omnigenome 0.3.1a0__py3-none-any.whl → 1.0.0b0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (79) hide show
  1. omnigenome/__init__.py +26 -266
  2. {omnigenome-0.3.1a0.dist-info → omnigenome-1.0.0b0.dist-info}/METADATA +8 -9
  3. omnigenome-1.0.0b0.dist-info/RECORD +6 -0
  4. omnigenome/auto/__init__.py +0 -3
  5. omnigenome/auto/auto_bench/__init__.py +0 -11
  6. omnigenome/auto/auto_bench/auto_bench.py +0 -494
  7. omnigenome/auto/auto_bench/auto_bench_cli.py +0 -230
  8. omnigenome/auto/auto_bench/auto_bench_config.py +0 -216
  9. omnigenome/auto/auto_bench/config_check.py +0 -34
  10. omnigenome/auto/auto_train/__init__.py +0 -12
  11. omnigenome/auto/auto_train/auto_train.py +0 -429
  12. omnigenome/auto/auto_train/auto_train_cli.py +0 -222
  13. omnigenome/auto/bench_hub/__init__.py +0 -11
  14. omnigenome/auto/bench_hub/bench_hub.py +0 -25
  15. omnigenome/cli/__init__.py +0 -12
  16. omnigenome/cli/commands/__init__.py +0 -12
  17. omnigenome/cli/commands/base.py +0 -83
  18. omnigenome/cli/commands/bench/__init__.py +0 -12
  19. omnigenome/cli/commands/bench/bench_cli.py +0 -202
  20. omnigenome/cli/commands/rna/__init__.py +0 -12
  21. omnigenome/cli/commands/rna/rna_design.py +0 -177
  22. omnigenome/cli/omnigenome_cli.py +0 -128
  23. omnigenome/src/__init__.py +0 -11
  24. omnigenome/src/abc/__init__.py +0 -11
  25. omnigenome/src/abc/abstract_dataset.py +0 -641
  26. omnigenome/src/abc/abstract_metric.py +0 -114
  27. omnigenome/src/abc/abstract_model.py +0 -690
  28. omnigenome/src/abc/abstract_tokenizer.py +0 -269
  29. omnigenome/src/dataset/__init__.py +0 -16
  30. omnigenome/src/dataset/omni_dataset.py +0 -437
  31. omnigenome/src/lora/__init__.py +0 -12
  32. omnigenome/src/lora/lora_model.py +0 -300
  33. omnigenome/src/metric/__init__.py +0 -15
  34. omnigenome/src/metric/classification_metric.py +0 -184
  35. omnigenome/src/metric/metric.py +0 -199
  36. omnigenome/src/metric/ranking_metric.py +0 -142
  37. omnigenome/src/metric/regression_metric.py +0 -191
  38. omnigenome/src/misc/__init__.py +0 -3
  39. omnigenome/src/misc/utils.py +0 -503
  40. omnigenome/src/model/__init__.py +0 -19
  41. omnigenome/src/model/augmentation/__init__.py +0 -11
  42. omnigenome/src/model/augmentation/model.py +0 -219
  43. omnigenome/src/model/classification/__init__.py +0 -11
  44. omnigenome/src/model/classification/model.py +0 -638
  45. omnigenome/src/model/embedding/__init__.py +0 -11
  46. omnigenome/src/model/embedding/model.py +0 -263
  47. omnigenome/src/model/mlm/__init__.py +0 -11
  48. omnigenome/src/model/mlm/model.py +0 -177
  49. omnigenome/src/model/module_utils.py +0 -232
  50. omnigenome/src/model/regression/__init__.py +0 -11
  51. omnigenome/src/model/regression/model.py +0 -781
  52. omnigenome/src/model/regression/resnet.py +0 -483
  53. omnigenome/src/model/rna_design/__init__.py +0 -11
  54. omnigenome/src/model/rna_design/model.py +0 -476
  55. omnigenome/src/model/seq2seq/__init__.py +0 -11
  56. omnigenome/src/model/seq2seq/model.py +0 -44
  57. omnigenome/src/tokenizer/__init__.py +0 -16
  58. omnigenome/src/tokenizer/bpe_tokenizer.py +0 -226
  59. omnigenome/src/tokenizer/kmers_tokenizer.py +0 -247
  60. omnigenome/src/tokenizer/single_nucleotide_tokenizer.py +0 -249
  61. omnigenome/src/trainer/__init__.py +0 -14
  62. omnigenome/src/trainer/accelerate_trainer.py +0 -747
  63. omnigenome/src/trainer/hf_trainer.py +0 -75
  64. omnigenome/src/trainer/trainer.py +0 -591
  65. omnigenome/utility/__init__.py +0 -3
  66. omnigenome/utility/dataset_hub/__init__.py +0 -12
  67. omnigenome/utility/dataset_hub/dataset_hub.py +0 -178
  68. omnigenome/utility/ensemble.py +0 -324
  69. omnigenome/utility/hub_utils.py +0 -517
  70. omnigenome/utility/model_hub/__init__.py +0 -11
  71. omnigenome/utility/model_hub/model_hub.py +0 -232
  72. omnigenome/utility/pipeline_hub/__init__.py +0 -11
  73. omnigenome/utility/pipeline_hub/pipeline.py +0 -483
  74. omnigenome/utility/pipeline_hub/pipeline_hub.py +0 -129
  75. omnigenome-0.3.1a0.dist-info/RECORD +0 -78
  76. omnigenome-0.3.1a0.dist-info/entry_points.txt +0 -3
  77. {omnigenome-0.3.1a0.dist-info → omnigenome-1.0.0b0.dist-info}/WHEEL +0 -0
  78. {omnigenome-0.3.1a0.dist-info → omnigenome-1.0.0b0.dist-info}/licenses/LICENSE +0 -0
  79. {omnigenome-0.3.1a0.dist-info → omnigenome-1.0.0b0.dist-info}/top_level.txt +0 -0
omnigenome-0.3.1a0.dist-info/RECORD DELETED
@@ -1,78 +0,0 @@
1
- omnigenome/__init__.py,sha256=2tXjLkxTWA1Akx9iks04X-JZckhVmkIEPDO5wKTucF8,9897
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- omnigenome/auto/__init__.py,sha256=UhcuYy43WsR7IowjajlcGwNVFFFDaufl8KqtNDmVqz0,97
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- omnigenome/auto/auto_bench/__init__.py,sha256=M2roe3FdlmRLeXs9cOH00KrccLrazkDvlYGSg_N9upo,410
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- omnigenome/auto/auto_bench/auto_bench.py,sha256=BdCzS-KF_Eos22TGlNdTtLFXlNt0Hd6yYpfvb1TawjE,20997
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- omnigenome/auto/auto_bench/auto_bench_cli.py,sha256=B3iJiTKuAc6dkEu2h9ApGFpJJwS0I2zwxXtZ6bWfarM,7608
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- omnigenome/auto/auto_bench/auto_bench_config.py,sha256=2mw6VFcWCSR6dJVAGDejlwmK_VmAZgqMvYlqznl5Ck8,7723
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- omnigenome/auto/auto_bench/config_check.py,sha256=5RYOOOC-CqvU-46-3uSK6vspLtPSVxdZsFMnNa-3rj0,1086
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- omnigenome/auto/auto_train/__init__.py,sha256=JClK_1E1_YVAy2rNzQewYzYxvLanqm71-swdXAx8uZs,447
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- omnigenome/auto/auto_train/auto_train.py,sha256=af5ca6SGyxn8apIxwU0vKPoAC0mKDP2CFqN9w1N_a2M,17506
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- omnigenome/auto/auto_train/auto_train_cli.py,sha256=vSjQ1t3hfe4HEvIWVB7V6cmYf-47_obKZGHWrk_LWDc,7298
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- omnigenome/auto/bench_hub/__init__.py,sha256=JryopzWvewnBtN_EZKNEDKvIsc6x0wCsntNFyCGhpmU,395
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- omnigenome/auto/bench_hub/bench_hub.py,sha256=eTxcVrKQdb-tdgt4CZDmD7zsUxMdw6McOeDAuaDiQZc,740
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- omnigenome/cli/__init__.py,sha256=sLM_HMGX4lK8LKvIsIBmQUAbZKih6bfYoHmqQFKfGBM,445
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- omnigenome/cli/omnigenome_cli.py,sha256=fvpxWqowa7IFSU097EXrhChYcMN4yekGS9UA5nsbpz4,4386
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- omnigenome/cli/commands/__init__.py,sha256=nnD9NFBNHGYhUt7nI5y4iuylIn2JOdvn6iEhlDJjhes,435
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- omnigenome/cli/commands/base.py,sha256=KU_lhhZpjCMRAK0LZz_txV3R9ZfzCAo_k3u44cBztMk,2858
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- omnigenome/cli/commands/bench/__init__.py,sha256=dAVl47_QKktT5DpHjv0VMY18vlmxkNMSXbfIWZ1l69k,440
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- omnigenome/cli/commands/bench/bench_cli.py,sha256=N4mkhg2MRo3beAWmUDJe2NsB5vL3hquxs8fBN-c9Z-A,7523
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- omnigenome/cli/commands/rna/__init__.py,sha256=rUyJljDj9JGcn83iyRSB2qC2BAXkgsbb24SWsimOFVE,434
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- omnigenome/cli/commands/rna/rna_design.py,sha256=Vb9jhh4Aj8RlUsBSHirQY5supkmMYzaXNIbs32Jjsyo,6408
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- omnigenome/src/__init__.py,sha256=MtntWq77RoL1K6iUQQlVcwgfDZIrykvjcpP4O4_7jgM,412
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- omnigenome/src/abc/__init__.py,sha256=4E5Ba2Fwf9VlxmjwZ50kku-YPGU00JZPgAcNuesaG3g,424
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- omnigenome/src/abc/abstract_dataset.py,sha256=YEHMwqohAPozmmbVemzA7CoA2hKyvrkW1wIB1msEQqA,24254
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- omnigenome/src/abc/abstract_metric.py,sha256=nRISSO93i1L9Q-TDL0ZnhtKAXgLRKVlzL6oKHknFU-4,4326
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- omnigenome/src/abc/abstract_model.py,sha256=t1XqLqs7VLJ4I9Tzu0chWYyFr3_ElaHk5vzQK5JGa7E,28639
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- omnigenome/src/abc/abstract_tokenizer.py,sha256=5z5dhL2qSswTa5W7Gdn7u8q7sC8cBfv2JuJf3G-F8Gw,9888
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- omnigenome/src/dataset/__init__.py,sha256=2Lz3xfGaiP5hl2Pf1eW0eenpzrDk3zDyyi63CXbC4hE,628
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- omnigenome/src/dataset/omni_dataset.py,sha256=dFsDraF3x9N-JIsxbAyPiDhY74BIdWn2pg0A_bV8iuc,17609
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- omnigenome/src/lora/__init__.py,sha256=EncdIW5iV7LWh8JndQqoXIDTZgHWAIGaeNUEyMa1SlU,457
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- omnigenome/src/lora/lora_model.py,sha256=HX_CW_ZlwHjGWLY-wcL01_6X6fIQKS7QxDZrmdmll44,10101
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- omnigenome/src/metric/__init__.py,sha256=lZr6uiL44G8ujmCz98wTH_anHRv9QUdO3tUiBHriZXA,543
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- omnigenome/src/metric/classification_metric.py,sha256=9AEBqtwga6cojFcS1lP_i-LGkbmn3QLAD7JGFz2Z6bY,8030
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- omnigenome/src/metric/metric.py,sha256=lAn7brhugv-gOEnE3SatnhczjWDgV8JTLfWxJU-regc,7724
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- omnigenome/src/metric/ranking_metric.py,sha256=iQZd7DIHIiNqykQJPNPVVjmGlrV-6nSEeKIh5o2XUt4,5670
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- omnigenome/src/metric/regression_metric.py,sha256=hfUPD6TnrfrQ_wpW5Lyk6t6xdHyMWhJ0rthsk3MXJkw,7585
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- omnigenome/src/misc/__init__.py,sha256=Dpa-uCQdwKVKkprqy26Np71mRobcWglCjgtITjU6yw0,63
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- omnigenome/src/misc/utils.py,sha256=WHoXcRpwliV1-9YO5ZfttvJNzUGib77uHS6oNVUnVjo,17108
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- omnigenome/src/model/__init__.py,sha256=vu1vJVYp8FR9BgF7X2msKkwMfa6jbzsfAsUHduTB21w,621
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- omnigenome/src/model/module_utils.py,sha256=dmiORa835Jg6cGS24h8e1ZrwfB9_tGiz30IbwUagdaw,9158
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- omnigenome/src/model/augmentation/__init__.py,sha256=Q1uTFVJjlDV_nJZ9YP44gq6LSolz9b8_6gJ0Iz0RtAc,395
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- omnigenome/src/model/augmentation/model.py,sha256=rA-NZGzydqvpZuHy4fq4xVJcFA97rjb6NcoV-Leeaqg,8174
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- omnigenome/src/model/classification/__init__.py,sha256=T1pW6HLdjUywf4-mN9d4ERRWPiZsGpDqsbalFPtyVCc,399
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- omnigenome/src/model/classification/model.py,sha256=wAets3HAF_T66LbBmdoEutKMYAwaIvWvMffDgGhnUbU,25022
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- omnigenome/src/model/embedding/__init__.py,sha256=Q6UqgzCEOujfAvYKcHnYhCa6kMIzFFFIa_5Ut8iHQgg,394
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- omnigenome/src/model/embedding/model.py,sha256=JJIjQTy50U8fVzeeXbgvUdJv_W59dF-f0gZD6qB8ha8,10140
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- omnigenome/src/model/mlm/__init__.py,sha256=PqKckKLXhvkJr8dLkSpKTwFYsclGv51nhXBKjI55oYw,406
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- omnigenome/src/model/mlm/model.py,sha256=rFYjn_QYFcREqHzSGO8GsbdUGGMzjOkAcooa-P9SaQ8,6435
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- omnigenome/src/model/regression/__init__.py,sha256=9_PEGxaiJrwPXvzOf6jGx6Wl1x4UQlOsCGUwNYPUDbc,395
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- omnigenome/src/model/regression/model.py,sha256=lXLg1Z0B7jzXHRkt8F1sP3KAitfSIAvhe8EAOFiUMFI,27591
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- omnigenome/src/model/regression/resnet.py,sha256=Xvpssyo3LmmPMJYHwdqKHU0x9F39dllkKY94aI9mHO0,16861
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- omnigenome/src/model/rna_design/__init__.py,sha256=cqC0Ap954sBDOe3RI8nVlYahx_gIg0nqwoBg8CRQ62E,395
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- omnigenome/src/model/rna_design/model.py,sha256=kDDM0BHpoFN9nlGxNWrjTjsFWn7E6CPYjfAfkJyLxGY,16939
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- omnigenome/src/model/seq2seq/__init__.py,sha256=38YtCYxAQRytOsW98G8cqgCXB6mmzrSGPKs1DbwzZ40,405
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- omnigenome/src/model/seq2seq/model.py,sha256=UC7j691BSbr6He3kCYwO_93V4RLWLt3fQOCQnnwJwgQ,1695
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- omnigenome/src/tokenizer/__init__.py,sha256=zYUgX-FJ-fw0GNJuuW8ovo9kflDmGDd8Z0F3AMDFXF4,556
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- omnigenome/src/tokenizer/bpe_tokenizer.py,sha256=_g1x3jJ3wzGgDu3_y2pW-KghYllgbiqoJfjMUF3sNTE,7646
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- omnigenome/src/tokenizer/kmers_tokenizer.py,sha256=KpPA5_MSP-Wvbp2aeRGD67al6xS1unhbreIQOio-1U4,9155
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- omnigenome/src/tokenizer/single_nucleotide_tokenizer.py,sha256=alwWeXuvGvzGflsyzm_V0AelAbdfMs79FGSo4pL5roo,9710
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- omnigenome/src/trainer/__init__.py,sha256=adib_MJlED-EXXkNCt9MhV1U9mPPoOrLReA-dxhgdT0,453
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- omnigenome/src/trainer/accelerate_trainer.py,sha256=u0gU1MRLjEcj3zPAkDztjxU1aNWDA_XTl6k_Wk3esIs,28377
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- omnigenome/src/trainer/hf_trainer.py,sha256=eRw0v21lBZW1gTi-5zmagLuR0A1X7OOb0bZlmzROcMI,2591
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- omnigenome/src/trainer/trainer.py,sha256=wyHJcb8IhrIrSW9dE7uK5MU_EL0_LRHJBP65z7RW9gA,21333
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- omnigenome/utility/__init__.py,sha256=UvgBH3hsW2JoXfGG6dHJeQLHVF7rXdzK39wGCoJOEKI,101
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- omnigenome/utility/ensemble.py,sha256=z9opb_9H213OeeNn4VJbKQfXVK_Kzig3mNDIjviG1oQ,13141
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- omnigenome/utility/hub_utils.py,sha256=iYxt1iAKW2OTsQ0rYxMixRiarwIxjYzCQtaDyijFnWw,20269
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- omnigenome/utility/dataset_hub/__init__.py,sha256=86rjBJixstpSiTbtprf0RnaC1V5lykh2Bs2cnZG9j3s,433
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- omnigenome/utility/dataset_hub/dataset_hub.py,sha256=aTPfk5Owoa5OtSGbFPM34WmZ3Oy9x8ZrILQgF6VXI3g,6960
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- omnigenome/utility/model_hub/__init__.py,sha256=Y5AcnzrtX9zPVbsAZy-6kLPJef-eddcPtZRAe8N7BOE,391
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- omnigenome/utility/model_hub/model_hub.py,sha256=0K0XOQvPLiscHt0LRphF7Gja6MXHDgBARbdQzr1G8mI,8574
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- omnigenome/utility/pipeline_hub/__init__.py,sha256=lz9kdc_arVwqDENvt_dN0h8fAhBeTRyG6LQRQrQAjGE,394
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- omnigenome/utility/pipeline_hub/pipeline.py,sha256=Ft56dolrLJWSLBj7jba8Fka3yCwtBso2Vx_Nt17ZB7A,19756
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- omnigenome/utility/pipeline_hub/pipeline_hub.py,sha256=bt2QLg4cld8QT2fbMZXJKL0vE3ReuNWHsqhLgiwc6HI,5268
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- omnigenome-0.3.1a0.dist-info/licenses/LICENSE,sha256=oQoefBV6siHctF0ET-OO3EaSZgtqGtf-wdIAmokS8iY,11560
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- omnigenome-0.3.1a0.dist-info/METADATA,sha256=LA0FxjRSjsEhsXvOV3noKYAis1t4_JY-wqTDjV9Fszo,10315
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- omnigenome-0.3.1a0.dist-info/WHEEL,sha256=lTU6B6eIfYoiQJTZNc-fyaR6BpL6ehTzU3xGYxn2n8k,91
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- omnigenome-0.3.1a0.dist-info/entry_points.txt,sha256=uu40UgMPxY65ASdRbrhkwH94r7CIYgyG_iDBmqFQbD8,84
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- omnigenome-0.3.1a0.dist-info/top_level.txt,sha256=LVFxm_WPaxjj9KnAqdW94W4D4lbOk30gdsaKlJiSzTo,11
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- omnigenome-0.3.1a0.dist-info/RECORD,,
omnigenome-0.3.1a0.dist-info/entry_points.txt DELETED
@@ -1,3 +0,0 @@
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- [console_scripts]
2
- autobench = omnigenome:run_bench
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- autotrain = omnigenome:run_train