omicverse 2.2.2__tar.gz → 2.2.4__tar.gz

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 (1809) hide show
  1. omicverse-2.2.4/MANIFEST.in +30 -0
  2. omicverse-2.2.4/PKG-INFO +1284 -0
  3. omicverse-2.2.4/README.md +392 -0
  4. omicverse-2.2.4/omicverse/__init__.py +425 -0
  5. omicverse-2.2.4/omicverse/_registry.py +1588 -0
  6. omicverse-2.2.4/omicverse/_settings.py +889 -0
  7. omicverse-2.2.4/omicverse/bulk/_Deseq2.py +1640 -0
  8. omicverse-2.2.4/omicverse/bulk/_dynamicTree.py +963 -0
  9. omicverse-2.2.4/omicverse/bulk2single/_bulk2single.py +663 -0
  10. omicverse-2.2.4/omicverse/bulk2single/_map_utils.py +946 -0
  11. omicverse-2.2.4/omicverse/datasets/__init__.py +152 -0
  12. omicverse-2.2.4/omicverse/datasets/_crossspecies.py +59 -0
  13. omicverse-2.2.4/omicverse/external/PyWGCNA/wgcna.py +4484 -0
  14. omicverse-2.2.4/omicverse/external/STT/pl/_plot_tensor.py +255 -0
  15. omicverse-2.2.4/omicverse/external/VIA/core.py +3091 -0
  16. omicverse-2.2.4/omicverse/external/camex/__init__.py +63 -0
  17. omicverse-2.2.4/omicverse/external/camex/_run.py +278 -0
  18. omicverse-2.2.4/omicverse/external/camex/base.py +809 -0
  19. omicverse-2.2.4/omicverse/external/camex/integration_metrics.py +80 -0
  20. omicverse-2.2.4/omicverse/external/camex/layer.py +52 -0
  21. omicverse-2.2.4/omicverse/external/camex/loss.py +96 -0
  22. omicverse-2.2.4/omicverse/external/camex/model.py +701 -0
  23. omicverse-2.2.4/omicverse/external/camex/params.py +135 -0
  24. omicverse-2.2.4/omicverse/external/camex/preprocess_untils.py +341 -0
  25. omicverse-2.2.4/omicverse/external/camex/train_untils.py +263 -0
  26. omicverse-2.2.4/omicverse/external/camex/trainer.py +722 -0
  27. omicverse-2.2.4/omicverse/external/cnmf/cnmf.py +1985 -0
  28. omicverse-2.2.4/omicverse/external/flowsig/tools/_network.py +389 -0
  29. omicverse-2.2.4/omicverse/external/gsmap/_jackknife.py +118 -0
  30. omicverse-2.2.4/omicverse/external/gsmap/diagnosis.py +280 -0
  31. omicverse-2.2.4/omicverse/external/latentvelo/utils.py +892 -0
  32. omicverse-2.2.4/omicverse/external/pyscenic/binarization.py +134 -0
  33. omicverse-2.2.4/omicverse/external/samap/__init__.py +52 -0
  34. omicverse-2.2.4/omicverse/external/samap/_run.py +222 -0
  35. omicverse-2.2.4/omicverse/external/samap/analysis.py +1603 -0
  36. omicverse-2.2.4/omicverse/external/samap/mapping.py +1886 -0
  37. omicverse-2.2.4/omicverse/external/samap/samalg/__init__.py +1837 -0
  38. omicverse-2.2.4/omicverse/external/samap/samalg/gui.py +1987 -0
  39. omicverse-2.2.4/omicverse/external/samap/samalg/utilities.py +453 -0
  40. omicverse-2.2.4/omicverse/external/samap/utils.py +143 -0
  41. omicverse-2.2.4/omicverse/external/saturn/__init__.py +37 -0
  42. omicverse-2.2.4/omicverse/external/saturn/_run.py +416 -0
  43. omicverse-2.2.4/omicverse/external/saturn/_train_saturn.py +1078 -0
  44. omicverse-2.2.4/omicverse/external/saturn/data/__init__.py +1 -0
  45. omicverse-2.2.4/omicverse/external/saturn/data/gene_embeddings.py +122 -0
  46. omicverse-2.2.4/omicverse/external/saturn/data/multi_species_data.py +265 -0
  47. omicverse-2.2.4/omicverse/external/saturn/distances/__init__.py +5 -0
  48. omicverse-2.2.4/omicverse/external/saturn/distances/base_distance.py +89 -0
  49. omicverse-2.2.4/omicverse/external/saturn/distances/cosine_similarity.py +8 -0
  50. omicverse-2.2.4/omicverse/external/saturn/distances/dot_product_similarity.py +15 -0
  51. omicverse-2.2.4/omicverse/external/saturn/distances/lp_distance.py +27 -0
  52. omicverse-2.2.4/omicverse/external/saturn/distances/snr_distance.py +21 -0
  53. omicverse-2.2.4/omicverse/external/saturn/losses/__init__.py +27 -0
  54. omicverse-2.2.4/omicverse/external/saturn/losses/angular_loss.py +72 -0
  55. omicverse-2.2.4/omicverse/external/saturn/losses/arcface_loss.py +27 -0
  56. omicverse-2.2.4/omicverse/external/saturn/losses/base_metric_loss_function.py +122 -0
  57. omicverse-2.2.4/omicverse/external/saturn/losses/circle_loss.py +87 -0
  58. omicverse-2.2.4/omicverse/external/saturn/losses/contrastive_loss.py +54 -0
  59. omicverse-2.2.4/omicverse/external/saturn/losses/cosface_loss.py +30 -0
  60. omicverse-2.2.4/omicverse/external/saturn/losses/cross_batch_memory.py +161 -0
  61. omicverse-2.2.4/omicverse/external/saturn/losses/fast_ap_loss.py +68 -0
  62. omicverse-2.2.4/omicverse/external/saturn/losses/generic_pair_loss.py +38 -0
  63. omicverse-2.2.4/omicverse/external/saturn/losses/intra_pair_variance_loss.py +56 -0
  64. omicverse-2.2.4/omicverse/external/saturn/losses/large_margin_softmax_loss.py +130 -0
  65. omicverse-2.2.4/omicverse/external/saturn/losses/lifted_structure_loss.py +80 -0
  66. omicverse-2.2.4/omicverse/external/saturn/losses/margin_loss.py +101 -0
  67. omicverse-2.2.4/omicverse/external/saturn/losses/mixins.py +72 -0
  68. omicverse-2.2.4/omicverse/external/saturn/losses/multi_similarity_loss.py +43 -0
  69. omicverse-2.2.4/omicverse/external/saturn/losses/n_pairs_loss.py +36 -0
  70. omicverse-2.2.4/omicverse/external/saturn/losses/nca_loss.py +51 -0
  71. omicverse-2.2.4/omicverse/external/saturn/losses/normalized_softmax_loss.py +46 -0
  72. omicverse-2.2.4/omicverse/external/saturn/losses/ntxent_loss.py +46 -0
  73. omicverse-2.2.4/omicverse/external/saturn/losses/proxy_anchor_loss.py +92 -0
  74. omicverse-2.2.4/omicverse/external/saturn/losses/proxy_losses.py +30 -0
  75. omicverse-2.2.4/omicverse/external/saturn/losses/signal_to_noise_ratio_losses.py +12 -0
  76. omicverse-2.2.4/omicverse/external/saturn/losses/soft_triple_loss.py +85 -0
  77. omicverse-2.2.4/omicverse/external/saturn/losses/sphereface_loss.py +10 -0
  78. omicverse-2.2.4/omicverse/external/saturn/losses/triplet_margin_loss.py +62 -0
  79. omicverse-2.2.4/omicverse/external/saturn/losses/triplet_margin_mmd_loss.py +73 -0
  80. omicverse-2.2.4/omicverse/external/saturn/losses/tuplet_margin_loss.py +53 -0
  81. omicverse-2.2.4/omicverse/external/saturn/miners/__init__.py +12 -0
  82. omicverse-2.2.4/omicverse/external/saturn/miners/angular_miner.py +73 -0
  83. omicverse-2.2.4/omicverse/external/saturn/miners/base_miner.py +86 -0
  84. omicverse-2.2.4/omicverse/external/saturn/miners/batch_easy_hard_miner.py +199 -0
  85. omicverse-2.2.4/omicverse/external/saturn/miners/batch_hard_miner.py +14 -0
  86. omicverse-2.2.4/omicverse/external/saturn/miners/distance_weighted_miner.py +56 -0
  87. omicverse-2.2.4/omicverse/external/saturn/miners/embeddings_already_packaged_as_triplets.py +14 -0
  88. omicverse-2.2.4/omicverse/external/saturn/miners/hdc_miner.py +65 -0
  89. omicverse-2.2.4/omicverse/external/saturn/miners/maximum_loss_miner.py +43 -0
  90. omicverse-2.2.4/omicverse/external/saturn/miners/multi_similarity_miner.py +66 -0
  91. omicverse-2.2.4/omicverse/external/saturn/miners/pair_margin_miner.py +50 -0
  92. omicverse-2.2.4/omicverse/external/saturn/miners/triplet_margin_miner.py +68 -0
  93. omicverse-2.2.4/omicverse/external/saturn/miners/uniform_histogram_miner.py +66 -0
  94. omicverse-2.2.4/omicverse/external/saturn/model/__init__.py +1 -0
  95. omicverse-2.2.4/omicverse/external/saturn/model/saturn_model.py +595 -0
  96. omicverse-2.2.4/omicverse/external/saturn/pretrain_utils.py +47 -0
  97. omicverse-2.2.4/omicverse/external/saturn/reducers/__init__.py +9 -0
  98. omicverse-2.2.4/omicverse/external/saturn/reducers/avg_non_zero_reducer.py +6 -0
  99. omicverse-2.2.4/omicverse/external/saturn/reducers/base_reducer.py +102 -0
  100. omicverse-2.2.4/omicverse/external/saturn/reducers/class_weighted_reducer.py +28 -0
  101. omicverse-2.2.4/omicverse/external/saturn/reducers/divisor_reducer.py +32 -0
  102. omicverse-2.2.4/omicverse/external/saturn/reducers/do_nothing_reducer.py +6 -0
  103. omicverse-2.2.4/omicverse/external/saturn/reducers/mean_reducer.py +17 -0
  104. omicverse-2.2.4/omicverse/external/saturn/reducers/multiple_reducers.py +32 -0
  105. omicverse-2.2.4/omicverse/external/saturn/reducers/per_anchor_reducer.py +63 -0
  106. omicverse-2.2.4/omicverse/external/saturn/reducers/threshold_reducer.py +56 -0
  107. omicverse-2.2.4/omicverse/external/saturn/requirements.txt +25 -0
  108. omicverse-2.2.4/omicverse/external/saturn/saturn_multiple_seeds.py +114 -0
  109. omicverse-2.2.4/omicverse/external/saturn/score_adata.py +1111 -0
  110. omicverse-2.2.4/omicverse/external/saturn/testers/__init__.py +4 -0
  111. omicverse-2.2.4/omicverse/external/saturn/testers/base_tester.py +314 -0
  112. omicverse-2.2.4/omicverse/external/saturn/testers/global_embedding_space.py +36 -0
  113. omicverse-2.2.4/omicverse/external/saturn/testers/global_twostream_embedding_space.py +63 -0
  114. omicverse-2.2.4/omicverse/external/saturn/testers/with_same_parent_label.py +69 -0
  115. omicverse-2.2.4/omicverse/external/saturn/utils/accuracy_calculator.py +431 -0
  116. omicverse-2.2.4/omicverse/external/saturn/utils/common_functions.py +473 -0
  117. omicverse-2.2.4/omicverse/external/saturn/utils/distributed.py +71 -0
  118. omicverse-2.2.4/omicverse/external/saturn/utils/inference.py +175 -0
  119. omicverse-2.2.4/omicverse/external/saturn/utils/logging_presets.py +427 -0
  120. omicverse-2.2.4/omicverse/external/saturn/utils/loss_and_miner_utils.py +682 -0
  121. omicverse-2.2.4/omicverse/external/saturn/utils/loss_tracker.py +33 -0
  122. omicverse-2.2.4/omicverse/external/saturn/utils/module_with_records.py +22 -0
  123. omicverse-2.2.4/omicverse/external/saturn/utils/module_with_records_and_reducer.py +55 -0
  124. omicverse-2.2.4/omicverse/external/saturn/utils/stat_utils.py +69 -0
  125. omicverse-2.2.4/omicverse/external/saturn/utils/stop_conditions.py +67 -0
  126. omicverse-2.2.4/omicverse/external/saturn/utils/transformations.py +265 -0
  127. omicverse-2.2.4/omicverse/external/scMulan/utils/meta_info.pt +0 -0
  128. {omicverse-2.2.2/omicverse/external/space/cell2location/cell_comm → omicverse-2.2.4/omicverse/external/single/arboreto}/__init__.py +0 -0
  129. {omicverse-2.2.2/omicverse/external/space/cell2location/distributions → omicverse-2.2.4/omicverse/external/space/cell2location/cell_comm}/__init__.py +0 -0
  130. {omicverse-2.2.2/omicverse/external/space/cell2location/models/base → omicverse-2.2.4/omicverse/external/space/cell2location/distributions}/__init__.py +0 -0
  131. {omicverse-2.2.2/omicverse/llm/CellPLM → omicverse-2.2.4/omicverse/external/space/cell2location/models/simplified}/__init__.py +0 -0
  132. omicverse-2.2.4/omicverse/genetics/_gsmap.py +959 -0
  133. omicverse-2.2.4/omicverse/llm/UCE/__init__.py +0 -0
  134. omicverse-2.2.4/omicverse/pl/__init__.py +476 -0
  135. omicverse-2.2.4/omicverse/pl/_dotplot.py +895 -0
  136. omicverse-2.2.4/omicverse/pl/_perturbation.py +1549 -0
  137. omicverse-2.2.4/omicverse/pl/_plot_backend.py +1728 -0
  138. omicverse-2.2.4/omicverse/pl/_qc.py +254 -0
  139. omicverse-2.2.4/omicverse/pl/_scatterplot_backend.py +2152 -0
  140. omicverse-2.2.4/omicverse/pp/_doubletfinder.py +142 -0
  141. omicverse-2.2.4/omicverse/pp/_leiden_gpu.py +473 -0
  142. omicverse-2.2.4/omicverse/pp/_preprocess.py +2702 -0
  143. omicverse-2.2.4/omicverse/pp/_qc.py +2113 -0
  144. omicverse-2.2.4/omicverse/pp/_sccomposite.py +370 -0
  145. omicverse-2.2.4/omicverse/pp/_scdblfinder.py +142 -0
  146. omicverse-2.2.4/omicverse/single/__init__.py +458 -0
  147. omicverse-2.2.4/omicverse/single/_batch.py +708 -0
  148. omicverse-2.2.4/omicverse/single/_cross_species.py +576 -0
  149. omicverse-2.2.4/omicverse/single/_milo_dev.py +1244 -0
  150. omicverse-2.2.4/omicverse/single/_rpca.py +691 -0
  151. omicverse-2.2.4/omicverse/space/_deconvolution.py +985 -0
  152. omicverse-2.2.4/omicverse/space/_svg.py +885 -0
  153. omicverse-2.2.4/omicverse/synbio/__init__.py +204 -0
  154. omicverse-2.2.4/omicverse/synbio/_assembly.py +318 -0
  155. omicverse-2.2.4/omicverse/synbio/_binder.py +234 -0
  156. omicverse-2.2.4/omicverse/synbio/_boltz.py +197 -0
  157. omicverse-2.2.4/omicverse/synbio/_cfd.py +63 -0
  158. omicverse-2.2.4/omicverse/synbio/_circuit.py +340 -0
  159. omicverse-2.2.4/omicverse/synbio/_clean.py +123 -0
  160. omicverse-2.2.4/omicverse/synbio/_codon.py +249 -0
  161. omicverse-2.2.4/omicverse/synbio/_crispr.py +391 -0
  162. omicverse-2.2.4/omicverse/synbio/_design.py +198 -0
  163. omicverse-2.2.4/omicverse/synbio/_device.py +112 -0
  164. omicverse-2.2.4/omicverse/synbio/_dynamic.py +177 -0
  165. omicverse-2.2.4/omicverse/synbio/_ec.py +241 -0
  166. omicverse-2.2.4/omicverse/synbio/_editing.py +302 -0
  167. omicverse-2.2.4/omicverse/synbio/_embed.py +113 -0
  168. omicverse-2.2.4/omicverse/synbio/_esm_common.py +102 -0
  169. omicverse-2.2.4/omicverse/synbio/_evaluate.py +253 -0
  170. omicverse-2.2.4/omicverse/synbio/_expression.py +272 -0
  171. omicverse-2.2.4/omicverse/synbio/_function.py +196 -0
  172. omicverse-2.2.4/omicverse/synbio/_gem.py +330 -0
  173. omicverse-2.2.4/omicverse/synbio/_kcat.py +215 -0
  174. omicverse-2.2.4/omicverse/synbio/_library.py +245 -0
  175. omicverse-2.2.4/omicverse/synbio/_mrna.py +174 -0
  176. omicverse-2.2.4/omicverse/synbio/_plot.py +416 -0
  177. omicverse-2.2.4/omicverse/synbio/_primedesign.py +131 -0
  178. omicverse-2.2.4/omicverse/synbio/_proteinmpnn.py +226 -0
  179. omicverse-2.2.4/omicverse/synbio/_retro.py +158 -0
  180. omicverse-2.2.4/omicverse/synbio/_retrobio.py +244 -0
  181. omicverse-2.2.4/omicverse/synbio/_rna.py +136 -0
  182. omicverse-2.2.4/omicverse/synbio/_rnadesign.py +316 -0
  183. omicverse-2.2.4/omicverse/synbio/_sbol.py +141 -0
  184. omicverse-2.2.4/omicverse/synbio/_seqview.py +379 -0
  185. omicverse-2.2.4/omicverse/synbio/_stability.py +137 -0
  186. omicverse-2.2.4/omicverse/synbio/_strain.py +408 -0
  187. omicverse-2.2.4/omicverse/synbio/_structure.py +155 -0
  188. omicverse-2.2.4/omicverse/synbio/_thermo.py +281 -0
  189. omicverse-2.2.4/omicverse/synbio/_thermompnn.py +110 -0
  190. omicverse-2.2.4/omicverse/synbio/_variant.py +147 -0
  191. omicverse-2.2.4/omicverse/synbio/external/cfd/mismatch_score.pkl +722 -0
  192. omicverse-2.2.4/omicverse/synbio/external/cfd/pam_scores.pkl +50 -0
  193. omicverse-2.2.4/omicverse/synbio/external/ec_reference.fasta +14 -0
  194. omicverse-2.2.4/omicverse/tl/__init__.py +9 -0
  195. omicverse-2.2.4/omicverse/tl/_cross_species.py +122 -0
  196. omicverse-2.2.4/omicverse/utils/__init__.py +394 -0
  197. omicverse-2.2.4/omicverse/utils/_heatmap.py +659 -0
  198. omicverse-2.2.4/omicverse/utils/_plot.py +135 -0
  199. omicverse-2.2.4/omicverse/utils/_versions.py +80 -0
  200. omicverse-2.2.4/omicverse/utils/ovagent/registry_scanner.py +893 -0
  201. omicverse-2.2.4/omicverse.egg-info/PKG-INFO +1284 -0
  202. omicverse-2.2.4/omicverse.egg-info/SOURCES.txt +1757 -0
  203. omicverse-2.2.4/omicverse.egg-info/requires.txt +227 -0
  204. omicverse-2.2.4/pyproject.toml +445 -0
  205. omicverse-2.2.2/MANIFEST.in +0 -29
  206. omicverse-2.2.2/PKG-INFO +0 -1237
  207. omicverse-2.2.2/README.md +0 -367
  208. omicverse-2.2.2/omicverse/__init__.py +0 -422
  209. omicverse-2.2.2/omicverse/_registry.py +0 -1557
  210. omicverse-2.2.2/omicverse/_settings.py +0 -829
  211. omicverse-2.2.2/omicverse/bulk/.ipynb_checkpoints/_wgcna-checkpoint.py +0 -138
  212. omicverse-2.2.2/omicverse/bulk/_Deseq2.py +0 -1653
  213. omicverse-2.2.2/omicverse/bulk/_dynamicTree.py +0 -955
  214. omicverse-2.2.2/omicverse/bulk2single/_bulk2single.py +0 -654
  215. omicverse-2.2.2/omicverse/bulk2single/_map_utils.py +0 -946
  216. omicverse-2.2.2/omicverse/datasets/__init__.py +0 -151
  217. omicverse-2.2.2/omicverse/external/PyWGCNA/wgcna.py +0 -4468
  218. omicverse-2.2.2/omicverse/external/STT/pl/_plot_tensor.py +0 -255
  219. omicverse-2.2.2/omicverse/external/VIA/core.py +0 -3094
  220. omicverse-2.2.2/omicverse/external/cnmf/cnmf.py +0 -1976
  221. omicverse-2.2.2/omicverse/external/flowsig/tools/_network.py +0 -434
  222. omicverse-2.2.2/omicverse/external/gsmap/_jackknife.py +0 -116
  223. omicverse-2.2.2/omicverse/external/gsmap/diagnosis.py +0 -280
  224. omicverse-2.2.2/omicverse/external/latentvelo/utils.py +0 -846
  225. omicverse-2.2.2/omicverse/external/pyscenic/binarization.py +0 -97
  226. omicverse-2.2.2/omicverse/external/scTenifold/data/__init__.py +0 -6
  227. omicverse-2.2.2/omicverse/external/scTenifold/data/_get.py +0 -122
  228. omicverse-2.2.2/omicverse/external/scTenifold/data/_io.py +0 -162
  229. omicverse-2.2.2/omicverse/external/scTenifold/data/_sim.py +0 -171
  230. omicverse-2.2.2/omicverse/genetics/_gsmap.py +0 -959
  231. omicverse-2.2.2/omicverse/pl/__init__.py +0 -472
  232. omicverse-2.2.2/omicverse/pl/_dotplot.py +0 -885
  233. omicverse-2.2.2/omicverse/pl/_perturbation.py +0 -1550
  234. omicverse-2.2.2/omicverse/pl/_plot_backend.py +0 -1728
  235. omicverse-2.2.2/omicverse/pl/_qc.py +0 -193
  236. omicverse-2.2.2/omicverse/pl/_scatterplot_backend.py +0 -2149
  237. omicverse-2.2.2/omicverse/pp/_doubletfinder.py +0 -123
  238. omicverse-2.2.2/omicverse/pp/_leiden_gpu.py +0 -429
  239. omicverse-2.2.2/omicverse/pp/_preprocess.py +0 -2668
  240. omicverse-2.2.2/omicverse/pp/_qc.py +0 -2071
  241. omicverse-2.2.2/omicverse/pp/_sccomposite.py +0 -374
  242. omicverse-2.2.2/omicverse/pp/_scdblfinder.py +0 -116
  243. omicverse-2.2.2/omicverse/single/__init__.py +0 -444
  244. omicverse-2.2.2/omicverse/single/_batch.py +0 -679
  245. omicverse-2.2.2/omicverse/single/_milo_dev.py +0 -1257
  246. omicverse-2.2.2/omicverse/space/_deconvolution.py +0 -965
  247. omicverse-2.2.2/omicverse/space/_svg.py +0 -868
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@@ -0,0 +1,30 @@
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+ include README.md
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+ include LICENSE
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+ include pyproject.toml
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+ include setup.py
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+ include setup.cfg
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+ include requirements.txt
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+ include requirements-latest.txt
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+
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+ recursive-include omicverse *.py *.pyi *.json *.txt *.yaml *.yml *.csv *.tsv *.md *.ipynb *.html *.css *.js *.png *.jpg *.jpeg *.svg *.ico *.db *.npz *.gz *.fasta *.pkl
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+ include omicverse/external/scMulan/utils/meta_info.pt
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+
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+ prune .git
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+ prune .github
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+ prune .claude
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+ prune .pytest_cache
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+ prune .ruff_cache
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+ prune .vscode
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+ prune docs
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+ prune tests
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+ prune OvIntelligence
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+ prune READMEM
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+ prune omicverse_guide
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+ prune omicverse_web
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+ prune tmp
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+ prune tmp_omicverse
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+ prune Skill_Seekers
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+
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+ global-exclude .DS_Store
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+ global-exclude *.py[cod]
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+ global-exclude __pycache__