pybiolib 1.2.1173__tar.gz → 1.2.1180__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 (163) hide show
  1. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/PKG-INFO +1 -1
  2. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/push_application.py +2 -1
  3. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/utils/seq_util.py +1 -1
  4. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/pyproject.toml +1 -1
  5. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/LICENSE +0 -0
  6. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/PYPI_README.md +0 -0
  7. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/__init__.py +0 -0
  8. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_data_record/data_record.py +0 -0
  9. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/__init__.py +0 -0
  10. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/add_copilot_prompts.py +0 -0
  11. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/add_gui_files.py +0 -0
  12. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/data_record/__init__.py +0 -0
  13. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/data_record/data_record.py +0 -0
  14. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/data_record/push_data.py +0 -0
  15. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
  16. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/errors.py +0 -0
  17. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/file_utils.py +0 -0
  18. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/fuse_mount/__init__.py +0 -0
  19. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +0 -0
  20. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/http_client.py +0 -0
  21. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/lfs/__init__.py +0 -0
  22. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/lfs/cache.py +0 -0
  23. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/libs/__init__.py +0 -0
  24. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/libs/fusepy/__init__.py +0 -0
  25. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/runtime.py +0 -0
  26. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/string_utils.py +0 -0
  27. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/__init__.py +0 -0
  28. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/copilot_template/.github/instructions/general-app-knowledge.instructions.md +0 -0
  29. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/copilot_template/.github/instructions/style-general.instructions.md +0 -0
  30. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/copilot_template/.github/instructions/style-python.instructions.md +0 -0
  31. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/copilot_template/.github/instructions/style-react-ts.instructions.md +0 -0
  32. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/copilot_template/.github/prompts/biolib_app_inputs.prompt.md +0 -0
  33. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/copilot_template/.github/prompts/biolib_onboard_repo.prompt.md +0 -0
  34. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/copilot_template/.github/prompts/biolib_run_apps.prompt.md +0 -0
  35. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/.yarnrc.yml +0 -0
  36. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/App.tsx +0 -0
  37. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/Dockerfile +0 -0
  38. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/index.css +0 -0
  39. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/index.html +0 -0
  40. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/index.tsx +0 -0
  41. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/package.json +0 -0
  42. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/tsconfig.json +0 -0
  43. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/gui_template/vite.config.mts +0 -0
  44. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/init_template/.biolib/config.yml +0 -0
  45. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/init_template/.github/workflows/biolib.yml +0 -0
  46. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/init_template/.gitignore +0 -0
  47. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/init_template/Dockerfile +0 -0
  48. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/init_template/requirements.txt +0 -0
  49. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/init_template/run.py +0 -0
  50. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/init_template/run.sh +0 -0
  51. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/templates/templates.py +0 -0
  52. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/tree_utils.py +0 -0
  53. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/__init__.py +0 -0
  54. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/account.py +0 -0
  55. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/account_member.py +0 -0
  56. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/app.py +0 -0
  57. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/data_record.py +0 -0
  58. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/experiment.py +0 -0
  59. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/file_node.py +0 -0
  60. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/push.py +0 -0
  61. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/resource.py +0 -0
  62. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/resource_permission.py +0 -0
  63. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/resource_version.py +0 -0
  64. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/result.py +0 -0
  65. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/typing.py +0 -0
  66. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/types/user.py +0 -0
  67. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/utils/__init__.py +0 -0
  68. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/utils/multinode.py +0 -0
  69. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_runtime/runtime.py +0 -0
  70. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_session/session.py +0 -0
  71. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/api/__init__.py +0 -0
  72. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/api/client.py +0 -0
  73. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/app/__init__.py +0 -0
  74. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/app/app.py +0 -0
  75. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/app/search_apps.py +0 -0
  76. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/__init__.py +0 -0
  77. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/api_client.py +0 -0
  78. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/app_types.py +0 -0
  79. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/auth.py +0 -0
  80. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  81. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  82. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/common_types.py +0 -0
  83. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/job_types.py +0 -0
  84. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/lfs_types.py +0 -0
  85. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_api_client/user_state.py +0 -0
  86. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/__init__.py +0 -0
  87. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  88. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/file_in_container.py +0 -0
  89. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/module_input.py +0 -0
  90. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/module_output_v2.py +0 -0
  91. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
  92. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
  93. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/saved_job.py +0 -0
  94. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  95. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/system_exception.py +0 -0
  96. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/system_status_update.py +0 -0
  97. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_binary_format/utils.py +0 -0
  98. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_docker_client/__init__.py +0 -0
  99. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_download_container.py +0 -0
  100. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_errors.py +0 -0
  101. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/biolib_logging.py +0 -0
  102. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/__init__.py +0 -0
  103. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/auth.py +0 -0
  104. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/data_record.py +0 -0
  105. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/download_container.py +0 -0
  106. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/init.py +0 -0
  107. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/lfs.py +0 -0
  108. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/push.py +0 -0
  109. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/run.py +0 -0
  110. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/runtime.py +0 -0
  111. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/sdk.py +0 -0
  112. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/cli/start.py +0 -0
  113. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/.gitignore +0 -0
  114. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/__init__.py +0 -0
  115. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  116. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  117. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/__init__.py +0 -0
  118. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/cache_state.py +0 -0
  119. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/cache_types.py +0 -0
  120. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  121. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  122. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
  123. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  124. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  125. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/executors/types.py +0 -0
  126. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  127. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  128. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/job_storage.py +0 -0
  129. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/job_worker.py +0 -0
  130. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  131. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/mappings.py +0 -0
  132. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
  133. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/job_worker/utils.py +0 -0
  134. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/remote_host_proxy.py +0 -0
  135. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/socker_listener_thread.py +0 -0
  136. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/socket_sender_thread.py +0 -0
  137. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/utils.py +0 -0
  138. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/__init__.py +0 -0
  139. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/compute_node_results_proxy.py +0 -0
  140. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  141. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/proxy_utils.py +0 -0
  142. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/webserver.py +0 -0
  143. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/webserver_types.py +0 -0
  144. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  145. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/compute_node/webserver/worker_thread.py +0 -0
  146. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/experiments/__init__.py +0 -0
  147. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/experiments/experiment.py +0 -0
  148. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/jobs/__init__.py +0 -0
  149. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/jobs/job.py +0 -0
  150. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/jobs/job_result.py +0 -0
  151. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/jobs/types.py +0 -0
  152. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/py.typed +0 -0
  153. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/runtime/__init__.py +0 -0
  154. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/sdk/__init__.py +0 -0
  155. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/tables.py +0 -0
  156. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/typing_utils.py +0 -0
  157. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/user/__init__.py +0 -0
  158. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/user/sign_in.py +0 -0
  159. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/utils/__init__.py +0 -0
  160. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/utils/app_uri.py +0 -0
  161. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/utils/cache_state.py +0 -0
  162. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/utils/multipart_uploader.py +0 -0
  163. {pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/utils/zip/remote_zip.py +0 -0
{pybiolib-1.2.1173 → pybiolib-1.2.1180}/PKG-INFO RENAMED
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  Metadata-Version: 2.3
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  Name: pybiolib
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- Version: 1.2.1173
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+ Version: 1.2.1180
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  Summary: BioLib Python Client
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  License: MIT
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  Keywords: biolib
{pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/_internal/push_application.py RENAMED
@@ -1,3 +1,4 @@
1
+ import copy
1
2
  import os
2
3
  import re
3
4
  import sys
@@ -238,7 +239,7 @@ def push_application(
238
239
  app_data_path: Optional[Path] = None
239
240
  try:
240
241
  with open(config_yml_path) as config_yml_file:
241
- config = yaml.safe_load(config_yml_file.read())
242
+ config = copy.deepcopy(yaml.safe_load(config_yml_file.read()))
242
243
 
243
244
  app_data = config.get('app_data') or config.get('assets')
244
245
  if app_data:
{pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/utils/seq_util.py RENAMED
@@ -9,7 +9,7 @@ class SeqUtilRecord:
9
9
  self,
10
10
  sequence: str,
11
11
  sequence_id: str,
12
- description: Optional['str'],
12
+ description: Optional['str'] = None,
13
13
  properties: Optional[Dict[str, str]] = None,
14
14
  ):
15
15
  self.sequence = sequence
{pybiolib-1.2.1173 → pybiolib-1.2.1180}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "pybiolib"
3
- version = "1.2.1173"
3
+ version = "1.2.1180"
4
4
  description = "BioLib Python Client"
5
5
  readme = "PYPI_README.md"
6
6
  license = "MIT"
{pybiolib-1.2.1173 → pybiolib-1.2.1180}/LICENSE RENAMED
File without changes
{pybiolib-1.2.1173 → pybiolib-1.2.1180}/PYPI_README.md RENAMED
File without changes
{pybiolib-1.2.1173 → pybiolib-1.2.1180}/biolib/py.typed RENAMED
File without changes