pybiolib 0.2.951__py3-none-any.whl → 1.2.1890__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 (262) hide show
  1. biolib/__init__.py +357 -11
  2. biolib/_data_record/data_record.py +380 -0
  3. biolib/_index/__init__.py +0 -0
  4. biolib/_index/index.py +55 -0
  5. biolib/_index/query_result.py +103 -0
  6. biolib/_internal/__init__.py +0 -0
  7. biolib/_internal/add_copilot_prompts.py +58 -0
  8. biolib/_internal/add_gui_files.py +81 -0
  9. biolib/_internal/data_record/__init__.py +1 -0
  10. biolib/_internal/data_record/data_record.py +85 -0
  11. biolib/_internal/data_record/push_data.py +116 -0
  12. biolib/_internal/data_record/remote_storage_endpoint.py +43 -0
  13. biolib/_internal/errors.py +5 -0
  14. biolib/_internal/file_utils.py +125 -0
  15. biolib/_internal/fuse_mount/__init__.py +1 -0
  16. biolib/_internal/fuse_mount/experiment_fuse_mount.py +209 -0
  17. biolib/_internal/http_client.py +159 -0
  18. biolib/_internal/lfs/__init__.py +1 -0
  19. biolib/_internal/lfs/cache.py +51 -0
  20. biolib/_internal/libs/__init__.py +1 -0
  21. biolib/_internal/libs/fusepy/__init__.py +1257 -0
  22. biolib/_internal/push_application.py +488 -0
  23. biolib/_internal/runtime.py +22 -0
  24. biolib/_internal/string_utils.py +13 -0
  25. biolib/_internal/templates/__init__.py +1 -0
  26. biolib/_internal/templates/copilot_template/.github/instructions/general-app-knowledge.instructions.md +10 -0
  27. biolib/_internal/templates/copilot_template/.github/instructions/style-general.instructions.md +20 -0
  28. biolib/_internal/templates/copilot_template/.github/instructions/style-python.instructions.md +16 -0
  29. biolib/_internal/templates/copilot_template/.github/instructions/style-react-ts.instructions.md +47 -0
  30. biolib/_internal/templates/copilot_template/.github/prompts/biolib_app_inputs.prompt.md +11 -0
  31. biolib/_internal/templates/copilot_template/.github/prompts/biolib_onboard_repo.prompt.md +19 -0
  32. biolib/_internal/templates/copilot_template/.github/prompts/biolib_run_apps.prompt.md +12 -0
  33. biolib/_internal/templates/dashboard_template/.biolib/config.yml +5 -0
  34. biolib/_internal/templates/github_workflow_template/.github/workflows/biolib.yml +21 -0
  35. biolib/_internal/templates/gitignore_template/.gitignore +10 -0
  36. biolib/_internal/templates/gui_template/.yarnrc.yml +1 -0
  37. biolib/_internal/templates/gui_template/App.tsx +53 -0
  38. biolib/_internal/templates/gui_template/Dockerfile +27 -0
  39. biolib/_internal/templates/gui_template/biolib-sdk.ts +82 -0
  40. biolib/_internal/templates/gui_template/dev-data/output.json +7 -0
  41. biolib/_internal/templates/gui_template/index.css +5 -0
  42. biolib/_internal/templates/gui_template/index.html +13 -0
  43. biolib/_internal/templates/gui_template/index.tsx +10 -0
  44. biolib/_internal/templates/gui_template/package.json +27 -0
  45. biolib/_internal/templates/gui_template/tsconfig.json +24 -0
  46. biolib/_internal/templates/gui_template/vite-plugin-dev-data.ts +50 -0
  47. biolib/_internal/templates/gui_template/vite.config.mts +10 -0
  48. biolib/_internal/templates/init_template/.biolib/config.yml +19 -0
  49. biolib/_internal/templates/init_template/Dockerfile +14 -0
  50. biolib/_internal/templates/init_template/requirements.txt +1 -0
  51. biolib/_internal/templates/init_template/run.py +12 -0
  52. biolib/_internal/templates/init_template/run.sh +4 -0
  53. biolib/_internal/templates/templates.py +25 -0
  54. biolib/_internal/tree_utils.py +106 -0
  55. biolib/_internal/utils/__init__.py +65 -0
  56. biolib/_internal/utils/auth.py +46 -0
  57. biolib/_internal/utils/job_url.py +33 -0
  58. biolib/_internal/utils/multinode.py +263 -0
  59. biolib/_runtime/runtime.py +157 -0
  60. biolib/_session/session.py +44 -0
  61. biolib/_shared/__init__.py +0 -0
  62. biolib/_shared/types/__init__.py +74 -0
  63. biolib/_shared/types/account.py +12 -0
  64. biolib/_shared/types/account_member.py +8 -0
  65. biolib/_shared/types/app.py +9 -0
  66. biolib/_shared/types/data_record.py +40 -0
  67. biolib/_shared/types/experiment.py +32 -0
  68. biolib/_shared/types/file_node.py +17 -0
  69. biolib/_shared/types/push.py +6 -0
  70. biolib/_shared/types/resource.py +37 -0
  71. biolib/_shared/types/resource_deploy_key.py +11 -0
  72. biolib/_shared/types/resource_permission.py +14 -0
  73. biolib/_shared/types/resource_version.py +19 -0
  74. biolib/_shared/types/result.py +14 -0
  75. biolib/_shared/types/typing.py +10 -0
  76. biolib/_shared/types/user.py +19 -0
  77. biolib/_shared/utils/__init__.py +7 -0
  78. biolib/_shared/utils/resource_uri.py +75 -0
  79. biolib/api/__init__.py +6 -0
  80. biolib/api/client.py +168 -0
  81. biolib/app/app.py +252 -49
  82. biolib/app/search_apps.py +45 -0
  83. biolib/biolib_api_client/api_client.py +126 -31
  84. biolib/biolib_api_client/app_types.py +24 -4
  85. biolib/biolib_api_client/auth.py +31 -8
  86. biolib/biolib_api_client/biolib_app_api.py +147 -52
  87. biolib/biolib_api_client/biolib_job_api.py +161 -141
  88. biolib/biolib_api_client/job_types.py +21 -5
  89. biolib/biolib_api_client/lfs_types.py +7 -23
  90. biolib/biolib_api_client/user_state.py +56 -0
  91. biolib/biolib_binary_format/__init__.py +1 -4
  92. biolib/biolib_binary_format/file_in_container.py +105 -0
  93. biolib/biolib_binary_format/module_input.py +24 -7
  94. biolib/biolib_binary_format/module_output_v2.py +149 -0
  95. biolib/biolib_binary_format/remote_endpoints.py +34 -0
  96. biolib/biolib_binary_format/remote_stream_seeker.py +59 -0
  97. biolib/biolib_binary_format/saved_job.py +3 -2
  98. biolib/biolib_binary_format/{attestation_document.py → stdout_and_stderr.py} +8 -8
  99. biolib/biolib_binary_format/system_status_update.py +3 -2
  100. biolib/biolib_binary_format/utils.py +175 -0
  101. biolib/biolib_docker_client/__init__.py +11 -2
  102. biolib/biolib_errors.py +36 -0
  103. biolib/biolib_logging.py +27 -10
  104. biolib/cli/__init__.py +38 -0
  105. biolib/cli/auth.py +46 -0
  106. biolib/cli/data_record.py +164 -0
  107. biolib/cli/index.py +32 -0
  108. biolib/cli/init.py +421 -0
  109. biolib/cli/lfs.py +101 -0
  110. biolib/cli/push.py +50 -0
  111. biolib/cli/run.py +63 -0
  112. biolib/cli/runtime.py +14 -0
  113. biolib/cli/sdk.py +16 -0
  114. biolib/cli/start.py +56 -0
  115. biolib/compute_node/cloud_utils/cloud_utils.py +110 -161
  116. biolib/compute_node/job_worker/cache_state.py +66 -88
  117. biolib/compute_node/job_worker/cache_types.py +1 -6
  118. biolib/compute_node/job_worker/docker_image_cache.py +112 -37
  119. biolib/compute_node/job_worker/executors/__init__.py +0 -3
  120. biolib/compute_node/job_worker/executors/docker_executor.py +532 -199
  121. biolib/compute_node/job_worker/executors/docker_types.py +9 -1
  122. biolib/compute_node/job_worker/executors/types.py +19 -9
  123. biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +30 -0
  124. biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +3 -5
  125. biolib/compute_node/job_worker/job_storage.py +108 -0
  126. biolib/compute_node/job_worker/job_worker.py +397 -212
  127. biolib/compute_node/job_worker/large_file_system.py +87 -38
  128. biolib/compute_node/job_worker/network_alloc.py +99 -0
  129. biolib/compute_node/job_worker/network_buffer.py +240 -0
  130. biolib/compute_node/job_worker/utilization_reporter_thread.py +197 -0
  131. biolib/compute_node/job_worker/utils.py +9 -24
  132. biolib/compute_node/remote_host_proxy.py +400 -98
  133. biolib/compute_node/utils.py +31 -9
  134. biolib/compute_node/webserver/compute_node_results_proxy.py +189 -0
  135. biolib/compute_node/webserver/proxy_utils.py +28 -0
  136. biolib/compute_node/webserver/webserver.py +130 -44
  137. biolib/compute_node/webserver/webserver_types.py +2 -6
  138. biolib/compute_node/webserver/webserver_utils.py +77 -12
  139. biolib/compute_node/webserver/worker_thread.py +183 -42
  140. biolib/experiments/__init__.py +0 -0
  141. biolib/experiments/experiment.py +356 -0
  142. biolib/jobs/__init__.py +1 -0
  143. biolib/jobs/job.py +741 -0
  144. biolib/jobs/job_result.py +185 -0
  145. biolib/jobs/types.py +50 -0
  146. biolib/py.typed +0 -0
  147. biolib/runtime/__init__.py +14 -0
  148. biolib/sdk/__init__.py +91 -0
  149. biolib/tables.py +34 -0
  150. biolib/typing_utils.py +2 -7
  151. biolib/user/__init__.py +1 -0
  152. biolib/user/sign_in.py +54 -0
  153. biolib/utils/__init__.py +162 -0
  154. biolib/utils/cache_state.py +94 -0
  155. biolib/utils/multipart_uploader.py +194 -0
  156. biolib/utils/seq_util.py +150 -0
  157. biolib/utils/zip/remote_zip.py +640 -0
  158. pybiolib-1.2.1890.dist-info/METADATA +41 -0
  159. pybiolib-1.2.1890.dist-info/RECORD +177 -0
  160. {pybiolib-0.2.951.dist-info → pybiolib-1.2.1890.dist-info}/WHEEL +1 -1
  161. pybiolib-1.2.1890.dist-info/entry_points.txt +2 -0
  162. README.md +0 -17
  163. biolib/app/app_result.py +0 -68
  164. biolib/app/utils.py +0 -62
  165. biolib/biolib-js/0-biolib.worker.js +0 -1
  166. biolib/biolib-js/1-biolib.worker.js +0 -1
  167. biolib/biolib-js/2-biolib.worker.js +0 -1
  168. biolib/biolib-js/3-biolib.worker.js +0 -1
  169. biolib/biolib-js/4-biolib.worker.js +0 -1
  170. biolib/biolib-js/5-biolib.worker.js +0 -1
  171. biolib/biolib-js/6-biolib.worker.js +0 -1
  172. biolib/biolib-js/index.html +0 -10
  173. biolib/biolib-js/main-biolib.js +0 -1
  174. biolib/biolib_api_client/biolib_account_api.py +0 -21
  175. biolib/biolib_api_client/biolib_large_file_system_api.py +0 -108
  176. biolib/biolib_binary_format/aes_encrypted_package.py +0 -42
  177. biolib/biolib_binary_format/module_output.py +0 -58
  178. biolib/biolib_binary_format/rsa_encrypted_aes_package.py +0 -57
  179. biolib/biolib_push.py +0 -114
  180. biolib/cli.py +0 -203
  181. biolib/cli_utils.py +0 -273
  182. biolib/compute_node/cloud_utils/enclave_parent_types.py +0 -7
  183. biolib/compute_node/enclave/__init__.py +0 -2
  184. biolib/compute_node/enclave/enclave_remote_hosts.py +0 -53
  185. biolib/compute_node/enclave/nitro_secure_module_utils.py +0 -64
  186. biolib/compute_node/job_worker/executors/base_executor.py +0 -18
  187. biolib/compute_node/job_worker/executors/pyppeteer_executor.py +0 -173
  188. biolib/compute_node/job_worker/executors/remote/__init__.py +0 -1
  189. biolib/compute_node/job_worker/executors/remote/nitro_enclave_utils.py +0 -81
  190. biolib/compute_node/job_worker/executors/remote/remote_executor.py +0 -51
  191. biolib/lfs.py +0 -196
  192. biolib/pyppeteer/.circleci/config.yml +0 -100
  193. biolib/pyppeteer/.coveragerc +0 -3
  194. biolib/pyppeteer/.gitignore +0 -89
  195. biolib/pyppeteer/.pre-commit-config.yaml +0 -28
  196. biolib/pyppeteer/CHANGES.md +0 -253
  197. biolib/pyppeteer/CONTRIBUTING.md +0 -26
  198. biolib/pyppeteer/LICENSE +0 -12
  199. biolib/pyppeteer/README.md +0 -137
  200. biolib/pyppeteer/docs/Makefile +0 -177
  201. biolib/pyppeteer/docs/_static/custom.css +0 -28
  202. biolib/pyppeteer/docs/_templates/layout.html +0 -10
  203. biolib/pyppeteer/docs/changes.md +0 -1
  204. biolib/pyppeteer/docs/conf.py +0 -299
  205. biolib/pyppeteer/docs/index.md +0 -21
  206. biolib/pyppeteer/docs/make.bat +0 -242
  207. biolib/pyppeteer/docs/reference.md +0 -211
  208. biolib/pyppeteer/docs/server.py +0 -60
  209. biolib/pyppeteer/poetry.lock +0 -1699
  210. biolib/pyppeteer/pyppeteer/__init__.py +0 -135
  211. biolib/pyppeteer/pyppeteer/accessibility.py +0 -286
  212. biolib/pyppeteer/pyppeteer/browser.py +0 -401
  213. biolib/pyppeteer/pyppeteer/browser_fetcher.py +0 -194
  214. biolib/pyppeteer/pyppeteer/command.py +0 -22
  215. biolib/pyppeteer/pyppeteer/connection/__init__.py +0 -242
  216. biolib/pyppeteer/pyppeteer/connection/cdpsession.py +0 -101
  217. biolib/pyppeteer/pyppeteer/coverage.py +0 -346
  218. biolib/pyppeteer/pyppeteer/device_descriptors.py +0 -787
  219. biolib/pyppeteer/pyppeteer/dialog.py +0 -79
  220. biolib/pyppeteer/pyppeteer/domworld.py +0 -597
  221. biolib/pyppeteer/pyppeteer/emulation_manager.py +0 -53
  222. biolib/pyppeteer/pyppeteer/errors.py +0 -48
  223. biolib/pyppeteer/pyppeteer/events.py +0 -63
  224. biolib/pyppeteer/pyppeteer/execution_context.py +0 -156
  225. biolib/pyppeteer/pyppeteer/frame/__init__.py +0 -299
  226. biolib/pyppeteer/pyppeteer/frame/frame_manager.py +0 -306
  227. biolib/pyppeteer/pyppeteer/helpers.py +0 -245
  228. biolib/pyppeteer/pyppeteer/input.py +0 -371
  229. biolib/pyppeteer/pyppeteer/jshandle.py +0 -598
  230. biolib/pyppeteer/pyppeteer/launcher.py +0 -683
  231. biolib/pyppeteer/pyppeteer/lifecycle_watcher.py +0 -169
  232. biolib/pyppeteer/pyppeteer/models/__init__.py +0 -103
  233. biolib/pyppeteer/pyppeteer/models/_protocol.py +0 -12460
  234. biolib/pyppeteer/pyppeteer/multimap.py +0 -82
  235. biolib/pyppeteer/pyppeteer/network_manager.py +0 -678
  236. biolib/pyppeteer/pyppeteer/options.py +0 -8
  237. biolib/pyppeteer/pyppeteer/page.py +0 -1728
  238. biolib/pyppeteer/pyppeteer/pipe_transport.py +0 -59
  239. biolib/pyppeteer/pyppeteer/target.py +0 -147
  240. biolib/pyppeteer/pyppeteer/task_queue.py +0 -24
  241. biolib/pyppeteer/pyppeteer/timeout_settings.py +0 -36
  242. biolib/pyppeteer/pyppeteer/tracing.py +0 -93
  243. biolib/pyppeteer/pyppeteer/us_keyboard_layout.py +0 -305
  244. biolib/pyppeteer/pyppeteer/util.py +0 -18
  245. biolib/pyppeteer/pyppeteer/websocket_transport.py +0 -47
  246. biolib/pyppeteer/pyppeteer/worker.py +0 -101
  247. biolib/pyppeteer/pyproject.toml +0 -97
  248. biolib/pyppeteer/spell.txt +0 -137
  249. biolib/pyppeteer/tox.ini +0 -72
  250. biolib/pyppeteer/utils/generate_protocol_types.py +0 -603
  251. biolib/start_cli.py +0 -7
  252. biolib/utils.py +0 -47
  253. biolib/validators/validate_app_version.py +0 -183
  254. biolib/validators/validate_argument.py +0 -134
  255. biolib/validators/validate_module.py +0 -323
  256. biolib/validators/validate_zip_file.py +0 -40
  257. biolib/validators/validator_utils.py +0 -103
  258. pybiolib-0.2.951.dist-info/LICENSE +0 -21
  259. pybiolib-0.2.951.dist-info/METADATA +0 -61
  260. pybiolib-0.2.951.dist-info/RECORD +0 -153
  261. pybiolib-0.2.951.dist-info/entry_points.txt +0 -3
  262. /LICENSE → /pybiolib-1.2.1890.dist-info/licenses/LICENSE +0 -0

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