+ ray==2.10.0
322
+ rdkit==2024.3.5
323
+ redis==6.1.1
324
+ referencing==0.35.1
325
+ regex==2022.4.24
326
+ requests==2.32.4
327
+ requests-oauthlib==1.3.0
328
+ responses==0.16.0
329
+ rich==13.7.1
330
+ rouge-score==0.1.2
331
+ rpds-py==0.20.1
332
+ rq==2.3.3
333
+ rsa==4.7.2
334
+ ruff==0.4.2
335
+ rustworkx==0.15.1
336
+ s3transfer==0.11.3
337
+ sacrebleu==2.1.0
338
+ sacremoses==0.0.46
339
+ safetensors==0.4.3
340
+ scooby==0.10.1
341
+ seaborn==0.13.2
342
+ semantic-version==2.10.0
343
+ sentence-transformers==2.2.2
344
+ sentencepiece==0.1.91
345
+ sentry-sdk==2.39.0
346
+ session_info==1.0.1
347
+ sgmllib3k==1.0.0
348
+ shapely==2.0.4
349
+ shellingham==1.5.4
350
+ shortuuid==1.0.13
351
+ six==1.17.0
352
+ smart-open==6.4.0
353
+ smmap==5.0.1
354
+ sniffio==1.3.1
355
+ snowballstemmer==2.2.0
356
+ sobol-seq==0.2.0
357
+ socksio==1.0.0
358
+ soupsieve==2.5
359
+ spacy-legacy==3.0.12
360
+ spacy-loggers==1.0.5
361
+ Sphinx==4.3.1
362
+ sphinxcontrib-applehelp==1.0.2
363
+ sphinxcontrib-devhelp==1.0.2
364
+ sphinxcontrib-htmlhelp==2.0.0
365
+ sphinxcontrib-jsmath==1.0.1
366
+ sphinxcontrib-qthelp==1.0.3
367
+ sphinxcontrib-serializinghtml==1.1.5
368
+ SQLAlchemy==2.0.19
369
+ sqlparse==0.4.2
370
+ sse-starlette==1.8.2
371
+ starlette==0.44.0
372
+ statsmodels==0.14.1
373
+ stdlib-list==0.10.0
374
+ streamlit==1.30.0
375
+ streamlit-aggrid==0.3.4.post3
376
+ streamlit-antd-components==0.3.1
377
+ streamlit-chatbox==1.1.11
378
+ streamlit-feedback==0.1.3
379
+ streamlit-modal==0.1.0
380
+ streamlit-option-menu==0.3.12
381
+ strsimpy==0.2.1
382
+ svgwrite==1.4.3
383
+ sympy==1.13.3
384
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
385
+ tabulate==0.8.9
386
+ tenacity==8.2.3
387
+ tensorboard-plugin-wit==1.8.0
388
+ tensorboardX==2.4.1
389
+ text-unidecode==1.3
390
+ texttable==1.7.0
391
+ thefuzz==0.22.1
392
+ threadpoolctl==3.5.0
393
+ tifffile==2023.7.10
394
+ tiktoken==0.7.0
395
+ timm==0.9.16
396
+ tk==0.1.0
397
+ tokenizers==0.20.3
398
+ toml==0.10.2
399
+ tomlkit==0.12.0
400
+ toolz==0.12.1
401
+ torch==2.4.1+cpu
402
+ torch-geometric==2.6.1
403
+ torchaudio==2.1.2+cu118
404
+ torchtext==0.4.0
405
+ tornado==6.4
406
+ tqdm==4.67.1
407
+ transformer-lens==2.16.1
408
+ transformers==4.46.3
409
+ transformers-stream-generator==0.0.5
410
+ typed-argument-parser==1.10.1
411
+ typeguard==4.4.0
412
+ typer==0.9.4
413
+ types-requests==2.31.0.20240406
414
+ typing-inspect==0.9.0
415
+ typing-utils==0.1.0
416
+ typing_extensions==4.13.2
417
+ tzdata==2024.1
418
+ tzlocal==5.2
419
+ umap-learn==0.5.7
420
+ Unidecode==1.3.2
421
+ unittest-xml-reporting==3.2.0
422
+ unstructured==0.11.0
423
+ unstructured-client==0.22.0
424
+ unstructured-inference==0.7.15
425
+ unstructured.pytesseract==0.3.12
426
+ uvicorn==0.29.0
427
+ uvloop==0.21.0
428
+ validators==0.28.1
429
+ vllm==0.2.7
430
+ vtk==9.3.1
431
+ wandb==0.22.0
432
+ watchdog==3.0.0
433
+ watchfiles==0.21.0
434
+ wavedrom==2.0.3.post3
435
+ weasel==0.3.4
436
+ websocket-client==1.8.0
437
+ websockets==13.1
438
+ Werkzeug==2.0.2
439
+ word2number==1.1
440
+ xlrd==2.0.1
441
+ XlsxWriter==3.0.2
442
+ xxhash==2.0.2
443
+ Yapsy==1.12.2
444
+ yarl==1.15.2
445
+ youtube-search==2.1.2
446
+ zipp==3.20.2
447
+ zope.event==4.5.0
448
+ zstandard==0.23.0
configs/021_test/pip-freeze.txt ADDED
@@ -0,0 +1,448 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filelock==3.13.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gdown==5.2.0
109
+ geosketch==1.3
110
+ geotorch==0.3.0
111
+ get-annotations==0.1.2
112
+ gevent==21.12.0
113
+ gitdb==4.0.11
114
+ GitPython==3.1.43
115
+ google-pasta==0.2.0
116
+ googleapis-common-protos==1.63.0
117
+ gpustat==1.1.1
118
+ gpytorch==1.10
119
+ gradio_client==0.16.0
120
+ graphlib_backport==1.1.0
121
+ greenlet==1.1.2
122
+ gunicorn==23.0.0
123
+ h11==0.14.0
124
+ h2==4.1.0
125
+ hf-xet==1.2.0
126
+ hf_transfer==0.1.9
127
+ hpack==4.0.0
128
+ httpcore==1.0.5
129
+ httptools==0.6.1
130
+ httpx==0.28.1
131
+ httpx-sse==0.4.0
132
+ huggingface_hub==0.36.1
133
+ humanfriendly==10.0
134
+ hyperframe==6.0.1
135
+ icetk==0.0.4
136
+ igraph==0.11.8
137
+ imageio==2.35.1
138
+ imagesize==1.3.0
139
+ imgaug==0.4.0
140
+ importlib-metadata==7.0.0
141
+ importlib_resources==6.4.5
142
+ inequalipy==1.0.5
143
+ iniconfig==1.1.1
144
+ inquirerpy==0.3.4
145
+ iopath==0.1.10
146
+ isodate==0.7.2
147
+ itsdangerous==2.0.1
148
+ jax==0.4.13
149
+ jaxlib==0.4.13
150
+ jaxtyping==0.2.19
151
+ Jinja2==3.1.6
152
+ jiter==0.9.1
153
+ jmespath==0.10.0
154
+ joblib==1.4.2
155
+ jsonnet==0.17.0
156
+ jsonpatch==1.33
157
+ jsonpath-python==1.0.6
158
+ jsonpickle==2.0.0
159
+ jsonschema==4.23.0
160
+ jsonschema-specifications==2023.12.1
161
+ kaggle==1.7.4.5
162
+ Keras-Preprocessing==1.1.2
163
+ kubernetes==29.0.0
164
+ langchain==0.1.16
165
+ langchain-community==0.0.34
166
+ langchain-core==0.1.46
167
+ langchain-experimental==0.0.57
168
+ langchain-text-splitters==0.0.1
169
+ langcodes==3.4.0
170
+ langdetect==1.0.9
171
+ langsmith==0.1.51
172
+ language_data==1.2.0
173
+ layoutparser==0.3.4
174
+ lazy_loader==0.4
175
+ leidenalg==0.10.2
176
+ Levenshtein==0.25.1
177
+ linear-operator==0.4.0
178
+ litellm==1.77.4
179
+ litellm-enterprise==0.1.20
180
+ litellm-proxy-extras==0.2.19
181
+ llama-index==0.9.35
182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
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203
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204
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205
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206
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207
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208
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209
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210
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211
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212
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213
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214
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215
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216
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217
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218
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219
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220
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221
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222
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223
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224
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225
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226
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227
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228
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229
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230
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231
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232
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233
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234
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235
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236
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237
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238
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239
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240
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241
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242
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243
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244
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245
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246
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247
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248
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249
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250
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251
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252
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253
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254
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255
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256
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257
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258
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259
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260
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261
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262
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263
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264
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265
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266
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267
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268
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269
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270
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271
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272
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273
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274
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275
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276
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277
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278
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279
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280
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281
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282
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284
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285
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286
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287
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288
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289
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290
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292
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293
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294
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295
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296
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297
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298
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299
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300
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301
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302
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303
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304
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305
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306
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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318
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319
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320
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322
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323
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324
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325
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326
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327
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328
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329
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330
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342
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346
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349
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350
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351
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354
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362
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363
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364
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365
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368
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369
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384
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388
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389
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392
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393
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394
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395
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396
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397
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398
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399
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400
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401
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403
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405
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415
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417
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418
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421
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422
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423
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427
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428
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429
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431
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432
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433
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434
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435
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437
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438
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439
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441
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442
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443
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444
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445
+ youtube-search==2.1.2
446
+ zipp==3.20.2
447
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448
+ zstandard==0.23.0
configs/069_test/editable.txt ADDED
File without changes
configs/069_test/env.yml ADDED
@@ -0,0 +1,62 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: 069_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
+ - bzip2=1.0.8
9
+ - ca-certificates=2025.8.3
10
+ - ld_impl_linux-64=2.44
11
+ - libffi=3.4.6
12
+ - libgcc=15.1.0
13
+ - libgcc-ng=15.1.0
14
+ - libgomp=15.1.0
15
+ - liblzma=5.8.1
16
+ - liblzma-devel=5.8.1
17
+ - libnsl=2.0.1
18
+ - libsqlite=3.50.4
19
+ - libuuid=2.41.2
20
+ - libxcrypt=4.4.36
21
+ - libzlib=1.3.1
22
+ - ncurses=6.5
23
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24
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25
+ - python=3.8.20
26
+ - readline=8.2
27
+ - setuptools=70.3.0
28
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29
+ - wheel=0.45.1
30
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31
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32
+ - xz-tools=5.8.1
33
+ - pip:
34
+ - certifi==2026.2.25
35
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36
+ - fsspec==2025.3.0
37
+ - idna==3.10
38
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39
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40
+ - mpmath==1.3.0
41
+ - networkx==3.1
42
+ - numpy==1.24.4
43
+ - nvidia-cublas-cu12==12.9.2.10
44
+ - nvidia-cuda-cupti-cu12==12.9.79
45
+ - nvidia-cuda-nvrtc-cu12==12.9.86
46
+ - nvidia-cuda-runtime-cu12==12.9.79
47
+ - nvidia-cudnn-cu12==9.1.0.70
48
+ - nvidia-cufft-cu12==11.4.1.4
49
+ - nvidia-curand-cu12==10.3.10.19
50
+ - nvidia-cusparse-cu12==12.5.10.65
51
+ - nvidia-nccl-cu12==2.20.5
52
+ - nvidia-nvjitlink-cu12==12.9.86
53
+ - nvidia-nvtx-cu12==12.9.79
54
+ - packaging==25.0
55
+ - pyyaml==6.0.3
56
+ - requests==2.32.4
57
+ - six==1.17.0
58
+ - sympy==1.13.3
59
+ - torch==2.4.1
60
+ - triton==3.0.0
61
+ - urllib3==2.2.3
62
+ prefix: /home/lily/yz979/anaconda3/envs/069_test
configs/069_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
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8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
9
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
10
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
11
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12
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13
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
14
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
15
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16
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17
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18
+ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
19
+ https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
20
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21
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22
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+ https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
configs/069_test/meta.json ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "env": "069_test",
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+ "python_version": "3.8.20",
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+ "has_cuda_hint": false,
5
+ "editable_count": 0,
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+ "source_prefix": "/home/lily/yz979/anaconda3/envs/069_test",
7
+ "exported_at": "2026-05-17T04:04:16Z"
8
+ }
configs/069_test/pip-clean.txt ADDED
@@ -0,0 +1,463 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
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4
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+ annotated-types==0.6.0
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+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ certifi==2026.2.25
43
+ cffi==1.15.0
44
+ cftime==1.6.4.post1
45
+ chaospy==3.3.9
46
+ charset-normalizer==3.4.7
47
+ chex==0.1.7
48
+ chroma-hnswlib==0.7.3
49
+ chromadb==0.4.15
50
+ click==8.1.7
51
+ cloudpathlib==0.16.0
52
+ cobra==0.29.1
53
+ cohere==5.3.3
54
+ coloredlogs==15.0.1
55
+ confection==0.1.4
56
+ ConfigArgParse==1.5.3
57
+ conllu==0.11
58
+ coverage==7.6.1
59
+ cpm-kernels==1.0.11
60
+ cryptography==42.0.5
61
+ cvxopt==1.3.2
62
+ cymem==2.0.8
63
+ Cython==0.29.30
64
+ dataclasses==0.6
65
+ dataclasses-json==0.6.4
66
+ datasets==2.19.0
67
+ deepdiff==7.0.1
68
+ Deprecated==1.2.14
69
+ deprecation==2.1.0
70
+ dill==0.3.8
71
+ distro==1.9.0
72
+ dm-tree==0.1.8
73
+ dnspython==2.6.1
74
+ docstring_parser==0.17.0
75
+ docutils==0.15.2
76
+ dotenv==0.9.9
77
+ duckduckgo-search==3.9.9
78
+ editdistance==0.6.0
79
+ effdet==0.4.1
80
+ einops==0.7.0
81
+ email-validator==2.3.0
82
+ emoji==2.11.1
83
+ equinox==0.10.4
84
+ et-xmlfile==1.1.0
85
+ eval_type_backport==0.2.2
86
+ exceptiongroup==1.2.1
87
+ fairseq==0.10.2
88
+ faiss-cpu==1.7.4
89
+ faiss-gpu==1.7.2
90
+ fancy-einsum==0.0.3
91
+ fastapi==0.115.14
92
+ fastapi-sso==0.16.0
93
+ fastavro==1.9.4
94
+ fastuuid==0.13.5
95
+ fbpca==1.0
96
+ feedparser==6.0.10
97
+ ffmpy==0.3.2
98
+ filelock==3.16.1
99
+ filetype==1.2.0
100
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
101
+ flaky==3.7.0
102
+ Flask-Cors==3.0.10
103
+ frozenlist==1.4.1
104
+ fschat==0.2.35
105
+ fsspec==2025.3.0
106
+ ftfy==6.0.3
107
+ future==0.18.2
108
+ fuzzywuzzy==0.18.0
109
+ gdown==5.2.0
110
+ geosketch==1.3
111
+ geotorch==0.3.0
112
+ get-annotations==0.1.2
113
+ gevent==21.12.0
114
+ gitdb==4.0.11
115
+ GitPython==3.1.43
116
+ google-pasta==0.2.0
117
+ googleapis-common-protos==1.63.0
118
+ gpustat==1.1.1
119
+ gpytorch==1.10
120
+ gradio_client==0.16.0
121
+ graphlib_backport==1.1.0
122
+ greenlet==1.1.2
123
+ gunicorn==23.0.0
124
+ h11==0.14.0
125
+ h2==4.1.0
126
+ hf-xet==1.2.0
127
+ hf_transfer==0.1.9
128
+ hpack==4.0.0
129
+ httpcore==1.0.5
130
+ httptools==0.6.1
131
+ httpx==0.28.1
132
+ httpx-sse==0.4.0
133
+ huggingface_hub==0.36.1
134
+ humanfriendly==10.0
135
+ hyperframe==6.0.1
136
+ icetk==0.0.4
137
+ idna==3.10
138
+ igraph==0.11.8
139
+ imageio==2.35.1
140
+ imagesize==1.3.0
141
+ imgaug==0.4.0
142
+ importlib-metadata==7.0.0
143
+ importlib_resources==6.4.5
144
+ inequalipy==1.0.5
145
+ iniconfig==1.1.1
146
+ inquirerpy==0.3.4
147
+ iopath==0.1.10
148
+ isodate==0.7.2
149
+ itsdangerous==2.0.1
150
+ jax==0.4.13
151
+ jaxlib==0.4.13
152
+ jaxtyping==0.2.19
153
+ Jinja2==3.1.6
154
+ jiter==0.9.1
155
+ jmespath==0.10.0
156
+ joblib==1.4.2
157
+ jsonnet==0.17.0
158
+ jsonpatch==1.33
159
+ jsonpath-python==1.0.6
160
+ jsonpickle==2.0.0
161
+ jsonschema==4.23.0
162
+ jsonschema-specifications==2023.12.1
163
+ kaggle==1.7.4.5
164
+ Keras-Preprocessing==1.1.2
165
+ kubernetes==29.0.0
166
+ langchain==0.1.16
167
+ langchain-community==0.0.34
168
+ langchain-core==0.1.46
169
+ langchain-experimental==0.0.57
170
+ langchain-text-splitters==0.0.1
171
+ langcodes==3.4.0
172
+ langdetect==1.0.9
173
+ langsmith==0.1.51
174
+ language_data==1.2.0
175
+ layoutparser==0.3.4
176
+ lazy_loader==0.4
177
+ leidenalg==0.10.2
178
+ Levenshtein==0.25.1
179
+ linear-operator==0.4.0
180
+ litellm==1.77.4
181
+ litellm-enterprise==0.1.20
182
+ litellm-proxy-extras==0.2.19
183
+ llama-index==0.9.35
184
+ llvmlite==0.41.1
185
+ lmdb==1.7.3
186
+ lxml==5.2.1
187
+ madoka==0.7.1
188
+ marisa-trie==1.1.0
189
+ Markdown==3.3.6
190
+ markdown-it-py==3.0.0
191
+ markdown2==2.4.13
192
+ markdownify==0.11.6
193
+ MarkupSafe==2.1.5
194
+ marshmallow==3.21.1
195
+ mdtex2html==1.3.0
196
+ mdurl==0.1.2
197
+ metaphor-python==0.1.23
198
+ ml-dtypes==0.2.0
199
+ monotonic==1.6
200
+ mpmath==1.3.0
201
+ mrcfile==1.5.4
202
+ msal==1.36.0
203
+ msal-extensions==1.3.0
204
+ msg-parser==1.2.0
205
+ msgpack==1.0.8
206
+ msgpack-numpy==0.4.3.2
207
+ multidict==6.0.5
208
+ multipledispatch==1.0.0
209
+ multiprocess==0.70.16
210
+ murmurhash==1.0.10
211
+ mypy-extensions==1.0.0
212
+ narwhals==1.42.1
213
+ natsort==8.4.0
214
+ nest-asyncio==1.6.0
215
+ netCDF4==1.7.2
216
+ networkx==3.1
217
+ neuroHarmonize==2.4.5
218
+ nh3==0.2.17
219
+ ninja==1.11.1.1
220
+ nltk==3.8.1
221
+ numba==0.58.1
222
+ numexpr==2.8.6
223
+ numpoly==1.0.6
224
+ numpy==1.24.4
225
+ numpydoc==1.1.0
226
+ nvidia-cublas-cu12==12.9.2.10
227
+ nvidia-cuda-cupti-cu12==12.9.79
228
+ nvidia-cuda-nvrtc-cu12==12.9.86
229
+ nvidia-cuda-runtime-cu12==12.9.79
230
+ nvidia-cudnn-cu12==9.1.0.70
231
+ nvidia-cufft-cu12==11.4.1.4
232
+ nvidia-curand-cu12==10.3.10.19
233
+ nvidia-cusparse-cu12==12.5.10.65
234
+ nvidia-ml-py==12.535.133
235
+ nvidia-nccl-cu12==2.20.5
236
+ nvidia-nvjitlink-cu12==12.9.86
237
+ nvidia-nvtx-cu12==12.9.79
238
+ nvitop==1.3.2
239
+ oauthlib==3.2.2
240
+ onnx==1.16.0
241
+ onnxruntime==1.15.1
242
+ openai==1.101.0
243
+ openpyxl==3.0.9
244
+ opentelemetry-api==1.24.0
245
+ opentelemetry-exporter-otlp-proto-common==1.24.0
246
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
247
+ opentelemetry-proto==1.24.0
248
+ opentelemetry-sdk==1.24.0
249
+ opentelemetry-semantic-conventions==0.45b0
250
+ opt-einsum==3.3.0
251
+ optax==0.1.5
252
+ ordered-set==4.1.0
253
+ orjson==3.10.1
254
+ overrides==7.7.0
255
+ packaging==26.2
256
+ pandas==2.0.3
257
+ pandas-stubs==1.2.0.45
258
+ parsimonious==0.8.1
259
+ pathlib==1.0.1
260
+ patsy==1.0.1
261
+ pdf2image==1.17.0
262
+ pfzy==0.3.4
263
+ PICOS==2.6.1
264
+ pikepdf==8.4.1
265
+ pip-search==0.0.12
266
+ pkgutil_resolve_name==1.3.10
267
+ plac==0.9.6
268
+ plotly==6.3.0
269
+ pluggy==1.5.0
270
+ ply==3.11
271
+ pondpond==1.4.1
272
+ pooch==1.8.2
273
+ portalocker==2.4.0
274
+ posthog==3.5.0
275
+ preshed==3.0.9
276
+ prettytable==3.11.0
277
+ primer3-py==2.2.0
278
+ prompt-toolkit==3.0.43
279
+ propcache==0.2.0
280
+ PuLP==3.1.1
281
+ pulsar-client==3.5.0
282
+ pyarrow==17.0.0
283
+ pyarrow-hotfix==0.6
284
+ pyclipper==1.3.0.post5
285
+ pycocotools==2.0.7
286
+ pycparser==2.21
287
+ pydantic==2.10.6
288
+ pydantic_core==2.27.2
289
+ pydeck==0.9.0b1
290
+ pyDOE2==1.3.0
291
+ pydub==0.25.1
292
+ pyfaidx==0.9.0.1
293
+ Pygments==2.19.2
294
+ PyJWT==2.8.0
295
+ pymodbus==3.6.9
296
+ PyMuPDF==1.23.16
297
+ PyMuPDFb==1.23.9
298
+ PyNaCl==1.6.2
299
+ pynndescent==0.5.13
300
+ Pyomo==6.8.2
301
+ pyOpenSSL==24.1.0
302
+ pypandoc==1.13
303
+ pypdf==4.2.0
304
+ pypdfium2==4.29.0
305
+ PyPika==0.48.9
306
+ PyQt5==5.15.7
307
+ PyQt5-Qt5==5.15.17
308
+ PyQt5_sip==12.15.0
309
+ pyro-api==0.1.2
310
+ pyro-ppl==1.9.1
311
+ pysam==0.23.3
312
+ PySocks==1.7.1
313
+ pysqlite3-binary==0.5.2.post3
314
+ pystan==2.19.1.1
315
+ pytesseract==0.3.10
316
+ pytest-cov==5.0.0
317
+ python-dateutil==2.9.0.post0
318
+ python-decouple==3.8
319
+ python-docx==1.1.0
320
+ python-dotenv==1.0.1
321
+ python-iso639==2024.4.27
322
+ python-Levenshtein==0.25.1
323
+ python-multipart==0.0.18
324
+ python-pptx==0.6.23
325
+ python-slugify==8.0.4
326
+ pytorch-pretrained-bert==0.6.2
327
+ pytz==2025.2
328
+ pyvista==0.44.2
329
+ PyWavelets==1.4.1
330
+ PyYAML==6.0.3
331
+ quantile-python==1.1
332
+ rapidfuzz==3.8.1
333
+ rapidocr-onnxruntime==1.3.8
334
+ ray==2.10.0
335
+ rdkit==2024.3.5
336
+ redis==6.1.1
337
+ referencing==0.35.1
338
+ regex==2022.4.24
339
+ requests==2.32.4
340
+ requests-oauthlib==1.3.0
341
+ responses==0.16.0
342
+ rich==13.7.1
343
+ rouge-score==0.1.2
344
+ rpds-py==0.20.1
345
+ rq==2.3.3
346
+ rsa==4.7.2
347
+ ruff==0.4.2
348
+ rustworkx==0.15.1
349
+ s3transfer==0.11.3
350
+ sacrebleu==2.1.0
351
+ sacremoses==0.0.46
352
+ safetensors==0.4.3
353
+ scooby==0.10.1
354
+ seaborn==0.13.2
355
+ semantic-version==2.10.0
356
+ sentence-transformers==2.2.2
357
+ sentencepiece==0.1.91
358
+ sentry-sdk==2.39.0
359
+ session_info==1.0.1
360
+ sgmllib3k==1.0.0
361
+ shapely==2.0.4
362
+ shellingham==1.5.4
363
+ shortuuid==1.0.13
364
+ six==1.17.0
365
+ smart-open==6.4.0
366
+ smmap==5.0.1
367
+ sniffio==1.3.1
368
+ snowballstemmer==2.2.0
369
+ sobol-seq==0.2.0
370
+ socksio==1.0.0
371
+ soupsieve==2.5
372
+ spacy-legacy==3.0.12
373
+ spacy-loggers==1.0.5
374
+ Sphinx==4.3.1
375
+ sphinxcontrib-applehelp==1.0.2
376
+ sphinxcontrib-devhelp==1.0.2
377
+ sphinxcontrib-htmlhelp==2.0.0
378
+ sphinxcontrib-jsmath==1.0.1
379
+ sphinxcontrib-qthelp==1.0.3
380
+ sphinxcontrib-serializinghtml==1.1.5
381
+ SQLAlchemy==2.0.19
382
+ sqlparse==0.4.2
383
+ sse-starlette==1.8.2
384
+ starlette==0.44.0
385
+ statsmodels==0.14.1
386
+ stdlib-list==0.10.0
387
+ streamlit==1.30.0
388
+ streamlit-aggrid==0.3.4.post3
389
+ streamlit-antd-components==0.3.1
390
+ streamlit-chatbox==1.1.11
391
+ streamlit-feedback==0.1.3
392
+ streamlit-modal==0.1.0
393
+ streamlit-option-menu==0.3.12
394
+ strsimpy==0.2.1
395
+ svgwrite==1.4.3
396
+ sympy==1.13.3
397
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
398
+ tabulate==0.8.9
399
+ tenacity==8.2.3
400
+ tensorboard-plugin-wit==1.8.0
401
+ tensorboardX==2.4.1
402
+ text-unidecode==1.3
403
+ texttable==1.7.0
404
+ thefuzz==0.22.1
405
+ threadpoolctl==3.5.0
406
+ tifffile==2023.7.10
407
+ tiktoken==0.7.0
408
+ timm==0.9.16
409
+ tk==0.1.0
410
+ tokenizers==0.20.3
411
+ toml==0.10.2
412
+ tomlkit==0.12.0
413
+ toolz==0.12.1
414
+ torch==2.4.1
415
+ torch-geometric==2.6.1
416
+ torchaudio==2.1.2+cu118
417
+ torchtext==0.4.0
418
+ tornado==6.4
419
+ tqdm==4.67.1
420
+ transformer-lens==2.16.1
421
+ transformers==4.46.3
422
+ transformers-stream-generator==0.0.5
423
+ triton==3.0.0
424
+ typed-argument-parser==1.10.1
425
+ typeguard==4.4.0
426
+ typer==0.9.4
427
+ types-requests==2.31.0.20240406
428
+ typing-inspect==0.9.0
429
+ typing-utils==0.1.0
430
+ typing_extensions==4.13.2
431
+ tzdata==2024.1
432
+ tzlocal==5.2
433
+ umap-learn==0.5.7
434
+ Unidecode==1.3.2
435
+ unittest-xml-reporting==3.2.0
436
+ unstructured==0.11.0
437
+ unstructured-client==0.22.0
438
+ unstructured-inference==0.7.15
439
+ unstructured.pytesseract==0.3.12
440
+ urllib3==2.2.3
441
+ uvicorn==0.29.0
442
+ uvloop==0.21.0
443
+ validators==0.28.1
444
+ vllm==0.2.7
445
+ vtk==9.3.1
446
+ wandb==0.22.0
447
+ watchdog==3.0.0
448
+ watchfiles==0.21.0
449
+ wavedrom==2.0.3.post3
450
+ weasel==0.3.4
451
+ websocket-client==1.8.0
452
+ websockets==13.1
453
+ Werkzeug==2.0.2
454
+ word2number==1.1
455
+ xlrd==2.0.1
456
+ XlsxWriter==3.0.2
457
+ xxhash==2.0.2
458
+ Yapsy==1.12.2
459
+ yarl==1.15.2
460
+ youtube-search==2.1.2
461
+ zipp==3.20.2
462
+ zope.event==4.5.0
463
+ zstandard==0.23.0
configs/069_test/pip-freeze.txt ADDED
@@ -0,0 +1,463 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ certifi==2026.2.25
43
+ cffi==1.15.0
44
+ cftime==1.6.4.post1
45
+ chaospy==3.3.9
46
+ charset-normalizer==3.4.7
47
+ chex==0.1.7
48
+ chroma-hnswlib==0.7.3
49
+ chromadb==0.4.15
50
+ click==8.1.7
51
+ cloudpathlib==0.16.0
52
+ cobra==0.29.1
53
+ cohere==5.3.3
54
+ coloredlogs==15.0.1
55
+ confection==0.1.4
56
+ ConfigArgParse==1.5.3
57
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59
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60
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61
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62
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63
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64
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66
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67
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68
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69
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70
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71
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72
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73
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78
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79
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80
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81
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82
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83
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84
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85
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86
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87
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88
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89
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90
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91
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92
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93
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94
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95
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96
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97
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98
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99
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100
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101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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143
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144
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145
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146
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147
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148
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149
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150
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151
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152
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153
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154
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155
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156
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157
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158
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159
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160
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161
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162
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163
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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177
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178
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
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203
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204
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205
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206
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207
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208
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209
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210
+ murmurhash==1.0.10
211
+ mypy-extensions==1.0.0
212
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213
+ natsort==8.4.0
214
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215
+ netCDF4==1.7.2
216
+ networkx==3.1
217
+ neuroHarmonize==2.4.5
218
+ nh3==0.2.17
219
+ ninja==1.11.1.1
220
+ nltk==3.8.1
221
+ numba==0.58.1
222
+ numexpr==2.8.6
223
+ numpoly==1.0.6
224
+ numpy==1.24.4
225
+ numpydoc==1.1.0
226
+ nvidia-cublas-cu12==12.9.2.10
227
+ nvidia-cuda-cupti-cu12==12.9.79
228
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229
+ nvidia-cuda-runtime-cu12==12.9.79
230
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231
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232
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233
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234
+ nvidia-ml-py==12.535.133
235
+ nvidia-nccl-cu12==2.20.5
236
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237
+ nvidia-nvtx-cu12==12.9.79
238
+ nvitop==1.3.2
239
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240
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241
+ onnxruntime==1.15.1
242
+ openai==1.101.0
243
+ openpyxl==3.0.9
244
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245
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246
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247
+ opentelemetry-proto==1.24.0
248
+ opentelemetry-sdk==1.24.0
249
+ opentelemetry-semantic-conventions==0.45b0
250
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251
+ optax==0.1.5
252
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253
+ orjson==3.10.1
254
+ overrides==7.7.0
255
+ packaging==26.2
256
+ pandas==2.0.3
257
+ pandas-stubs==1.2.0.45
258
+ parsimonious==0.8.1
259
+ pathlib==1.0.1
260
+ patsy==1.0.1
261
+ pdf2image==1.17.0
262
+ pfzy==0.3.4
263
+ PICOS==2.6.1
264
+ pikepdf==8.4.1
265
+ pip-search==0.0.12
266
+ pkgutil_resolve_name==1.3.10
267
+ plac==0.9.6
268
+ plotly==6.3.0
269
+ pluggy==1.5.0
270
+ ply==3.11
271
+ pondpond==1.4.1
272
+ pooch==1.8.2
273
+ portalocker==2.4.0
274
+ posthog==3.5.0
275
+ preshed==3.0.9
276
+ prettytable==3.11.0
277
+ primer3-py==2.2.0
278
+ prompt-toolkit==3.0.43
279
+ propcache==0.2.0
280
+ PuLP==3.1.1
281
+ pulsar-client==3.5.0
282
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283
+ pyarrow-hotfix==0.6
284
+ pyclipper==1.3.0.post5
285
+ pycocotools==2.0.7
286
+ pycparser==2.21
287
+ pydantic==2.10.6
288
+ pydantic_core==2.27.2
289
+ pydeck==0.9.0b1
290
+ pyDOE2==1.3.0
291
+ pydub==0.25.1
292
+ pyfaidx==0.9.0.1
293
+ Pygments==2.19.2
294
+ PyJWT==2.8.0
295
+ pymodbus==3.6.9
296
+ PyMuPDF==1.23.16
297
+ PyMuPDFb==1.23.9
298
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299
+ pynndescent==0.5.13
300
+ Pyomo==6.8.2
301
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302
+ pypandoc==1.13
303
+ pypdf==4.2.0
304
+ pypdfium2==4.29.0
305
+ PyPika==0.48.9
306
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307
+ PyQt5-Qt5==5.15.17
308
+ PyQt5_sip==12.15.0
309
+ pyro-api==0.1.2
310
+ pyro-ppl==1.9.1
311
+ pysam==0.23.3
312
+ PySocks==1.7.1
313
+ pysqlite3-binary==0.5.2.post3
314
+ pystan==2.19.1.1
315
+ pytesseract==0.3.10
316
+ pytest-cov==5.0.0
317
+ python-dateutil==2.9.0.post0
318
+ python-decouple==3.8
319
+ python-docx==1.1.0
320
+ python-dotenv==1.0.1
321
+ python-iso639==2024.4.27
322
+ python-Levenshtein==0.25.1
323
+ python-multipart==0.0.18
324
+ python-pptx==0.6.23
325
+ python-slugify==8.0.4
326
+ pytorch-pretrained-bert==0.6.2
327
+ pytz==2025.2
328
+ pyvista==0.44.2
329
+ PyWavelets==1.4.1
330
+ PyYAML==6.0.3
331
+ quantile-python==1.1
332
+ rapidfuzz==3.8.1
333
+ rapidocr-onnxruntime==1.3.8
334
+ ray==2.10.0
335
+ rdkit==2024.3.5
336
+ redis==6.1.1
337
+ referencing==0.35.1
338
+ regex==2022.4.24
339
+ requests==2.32.4
340
+ requests-oauthlib==1.3.0
341
+ responses==0.16.0
342
+ rich==13.7.1
343
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344
+ rpds-py==0.20.1
345
+ rq==2.3.3
346
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347
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348
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349
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350
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351
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352
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353
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354
+ seaborn==0.13.2
355
+ semantic-version==2.10.0
356
+ sentence-transformers==2.2.2
357
+ sentencepiece==0.1.91
358
+ sentry-sdk==2.39.0
359
+ session_info==1.0.1
360
+ sgmllib3k==1.0.0
361
+ shapely==2.0.4
362
+ shellingham==1.5.4
363
+ shortuuid==1.0.13
364
+ six==1.17.0
365
+ smart-open==6.4.0
366
+ smmap==5.0.1
367
+ sniffio==1.3.1
368
+ snowballstemmer==2.2.0
369
+ sobol-seq==0.2.0
370
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371
+ soupsieve==2.5
372
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373
+ spacy-loggers==1.0.5
374
+ Sphinx==4.3.1
375
+ sphinxcontrib-applehelp==1.0.2
376
+ sphinxcontrib-devhelp==1.0.2
377
+ sphinxcontrib-htmlhelp==2.0.0
378
+ sphinxcontrib-jsmath==1.0.1
379
+ sphinxcontrib-qthelp==1.0.3
380
+ sphinxcontrib-serializinghtml==1.1.5
381
+ SQLAlchemy==2.0.19
382
+ sqlparse==0.4.2
383
+ sse-starlette==1.8.2
384
+ starlette==0.44.0
385
+ statsmodels==0.14.1
386
+ stdlib-list==0.10.0
387
+ streamlit==1.30.0
388
+ streamlit-aggrid==0.3.4.post3
389
+ streamlit-antd-components==0.3.1
390
+ streamlit-chatbox==1.1.11
391
+ streamlit-feedback==0.1.3
392
+ streamlit-modal==0.1.0
393
+ streamlit-option-menu==0.3.12
394
+ strsimpy==0.2.1
395
+ svgwrite==1.4.3
396
+ sympy==1.13.3
397
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
398
+ tabulate==0.8.9
399
+ tenacity==8.2.3
400
+ tensorboard-plugin-wit==1.8.0
401
+ tensorboardX==2.4.1
402
+ text-unidecode==1.3
403
+ texttable==1.7.0
404
+ thefuzz==0.22.1
405
+ threadpoolctl==3.5.0
406
+ tifffile==2023.7.10
407
+ tiktoken==0.7.0
408
+ timm==0.9.16
409
+ tk==0.1.0
410
+ tokenizers==0.20.3
411
+ toml==0.10.2
412
+ tomlkit==0.12.0
413
+ toolz==0.12.1
414
+ torch==2.4.1
415
+ torch-geometric==2.6.1
416
+ torchaudio==2.1.2+cu118
417
+ torchtext==0.4.0
418
+ tornado==6.4
419
+ tqdm==4.67.1
420
+ transformer-lens==2.16.1
421
+ transformers==4.46.3
422
+ transformers-stream-generator==0.0.5
423
+ triton==3.0.0
424
+ typed-argument-parser==1.10.1
425
+ typeguard==4.4.0
426
+ typer==0.9.4
427
+ types-requests==2.31.0.20240406
428
+ typing-inspect==0.9.0
429
+ typing-utils==0.1.0
430
+ typing_extensions==4.13.2
431
+ tzdata==2024.1
432
+ tzlocal==5.2
433
+ umap-learn==0.5.7
434
+ Unidecode==1.3.2
435
+ unittest-xml-reporting==3.2.0
436
+ unstructured==0.11.0
437
+ unstructured-client==0.22.0
438
+ unstructured-inference==0.7.15
439
+ unstructured.pytesseract==0.3.12
440
+ urllib3==2.2.3
441
+ uvicorn==0.29.0
442
+ uvloop==0.21.0
443
+ validators==0.28.1
444
+ vllm==0.2.7
445
+ vtk==9.3.1
446
+ wandb==0.22.0
447
+ watchdog==3.0.0
448
+ watchfiles==0.21.0
449
+ wavedrom==2.0.3.post3
450
+ weasel==0.3.4
451
+ websocket-client==1.8.0
452
+ websockets==13.1
453
+ Werkzeug==2.0.2
454
+ word2number==1.1
455
+ xlrd==2.0.1
456
+ XlsxWriter==3.0.2
457
+ xxhash==2.0.2
458
+ Yapsy==1.12.2
459
+ yarl==1.15.2
460
+ youtube-search==2.1.2
461
+ zipp==3.20.2
462
+ zope.event==4.5.0
463
+ zstandard==0.23.0
configs/s41467_024_44930_y_test/editable.txt ADDED
File without changes
configs/s41467_024_44930_y_test/env.yml ADDED
@@ -0,0 +1,63 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: s41467_024_44930_y_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
+ - bzip2=1.0.8
9
+ - ca-certificates=2025.8.3
10
+ - ld_impl_linux-64=2.44
11
+ - libffi=3.4.6
12
+ - libgcc=15.1.0
13
+ - libgcc-ng=15.1.0
14
+ - libgomp=15.1.0
15
+ - liblzma=5.8.1
16
+ - liblzma-devel=5.8.1
17
+ - libnsl=2.0.1
18
+ - libsqlite=3.50.4
19
+ - libuuid=2.38.1
20
+ - libxcrypt=4.4.36
21
+ - libzlib=1.3.1
22
+ - ncurses=6.5
23
+ - openssl=3.5.2
24
+ - pip=22.1.2
25
+ - python=3.8.20
26
+ - readline=8.2
27
+ - setuptools=70.3.0
28
+ - tk=8.6.13
29
+ - wheel=0.45.1
30
+ - xz=5.8.1
31
+ - xz-gpl-tools=5.8.1
32
+ - xz-tools=5.8.1
33
+ - pip:
34
+ - charset-normalizer==3.4.3
35
+ - coverage==7.6.1
36
+ - flatbuffers==25.2.10
37
+ - gast==0.4.0
38
+ - google-auth==2.40.3
39
+ - google-auth-oauthlib==1.0.0
40
+ - h5py==3.9.0
41
+ - idna==3.10
42
+ - keras==2.13.1
43
+ - libclang==18.1.1
44
+ - numpy==1.24.3
45
+ - packaging==25.0
46
+ - protobuf==4.25.8
47
+ - pyasn1==0.6.1
48
+ - pyasn1-modules==0.4.2
49
+ - pytest-cov==5.0.0
50
+ - requests==2.32.4
51
+ - scipy==1.4.1
52
+ - six==1.17.0
53
+ - tensorboard==2.13.0
54
+ - tensorboard-data-server==0.7.2
55
+ - tensorflow==2.13.1
56
+ - tensorflow-estimator==2.13.0
57
+ - tensorflow-io-gcs-filesystem==0.34.0
58
+ - termcolor==2.4.0
59
+ - typing-extensions==4.5.0
60
+ - unittest-xml-reporting==3.2.0
61
+ - urllib3==2.2.3
62
+ - wrapt==1.17.3
63
+ prefix: /home/lily/yz979/anaconda3/envs/s41467_024_44930_y_test
configs/s41467_024_44930_y_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
+ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
9
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
10
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
11
+ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
12
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399
+ tensorflow==2.13.1
400
+ tensorflow-estimator==2.13.0
401
+ tensorflow-io-gcs-filesystem==0.34.0
402
+ termcolor==2.4.0
403
+ text-unidecode==1.3
404
+ texttable==1.7.0
405
+ thefuzz==0.22.1
406
+ threadpoolctl==3.5.0
407
+ tifffile==2023.7.10
408
+ tiktoken==0.7.0
409
+ timm==0.9.16
410
+ tk==0.1.0
411
+ tokenizers==0.20.3
412
+ toml==0.10.2
413
+ tomlkit==0.12.0
414
+ toolz==0.12.1
415
+ torch-geometric==2.6.1
416
+ torchaudio==2.1.2+cu118
417
+ torchtext==0.4.0
418
+ tornado==6.4
419
+ tqdm==4.67.1
420
+ transformer-lens==2.16.1
421
+ transformers==4.46.3
422
+ transformers-stream-generator==0.0.5
423
+ typed-argument-parser==1.10.1
424
+ typeguard==4.4.0
425
+ typer==0.9.4
426
+ types-requests==2.31.0.20240406
427
+ typing-inspect==0.9.0
428
+ typing-utils==0.1.0
429
+ typing_extensions==4.13.2
430
+ tzdata==2024.1
431
+ tzlocal==5.2
432
+ umap-learn==0.5.7
433
+ Unidecode==1.3.2
434
+ unittest-xml-reporting==3.2.0
435
+ unstructured==0.11.0
436
+ unstructured-client==0.22.0
437
+ unstructured-inference==0.7.15
438
+ unstructured.pytesseract==0.3.12
439
+ urllib3==2.2.3
440
+ uvicorn==0.29.0
441
+ uvloop==0.21.0
442
+ validators==0.28.1
443
+ vllm==0.2.7
444
+ vtk==9.3.1
445
+ wandb==0.22.0
446
+ watchdog==3.0.0
447
+ watchfiles==0.21.0
448
+ wavedrom==2.0.3.post3
449
+ weasel==0.3.4
450
+ websocket-client==1.8.0
451
+ websockets==13.1
452
+ Werkzeug==2.0.2
453
+ word2number==1.1
454
+ wrapt==1.17.3
455
+ xlrd==2.0.1
456
+ XlsxWriter==3.0.2
457
+ xxhash==2.0.2
458
+ Yapsy==1.12.2
459
+ yarl==1.15.2
460
+ youtube-search==2.1.2
461
+ zipp==3.20.2
462
+ zope.event==4.5.0
463
+ zstandard==0.23.0
configs/s41467_024_44930_y_test/pip-freeze.txt ADDED
@@ -0,0 +1,463 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filetype==1.2.0
98
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
99
+ flaky==3.7.0
100
+ Flask-Cors==3.0.10
101
+ flatbuffers==25.2.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gast==0.4.0
109
+ gdown==5.2.0
110
+ geosketch==1.3
111
+ geotorch==0.3.0
112
+ get-annotations==0.1.2
113
+ gevent==21.12.0
114
+ gitdb==4.0.11
115
+ GitPython==3.1.43
116
+ google-auth==2.40.3
117
+ google-auth-oauthlib==1.0.0
118
+ google-pasta==0.2.0
119
+ googleapis-common-protos==1.63.0
120
+ gpustat==1.1.1
121
+ gpytorch==1.10
122
+ gradio_client==0.16.0
123
+ graphlib_backport==1.1.0
124
+ greenlet==1.1.2
125
+ gunicorn==23.0.0
126
+ h11==0.14.0
127
+ h2==4.1.0
128
+ h5py==3.9.0
129
+ hf-xet==1.2.0
130
+ hf_transfer==0.1.9
131
+ hpack==4.0.0
132
+ httpcore==1.0.5
133
+ httptools==0.6.1
134
+ httpx==0.28.1
135
+ httpx-sse==0.4.0
136
+ huggingface_hub==0.36.1
137
+ humanfriendly==10.0
138
+ hyperframe==6.0.1
139
+ icetk==0.0.4
140
+ idna==3.10
141
+ igraph==0.11.8
142
+ imageio==2.35.1
143
+ imagesize==1.3.0
144
+ imgaug==0.4.0
145
+ importlib-metadata==7.0.0
146
+ importlib_resources==6.4.5
147
+ inequalipy==1.0.5
148
+ iniconfig==1.1.1
149
+ inquirerpy==0.3.4
150
+ iopath==0.1.10
151
+ isodate==0.7.2
152
+ itsdangerous==2.0.1
153
+ jax==0.4.13
154
+ jaxlib==0.4.13
155
+ jaxtyping==0.2.19
156
+ Jinja2==3.1.6
157
+ jiter==0.9.1
158
+ jmespath==0.10.0
159
+ joblib==1.4.2
160
+ jsonnet==0.17.0
161
+ jsonpatch==1.33
162
+ jsonpath-python==1.0.6
163
+ jsonpickle==2.0.0
164
+ jsonschema==4.23.0
165
+ jsonschema-specifications==2023.12.1
166
+ kaggle==1.7.4.5
167
+ keras==2.13.1
168
+ Keras-Preprocessing==1.1.2
169
+ kubernetes==29.0.0
170
+ langchain==0.1.16
171
+ langchain-community==0.0.34
172
+ langchain-core==0.1.46
173
+ langchain-experimental==0.0.57
174
+ langchain-text-splitters==0.0.1
175
+ langcodes==3.4.0
176
+ langdetect==1.0.9
177
+ langsmith==0.1.51
178
+ language_data==1.2.0
179
+ layoutparser==0.3.4
180
+ lazy_loader==0.4
181
+ leidenalg==0.10.2
182
+ Levenshtein==0.25.1
183
+ libclang==18.1.1
184
+ linear-operator==0.4.0
185
+ litellm==1.77.4
186
+ litellm-enterprise==0.1.20
187
+ litellm-proxy-extras==0.2.19
188
+ llama-index==0.9.35
189
+ llvmlite==0.41.1
190
+ lmdb==1.7.3
191
+ lxml==5.2.1
192
+ madoka==0.7.1
193
+ marisa-trie==1.1.0
194
+ Markdown==3.3.6
195
+ markdown-it-py==3.0.0
196
+ markdown2==2.4.13
197
+ markdownify==0.11.6
198
+ MarkupSafe==2.1.5
199
+ marshmallow==3.21.1
200
+ mdtex2html==1.3.0
201
+ mdurl==0.1.2
202
+ metaphor-python==0.1.23
203
+ ml-dtypes==0.2.0
204
+ monotonic==1.6
205
+ mrcfile==1.5.4
206
+ msal==1.36.0
207
+ msal-extensions==1.3.0
208
+ msg-parser==1.2.0
209
+ msgpack==1.0.8
210
+ msgpack-numpy==0.4.3.2
211
+ multidict==6.0.5
212
+ multipledispatch==1.0.0
213
+ multiprocess==0.70.16
214
+ murmurhash==1.0.10
215
+ mypy-extensions==1.0.0
216
+ narwhals==1.42.1
217
+ natsort==8.4.0
218
+ nest-asyncio==1.6.0
219
+ netCDF4==1.7.2
220
+ neuroHarmonize==2.4.5
221
+ nh3==0.2.17
222
+ ninja==1.11.1.1
223
+ nltk==3.8.1
224
+ numba==0.58.1
225
+ numexpr==2.8.6
226
+ numpoly==1.0.6
227
+ numpy==1.24.3
228
+ numpydoc==1.1.0
229
+ nvidia-ml-py==12.535.133
230
+ nvitop==1.3.2
231
+ oauthlib==3.2.2
232
+ onnx==1.16.0
233
+ onnxruntime==1.15.1
234
+ openai==1.101.0
235
+ openpyxl==3.0.9
236
+ opentelemetry-api==1.24.0
237
+ opentelemetry-exporter-otlp-proto-common==1.24.0
238
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
239
+ opentelemetry-proto==1.24.0
240
+ opentelemetry-sdk==1.24.0
241
+ opentelemetry-semantic-conventions==0.45b0
242
+ opt-einsum==3.3.0
243
+ optax==0.1.5
244
+ ordered-set==4.1.0
245
+ orjson==3.10.1
246
+ overrides==7.7.0
247
+ packaging==26.2
248
+ pandas==2.0.3
249
+ pandas-stubs==1.2.0.45
250
+ parsimonious==0.8.1
251
+ pathlib==1.0.1
252
+ patsy==1.0.1
253
+ pdf2image==1.17.0
254
+ pfzy==0.3.4
255
+ PICOS==2.6.1
256
+ pikepdf==8.4.1
257
+ pip-search==0.0.12
258
+ pkgutil_resolve_name==1.3.10
259
+ plac==0.9.6
260
+ plotly==6.3.0
261
+ pluggy==1.5.0
262
+ ply==3.11
263
+ pondpond==1.4.1
264
+ pooch==1.8.2
265
+ portalocker==2.4.0
266
+ posthog==3.5.0
267
+ preshed==3.0.9
268
+ prettytable==3.11.0
269
+ primer3-py==2.2.0
270
+ prompt-toolkit==3.0.43
271
+ propcache==0.2.0
272
+ protobuf==3.20.3
273
+ PuLP==3.1.1
274
+ pulsar-client==3.5.0
275
+ pyarrow==17.0.0
276
+ pyarrow-hotfix==0.6
277
+ pyasn1==0.6.1
278
+ pyasn1_modules==0.4.2
279
+ pyclipper==1.3.0.post5
280
+ pycocotools==2.0.7
281
+ pycparser==2.21
282
+ pydantic==2.10.6
283
+ pydantic_core==2.27.2
284
+ pydeck==0.9.0b1
285
+ pyDOE2==1.3.0
286
+ pydub==0.25.1
287
+ pyfaidx==0.9.0.1
288
+ Pygments==2.19.2
289
+ PyJWT==2.8.0
290
+ pymodbus==3.6.9
291
+ PyMuPDF==1.23.16
292
+ PyMuPDFb==1.23.9
293
+ PyNaCl==1.6.2
294
+ pynndescent==0.5.13
295
+ Pyomo==6.8.2
296
+ pyOpenSSL==24.1.0
297
+ pypandoc==1.13
298
+ pypdf==4.2.0
299
+ pypdfium2==4.29.0
300
+ PyPika==0.48.9
301
+ PyQt5==5.15.7
302
+ PyQt5-Qt5==5.15.17
303
+ PyQt5_sip==12.15.0
304
+ pyro-api==0.1.2
305
+ pyro-ppl==1.9.1
306
+ pysam==0.23.3
307
+ PySocks==1.7.1
308
+ pysqlite3-binary==0.5.2.post3
309
+ pystan==2.19.1.1
310
+ pytesseract==0.3.10
311
+ pytest-cov==5.0.0
312
+ python-dateutil==2.9.0.post0
313
+ python-decouple==3.8
314
+ python-docx==1.1.0
315
+ python-dotenv==1.0.1
316
+ python-iso639==2024.4.27
317
+ python-Levenshtein==0.25.1
318
+ python-multipart==0.0.18
319
+ python-pptx==0.6.23
320
+ python-slugify==8.0.4
321
+ pytorch-pretrained-bert==0.6.2
322
+ pytz==2025.2
323
+ pyvista==0.44.2
324
+ PyWavelets==1.4.1
325
+ PyYAML==6.0.3
326
+ quantile-python==1.1
327
+ rapidfuzz==3.8.1
328
+ rapidocr-onnxruntime==1.3.8
329
+ ray==2.10.0
330
+ rdkit==2024.3.5
331
+ redis==6.1.1
332
+ referencing==0.35.1
333
+ regex==2022.4.24
334
+ requests==2.32.4
335
+ requests-oauthlib==1.3.0
336
+ responses==0.16.0
337
+ rich==13.7.1
338
+ rouge-score==0.1.2
339
+ rpds-py==0.20.1
340
+ rq==2.3.3
341
+ rsa==4.7.2
342
+ ruff==0.4.2
343
+ rustworkx==0.15.1
344
+ s3transfer==0.11.3
345
+ sacrebleu==2.1.0
346
+ sacremoses==0.0.46
347
+ safetensors==0.4.3
348
+ scipy==1.4.1
349
+ scooby==0.10.1
350
+ seaborn==0.13.2
351
+ semantic-version==2.10.0
352
+ sentence-transformers==2.2.2
353
+ sentencepiece==0.1.91
354
+ sentry-sdk==2.39.0
355
+ session_info==1.0.1
356
+ sgmllib3k==1.0.0
357
+ shapely==2.0.4
358
+ shellingham==1.5.4
359
+ shortuuid==1.0.13
360
+ six==1.17.0
361
+ smart-open==6.4.0
362
+ smmap==5.0.1
363
+ sniffio==1.3.1
364
+ snowballstemmer==2.2.0
365
+ sobol-seq==0.2.0
366
+ socksio==1.0.0
367
+ soupsieve==2.5
368
+ spacy-legacy==3.0.12
369
+ spacy-loggers==1.0.5
370
+ Sphinx==4.3.1
371
+ sphinxcontrib-applehelp==1.0.2
372
+ sphinxcontrib-devhelp==1.0.2
373
+ sphinxcontrib-htmlhelp==2.0.0
374
+ sphinxcontrib-jsmath==1.0.1
375
+ sphinxcontrib-qthelp==1.0.3
376
+ sphinxcontrib-serializinghtml==1.1.5
377
+ SQLAlchemy==2.0.19
378
+ sqlparse==0.4.2
379
+ sse-starlette==1.8.2
380
+ starlette==0.44.0
381
+ statsmodels==0.14.1
382
+ stdlib-list==0.10.0
383
+ streamlit==1.30.0
384
+ streamlit-aggrid==0.3.4.post3
385
+ streamlit-antd-components==0.3.1
386
+ streamlit-chatbox==1.1.11
387
+ streamlit-feedback==0.1.3
388
+ streamlit-modal==0.1.0
389
+ streamlit-option-menu==0.3.12
390
+ strsimpy==0.2.1
391
+ svgwrite==1.4.3
392
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
393
+ tabulate==0.8.9
394
+ tenacity==8.2.3
395
+ tensorboard==2.13.0
396
+ tensorboard-data-server==0.7.2
397
+ tensorboard-plugin-wit==1.8.0
398
+ tensorboardX==2.4.1
399
+ tensorflow==2.13.1
400
+ tensorflow-estimator==2.13.0
401
+ tensorflow-io-gcs-filesystem==0.34.0
402
+ termcolor==2.4.0
403
+ text-unidecode==1.3
404
+ texttable==1.7.0
405
+ thefuzz==0.22.1
406
+ threadpoolctl==3.5.0
407
+ tifffile==2023.7.10
408
+ tiktoken==0.7.0
409
+ timm==0.9.16
410
+ tk==0.1.0
411
+ tokenizers==0.20.3
412
+ toml==0.10.2
413
+ tomlkit==0.12.0
414
+ toolz==0.12.1
415
+ torch-geometric==2.6.1
416
+ torchaudio==2.1.2+cu118
417
+ torchtext==0.4.0
418
+ tornado==6.4
419
+ tqdm==4.67.1
420
+ transformer-lens==2.16.1
421
+ transformers==4.46.3
422
+ transformers-stream-generator==0.0.5
423
+ typed-argument-parser==1.10.1
424
+ typeguard==4.4.0
425
+ typer==0.9.4
426
+ types-requests==2.31.0.20240406
427
+ typing-inspect==0.9.0
428
+ typing-utils==0.1.0
429
+ typing_extensions==4.13.2
430
+ tzdata==2024.1
431
+ tzlocal==5.2
432
+ umap-learn==0.5.7
433
+ Unidecode==1.3.2
434
+ unittest-xml-reporting==3.2.0
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447
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449
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454
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457
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460
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461
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463
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configs/s41467_024_46879_4_test/editable.txt ADDED
File without changes
configs/s41467_024_46879_4_test/env.yml ADDED
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1
+ name: s41467_024_46879_4_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
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8
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9
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24
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25
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26
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54
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56
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62
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67
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68
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configs/s41467_024_46879_4_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
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7
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8
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1
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configs/s41467_024_46879_4_test/pip-clean.txt ADDED
@@ -0,0 +1,472 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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247
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248
+ openai==1.101.0
249
+ openpyxl==3.0.9
250
+ opentelemetry-api==1.24.0
251
+ opentelemetry-exporter-otlp-proto-common==1.24.0
252
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
253
+ opentelemetry-proto==1.24.0
254
+ opentelemetry-sdk==1.24.0
255
+ opentelemetry-semantic-conventions==0.45b0
256
+ opt-einsum==3.3.0
257
+ optax==0.1.5
258
+ ordered-set==4.1.0
259
+ orjson==3.10.1
260
+ overrides==7.7.0
261
+ packaging==26.2
262
+ pandas==2.0.3
263
+ pandas-stubs==1.2.0.45
264
+ parsimonious==0.8.1
265
+ pathlib==1.0.1
266
+ patsy==1.0.1
267
+ pdf2image==1.17.0
268
+ pfzy==0.3.4
269
+ PICOS==2.6.1
270
+ pikepdf==8.4.1
271
+ pillow==10.4.0
272
+ pip-search==0.0.12
273
+ pkgutil_resolve_name==1.3.10
274
+ plac==0.9.6
275
+ plotly==6.3.0
276
+ pluggy==1.5.0
277
+ ply==3.11
278
+ pondpond==1.4.1
279
+ pooch==1.8.2
280
+ portalocker==2.4.0
281
+ posthog==3.5.0
282
+ preshed==3.0.9
283
+ prettytable==3.11.0
284
+ primer3-py==2.2.0
285
+ prompt-toolkit==3.0.43
286
+ propcache==0.2.0
287
+ PuLP==3.1.1
288
+ pulsar-client==3.5.0
289
+ pyarrow==17.0.0
290
+ pyarrow-hotfix==0.6
291
+ pyclipper==1.3.0.post5
292
+ pycocotools==2.0.7
293
+ pycparser==2.21
294
+ pydantic==2.10.6
295
+ pydantic_core==2.27.2
296
+ pydeck==0.9.0b1
297
+ pyDOE2==1.3.0
298
+ pydub==0.25.1
299
+ pyfaidx==0.9.0.1
300
+ Pygments==2.19.2
301
+ PyJWT==2.8.0
302
+ pymodbus==3.6.9
303
+ PyMuPDF==1.23.16
304
+ PyMuPDFb==1.23.9
305
+ PyNaCl==1.6.2
306
+ pynndescent==0.5.13
307
+ Pyomo==6.8.2
308
+ pyOpenSSL==24.1.0
309
+ pypandoc==1.13
310
+ pyparsing==3.1.4
311
+ pypdf==4.2.0
312
+ pypdfium2==4.29.0
313
+ PyPika==0.48.9
314
+ PyQt5==5.15.7
315
+ PyQt5-Qt5==5.15.17
316
+ PyQt5_sip==12.15.0
317
+ pyro-api==0.1.2
318
+ pyro-ppl==1.9.1
319
+ pysam==0.23.3
320
+ PySocks==1.7.1
321
+ pysqlite3-binary==0.5.2.post3
322
+ pystan==2.19.1.1
323
+ pytesseract==0.3.10
324
+ pytest-cov==5.0.0
325
+ python-dateutil==2.9.0.post0
326
+ python-decouple==3.8
327
+ python-docx==1.1.0
328
+ python-dotenv==1.0.1
329
+ python-iso639==2024.4.27
330
+ python-Levenshtein==0.25.1
331
+ python-multipart==0.0.18
332
+ python-pptx==0.6.23
333
+ python-slugify==8.0.4
334
+ pytorch-pretrained-bert==0.6.2
335
+ pytz==2025.2
336
+ pyvista==0.44.2
337
+ PyWavelets==1.4.1
338
+ PyYAML==6.0.3
339
+ quantile-python==1.1
340
+ rapidfuzz==3.8.1
341
+ rapidocr-onnxruntime==1.3.8
342
+ ray==2.10.0
343
+ rdkit==2024.3.5
344
+ redis==6.1.1
345
+ referencing==0.35.1
346
+ regex==2022.4.24
347
+ requests==2.32.4
348
+ requests-oauthlib==1.3.0
349
+ responses==0.16.0
350
+ rich==13.7.1
351
+ rouge-score==0.1.2
352
+ rpds-py==0.20.1
353
+ rq==2.3.3
354
+ rsa==4.7.2
355
+ ruff==0.4.2
356
+ rustworkx==0.15.1
357
+ s3transfer==0.11.3
358
+ sacrebleu==2.1.0
359
+ sacremoses==0.0.46
360
+ safetensors==0.4.3
361
+ scipy==1.10.1
362
+ scooby==0.10.1
363
+ seaborn==0.13.2
364
+ semantic-version==2.10.0
365
+ sentence-transformers==2.2.2
366
+ sentencepiece==0.1.91
367
+ sentry-sdk==2.39.0
368
+ session_info==1.0.1
369
+ sgmllib3k==1.0.0
370
+ shapely==2.0.4
371
+ shellingham==1.5.4
372
+ shortuuid==1.0.13
373
+ six==1.17.0
374
+ smart-open==6.4.0
375
+ smmap==5.0.1
376
+ sniffio==1.3.1
377
+ snowballstemmer==2.2.0
378
+ sobol-seq==0.2.0
379
+ socksio==1.0.0
380
+ soupsieve==2.5
381
+ spacy-legacy==3.0.12
382
+ spacy-loggers==1.0.5
383
+ Sphinx==4.3.1
384
+ sphinxcontrib-applehelp==1.0.2
385
+ sphinxcontrib-devhelp==1.0.2
386
+ sphinxcontrib-htmlhelp==2.0.0
387
+ sphinxcontrib-jsmath==1.0.1
388
+ sphinxcontrib-qthelp==1.0.3
389
+ sphinxcontrib-serializinghtml==1.1.5
390
+ SQLAlchemy==2.0.19
391
+ sqlparse==0.4.2
392
+ sse-starlette==1.8.2
393
+ starlette==0.44.0
394
+ statsmodels==0.14.1
395
+ stdlib-list==0.10.0
396
+ streamlit==1.30.0
397
+ streamlit-aggrid==0.3.4.post3
398
+ streamlit-antd-components==0.3.1
399
+ streamlit-chatbox==1.1.11
400
+ streamlit-feedback==0.1.3
401
+ streamlit-modal==0.1.0
402
+ streamlit-option-menu==0.3.12
403
+ strsimpy==0.2.1
404
+ svgwrite==1.4.3
405
+ sympy==1.13.3
406
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
407
+ tabulate==0.8.9
408
+ tenacity==8.2.3
409
+ tensorboard-plugin-wit==1.8.0
410
+ tensorboardX==2.4.1
411
+ text-unidecode==1.3
412
+ texttable==1.7.0
413
+ thefuzz==0.22.1
414
+ threadpoolctl==3.5.0
415
+ tifffile==2023.7.10
416
+ tiktoken==0.7.0
417
+ timm==0.9.16
418
+ tk==0.1.0
419
+ tokenizers==0.20.3
420
+ toml==0.10.2
421
+ tomlkit==0.12.0
422
+ toolz==0.12.1
423
+ torch==2.4.1+cpu
424
+ torch-geometric==2.6.1
425
+ torchaudio==2.1.2+cu118
426
+ torchtext==0.4.0
427
+ tornado==6.4
428
+ tqdm==4.67.1
429
+ transformer-lens==2.16.1
430
+ transformers==4.46.3
431
+ transformers-stream-generator==0.0.5
432
+ triton==3.0.0
433
+ typed-argument-parser==1.10.1
434
+ typeguard==4.4.0
435
+ typer==0.9.4
436
+ types-requests==2.31.0.20240406
437
+ typing-inspect==0.9.0
438
+ typing-utils==0.1.0
439
+ typing_extensions==4.13.2
440
+ tzdata==2024.1
441
+ tzlocal==5.2
442
+ umap-learn==0.5.7
443
+ Unidecode==1.3.2
444
+ unittest-xml-reporting==3.2.0
445
+ unstructured==0.11.0
446
+ unstructured-client==0.22.0
447
+ unstructured-inference==0.7.15
448
+ unstructured.pytesseract==0.3.12
449
+ urllib3==2.2.3
450
+ uvicorn==0.29.0
451
+ uvloop==0.21.0
452
+ validators==0.28.1
453
+ vllm==0.2.7
454
+ vtk==9.3.1
455
+ wandb==0.22.0
456
+ watchdog==3.0.0
457
+ watchfiles==0.21.0
458
+ wavedrom==2.0.3.post3
459
+ weasel==0.3.4
460
+ websocket-client==1.8.0
461
+ websockets==13.1
462
+ Werkzeug==2.0.2
463
+ word2number==1.1
464
+ xlrd==2.0.1
465
+ XlsxWriter==3.0.2
466
+ xxhash==2.0.2
467
+ Yapsy==1.12.2
468
+ yarl==1.15.2
469
+ youtube-search==2.1.2
470
+ zipp==3.20.2
471
+ zope.event==4.5.0
472
+ zstandard==0.23.0
configs/s41467_024_46879_4_test/pip-freeze.txt ADDED
@@ -0,0 +1,472 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ contourpy==1.1.1
58
+ coverage==7.6.1
59
+ cpm-kernels==1.0.11
60
+ cryptography==42.0.5
61
+ cvxopt==1.3.2
62
+ cycler==0.12.1
63
+ cymem==2.0.8
64
+ Cython==0.29.30
65
+ dataclasses==0.6
66
+ dataclasses-json==0.6.4
67
+ datasets==2.19.0
68
+ deepdiff==7.0.1
69
+ Deprecated==1.2.14
70
+ deprecation==2.1.0
71
+ dill==0.3.8
72
+ dimod==0.12.17
73
+ distro==1.9.0
74
+ dm-tree==0.1.8
75
+ dnspython==2.6.1
76
+ docstring_parser==0.17.0
77
+ docutils==0.15.2
78
+ dotenv==0.9.9
79
+ duckduckgo-search==3.9.9
80
+ dwave-neal==0.6.0
81
+ dwave-samplers==1.3.0
82
+ editdistance==0.6.0
83
+ effdet==0.4.1
84
+ einops==0.7.0
85
+ email-validator==2.3.0
86
+ emoji==2.11.1
87
+ equinox==0.10.4
88
+ et-xmlfile==1.1.0
89
+ eval_type_backport==0.2.2
90
+ exceptiongroup==1.2.1
91
+ fairseq==0.10.2
92
+ faiss-cpu==1.7.4
93
+ faiss-gpu==1.7.2
94
+ fancy-einsum==0.0.3
95
+ fastapi==0.115.14
96
+ fastapi-sso==0.16.0
97
+ fastavro==1.9.4
98
+ fastuuid==0.13.5
99
+ fbpca==1.0
100
+ feedparser==6.0.10
101
+ ffmpy==0.3.2
102
+ filelock==3.16.1
103
+ filetype==1.2.0
104
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
105
+ flaky==3.7.0
106
+ Flask-Cors==3.0.10
107
+ fonttools==4.57.0
108
+ frozenlist==1.4.1
109
+ fschat==0.2.35
110
+ fsspec==2025.3.0
111
+ ftfy==6.0.3
112
+ future==0.18.2
113
+ fuzzywuzzy==0.18.0
114
+ gdown==5.2.0
115
+ geosketch==1.3
116
+ geotorch==0.3.0
117
+ get-annotations==0.1.2
118
+ gevent==21.12.0
119
+ gitdb==4.0.11
120
+ GitPython==3.1.43
121
+ google-pasta==0.2.0
122
+ googleapis-common-protos==1.63.0
123
+ gpustat==1.1.1
124
+ gpytorch==1.10
125
+ gradio_client==0.16.0
126
+ graphlib_backport==1.1.0
127
+ greenlet==1.1.2
128
+ gunicorn==23.0.0
129
+ h11==0.14.0
130
+ h2==4.1.0
131
+ hf-xet==1.2.0
132
+ hf_transfer==0.1.9
133
+ hpack==4.0.0
134
+ httpcore==1.0.5
135
+ httptools==0.6.1
136
+ httpx==0.28.1
137
+ httpx-sse==0.4.0
138
+ huggingface_hub==0.36.1
139
+ humanfriendly==10.0
140
+ hyperframe==6.0.1
141
+ icetk==0.0.4
142
+ idna==3.11
143
+ igraph==0.11.8
144
+ imageio==2.35.1
145
+ imagesize==1.3.0
146
+ imgaug==0.4.0
147
+ importlib-metadata==7.0.0
148
+ importlib_resources==6.4.5
149
+ inequalipy==1.0.5
150
+ iniconfig==1.1.1
151
+ inquirerpy==0.3.4
152
+ iopath==0.1.10
153
+ isodate==0.7.2
154
+ itsdangerous==2.0.1
155
+ jax==0.4.13
156
+ jaxlib==0.4.13
157
+ jaxtyping==0.2.19
158
+ Jinja2==3.1.6
159
+ jiter==0.9.1
160
+ jmespath==0.10.0
161
+ joblib==1.4.2
162
+ jsonnet==0.17.0
163
+ jsonpatch==1.33
164
+ jsonpath-python==1.0.6
165
+ jsonpickle==2.0.0
166
+ jsonschema==4.23.0
167
+ jsonschema-specifications==2023.12.1
168
+ kaggle==1.7.4.5
169
+ Keras-Preprocessing==1.1.2
170
+ kiwisolver==1.4.7
171
+ kubernetes==29.0.0
172
+ langchain==0.1.16
173
+ langchain-community==0.0.34
174
+ langchain-core==0.1.46
175
+ langchain-experimental==0.0.57
176
+ langchain-text-splitters==0.0.1
177
+ langcodes==3.4.0
178
+ langdetect==1.0.9
179
+ langsmith==0.1.51
180
+ language_data==1.2.0
181
+ layoutparser==0.3.4
182
+ lazy_loader==0.4
183
+ leidenalg==0.10.2
184
+ Levenshtein==0.25.1
185
+ linear-operator==0.4.0
186
+ litellm==1.77.4
187
+ litellm-enterprise==0.1.20
188
+ litellm-proxy-extras==0.2.19
189
+ llama-index==0.9.35
190
+ llvmlite==0.41.1
191
+ lmdb==1.7.3
192
+ lxml==5.2.1
193
+ madoka==0.7.1
194
+ marisa-trie==1.1.0
195
+ Markdown==3.3.6
196
+ markdown-it-py==3.0.0
197
+ markdown2==2.4.13
198
+ markdownify==0.11.6
199
+ MarkupSafe==2.1.5
200
+ marshmallow==3.21.1
201
+ matplotlib==3.7.5
202
+ mdtex2html==1.3.0
203
+ mdurl==0.1.2
204
+ metaphor-python==0.1.23
205
+ ml-dtypes==0.2.0
206
+ monotonic==1.6
207
+ mpmath==1.3.0
208
+ mrcfile==1.5.4
209
+ msal==1.36.0
210
+ msal-extensions==1.3.0
211
+ msg-parser==1.2.0
212
+ msgpack==1.0.8
213
+ msgpack-numpy==0.4.3.2
214
+ multidict==6.0.5
215
+ multipledispatch==1.0.0
216
+ multiprocess==0.70.16
217
+ murmurhash==1.0.10
218
+ mypy-extensions==1.0.0
219
+ narwhals==1.42.1
220
+ natsort==8.4.0
221
+ nest-asyncio==1.6.0
222
+ netCDF4==1.7.2
223
+ networkx==3.1
224
+ neuroHarmonize==2.4.5
225
+ nh3==0.2.17
226
+ ninja==1.11.1.1
227
+ nltk==3.8.1
228
+ numba==0.58.1
229
+ numexpr==2.8.6
230
+ numpoly==1.0.6
231
+ numpy==1.24.4
232
+ numpydoc==1.1.0
233
+ nvidia-cublas-cu12==12.1.3.1
234
+ nvidia-cuda-cupti-cu12==12.1.105
235
+ nvidia-cuda-nvrtc-cu12==12.1.105
236
+ nvidia-cuda-runtime-cu12==12.1.105
237
+ nvidia-cudnn-cu12==9.1.0.70
238
+ nvidia-cufft-cu12==11.0.2.54
239
+ nvidia-curand-cu12==10.3.2.106
240
+ nvidia-ml-py==12.535.133
241
+ nvidia-nccl-cu12==2.20.5
242
+ nvidia-nvjitlink-cu12==12.9.86
243
+ nvidia-nvtx-cu12==12.1.105
244
+ nvitop==1.3.2
245
+ oauthlib==3.2.2
246
+ onnx==1.16.0
247
+ onnxruntime==1.15.1
248
+ openai==1.101.0
249
+ openpyxl==3.0.9
250
+ opentelemetry-api==1.24.0
251
+ opentelemetry-exporter-otlp-proto-common==1.24.0
252
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
253
+ opentelemetry-proto==1.24.0
254
+ opentelemetry-sdk==1.24.0
255
+ opentelemetry-semantic-conventions==0.45b0
256
+ opt-einsum==3.3.0
257
+ optax==0.1.5
258
+ ordered-set==4.1.0
259
+ orjson==3.10.1
260
+ overrides==7.7.0
261
+ packaging==26.2
262
+ pandas==2.0.3
263
+ pandas-stubs==1.2.0.45
264
+ parsimonious==0.8.1
265
+ pathlib==1.0.1
266
+ patsy==1.0.1
267
+ pdf2image==1.17.0
268
+ pfzy==0.3.4
269
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270
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279
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406
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424
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configs/s41467_024_47677_8_test/editable.txt ADDED
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configs/s41467_024_47677_8_test/env.yml ADDED
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1
+ name: s41467_024_47677_8_test
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42
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43
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configs/s41467_024_47677_8_test/explicit.txt ADDED
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1
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2
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3
+ # platform: linux-64
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15
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configs/s41467_024_47677_8_test/meta.json ADDED
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configs/s41467_024_47677_8_test/pip-clean.txt ADDED
@@ -0,0 +1,451 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
101
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102
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103
+ fonttools==4.57.0
104
+ frozenlist==1.4.1
105
+ fschat==0.2.35
106
+ fsspec==2025.3.0
107
+ ftfy==6.0.3
108
+ future==0.18.2
109
+ fuzzywuzzy==0.18.0
110
+ gdown==5.2.0
111
+ geosketch==1.3
112
+ geotorch==0.3.0
113
+ get-annotations==0.1.2
114
+ gevent==21.12.0
115
+ gitdb==4.0.11
116
+ GitPython==3.1.43
117
+ google-pasta==0.2.0
118
+ googleapis-common-protos==1.63.0
119
+ gpustat==1.1.1
120
+ gpytorch==1.10
121
+ gradio_client==0.16.0
122
+ graphlib_backport==1.1.0
123
+ greenlet==1.1.2
124
+ gunicorn==23.0.0
125
+ h11==0.14.0
126
+ h2==4.1.0
127
+ hf-xet==1.2.0
128
+ hf_transfer==0.1.9
129
+ hpack==4.0.0
130
+ httpcore==1.0.5
131
+ httptools==0.6.1
132
+ httpx==0.28.1
133
+ httpx-sse==0.4.0
134
+ huggingface_hub==0.36.1
135
+ humanfriendly==10.0
136
+ hyperframe==6.0.1
137
+ icetk==0.0.4
138
+ igraph==0.11.8
139
+ imageio==2.35.1
140
+ imagesize==1.3.0
141
+ imgaug==0.4.0
142
+ importlib-metadata==7.0.0
143
+ importlib_resources==6.4.5
144
+ inequalipy==1.0.5
145
+ iniconfig==1.1.1
146
+ inquirerpy==0.3.4
147
+ iopath==0.1.10
148
+ isodate==0.7.2
149
+ itsdangerous==2.0.1
150
+ jax==0.4.13
151
+ jaxlib==0.4.13
152
+ jaxtyping==0.2.19
153
+ Jinja2==3.1.6
154
+ jiter==0.9.1
155
+ jmespath==0.10.0
156
+ joblib==1.4.2
157
+ jsonnet==0.17.0
158
+ jsonpatch==1.33
159
+ jsonpath-python==1.0.6
160
+ jsonpickle==2.0.0
161
+ jsonschema==4.23.0
162
+ jsonschema-specifications==2023.12.1
163
+ kaggle==1.7.4.5
164
+ Keras-Preprocessing==1.1.2
165
+ kiwisolver==1.4.7
166
+ kubernetes==29.0.0
167
+ langchain==0.1.16
168
+ langchain-community==0.0.34
169
+ langchain-core==0.1.46
170
+ langchain-experimental==0.0.57
171
+ langchain-text-splitters==0.0.1
172
+ langcodes==3.4.0
173
+ langdetect==1.0.9
174
+ langsmith==0.1.51
175
+ language_data==1.2.0
176
+ layoutparser==0.3.4
177
+ lazy_loader==0.4
178
+ leidenalg==0.10.2
179
+ Levenshtein==0.25.1
180
+ linear-operator==0.4.0
181
+ litellm==1.77.4
182
+ litellm-enterprise==0.1.20
183
+ litellm-proxy-extras==0.2.19
184
+ llama-index==0.9.35
185
+ llvmlite==0.41.1
186
+ lmdb==1.7.3
187
+ lxml==5.2.1
188
+ madoka==0.7.1
189
+ marisa-trie==1.1.0
190
+ Markdown==3.3.6
191
+ markdown-it-py==3.0.0
192
+ markdown2==2.4.13
193
+ markdownify==0.11.6
194
+ MarkupSafe==2.1.5
195
+ marshmallow==3.21.1
196
+ matplotlib==3.7.5
197
+ mdtex2html==1.3.0
198
+ mdurl==0.1.2
199
+ metaphor-python==0.1.23
200
+ ml-dtypes==0.2.0
201
+ monotonic==1.6
202
+ mrcfile==1.5.4
203
+ msal==1.36.0
204
+ msal-extensions==1.3.0
205
+ msg-parser==1.2.0
206
+ msgpack==1.0.8
207
+ msgpack-numpy==0.4.3.2
208
+ multidict==6.0.5
209
+ multipledispatch==1.0.0
210
+ multiprocess==0.70.16
211
+ murmurhash==1.0.10
212
+ mypy-extensions==1.0.0
213
+ narwhals==1.42.1
214
+ natsort==8.4.0
215
+ nest-asyncio==1.6.0
216
+ netCDF4==1.7.2
217
+ neuroHarmonize==2.4.5
218
+ nh3==0.2.17
219
+ ninja==1.11.1.1
220
+ nltk==3.8.1
221
+ numba==0.58.1
222
+ numexpr==2.8.6
223
+ numpoly==1.0.6
224
+ numpy==1.24.4
225
+ numpydoc==1.1.0
226
+ nvidia-ml-py==12.535.133
227
+ nvitop==1.3.2
228
+ oauthlib==3.2.2
229
+ onnx==1.16.0
230
+ onnxruntime==1.15.1
231
+ openai==1.101.0
232
+ openpyxl==3.0.9
233
+ opentelemetry-api==1.24.0
234
+ opentelemetry-exporter-otlp-proto-common==1.24.0
235
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
236
+ opentelemetry-proto==1.24.0
237
+ opentelemetry-sdk==1.24.0
238
+ opentelemetry-semantic-conventions==0.45b0
239
+ opt-einsum==3.3.0
240
+ optax==0.1.5
241
+ ordered-set==4.1.0
242
+ orjson==3.10.1
243
+ overrides==7.7.0
244
+ packaging==26.2
245
+ pandas==2.0.3
246
+ pandas-stubs==1.2.0.45
247
+ parsimonious==0.8.1
248
+ pathlib==1.0.1
249
+ patsy==1.0.1
250
+ pdf2image==1.17.0
251
+ pfzy==0.3.4
252
+ PICOS==2.6.1
253
+ pikepdf==8.4.1
254
+ pillow==10.4.0
255
+ pip-search==0.0.12
256
+ pkgutil_resolve_name==1.3.10
257
+ plac==0.9.6
258
+ plotly==6.3.0
259
+ pluggy==1.5.0
260
+ ply==3.11
261
+ pondpond==1.4.1
262
+ pooch==1.8.2
263
+ portalocker==2.4.0
264
+ posthog==3.5.0
265
+ preshed==3.0.9
266
+ prettytable==3.11.0
267
+ primer3-py==2.2.0
268
+ prompt-toolkit==3.0.43
269
+ propcache==0.2.0
270
+ PuLP==3.1.1
271
+ pulsar-client==3.5.0
272
+ pyarrow==17.0.0
273
+ pyarrow-hotfix==0.6
274
+ pyclipper==1.3.0.post5
275
+ pycocotools==2.0.7
276
+ pycparser==2.21
277
+ pydantic==2.10.6
278
+ pydantic_core==2.27.2
279
+ pydeck==0.9.0b1
280
+ pyDOE2==1.3.0
281
+ pydub==0.25.1
282
+ pyfaidx==0.9.0.1
283
+ Pygments==2.19.2
284
+ PyJWT==2.8.0
285
+ pymodbus==3.6.9
286
+ PyMuPDF==1.23.16
287
+ PyMuPDFb==1.23.9
288
+ PyNaCl==1.6.2
289
+ pynndescent==0.5.13
290
+ Pyomo==6.8.2
291
+ pyOpenSSL==24.1.0
292
+ pypandoc==1.13
293
+ pyparsing==3.1.4
294
+ pypdf==4.2.0
295
+ pypdfium2==4.29.0
296
+ PyPika==0.48.9
297
+ PyQt5==5.15.7
298
+ PyQt5-Qt5==5.15.17
299
+ PyQt5_sip==12.15.0
300
+ pyro-api==0.1.2
301
+ pyro-ppl==1.9.1
302
+ pysam==0.23.3
303
+ PySocks==1.7.1
304
+ pysqlite3-binary==0.5.2.post3
305
+ pystan==2.19.1.1
306
+ pytesseract==0.3.10
307
+ pytest-cov==5.0.0
308
+ python-dateutil==2.9.0.post0
309
+ python-decouple==3.8
310
+ python-docx==1.1.0
311
+ python-dotenv==1.0.1
312
+ python-iso639==2024.4.27
313
+ python-Levenshtein==0.25.1
314
+ python-multipart==0.0.18
315
+ python-pptx==0.6.23
316
+ python-slugify==8.0.4
317
+ pytorch-pretrained-bert==0.6.2
318
+ pytz==2025.2
319
+ pyvista==0.44.2
320
+ PyWavelets==1.4.1
321
+ PyYAML==6.0.3
322
+ quantile-python==1.1
323
+ rapidfuzz==3.8.1
324
+ rapidocr-onnxruntime==1.3.8
325
+ ray==2.10.0
326
+ rdkit==2024.3.5
327
+ redis==6.1.1
328
+ referencing==0.35.1
329
+ regex==2022.4.24
330
+ requests==2.32.4
331
+ requests-oauthlib==1.3.0
332
+ responses==0.16.0
333
+ rich==13.7.1
334
+ rouge-score==0.1.2
335
+ rpds-py==0.20.1
336
+ rq==2.3.3
337
+ rsa==4.7.2
338
+ ruff==0.4.2
339
+ rustworkx==0.15.1
340
+ s3transfer==0.11.3
341
+ sacrebleu==2.1.0
342
+ sacremoses==0.0.46
343
+ safetensors==0.4.3
344
+ scipy==1.10.1
345
+ scooby==0.10.1
346
+ seaborn==0.13.2
347
+ semantic-version==2.10.0
348
+ sentence-transformers==2.2.2
349
+ sentencepiece==0.1.91
350
+ sentry-sdk==2.39.0
351
+ session_info==1.0.1
352
+ sgmllib3k==1.0.0
353
+ shapely==2.0.4
354
+ shellingham==1.5.4
355
+ shortuuid==1.0.13
356
+ six==1.17.0
357
+ smart-open==6.4.0
358
+ smmap==5.0.1
359
+ sniffio==1.3.1
360
+ snowballstemmer==2.2.0
361
+ sobol-seq==0.2.0
362
+ socksio==1.0.0
363
+ soupsieve==2.5
364
+ spacy-legacy==3.0.12
365
+ spacy-loggers==1.0.5
366
+ Sphinx==4.3.1
367
+ sphinxcontrib-applehelp==1.0.2
368
+ sphinxcontrib-devhelp==1.0.2
369
+ sphinxcontrib-htmlhelp==2.0.0
370
+ sphinxcontrib-jsmath==1.0.1
371
+ sphinxcontrib-qthelp==1.0.3
372
+ sphinxcontrib-serializinghtml==1.1.5
373
+ SQLAlchemy==2.0.19
374
+ sqlparse==0.4.2
375
+ sse-starlette==1.8.2
376
+ starlette==0.44.0
377
+ statsmodels==0.14.1
378
+ stdlib-list==0.10.0
379
+ streamlit==1.30.0
380
+ streamlit-aggrid==0.3.4.post3
381
+ streamlit-antd-components==0.3.1
382
+ streamlit-chatbox==1.1.11
383
+ streamlit-feedback==0.1.3
384
+ streamlit-modal==0.1.0
385
+ streamlit-option-menu==0.3.12
386
+ strsimpy==0.2.1
387
+ svgwrite==1.4.3
388
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
389
+ tabulate==0.8.9
390
+ tenacity==8.2.3
391
+ tensorboard-plugin-wit==1.8.0
392
+ tensorboardX==2.4.1
393
+ text-unidecode==1.3
394
+ texttable==1.7.0
395
+ thefuzz==0.22.1
396
+ threadpoolctl==3.5.0
397
+ tifffile==2023.7.10
398
+ tiktoken==0.7.0
399
+ timm==0.9.16
400
+ tk==0.1.0
401
+ tokenizers==0.20.3
402
+ toml==0.10.2
403
+ tomlkit==0.12.0
404
+ toolz==0.12.1
405
+ torch-geometric==2.6.1
406
+ torchaudio==2.1.2+cu118
407
+ torchtext==0.4.0
408
+ tornado==6.4
409
+ tqdm==4.67.1
410
+ transformer-lens==2.16.1
411
+ transformers==4.46.3
412
+ transformers-stream-generator==0.0.5
413
+ typed-argument-parser==1.10.1
414
+ typeguard==4.4.0
415
+ typer==0.9.4
416
+ types-requests==2.31.0.20240406
417
+ typing-inspect==0.9.0
418
+ typing-utils==0.1.0
419
+ typing_extensions==4.13.2
420
+ tzdata==2024.1
421
+ tzlocal==5.2
422
+ umap-learn==0.5.7
423
+ Unidecode==1.3.2
424
+ unittest-xml-reporting==3.2.0
425
+ unstructured==0.11.0
426
+ unstructured-client==0.22.0
427
+ unstructured-inference==0.7.15
428
+ unstructured.pytesseract==0.3.12
429
+ uvicorn==0.29.0
430
+ uvloop==0.21.0
431
+ validators==0.28.1
432
+ vllm==0.2.7
433
+ vtk==9.3.1
434
+ wandb==0.22.0
435
+ watchdog==3.0.0
436
+ watchfiles==0.21.0
437
+ wavedrom==2.0.3.post3
438
+ weasel==0.3.4
439
+ websocket-client==1.8.0
440
+ websockets==13.1
441
+ Werkzeug==2.0.2
442
+ word2number==1.1
443
+ xlrd==2.0.1
444
+ XlsxWriter==3.0.2
445
+ xxhash==2.0.2
446
+ Yapsy==1.12.2
447
+ yarl==1.15.2
448
+ youtube-search==2.1.2
449
+ zipp==3.20.2
450
+ zope.event==4.5.0
451
+ zstandard==0.23.0
configs/s41467_024_47677_8_test/pip-freeze.txt ADDED
@@ -0,0 +1,451 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ contourpy==1.1.1
58
+ coverage==7.6.1
59
+ cpm-kernels==1.0.11
60
+ cryptography==42.0.5
61
+ cvxopt==1.3.2
62
+ cycler==0.12.1
63
+ cymem==2.0.8
64
+ Cython==0.29.30
65
+ dataclasses==0.6
66
+ dataclasses-json==0.6.4
67
+ datasets==2.19.0
68
+ deepdiff==7.0.1
69
+ Deprecated==1.2.14
70
+ deprecation==2.1.0
71
+ dill==0.3.8
72
+ distro==1.9.0
73
+ dm-tree==0.1.8
74
+ dnspython==2.6.1
75
+ docstring_parser==0.17.0
76
+ docutils==0.15.2
77
+ dotenv==0.9.9
78
+ duckduckgo-search==3.9.9
79
+ editdistance==0.6.0
80
+ effdet==0.4.1
81
+ einops==0.7.0
82
+ email-validator==2.3.0
83
+ emoji==2.11.1
84
+ equinox==0.10.4
85
+ et-xmlfile==1.1.0
86
+ eval_type_backport==0.2.2
87
+ exceptiongroup==1.2.1
88
+ fairseq==0.10.2
89
+ faiss-cpu==1.7.4
90
+ faiss-gpu==1.7.2
91
+ fancy-einsum==0.0.3
92
+ fastapi==0.115.14
93
+ fastapi-sso==0.16.0
94
+ fastavro==1.9.4
95
+ fastuuid==0.13.5
96
+ fbpca==1.0
97
+ feedparser==6.0.10
98
+ ffmpy==0.3.2
99
+ filetype==1.2.0
100
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
101
+ flaky==3.7.0
102
+ Flask-Cors==3.0.10
103
+ fonttools==4.57.0
104
+ frozenlist==1.4.1
105
+ fschat==0.2.35
106
+ fsspec==2025.3.0
107
+ ftfy==6.0.3
108
+ future==0.18.2
109
+ fuzzywuzzy==0.18.0
110
+ gdown==5.2.0
111
+ geosketch==1.3
112
+ geotorch==0.3.0
113
+ get-annotations==0.1.2
114
+ gevent==21.12.0
115
+ gitdb==4.0.11
116
+ GitPython==3.1.43
117
+ google-pasta==0.2.0
118
+ googleapis-common-protos==1.63.0
119
+ gpustat==1.1.1
120
+ gpytorch==1.10
121
+ gradio_client==0.16.0
122
+ graphlib_backport==1.1.0
123
+ greenlet==1.1.2
124
+ gunicorn==23.0.0
125
+ h11==0.14.0
126
+ h2==4.1.0
127
+ hf-xet==1.2.0
128
+ hf_transfer==0.1.9
129
+ hpack==4.0.0
130
+ httpcore==1.0.5
131
+ httptools==0.6.1
132
+ httpx==0.28.1
133
+ httpx-sse==0.4.0
134
+ huggingface_hub==0.36.1
135
+ humanfriendly==10.0
136
+ hyperframe==6.0.1
137
+ icetk==0.0.4
138
+ igraph==0.11.8
139
+ imageio==2.35.1
140
+ imagesize==1.3.0
141
+ imgaug==0.4.0
142
+ importlib-metadata==7.0.0
143
+ importlib_resources==6.4.5
144
+ inequalipy==1.0.5
145
+ iniconfig==1.1.1
146
+ inquirerpy==0.3.4
147
+ iopath==0.1.10
148
+ isodate==0.7.2
149
+ itsdangerous==2.0.1
150
+ jax==0.4.13
151
+ jaxlib==0.4.13
152
+ jaxtyping==0.2.19
153
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154
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182
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191
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207
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217
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218
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219
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221
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223
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246
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248
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249
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255
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291
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316
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451
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configs/s41467_024_52614_w_test/env.yml ADDED
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1
+ name: s41467_024_52614_w_test
2
+ channels:
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6
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7
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34
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35
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38
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39
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configs/s41467_024_52614_w_test/explicit.txt ADDED
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1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
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configs/s41467_024_52614_w_test/pip-clean.txt ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filetype==1.2.0
98
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
99
+ flaky==3.7.0
100
+ Flask-Cors==3.0.10
101
+ frozenlist==1.4.1
102
+ fschat==0.2.35
103
+ fsspec==2025.3.0
104
+ ftfy==6.0.3
105
+ future==0.18.2
106
+ fuzzywuzzy==0.18.0
107
+ gdown==5.2.0
108
+ geosketch==1.3
109
+ geotorch==0.3.0
110
+ get-annotations==0.1.2
111
+ gevent==21.12.0
112
+ gitdb==4.0.11
113
+ GitPython==3.1.43
114
+ google-pasta==0.2.0
115
+ googleapis-common-protos==1.63.0
116
+ gpustat==1.1.1
117
+ gpytorch==1.10
118
+ gradio_client==0.16.0
119
+ graphlib_backport==1.1.0
120
+ greenlet==1.1.2
121
+ gunicorn==23.0.0
122
+ h11==0.14.0
123
+ h2==4.1.0
124
+ hf-xet==1.2.0
125
+ hf_transfer==0.1.9
126
+ hpack==4.0.0
127
+ httpcore==1.0.5
128
+ httptools==0.6.1
129
+ httpx==0.28.1
130
+ httpx-sse==0.4.0
131
+ huggingface_hub==0.36.1
132
+ humanfriendly==10.0
133
+ hyperframe==6.0.1
134
+ icetk==0.0.4
135
+ igraph==0.11.8
136
+ imageio==2.35.1
137
+ imagesize==1.3.0
138
+ imgaug==0.4.0
139
+ importlib-metadata==7.0.0
140
+ importlib_resources==6.4.5
141
+ inequalipy==1.0.5
142
+ iniconfig==1.1.1
143
+ inquirerpy==0.3.4
144
+ iopath==0.1.10
145
+ isodate==0.7.2
146
+ itsdangerous==2.0.1
147
+ jax==0.4.13
148
+ jaxlib==0.4.13
149
+ jaxtyping==0.2.19
150
+ Jinja2==3.1.6
151
+ jiter==0.9.1
152
+ jmespath==0.10.0
153
+ joblib==1.4.2
154
+ jsonnet==0.17.0
155
+ jsonpatch==1.33
156
+ jsonpath-python==1.0.6
157
+ jsonpickle==2.0.0
158
+ jsonschema==4.23.0
159
+ jsonschema-specifications==2023.12.1
160
+ kaggle==1.7.4.5
161
+ Keras-Preprocessing==1.1.2
162
+ kubernetes==29.0.0
163
+ langchain==0.1.16
164
+ langchain-community==0.0.34
165
+ langchain-core==0.1.46
166
+ langchain-experimental==0.0.57
167
+ langchain-text-splitters==0.0.1
168
+ langcodes==3.4.0
169
+ langdetect==1.0.9
170
+ langsmith==0.1.51
171
+ language_data==1.2.0
172
+ layoutparser==0.3.4
173
+ lazy_loader==0.4
174
+ leidenalg==0.10.2
175
+ Levenshtein==0.25.1
176
+ linear-operator==0.4.0
177
+ litellm==1.77.4
178
+ litellm-enterprise==0.1.20
179
+ litellm-proxy-extras==0.2.19
180
+ llama-index==0.9.35
181
+ llvmlite==0.41.1
182
+ lmdb==1.7.3
183
+ lxml==5.2.1
184
+ madoka==0.7.1
185
+ marisa-trie==1.1.0
186
+ Markdown==3.3.6
187
+ markdown-it-py==3.0.0
188
+ markdown2==2.4.13
189
+ markdownify==0.11.6
190
+ MarkupSafe==2.1.5
191
+ marshmallow==3.21.1
192
+ mdtex2html==1.3.0
193
+ mdurl==0.1.2
194
+ metaphor-python==0.1.23
195
+ ml-dtypes==0.2.0
196
+ monotonic==1.6
197
+ mrcfile==1.5.4
198
+ msal==1.36.0
199
+ msal-extensions==1.3.0
200
+ msg-parser==1.2.0
201
+ msgpack==1.0.8
202
+ msgpack-numpy==0.4.3.2
203
+ multidict==6.0.5
204
+ multipledispatch==1.0.0
205
+ multiprocess==0.70.16
206
+ murmurhash==1.0.10
207
+ mypy-extensions==1.0.0
208
+ narwhals==1.42.1
209
+ natsort==8.4.0
210
+ nest-asyncio==1.6.0
211
+ netCDF4==1.7.2
212
+ networkx==3.1
213
+ neuroHarmonize==2.4.5
214
+ nh3==0.2.17
215
+ ninja==1.11.1.1
216
+ nltk==3.8.1
217
+ numba==0.58.1
218
+ numexpr==2.8.6
219
+ numpoly==1.0.6
220
+ numpy==1.24.4
221
+ numpydoc==1.1.0
222
+ nvidia-ml-py==12.535.133
223
+ nvitop==1.3.2
224
+ oauthlib==3.2.2
225
+ onnx==1.16.0
226
+ onnxruntime==1.15.1
227
+ openai==1.101.0
228
+ openpyxl==3.0.9
229
+ opentelemetry-api==1.24.0
230
+ opentelemetry-exporter-otlp-proto-common==1.24.0
231
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
232
+ opentelemetry-proto==1.24.0
233
+ opentelemetry-sdk==1.24.0
234
+ opentelemetry-semantic-conventions==0.45b0
235
+ opt-einsum==3.3.0
236
+ optax==0.1.5
237
+ ordered-set==4.1.0
238
+ orjson==3.10.1
239
+ overrides==7.7.0
240
+ packaging==26.2
241
+ pandas==2.0.3
242
+ pandas-stubs==1.2.0.45
243
+ parsimonious==0.8.1
244
+ pathlib==1.0.1
245
+ patsy==1.0.1
246
+ pdf2image==1.17.0
247
+ pfzy==0.3.4
248
+ PICOS==2.6.1
249
+ pikepdf==8.4.1
250
+ pip-search==0.0.12
251
+ pkgutil_resolve_name==1.3.10
252
+ plac==0.9.6
253
+ plotly==6.3.0
254
+ pluggy==1.5.0
255
+ ply==3.11
256
+ pondpond==1.4.1
257
+ pooch==1.8.2
258
+ portalocker==2.4.0
259
+ posthog==3.5.0
260
+ preshed==3.0.9
261
+ prettytable==3.11.0
262
+ primer3-py==2.2.0
263
+ prompt-toolkit==3.0.43
264
+ propcache==0.2.0
265
+ PuLP==3.1.1
266
+ pulsar-client==3.5.0
267
+ pyarrow==17.0.0
268
+ pyarrow-hotfix==0.6
269
+ pyclipper==1.3.0.post5
270
+ pycocotools==2.0.7
271
+ pycparser==2.21
272
+ pydantic==2.10.6
273
+ pydantic_core==2.27.2
274
+ pydeck==0.9.0b1
275
+ pyDOE2==1.3.0
276
+ pydub==0.25.1
277
+ pyfaidx==0.9.0.1
278
+ Pygments==2.19.2
279
+ PyJWT==2.8.0
280
+ pymodbus==3.6.9
281
+ PyMuPDF==1.23.16
282
+ PyMuPDFb==1.23.9
283
+ PyNaCl==1.6.2
284
+ pynndescent==0.5.13
285
+ Pyomo==6.8.2
286
+ pyOpenSSL==24.1.0
287
+ pypandoc==1.13
288
+ pypdf==4.2.0
289
+ pypdfium2==4.29.0
290
+ PyPika==0.48.9
291
+ PyQt5==5.15.7
292
+ PyQt5-Qt5==5.15.17
293
+ PyQt5_sip==12.15.0
294
+ pyro-api==0.1.2
295
+ pyro-ppl==1.9.1
296
+ pysam==0.23.3
297
+ PySocks==1.7.1
298
+ pysqlite3-binary==0.5.2.post3
299
+ pystan==2.19.1.1
300
+ pytesseract==0.3.10
301
+ pytest-cov==5.0.0
302
+ python-dateutil==2.9.0.post0
303
+ python-decouple==3.8
304
+ python-docx==1.1.0
305
+ python-dotenv==1.0.1
306
+ python-iso639==2024.4.27
307
+ python-Levenshtein==0.25.1
308
+ python-multipart==0.0.18
309
+ python-pptx==0.6.23
310
+ python-slugify==8.0.4
311
+ pytorch-pretrained-bert==0.6.2
312
+ pytz==2025.2
313
+ pyvista==0.44.2
314
+ PyWavelets==1.4.1
315
+ PyYAML==6.0.3
316
+ quantile-python==1.1
317
+ rapidfuzz==3.8.1
318
+ rapidocr-onnxruntime==1.3.8
319
+ ray==2.10.0
320
+ rdkit==2024.3.5
321
+ redis==6.1.1
322
+ referencing==0.35.1
323
+ regex==2022.4.24
324
+ requests==2.32.4
325
+ requests-oauthlib==1.3.0
326
+ responses==0.16.0
327
+ rich==13.7.1
328
+ rouge-score==0.1.2
329
+ rpds-py==0.20.1
330
+ rq==2.3.3
331
+ rsa==4.7.2
332
+ ruff==0.4.2
333
+ rustworkx==0.15.1
334
+ s3transfer==0.11.3
335
+ sacrebleu==2.1.0
336
+ sacremoses==0.0.46
337
+ safetensors==0.4.3
338
+ scooby==0.10.1
339
+ seaborn==0.13.2
340
+ semantic-version==2.10.0
341
+ sentence-transformers==2.2.2
342
+ sentencepiece==0.1.91
343
+ sentry-sdk==2.39.0
344
+ session_info==1.0.1
345
+ sgmllib3k==1.0.0
346
+ shapely==2.0.4
347
+ shellingham==1.5.4
348
+ shortuuid==1.0.13
349
+ six==1.17.0
350
+ smart-open==6.4.0
351
+ smmap==5.0.1
352
+ sniffio==1.3.1
353
+ snowballstemmer==2.2.0
354
+ sobol-seq==0.2.0
355
+ socksio==1.0.0
356
+ soupsieve==2.5
357
+ spacy-legacy==3.0.12
358
+ spacy-loggers==1.0.5
359
+ Sphinx==4.3.1
360
+ sphinxcontrib-applehelp==1.0.2
361
+ sphinxcontrib-devhelp==1.0.2
362
+ sphinxcontrib-htmlhelp==2.0.0
363
+ sphinxcontrib-jsmath==1.0.1
364
+ sphinxcontrib-qthelp==1.0.3
365
+ sphinxcontrib-serializinghtml==1.1.5
366
+ SQLAlchemy==2.0.19
367
+ sqlparse==0.4.2
368
+ sse-starlette==1.8.2
369
+ starlette==0.44.0
370
+ statsmodels==0.14.1
371
+ stdlib-list==0.10.0
372
+ streamlit==1.30.0
373
+ streamlit-aggrid==0.3.4.post3
374
+ streamlit-antd-components==0.3.1
375
+ streamlit-chatbox==1.1.11
376
+ streamlit-feedback==0.1.3
377
+ streamlit-modal==0.1.0
378
+ streamlit-option-menu==0.3.12
379
+ strsimpy==0.2.1
380
+ svgwrite==1.4.3
381
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
382
+ tabulate==0.8.9
383
+ tenacity==8.2.3
384
+ tensorboard-plugin-wit==1.8.0
385
+ tensorboardX==2.4.1
386
+ text-unidecode==1.3
387
+ texttable==1.7.0
388
+ thefuzz==0.22.1
389
+ threadpoolctl==3.5.0
390
+ tifffile==2023.7.10
391
+ tiktoken==0.7.0
392
+ timm==0.9.16
393
+ tk==0.1.0
394
+ tokenizers==0.20.3
395
+ toml==0.10.2
396
+ tomlkit==0.12.0
397
+ toolz==0.12.1
398
+ torch-geometric==2.6.1
399
+ torchaudio==2.1.2+cu118
400
+ torchtext==0.4.0
401
+ tornado==6.4
402
+ tqdm==4.67.1
403
+ transformer-lens==2.16.1
404
+ transformers==4.46.3
405
+ transformers-stream-generator==0.0.5
406
+ typed-argument-parser==1.10.1
407
+ typeguard==4.4.0
408
+ typer==0.9.4
409
+ types-requests==2.31.0.20240406
410
+ typing-inspect==0.9.0
411
+ typing-utils==0.1.0
412
+ typing_extensions==4.13.2
413
+ tzdata==2024.1
414
+ tzlocal==5.2
415
+ umap-learn==0.5.7
416
+ Unidecode==1.3.2
417
+ unittest-xml-reporting==3.2.0
418
+ unstructured==0.11.0
419
+ unstructured-client==0.22.0
420
+ unstructured-inference==0.7.15
421
+ unstructured.pytesseract==0.3.12
422
+ uvicorn==0.29.0
423
+ uvloop==0.21.0
424
+ validators==0.28.1
425
+ vllm==0.2.7
426
+ vtk==9.3.1
427
+ wandb==0.22.0
428
+ watchdog==3.0.0
429
+ watchfiles==0.21.0
430
+ wavedrom==2.0.3.post3
431
+ weasel==0.3.4
432
+ websocket-client==1.8.0
433
+ websockets==13.1
434
+ Werkzeug==2.0.2
435
+ word2number==1.1
436
+ xlrd==2.0.1
437
+ XlsxWriter==3.0.2
438
+ xxhash==2.0.2
439
+ Yapsy==1.12.2
440
+ yarl==1.15.2
441
+ youtube-search==2.1.2
442
+ zipp==3.20.2
443
+ zope.event==4.5.0
444
+ zstandard==0.23.0
configs/s41467_024_52614_w_test/pip-freeze.txt ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
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76
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77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filetype==1.2.0
98
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
99
+ flaky==3.7.0
100
+ Flask-Cors==3.0.10
101
+ frozenlist==1.4.1
102
+ fschat==0.2.35
103
+ fsspec==2025.3.0
104
+ ftfy==6.0.3
105
+ future==0.18.2
106
+ fuzzywuzzy==0.18.0
107
+ gdown==5.2.0
108
+ geosketch==1.3
109
+ geotorch==0.3.0
110
+ get-annotations==0.1.2
111
+ gevent==21.12.0
112
+ gitdb==4.0.11
113
+ GitPython==3.1.43
114
+ google-pasta==0.2.0
115
+ googleapis-common-protos==1.63.0
116
+ gpustat==1.1.1
117
+ gpytorch==1.10
118
+ gradio_client==0.16.0
119
+ graphlib_backport==1.1.0
120
+ greenlet==1.1.2
121
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122
+ h11==0.14.0
123
+ h2==4.1.0
124
+ hf-xet==1.2.0
125
+ hf_transfer==0.1.9
126
+ hpack==4.0.0
127
+ httpcore==1.0.5
128
+ httptools==0.6.1
129
+ httpx==0.28.1
130
+ httpx-sse==0.4.0
131
+ huggingface_hub==0.36.1
132
+ humanfriendly==10.0
133
+ hyperframe==6.0.1
134
+ icetk==0.0.4
135
+ igraph==0.11.8
136
+ imageio==2.35.1
137
+ imagesize==1.3.0
138
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139
+ importlib-metadata==7.0.0
140
+ importlib_resources==6.4.5
141
+ inequalipy==1.0.5
142
+ iniconfig==1.1.1
143
+ inquirerpy==0.3.4
144
+ iopath==0.1.10
145
+ isodate==0.7.2
146
+ itsdangerous==2.0.1
147
+ jax==0.4.13
148
+ jaxlib==0.4.13
149
+ jaxtyping==0.2.19
150
+ Jinja2==3.1.6
151
+ jiter==0.9.1
152
+ jmespath==0.10.0
153
+ joblib==1.4.2
154
+ jsonnet==0.17.0
155
+ jsonpatch==1.33
156
+ jsonpath-python==1.0.6
157
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158
+ jsonschema==4.23.0
159
+ jsonschema-specifications==2023.12.1
160
+ kaggle==1.7.4.5
161
+ Keras-Preprocessing==1.1.2
162
+ kubernetes==29.0.0
163
+ langchain==0.1.16
164
+ langchain-community==0.0.34
165
+ langchain-core==0.1.46
166
+ langchain-experimental==0.0.57
167
+ langchain-text-splitters==0.0.1
168
+ langcodes==3.4.0
169
+ langdetect==1.0.9
170
+ langsmith==0.1.51
171
+ language_data==1.2.0
172
+ layoutparser==0.3.4
173
+ lazy_loader==0.4
174
+ leidenalg==0.10.2
175
+ Levenshtein==0.25.1
176
+ linear-operator==0.4.0
177
+ litellm==1.77.4
178
+ litellm-enterprise==0.1.20
179
+ litellm-proxy-extras==0.2.19
180
+ llama-index==0.9.35
181
+ llvmlite==0.41.1
182
+ lmdb==1.7.3
183
+ lxml==5.2.1
184
+ madoka==0.7.1
185
+ marisa-trie==1.1.0
186
+ Markdown==3.3.6
187
+ markdown-it-py==3.0.0
188
+ markdown2==2.4.13
189
+ markdownify==0.11.6
190
+ MarkupSafe==2.1.5
191
+ marshmallow==3.21.1
192
+ mdtex2html==1.3.0
193
+ mdurl==0.1.2
194
+ metaphor-python==0.1.23
195
+ ml-dtypes==0.2.0
196
+ monotonic==1.6
197
+ mrcfile==1.5.4
198
+ msal==1.36.0
199
+ msal-extensions==1.3.0
200
+ msg-parser==1.2.0
201
+ msgpack==1.0.8
202
+ msgpack-numpy==0.4.3.2
203
+ multidict==6.0.5
204
+ multipledispatch==1.0.0
205
+ multiprocess==0.70.16
206
+ murmurhash==1.0.10
207
+ mypy-extensions==1.0.0
208
+ narwhals==1.42.1
209
+ natsort==8.4.0
210
+ nest-asyncio==1.6.0
211
+ netCDF4==1.7.2
212
+ networkx==3.1
213
+ neuroHarmonize==2.4.5
214
+ nh3==0.2.17
215
+ ninja==1.11.1.1
216
+ nltk==3.8.1
217
+ numba==0.58.1
218
+ numexpr==2.8.6
219
+ numpoly==1.0.6
220
+ numpy==1.24.4
221
+ numpydoc==1.1.0
222
+ nvidia-ml-py==12.535.133
223
+ nvitop==1.3.2
224
+ oauthlib==3.2.2
225
+ onnx==1.16.0
226
+ onnxruntime==1.15.1
227
+ openai==1.101.0
228
+ openpyxl==3.0.9
229
+ opentelemetry-api==1.24.0
230
+ opentelemetry-exporter-otlp-proto-common==1.24.0
231
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
232
+ opentelemetry-proto==1.24.0
233
+ opentelemetry-sdk==1.24.0
234
+ opentelemetry-semantic-conventions==0.45b0
235
+ opt-einsum==3.3.0
236
+ optax==0.1.5
237
+ ordered-set==4.1.0
238
+ orjson==3.10.1
239
+ overrides==7.7.0
240
+ packaging==26.2
241
+ pandas==2.0.3
242
+ pandas-stubs==1.2.0.45
243
+ parsimonious==0.8.1
244
+ pathlib==1.0.1
245
+ patsy==1.0.1
246
+ pdf2image==1.17.0
247
+ pfzy==0.3.4
248
+ PICOS==2.6.1
249
+ pikepdf==8.4.1
250
+ pip-search==0.0.12
251
+ pkgutil_resolve_name==1.3.10
252
+ plac==0.9.6
253
+ plotly==6.3.0
254
+ pluggy==1.5.0
255
+ ply==3.11
256
+ pondpond==1.4.1
257
+ pooch==1.8.2
258
+ portalocker==2.4.0
259
+ posthog==3.5.0
260
+ preshed==3.0.9
261
+ prettytable==3.11.0
262
+ primer3-py==2.2.0
263
+ prompt-toolkit==3.0.43
264
+ propcache==0.2.0
265
+ PuLP==3.1.1
266
+ pulsar-client==3.5.0
267
+ pyarrow==17.0.0
268
+ pyarrow-hotfix==0.6
269
+ pyclipper==1.3.0.post5
270
+ pycocotools==2.0.7
271
+ pycparser==2.21
272
+ pydantic==2.10.6
273
+ pydantic_core==2.27.2
274
+ pydeck==0.9.0b1
275
+ pyDOE2==1.3.0
276
+ pydub==0.25.1
277
+ pyfaidx==0.9.0.1
278
+ Pygments==2.19.2
279
+ PyJWT==2.8.0
280
+ pymodbus==3.6.9
281
+ PyMuPDF==1.23.16
282
+ PyMuPDFb==1.23.9
283
+ PyNaCl==1.6.2
284
+ pynndescent==0.5.13
285
+ Pyomo==6.8.2
286
+ pyOpenSSL==24.1.0
287
+ pypandoc==1.13
288
+ pypdf==4.2.0
289
+ pypdfium2==4.29.0
290
+ PyPika==0.48.9
291
+ PyQt5==5.15.7
292
+ PyQt5-Qt5==5.15.17
293
+ PyQt5_sip==12.15.0
294
+ pyro-api==0.1.2
295
+ pyro-ppl==1.9.1
296
+ pysam==0.23.3
297
+ PySocks==1.7.1
298
+ pysqlite3-binary==0.5.2.post3
299
+ pystan==2.19.1.1
300
+ pytesseract==0.3.10
301
+ pytest-cov==5.0.0
302
+ python-dateutil==2.9.0.post0
303
+ python-decouple==3.8
304
+ python-docx==1.1.0
305
+ python-dotenv==1.0.1
306
+ python-iso639==2024.4.27
307
+ python-Levenshtein==0.25.1
308
+ python-multipart==0.0.18
309
+ python-pptx==0.6.23
310
+ python-slugify==8.0.4
311
+ pytorch-pretrained-bert==0.6.2
312
+ pytz==2025.2
313
+ pyvista==0.44.2
314
+ PyWavelets==1.4.1
315
+ PyYAML==6.0.3
316
+ quantile-python==1.1
317
+ rapidfuzz==3.8.1
318
+ rapidocr-onnxruntime==1.3.8
319
+ ray==2.10.0
320
+ rdkit==2024.3.5
321
+ redis==6.1.1
322
+ referencing==0.35.1
323
+ regex==2022.4.24
324
+ requests==2.32.4
325
+ requests-oauthlib==1.3.0
326
+ responses==0.16.0
327
+ rich==13.7.1
328
+ rouge-score==0.1.2
329
+ rpds-py==0.20.1
330
+ rq==2.3.3
331
+ rsa==4.7.2
332
+ ruff==0.4.2
333
+ rustworkx==0.15.1
334
+ s3transfer==0.11.3
335
+ sacrebleu==2.1.0
336
+ sacremoses==0.0.46
337
+ safetensors==0.4.3
338
+ scooby==0.10.1
339
+ seaborn==0.13.2
340
+ semantic-version==2.10.0
341
+ sentence-transformers==2.2.2
342
+ sentencepiece==0.1.91
343
+ sentry-sdk==2.39.0
344
+ session_info==1.0.1
345
+ sgmllib3k==1.0.0
346
+ shapely==2.0.4
347
+ shellingham==1.5.4
348
+ shortuuid==1.0.13
349
+ six==1.17.0
350
+ smart-open==6.4.0
351
+ smmap==5.0.1
352
+ sniffio==1.3.1
353
+ snowballstemmer==2.2.0
354
+ sobol-seq==0.2.0
355
+ socksio==1.0.0
356
+ soupsieve==2.5
357
+ spacy-legacy==3.0.12
358
+ spacy-loggers==1.0.5
359
+ Sphinx==4.3.1
360
+ sphinxcontrib-applehelp==1.0.2
361
+ sphinxcontrib-devhelp==1.0.2
362
+ sphinxcontrib-htmlhelp==2.0.0
363
+ sphinxcontrib-jsmath==1.0.1
364
+ sphinxcontrib-qthelp==1.0.3
365
+ sphinxcontrib-serializinghtml==1.1.5
366
+ SQLAlchemy==2.0.19
367
+ sqlparse==0.4.2
368
+ sse-starlette==1.8.2
369
+ starlette==0.44.0
370
+ statsmodels==0.14.1
371
+ stdlib-list==0.10.0
372
+ streamlit==1.30.0
373
+ streamlit-aggrid==0.3.4.post3
374
+ streamlit-antd-components==0.3.1
375
+ streamlit-chatbox==1.1.11
376
+ streamlit-feedback==0.1.3
377
+ streamlit-modal==0.1.0
378
+ streamlit-option-menu==0.3.12
379
+ strsimpy==0.2.1
380
+ svgwrite==1.4.3
381
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
382
+ tabulate==0.8.9
383
+ tenacity==8.2.3
384
+ tensorboard-plugin-wit==1.8.0
385
+ tensorboardX==2.4.1
386
+ text-unidecode==1.3
387
+ texttable==1.7.0
388
+ thefuzz==0.22.1
389
+ threadpoolctl==3.5.0
390
+ tifffile==2023.7.10
391
+ tiktoken==0.7.0
392
+ timm==0.9.16
393
+ tk==0.1.0
394
+ tokenizers==0.20.3
395
+ toml==0.10.2
396
+ tomlkit==0.12.0
397
+ toolz==0.12.1
398
+ torch-geometric==2.6.1
399
+ torchaudio==2.1.2+cu118
400
+ torchtext==0.4.0
401
+ tornado==6.4
402
+ tqdm==4.67.1
403
+ transformer-lens==2.16.1
404
+ transformers==4.46.3
405
+ transformers-stream-generator==0.0.5
406
+ typed-argument-parser==1.10.1
407
+ typeguard==4.4.0
408
+ typer==0.9.4
409
+ types-requests==2.31.0.20240406
410
+ typing-inspect==0.9.0
411
+ typing-utils==0.1.0
412
+ typing_extensions==4.13.2
413
+ tzdata==2024.1
414
+ tzlocal==5.2
415
+ umap-learn==0.5.7
416
+ Unidecode==1.3.2
417
+ unittest-xml-reporting==3.2.0
418
+ unstructured==0.11.0
419
+ unstructured-client==0.22.0
420
+ unstructured-inference==0.7.15
421
+ unstructured.pytesseract==0.3.12
422
+ uvicorn==0.29.0
423
+ uvloop==0.21.0
424
+ validators==0.28.1
425
+ vllm==0.2.7
426
+ vtk==9.3.1
427
+ wandb==0.22.0
428
+ watchdog==3.0.0
429
+ watchfiles==0.21.0
430
+ wavedrom==2.0.3.post3
431
+ weasel==0.3.4
432
+ websocket-client==1.8.0
433
+ websockets==13.1
434
+ Werkzeug==2.0.2
435
+ word2number==1.1
436
+ xlrd==2.0.1
437
+ XlsxWriter==3.0.2
438
+ xxhash==2.0.2
439
+ Yapsy==1.12.2
440
+ yarl==1.15.2
441
+ youtube-search==2.1.2
442
+ zipp==3.20.2
443
+ zope.event==4.5.0
444
+ zstandard==0.23.0
configs/s41467_024_53672_w_test/editable.txt ADDED
File without changes
configs/s41467_024_53672_w_test/env.yml ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: s41467_024_53672_w_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
+ - bzip2=1.0.8
9
+ - ca-certificates=2025.8.3
10
+ - ld_impl_linux-64=2.44
11
+ - libffi=3.4.6
12
+ - libgcc=15.1.0
13
+ - libgcc-ng=15.1.0
14
+ - libgomp=15.1.0
15
+ - liblzma=5.8.1
16
+ - liblzma-devel=5.8.1
17
+ - libnsl=2.0.1
18
+ - libsqlite=3.50.4
19
+ - libuuid=2.38.1
20
+ - libxcrypt=4.4.36
21
+ - libzlib=1.3.1
22
+ - ncurses=6.5
23
+ - openssl=3.5.2
24
+ - pip=22.1.2
25
+ - python=3.8.20
26
+ - readline=8.2
27
+ - setuptools=70.3.0
28
+ - tk=8.6.13
29
+ - wheel=0.45.1
30
+ - xz=5.8.1
31
+ - xz-gpl-tools=5.8.1
32
+ - xz-tools=5.8.1
33
+ - pip:
34
+ - numpy==1.24.4
35
+ - packaging==25.0
36
+ - six==1.17.0
37
+ - tqdm==4.67.1
38
+ prefix: /home/lily/yz979/anaconda3/envs/s41467_024_53672_w_test
configs/s41467_024_53672_w_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
+ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
9
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
10
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
11
+ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
12
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
13
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
14
+ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
15
+ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
16
+ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
17
+ https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
18
+ https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
19
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
20
+ https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
21
+ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
22
+ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
23
+ https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
24
+ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
25
+ https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
26
+ https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
27
+ https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
28
+ https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
29
+ https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
30
+ https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
31
+ https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
configs/s41467_024_53672_w_test/meta.json ADDED
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1
+ {
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+ "exported_at": "2026-05-17T04:05:53Z"
8
+ }
configs/s41467_024_53672_w_test/pip-clean.txt ADDED
@@ -0,0 +1,443 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
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6
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7
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8
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9
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10
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11
+ annotated-types==0.6.0
12
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13
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14
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15
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16
+ async-timeout==4.0.3
17
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18
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19
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21
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23
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24
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25
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26
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27
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31
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32
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33
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34
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35
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36
+ botocore==1.36.26
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38
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39
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40
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41
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42
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43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
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56
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57
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58
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59
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60
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61
+ cymem==2.0.8
62
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63
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64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
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67
+ Deprecated==1.2.14
68
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69
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70
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71
+ dm-tree==0.1.8
72
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73
+ docstring_parser==0.17.0
74
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75
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76
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77
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78
+ effdet==0.4.1
79
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80
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81
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82
+ equinox==0.10.4
83
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84
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85
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86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
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89
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90
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91
+ fastapi-sso==0.16.0
92
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93
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94
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95
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96
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97
+ filetype==1.2.0
98
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
99
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100
+ Flask-Cors==3.0.10
101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
+ gevent==21.12.0
112
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113
+ GitPython==3.1.43
114
+ google-pasta==0.2.0
115
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116
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117
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118
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119
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120
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121
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122
+ h11==0.14.0
123
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124
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125
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126
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127
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128
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129
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130
+ httpx-sse==0.4.0
131
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132
+ humanfriendly==10.0
133
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134
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135
+ igraph==0.11.8
136
+ imageio==2.35.1
137
+ imagesize==1.3.0
138
+ imgaug==0.4.0
139
+ importlib-metadata==7.0.0
140
+ importlib_resources==6.4.5
141
+ inequalipy==1.0.5
142
+ iniconfig==1.1.1
143
+ inquirerpy==0.3.4
144
+ iopath==0.1.10
145
+ isodate==0.7.2
146
+ itsdangerous==2.0.1
147
+ jax==0.4.13
148
+ jaxlib==0.4.13
149
+ jaxtyping==0.2.19
150
+ Jinja2==3.1.6
151
+ jiter==0.9.1
152
+ jmespath==0.10.0
153
+ joblib==1.4.2
154
+ jsonnet==0.17.0
155
+ jsonpatch==1.33
156
+ jsonpath-python==1.0.6
157
+ jsonpickle==2.0.0
158
+ jsonschema==4.23.0
159
+ jsonschema-specifications==2023.12.1
160
+ kaggle==1.7.4.5
161
+ Keras-Preprocessing==1.1.2
162
+ kubernetes==29.0.0
163
+ langchain==0.1.16
164
+ langchain-community==0.0.34
165
+ langchain-core==0.1.46
166
+ langchain-experimental==0.0.57
167
+ langchain-text-splitters==0.0.1
168
+ langcodes==3.4.0
169
+ langdetect==1.0.9
170
+ langsmith==0.1.51
171
+ language_data==1.2.0
172
+ layoutparser==0.3.4
173
+ lazy_loader==0.4
174
+ leidenalg==0.10.2
175
+ Levenshtein==0.25.1
176
+ linear-operator==0.4.0
177
+ litellm==1.77.4
178
+ litellm-enterprise==0.1.20
179
+ litellm-proxy-extras==0.2.19
180
+ llama-index==0.9.35
181
+ llvmlite==0.41.1
182
+ lmdb==1.7.3
183
+ lxml==5.2.1
184
+ madoka==0.7.1
185
+ marisa-trie==1.1.0
186
+ Markdown==3.3.6
187
+ markdown-it-py==3.0.0
188
+ markdown2==2.4.13
189
+ markdownify==0.11.6
190
+ MarkupSafe==2.1.5
191
+ marshmallow==3.21.1
192
+ mdtex2html==1.3.0
193
+ mdurl==0.1.2
194
+ metaphor-python==0.1.23
195
+ ml-dtypes==0.2.0
196
+ monotonic==1.6
197
+ mrcfile==1.5.4
198
+ msal==1.36.0
199
+ msal-extensions==1.3.0
200
+ msg-parser==1.2.0
201
+ msgpack==1.0.8
202
+ msgpack-numpy==0.4.3.2
203
+ multidict==6.0.5
204
+ multipledispatch==1.0.0
205
+ multiprocess==0.70.16
206
+ murmurhash==1.0.10
207
+ mypy-extensions==1.0.0
208
+ narwhals==1.42.1
209
+ natsort==8.4.0
210
+ nest-asyncio==1.6.0
211
+ netCDF4==1.7.2
212
+ neuroHarmonize==2.4.5
213
+ nh3==0.2.17
214
+ ninja==1.11.1.1
215
+ nltk==3.8.1
216
+ numba==0.58.1
217
+ numexpr==2.8.6
218
+ numpoly==1.0.6
219
+ numpy==1.24.4
220
+ numpydoc==1.1.0
221
+ nvidia-ml-py==12.535.133
222
+ nvitop==1.3.2
223
+ oauthlib==3.2.2
224
+ onnx==1.16.0
225
+ onnxruntime==1.15.1
226
+ openai==1.101.0
227
+ openpyxl==3.0.9
228
+ opentelemetry-api==1.24.0
229
+ opentelemetry-exporter-otlp-proto-common==1.24.0
230
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
231
+ opentelemetry-proto==1.24.0
232
+ opentelemetry-sdk==1.24.0
233
+ opentelemetry-semantic-conventions==0.45b0
234
+ opt-einsum==3.3.0
235
+ optax==0.1.5
236
+ ordered-set==4.1.0
237
+ orjson==3.10.1
238
+ overrides==7.7.0
239
+ packaging==26.2
240
+ pandas==2.0.3
241
+ pandas-stubs==1.2.0.45
242
+ parsimonious==0.8.1
243
+ pathlib==1.0.1
244
+ patsy==1.0.1
245
+ pdf2image==1.17.0
246
+ pfzy==0.3.4
247
+ PICOS==2.6.1
248
+ pikepdf==8.4.1
249
+ pip-search==0.0.12
250
+ pkgutil_resolve_name==1.3.10
251
+ plac==0.9.6
252
+ plotly==6.3.0
253
+ pluggy==1.5.0
254
+ ply==3.11
255
+ pondpond==1.4.1
256
+ pooch==1.8.2
257
+ portalocker==2.4.0
258
+ posthog==3.5.0
259
+ preshed==3.0.9
260
+ prettytable==3.11.0
261
+ primer3-py==2.2.0
262
+ prompt-toolkit==3.0.43
263
+ propcache==0.2.0
264
+ PuLP==3.1.1
265
+ pulsar-client==3.5.0
266
+ pyarrow==17.0.0
267
+ pyarrow-hotfix==0.6
268
+ pyclipper==1.3.0.post5
269
+ pycocotools==2.0.7
270
+ pycparser==2.21
271
+ pydantic==2.10.6
272
+ pydantic_core==2.27.2
273
+ pydeck==0.9.0b1
274
+ pyDOE2==1.3.0
275
+ pydub==0.25.1
276
+ pyfaidx==0.9.0.1
277
+ Pygments==2.19.2
278
+ PyJWT==2.8.0
279
+ pymodbus==3.6.9
280
+ PyMuPDF==1.23.16
281
+ PyMuPDFb==1.23.9
282
+ PyNaCl==1.6.2
283
+ pynndescent==0.5.13
284
+ Pyomo==6.8.2
285
+ pyOpenSSL==24.1.0
286
+ pypandoc==1.13
287
+ pypdf==4.2.0
288
+ pypdfium2==4.29.0
289
+ PyPika==0.48.9
290
+ PyQt5==5.15.7
291
+ PyQt5-Qt5==5.15.17
292
+ PyQt5_sip==12.15.0
293
+ pyro-api==0.1.2
294
+ pyro-ppl==1.9.1
295
+ pysam==0.23.3
296
+ PySocks==1.7.1
297
+ pysqlite3-binary==0.5.2.post3
298
+ pystan==2.19.1.1
299
+ pytesseract==0.3.10
300
+ pytest-cov==5.0.0
301
+ python-dateutil==2.9.0.post0
302
+ python-decouple==3.8
303
+ python-docx==1.1.0
304
+ python-dotenv==1.0.1
305
+ python-iso639==2024.4.27
306
+ python-Levenshtein==0.25.1
307
+ python-multipart==0.0.18
308
+ python-pptx==0.6.23
309
+ python-slugify==8.0.4
310
+ pytorch-pretrained-bert==0.6.2
311
+ pytz==2025.2
312
+ pyvista==0.44.2
313
+ PyWavelets==1.4.1
314
+ PyYAML==6.0.3
315
+ quantile-python==1.1
316
+ rapidfuzz==3.8.1
317
+ rapidocr-onnxruntime==1.3.8
318
+ ray==2.10.0
319
+ rdkit==2024.3.5
320
+ redis==6.1.1
321
+ referencing==0.35.1
322
+ regex==2022.4.24
323
+ requests==2.32.4
324
+ requests-oauthlib==1.3.0
325
+ responses==0.16.0
326
+ rich==13.7.1
327
+ rouge-score==0.1.2
328
+ rpds-py==0.20.1
329
+ rq==2.3.3
330
+ rsa==4.7.2
331
+ ruff==0.4.2
332
+ rustworkx==0.15.1
333
+ s3transfer==0.11.3
334
+ sacrebleu==2.1.0
335
+ sacremoses==0.0.46
336
+ safetensors==0.4.3
337
+ scooby==0.10.1
338
+ seaborn==0.13.2
339
+ semantic-version==2.10.0
340
+ sentence-transformers==2.2.2
341
+ sentencepiece==0.1.91
342
+ sentry-sdk==2.39.0
343
+ session_info==1.0.1
344
+ sgmllib3k==1.0.0
345
+ shapely==2.0.4
346
+ shellingham==1.5.4
347
+ shortuuid==1.0.13
348
+ six==1.17.0
349
+ smart-open==6.4.0
350
+ smmap==5.0.1
351
+ sniffio==1.3.1
352
+ snowballstemmer==2.2.0
353
+ sobol-seq==0.2.0
354
+ socksio==1.0.0
355
+ soupsieve==2.5
356
+ spacy-legacy==3.0.12
357
+ spacy-loggers==1.0.5
358
+ Sphinx==4.3.1
359
+ sphinxcontrib-applehelp==1.0.2
360
+ sphinxcontrib-devhelp==1.0.2
361
+ sphinxcontrib-htmlhelp==2.0.0
362
+ sphinxcontrib-jsmath==1.0.1
363
+ sphinxcontrib-qthelp==1.0.3
364
+ sphinxcontrib-serializinghtml==1.1.5
365
+ SQLAlchemy==2.0.19
366
+ sqlparse==0.4.2
367
+ sse-starlette==1.8.2
368
+ starlette==0.44.0
369
+ statsmodels==0.14.1
370
+ stdlib-list==0.10.0
371
+ streamlit==1.30.0
372
+ streamlit-aggrid==0.3.4.post3
373
+ streamlit-antd-components==0.3.1
374
+ streamlit-chatbox==1.1.11
375
+ streamlit-feedback==0.1.3
376
+ streamlit-modal==0.1.0
377
+ streamlit-option-menu==0.3.12
378
+ strsimpy==0.2.1
379
+ svgwrite==1.4.3
380
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
381
+ tabulate==0.8.9
382
+ tenacity==8.2.3
383
+ tensorboard-plugin-wit==1.8.0
384
+ tensorboardX==2.4.1
385
+ text-unidecode==1.3
386
+ texttable==1.7.0
387
+ thefuzz==0.22.1
388
+ threadpoolctl==3.5.0
389
+ tifffile==2023.7.10
390
+ tiktoken==0.7.0
391
+ timm==0.9.16
392
+ tk==0.1.0
393
+ tokenizers==0.20.3
394
+ toml==0.10.2
395
+ tomlkit==0.12.0
396
+ toolz==0.12.1
397
+ torch-geometric==2.6.1
398
+ torchaudio==2.1.2+cu118
399
+ torchtext==0.4.0
400
+ tornado==6.4
401
+ tqdm==4.67.1
402
+ transformer-lens==2.16.1
403
+ transformers==4.46.3
404
+ transformers-stream-generator==0.0.5
405
+ typed-argument-parser==1.10.1
406
+ typeguard==4.4.0
407
+ typer==0.9.4
408
+ types-requests==2.31.0.20240406
409
+ typing-inspect==0.9.0
410
+ typing-utils==0.1.0
411
+ typing_extensions==4.13.2
412
+ tzdata==2024.1
413
+ tzlocal==5.2
414
+ umap-learn==0.5.7
415
+ Unidecode==1.3.2
416
+ unittest-xml-reporting==3.2.0
417
+ unstructured==0.11.0
418
+ unstructured-client==0.22.0
419
+ unstructured-inference==0.7.15
420
+ unstructured.pytesseract==0.3.12
421
+ uvicorn==0.29.0
422
+ uvloop==0.21.0
423
+ validators==0.28.1
424
+ vllm==0.2.7
425
+ vtk==9.3.1
426
+ wandb==0.22.0
427
+ watchdog==3.0.0
428
+ watchfiles==0.21.0
429
+ wavedrom==2.0.3.post3
430
+ weasel==0.3.4
431
+ websocket-client==1.8.0
432
+ websockets==13.1
433
+ Werkzeug==2.0.2
434
+ word2number==1.1
435
+ xlrd==2.0.1
436
+ XlsxWriter==3.0.2
437
+ xxhash==2.0.2
438
+ Yapsy==1.12.2
439
+ yarl==1.15.2
440
+ youtube-search==2.1.2
441
+ zipp==3.20.2
442
+ zope.event==4.5.0
443
+ zstandard==0.23.0
configs/s41467_024_53672_w_test/pip-freeze.txt ADDED
@@ -0,0 +1,443 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filetype==1.2.0
98
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
99
+ flaky==3.7.0
100
+ Flask-Cors==3.0.10
101
+ frozenlist==1.4.1
102
+ fschat==0.2.35
103
+ fsspec==2025.3.0
104
+ ftfy==6.0.3
105
+ future==0.18.2
106
+ fuzzywuzzy==0.18.0
107
+ gdown==5.2.0
108
+ geosketch==1.3
109
+ geotorch==0.3.0
110
+ get-annotations==0.1.2
111
+ gevent==21.12.0
112
+ gitdb==4.0.11
113
+ GitPython==3.1.43
114
+ google-pasta==0.2.0
115
+ googleapis-common-protos==1.63.0
116
+ gpustat==1.1.1
117
+ gpytorch==1.10
118
+ gradio_client==0.16.0
119
+ graphlib_backport==1.1.0
120
+ greenlet==1.1.2
121
+ gunicorn==23.0.0
122
+ h11==0.14.0
123
+ h2==4.1.0
124
+ hf-xet==1.2.0
125
+ hf_transfer==0.1.9
126
+ hpack==4.0.0
127
+ httpcore==1.0.5
128
+ httptools==0.6.1
129
+ httpx==0.28.1
130
+ httpx-sse==0.4.0
131
+ huggingface_hub==0.36.1
132
+ humanfriendly==10.0
133
+ hyperframe==6.0.1
134
+ icetk==0.0.4
135
+ igraph==0.11.8
136
+ imageio==2.35.1
137
+ imagesize==1.3.0
138
+ imgaug==0.4.0
139
+ importlib-metadata==7.0.0
140
+ importlib_resources==6.4.5
141
+ inequalipy==1.0.5
142
+ iniconfig==1.1.1
143
+ inquirerpy==0.3.4
144
+ iopath==0.1.10
145
+ isodate==0.7.2
146
+ itsdangerous==2.0.1
147
+ jax==0.4.13
148
+ jaxlib==0.4.13
149
+ jaxtyping==0.2.19
150
+ Jinja2==3.1.6
151
+ jiter==0.9.1
152
+ jmespath==0.10.0
153
+ joblib==1.4.2
154
+ jsonnet==0.17.0
155
+ jsonpatch==1.33
156
+ jsonpath-python==1.0.6
157
+ jsonpickle==2.0.0
158
+ jsonschema==4.23.0
159
+ jsonschema-specifications==2023.12.1
160
+ kaggle==1.7.4.5
161
+ Keras-Preprocessing==1.1.2
162
+ kubernetes==29.0.0
163
+ langchain==0.1.16
164
+ langchain-community==0.0.34
165
+ langchain-core==0.1.46
166
+ langchain-experimental==0.0.57
167
+ langchain-text-splitters==0.0.1
168
+ langcodes==3.4.0
169
+ langdetect==1.0.9
170
+ langsmith==0.1.51
171
+ language_data==1.2.0
172
+ layoutparser==0.3.4
173
+ lazy_loader==0.4
174
+ leidenalg==0.10.2
175
+ Levenshtein==0.25.1
176
+ linear-operator==0.4.0
177
+ litellm==1.77.4
178
+ litellm-enterprise==0.1.20
179
+ litellm-proxy-extras==0.2.19
180
+ llama-index==0.9.35
181
+ llvmlite==0.41.1
182
+ lmdb==1.7.3
183
+ lxml==5.2.1
184
+ madoka==0.7.1
185
+ marisa-trie==1.1.0
186
+ Markdown==3.3.6
187
+ markdown-it-py==3.0.0
188
+ markdown2==2.4.13
189
+ markdownify==0.11.6
190
+ MarkupSafe==2.1.5
191
+ marshmallow==3.21.1
192
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193
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194
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195
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196
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197
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198
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199
+ msal-extensions==1.3.0
200
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201
+ msgpack==1.0.8
202
+ msgpack-numpy==0.4.3.2
203
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204
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205
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206
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207
+ mypy-extensions==1.0.0
208
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209
+ natsort==8.4.0
210
+ nest-asyncio==1.6.0
211
+ netCDF4==1.7.2
212
+ neuroHarmonize==2.4.5
213
+ nh3==0.2.17
214
+ ninja==1.11.1.1
215
+ nltk==3.8.1
216
+ numba==0.58.1
217
+ numexpr==2.8.6
218
+ numpoly==1.0.6
219
+ numpy==1.24.4
220
+ numpydoc==1.1.0
221
+ nvidia-ml-py==12.535.133
222
+ nvitop==1.3.2
223
+ oauthlib==3.2.2
224
+ onnx==1.16.0
225
+ onnxruntime==1.15.1
226
+ openai==1.101.0
227
+ openpyxl==3.0.9
228
+ opentelemetry-api==1.24.0
229
+ opentelemetry-exporter-otlp-proto-common==1.24.0
230
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
231
+ opentelemetry-proto==1.24.0
232
+ opentelemetry-sdk==1.24.0
233
+ opentelemetry-semantic-conventions==0.45b0
234
+ opt-einsum==3.3.0
235
+ optax==0.1.5
236
+ ordered-set==4.1.0
237
+ orjson==3.10.1
238
+ overrides==7.7.0
239
+ packaging==26.2
240
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241
+ pandas-stubs==1.2.0.45
242
+ parsimonious==0.8.1
243
+ pathlib==1.0.1
244
+ patsy==1.0.1
245
+ pdf2image==1.17.0
246
+ pfzy==0.3.4
247
+ PICOS==2.6.1
248
+ pikepdf==8.4.1
249
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250
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251
+ plac==0.9.6
252
+ plotly==6.3.0
253
+ pluggy==1.5.0
254
+ ply==3.11
255
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256
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257
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258
+ posthog==3.5.0
259
+ preshed==3.0.9
260
+ prettytable==3.11.0
261
+ primer3-py==2.2.0
262
+ prompt-toolkit==3.0.43
263
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264
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265
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266
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267
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268
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269
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270
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271
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272
+ pydantic_core==2.27.2
273
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274
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275
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276
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277
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278
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279
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280
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281
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282
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283
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284
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285
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286
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287
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288
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289
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290
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291
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292
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293
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294
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295
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296
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297
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298
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299
+ pytesseract==0.3.10
300
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301
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302
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303
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304
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305
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306
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307
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308
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309
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310
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311
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312
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313
+ PyWavelets==1.4.1
314
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315
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316
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317
+ rapidocr-onnxruntime==1.3.8
318
+ ray==2.10.0
319
+ rdkit==2024.3.5
320
+ redis==6.1.1
321
+ referencing==0.35.1
322
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323
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324
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325
+ responses==0.16.0
326
+ rich==13.7.1
327
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328
+ rpds-py==0.20.1
329
+ rq==2.3.3
330
+ rsa==4.7.2
331
+ ruff==0.4.2
332
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333
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334
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335
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336
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337
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338
+ seaborn==0.13.2
339
+ semantic-version==2.10.0
340
+ sentence-transformers==2.2.2
341
+ sentencepiece==0.1.91
342
+ sentry-sdk==2.39.0
343
+ session_info==1.0.1
344
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345
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346
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347
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348
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349
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350
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351
+ sniffio==1.3.1
352
+ snowballstemmer==2.2.0
353
+ sobol-seq==0.2.0
354
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355
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356
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357
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358
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359
+ sphinxcontrib-applehelp==1.0.2
360
+ sphinxcontrib-devhelp==1.0.2
361
+ sphinxcontrib-htmlhelp==2.0.0
362
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363
+ sphinxcontrib-qthelp==1.0.3
364
+ sphinxcontrib-serializinghtml==1.1.5
365
+ SQLAlchemy==2.0.19
366
+ sqlparse==0.4.2
367
+ sse-starlette==1.8.2
368
+ starlette==0.44.0
369
+ statsmodels==0.14.1
370
+ stdlib-list==0.10.0
371
+ streamlit==1.30.0
372
+ streamlit-aggrid==0.3.4.post3
373
+ streamlit-antd-components==0.3.1
374
+ streamlit-chatbox==1.1.11
375
+ streamlit-feedback==0.1.3
376
+ streamlit-modal==0.1.0
377
+ streamlit-option-menu==0.3.12
378
+ strsimpy==0.2.1
379
+ svgwrite==1.4.3
380
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
381
+ tabulate==0.8.9
382
+ tenacity==8.2.3
383
+ tensorboard-plugin-wit==1.8.0
384
+ tensorboardX==2.4.1
385
+ text-unidecode==1.3
386
+ texttable==1.7.0
387
+ thefuzz==0.22.1
388
+ threadpoolctl==3.5.0
389
+ tifffile==2023.7.10
390
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391
+ timm==0.9.16
392
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393
+ tokenizers==0.20.3
394
+ toml==0.10.2
395
+ tomlkit==0.12.0
396
+ toolz==0.12.1
397
+ torch-geometric==2.6.1
398
+ torchaudio==2.1.2+cu118
399
+ torchtext==0.4.0
400
+ tornado==6.4
401
+ tqdm==4.67.1
402
+ transformer-lens==2.16.1
403
+ transformers==4.46.3
404
+ transformers-stream-generator==0.0.5
405
+ typed-argument-parser==1.10.1
406
+ typeguard==4.4.0
407
+ typer==0.9.4
408
+ types-requests==2.31.0.20240406
409
+ typing-inspect==0.9.0
410
+ typing-utils==0.1.0
411
+ typing_extensions==4.13.2
412
+ tzdata==2024.1
413
+ tzlocal==5.2
414
+ umap-learn==0.5.7
415
+ Unidecode==1.3.2
416
+ unittest-xml-reporting==3.2.0
417
+ unstructured==0.11.0
418
+ unstructured-client==0.22.0
419
+ unstructured-inference==0.7.15
420
+ unstructured.pytesseract==0.3.12
421
+ uvicorn==0.29.0
422
+ uvloop==0.21.0
423
+ validators==0.28.1
424
+ vllm==0.2.7
425
+ vtk==9.3.1
426
+ wandb==0.22.0
427
+ watchdog==3.0.0
428
+ watchfiles==0.21.0
429
+ wavedrom==2.0.3.post3
430
+ weasel==0.3.4
431
+ websocket-client==1.8.0
432
+ websockets==13.1
433
+ Werkzeug==2.0.2
434
+ word2number==1.1
435
+ xlrd==2.0.1
436
+ XlsxWriter==3.0.2
437
+ xxhash==2.0.2
438
+ Yapsy==1.12.2
439
+ yarl==1.15.2
440
+ youtube-search==2.1.2
441
+ zipp==3.20.2
442
+ zope.event==4.5.0
443
+ zstandard==0.23.0
editable_manifest.tsv ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ env egg_name source_path status size_bytes
2
+ s41467_024_48567_9_test SchNet4AIM.egg-link /data/lily/yz979/xx/Python/s41467-024-48567-9/SchNet4AIM/src copied 71228729
3
+ s41467_024_48578_6_test hypergraphx-1.7.8.egg-link /data/lily/yz979/xx/Python/s41467-024-48578-6/hypergraphx copied 18828165
4
+ 006_map_alignment_test alignmap.egg-link /data/lily/yz979/xx/MMSciCode/data/Python/006_MAP_Multi-Human-Value_Alignment_Palette/code copied 17820432
5
+ s41467_024_44757_7_test sift_sc-0.1.0.egg-link /data/lily/yz979/xx/Python/s41467-024-44757-7/sift-sc copied 4463596