omnigenome 0.3.0a1__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 -258
  2. {omnigenome-0.3.0a1.dist-info → omnigenome-1.0.0b0.dist-info}/METADATA +9 -10
  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 -12
  6. omnigenome/auto/auto_bench/auto_bench.py +0 -484
  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 -13
  11. omnigenome/auto/auto_train/auto_train.py +0 -430
  12. omnigenome/auto/auto_train/auto_train_cli.py +0 -222
  13. omnigenome/auto/bench_hub/__init__.py +0 -12
  14. omnigenome/auto/bench_hub/bench_hub.py +0 -25
  15. omnigenome/cli/__init__.py +0 -13
  16. omnigenome/cli/commands/__init__.py +0 -13
  17. omnigenome/cli/commands/base.py +0 -83
  18. omnigenome/cli/commands/bench/__init__.py +0 -13
  19. omnigenome/cli/commands/bench/bench_cli.py +0 -202
  20. omnigenome/cli/commands/rna/__init__.py +0 -13
  21. omnigenome/cli/commands/rna/rna_design.py +0 -178
  22. omnigenome/cli/omnigenome_cli.py +0 -128
  23. omnigenome/src/__init__.py +0 -12
  24. omnigenome/src/abc/__init__.py +0 -12
  25. omnigenome/src/abc/abstract_dataset.py +0 -622
  26. omnigenome/src/abc/abstract_metric.py +0 -114
  27. omnigenome/src/abc/abstract_model.py +0 -689
  28. omnigenome/src/abc/abstract_tokenizer.py +0 -267
  29. omnigenome/src/dataset/__init__.py +0 -16
  30. omnigenome/src/dataset/omni_dataset.py +0 -435
  31. omnigenome/src/lora/__init__.py +0 -13
  32. omnigenome/src/lora/lora_model.py +0 -294
  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 -499
  40. omnigenome/src/model/__init__.py +0 -19
  41. omnigenome/src/model/augmentation/__init__.py +0 -12
  42. omnigenome/src/model/augmentation/model.py +0 -219
  43. omnigenome/src/model/classification/__init__.py +0 -12
  44. omnigenome/src/model/classification/model.py +0 -642
  45. omnigenome/src/model/embedding/__init__.py +0 -12
  46. omnigenome/src/model/embedding/model.py +0 -263
  47. omnigenome/src/model/mlm/__init__.py +0 -12
  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 -12
  51. omnigenome/src/model/regression/model.py +0 -786
  52. omnigenome/src/model/regression/resnet.py +0 -483
  53. omnigenome/src/model/rna_design/__init__.py +0 -12
  54. omnigenome/src/model/rna_design/model.py +0 -469
  55. omnigenome/src/model/seq2seq/__init__.py +0 -12
  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 -739
  63. omnigenome/src/trainer/hf_trainer.py +0 -75
  64. omnigenome/src/trainer/trainer.py +0 -579
  65. omnigenome/utility/__init__.py +0 -3
  66. omnigenome/utility/dataset_hub/__init__.py +0 -13
  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 -12
  71. omnigenome/utility/model_hub/model_hub.py +0 -231
  72. omnigenome/utility/pipeline_hub/__init__.py +0 -12
  73. omnigenome/utility/pipeline_hub/pipeline.py +0 -483
  74. omnigenome/utility/pipeline_hub/pipeline_hub.py +0 -129
  75. omnigenome-0.3.0a1.dist-info/RECORD +0 -78
  76. omnigenome-0.3.0a1.dist-info/entry_points.txt +0 -3
  77. {omnigenome-0.3.0a1.dist-info → omnigenome-1.0.0b0.dist-info}/WHEEL +0 -0
  78. {omnigenome-0.3.0a1.dist-info → omnigenome-1.0.0b0.dist-info}/licenses/LICENSE +0 -0
  79. {omnigenome-0.3.0a1.dist-info → omnigenome-1.0.0b0.dist-info}/top_level.txt +0 -0
omnigenome-0.3.0a1.dist-info/RECORD DELETED
@@ -1,78 +0,0 @@
1
- omnigenome/__init__.py,sha256=ueMMkmyP6EjSvPUwNGLupoWT0W673sRbMXULhjbPjnU,9863
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- omnigenome/auto/__init__.py,sha256=UhcuYy43WsR7IowjajlcGwNVFFFDaufl8KqtNDmVqz0,97
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- omnigenome/auto/auto_bench/__init__.py,sha256=o0sPxaZM_KP5lRgidFUySr12OWguqB6PlL9ZhvWV1DM,411
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- omnigenome/auto/auto_bench/auto_bench.py,sha256=nprUgDGLLh4OIG9Qys6Aing1j8n_aw3ndSmx4PzAYN4,20781
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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=piAuS6ry7obkTthpbBvn5u2kqqhtrTwiGsrWIPqE4w0,448
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- omnigenome/auto/auto_train/auto_train.py,sha256=ne2G9oOMsqYysDxpOQbrp-v29-aDqtuAu4fo_HG4D2A,17563
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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=lbqmvd01gyyaijag-cg_MqjIlKcXfDskf-vLaWKpxBM,396
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- omnigenome/auto/bench_hub/bench_hub.py,sha256=CsnONzpcDw2HWNszCa_Ak4zUpIqKhV72cENkG0qoB0U,744
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- omnigenome/cli/__init__.py,sha256=xDO_D_enpEDCkpOqIcgIBn_nA7Na1x3AIHFfw42w_XU,446
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- omnigenome/cli/omnigenome_cli.py,sha256=fvpxWqowa7IFSU097EXrhChYcMN4yekGS9UA5nsbpz4,4386
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- omnigenome/cli/commands/__init__.py,sha256=vKd5VEfonNnNc6k77q2lGyfpyA12Lgl9cI0soMU24Ns,436
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- omnigenome/cli/commands/base.py,sha256=cziPHmbzHyBlQ1t-SbDt3k1Mwkb9i6cba8i-MCaoRWw,2931
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- omnigenome/cli/commands/bench/__init__.py,sha256=BnoQ23hFXEkKy8GtNVQbynvGyKNkvVF8UFDSmSprSAI,441
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- omnigenome/cli/commands/bench/bench_cli.py,sha256=5tpPpV_pIBC4_oUoD2jz9GlMjEHR7f-zbThlIYkWrwU,7625
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- omnigenome/cli/commands/rna/__init__.py,sha256=hLyxZjMFFSGU8wuSEaxvWxM2plLbCGoI9B-sMcrxjvY,435
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- omnigenome/cli/commands/rna/rna_design.py,sha256=JQGaCMMTq45mTAxFXylFQ4gfpLWb9mvciTRGtapDpu8,6519
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- omnigenome/src/__init__.py,sha256=gciGhCbdgcNEVoyquqnWubNmN1X-Ir53dHT2cAgOZUk,413
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- omnigenome/src/abc/__init__.py,sha256=RdVIA2WOyGbt9aTdMWXDZIG3I_6M49BV_WP8ti887LM,425
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- omnigenome/src/abc/abstract_dataset.py,sha256=jZFRVnAmif4gwGvhi2uYApLPYyYTz6k-RENGeWizrfU,23816
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- omnigenome/src/abc/abstract_metric.py,sha256=bR5mBnEiDAzBbzd2kF8aYV59Kipej2wZ8QlZsPzFP7o,4353
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- omnigenome/src/abc/abstract_model.py,sha256=E_YuhScqBi8Qt_-wEbTtP0c_dxv0oz7fe7NfyFNszwk,28670
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- omnigenome/src/abc/abstract_tokenizer.py,sha256=tfiYddutKIuUZiQJ3ujiakehWINiGOYbrKV-tUwtF5U,9894
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- omnigenome/src/dataset/__init__.py,sha256=2Lz3xfGaiP5hl2Pf1eW0eenpzrDk3zDyyi63CXbC4hE,628
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- omnigenome/src/dataset/omni_dataset.py,sha256=1ryp9TZu7Josv3ua_8GZJbA6BOOIeQ3Ty_kBtj9FgRc,17633
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- omnigenome/src/lora/__init__.py,sha256=VRNwSjziZywM4bRegcho4y1zGNF-kvBgxYXyATSgRL0,458
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- omnigenome/src/lora/lora_model.py,sha256=cFE2SW-KW9G64tu8mb94ymwtZsg4N0Ykmj3p8V6fh1k,10293
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- omnigenome/src/metric/__init__.py,sha256=lZr6uiL44G8ujmCz98wTH_anHRv9QUdO3tUiBHriZXA,543
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- omnigenome/src/metric/classification_metric.py,sha256=ndv2MPx6xv0k0CaHVQoeWyUW5HkMCqqZ0okeUUsXtgs,8109
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- omnigenome/src/metric/metric.py,sha256=mDd-8huMv9PiyWSaVWiIqNIaXQC5yI-zc_5WOTXWAxY,7912
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- omnigenome/src/metric/ranking_metric.py,sha256=DTyNyhleDPDPEyg5HlDjlUpLS5uYne17SdDUejpXmCs,5826
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- omnigenome/src/metric/regression_metric.py,sha256=J_XOZ1jXSdqzkOgw4adHA-YLA4A_QcGlW8g0lgIm9xs,7753
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- omnigenome/src/misc/__init__.py,sha256=Dpa-uCQdwKVKkprqy26Np71mRobcWglCjgtITjU6yw0,63
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- omnigenome/src/misc/utils.py,sha256=U8wk7-F2YhODKfSWhzkP8aJuoWIm49H5pAt3jHoJmVE,17241
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- omnigenome/src/model/__init__.py,sha256=vu1vJVYp8FR9BgF7X2msKkwMfa6jbzsfAsUHduTB21w,621
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- omnigenome/src/model/module_utils.py,sha256=rPJJfAcA4C8KumxSBJRCrCRxUSrwiRvLdbilIYIPS5U,9286
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- omnigenome/src/model/augmentation/__init__.py,sha256=JEZ1rszRUq7NBzwyu02eyNb_TTph2K3lXnXOCbHTtJc,396
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- omnigenome/src/model/augmentation/model.py,sha256=VHfi4z1LX5mDKrjHqg_B7kCvykc-E-YZd-TMSSn8yV0,8318
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- omnigenome/src/model/classification/__init__.py,sha256=6LxPh0ROdvzxMRLyLiksuX32H3F72vIbm1N3VCPnz4A,400
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- omnigenome/src/model/classification/model.py,sha256=_XPiVhoF-7QD_VV9shG5c95F_XD6t8E-czg3Eb2xDdQ,25184
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- omnigenome/src/model/embedding/__init__.py,sha256=pxrepPcVIp5ZmkEC5M3vRnmBJJTB1qXII5Zot_WSA3k,395
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- omnigenome/src/model/embedding/model.py,sha256=H3XyIJ-HxgYDPFqnfd1XsWO3JYV5DnDAbMqgz6oe3g0,10355
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- omnigenome/src/model/mlm/__init__.py,sha256=_rVEdL3nec_7hze2nTG0jgoupDJYMyl8EVcb02ZNwRs,407
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- omnigenome/src/model/mlm/model.py,sha256=RaUiX66Kzinn6vE1Rp23paJSOJP78EpxS0a9QJinQn0,6547
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- omnigenome/src/model/regression/__init__.py,sha256=Qdd4ctbc6jqTJDxHLe5MzSA3eDvW4vdypJm28bMQkco,396
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- omnigenome/src/model/regression/model.py,sha256=sgFqZ00J_gmeP9eRt1JYlbNN_KZhWLP1m4bEKKzV1Z8,28177
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- omnigenome/src/model/regression/resnet.py,sha256=YgzUAhGdXG_pAmvjQOpEjjzwxtm7sOb-a4et0CPJ09Y,17093
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- omnigenome/src/model/rna_design/__init__.py,sha256=jHAhyxuJScz1h1HY1UfZ3_fSVmwJOwsSACQkTItAl38,396
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- omnigenome/src/model/rna_design/model.py,sha256=HW5KcJiN-SWCvLalYS3w5ZprDK3GXR1sGr_15OybRlM,17343
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- omnigenome/src/model/seq2seq/__init__.py,sha256=OAi4RVSwCbFOIvEwQZCDTImBOFrLkHs1JXwipL_4fqs,406
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- omnigenome/src/model/seq2seq/model.py,sha256=-dGUjg7uRmnbR4rPH_lF8SgpR-U5lCoVJm4oNqzCOGg,1715
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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=5_qIuTYOWkhZH4O1jRf-hm4C130SjyVQP6avQkAkUr4,7898
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- omnigenome/src/tokenizer/kmers_tokenizer.py,sha256=KqyoY3xxllhl2Ij3YZk_zuW16dtH96I0hU5OMvO-EtA,9359
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- omnigenome/src/tokenizer/single_nucleotide_tokenizer.py,sha256=MAIeTtqQUDn6LYbYMy8RTzIU6S40rM5IE-imyM2MgFE,9794
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- omnigenome/src/trainer/__init__.py,sha256=adib_MJlED-EXXkNCt9MhV1U9mPPoOrLReA-dxhgdT0,453
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- omnigenome/src/trainer/trainer.py,sha256=NByvYdcazND_c9Ot2RSxoFjOV-Wc6kReu099BZbk13A,21179
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- omnigenome/utility/__init__.py,sha256=UvgBH3hsW2JoXfGG6dHJeQLHVF7rXdzK39wGCoJOEKI,101
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- omnigenome/utility/ensemble.py,sha256=2xSDvGULKJwE5LfLWfnNjsWo2DFf_TFmvqyhrYFlC90,13413
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- omnigenome/utility/hub_utils.py,sha256=yJF5RVICFbWy9JQU2P0lM3NXumu7HxNLCjpTKAudZf4,20313
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- omnigenome/utility/dataset_hub/__init__.py,sha256=6OTdqTWgKkuPQRBCGycpS1BboBoyT8rF3jY1EBSSAmE,434
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- omnigenome/utility/dataset_hub/dataset_hub.py,sha256=OW0XE27nCbuVD18UatFwi1w4UEfKxnv77R61D7bd0Vg,7008
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- omnigenome/utility/model_hub/__init__.py,sha256=N0xf5urzb6MxR8g-xF1CTzX0OFpHjngfETk6cmn92sc,392
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- omnigenome/utility/model_hub/model_hub.py,sha256=kgyjrU9qUb_pflIKqOQOUrk3zlF5pM8JazBxJyiBTck,8792
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- omnigenome/utility/pipeline_hub/__init__.py,sha256=rm7k6GDXyrYGQyLO3ZFpYLnjAYf6s8xmJuOPypDNQ-g,395
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- omnigenome/utility/pipeline_hub/pipeline.py,sha256=F_pDC_JKJF3b8OZtqzKzl99Q1FLMRQdBaGURi8CjZzg,20121
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- omnigenome/utility/pipeline_hub/pipeline_hub.py,sha256=9HB5xZTr8HZtsuC6MrWWNbR4cg_5BW0CVXKQk2AwcWA,5384
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- omnigenome-0.3.0a1.dist-info/licenses/LICENSE,sha256=oQoefBV6siHctF0ET-OO3EaSZgtqGtf-wdIAmokS8iY,11560
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- omnigenome-0.3.0a1.dist-info/METADATA,sha256=yT37KTD8T7iMB8nrqAasko3IxhpVR5L3QIkRdT6Qf3o,10318
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- omnigenome-0.3.0a1.dist-info/WHEEL,sha256=lTU6B6eIfYoiQJTZNc-fyaR6BpL6ehTzU3xGYxn2n8k,91
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- omnigenome-0.3.0a1.dist-info/entry_points.txt,sha256=uu40UgMPxY65ASdRbrhkwH94r7CIYgyG_iDBmqFQbD8,84
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- omnigenome-0.3.0a1.dist-info/top_level.txt,sha256=LVFxm_WPaxjj9KnAqdW94W4D4lbOk30gdsaKlJiSzTo,11
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- omnigenome-0.3.0a1.dist-info/RECORD,,
omnigenome-0.3.0a1.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