pybiolib 1.1.2204__tar.gz → 1.1.2208__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 (120) hide show
  1. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/PKG-INFO +1 -1
  2. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/job_storage.py +14 -1
  3. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/pyproject.toml +1 -1
  4. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/LICENSE +0 -0
  5. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/README.md +0 -0
  6. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/__init__.py +0 -0
  7. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_data_record/data_record.py +0 -0
  8. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/__init__.py +0 -0
  9. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/data_record/__init__.py +0 -0
  10. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/data_record/data_record.py +0 -0
  11. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
  12. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/file_utils.py +0 -0
  13. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/fuse_mount/__init__.py +0 -0
  14. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +0 -0
  15. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/http_client.py +0 -0
  16. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/lfs/__init__.py +0 -0
  17. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/lfs/cache.py +0 -0
  18. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/libs/__init__.py +0 -0
  19. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/libs/fusepy/__init__.py +0 -0
  20. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/push_application.py +0 -0
  21. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/runtime.py +0 -0
  22. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/types/__init__.py +0 -0
  23. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/types/app.py +0 -0
  24. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/types/data_record.py +0 -0
  25. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/types/experiment.py +0 -0
  26. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/types/resource.py +0 -0
  27. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/types/typing.py +0 -0
  28. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_internal/utils/__init__.py +0 -0
  29. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/_runtime/runtime.py +0 -0
  30. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/api/__init__.py +0 -0
  31. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/api/client.py +0 -0
  32. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/app/__init__.py +0 -0
  33. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/app/app.py +0 -0
  34. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/app/search_apps.py +0 -0
  35. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/__init__.py +0 -0
  36. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/api_client.py +0 -0
  37. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/app_types.py +0 -0
  38. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/auth.py +0 -0
  39. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  40. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  41. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/common_types.py +0 -0
  42. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/job_types.py +0 -0
  43. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/lfs_types.py +0 -0
  44. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_api_client/user_state.py +0 -0
  45. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/__init__.py +0 -0
  46. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  47. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/file_in_container.py +0 -0
  48. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/module_input.py +0 -0
  49. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/module_output_v2.py +0 -0
  50. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
  51. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
  52. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/saved_job.py +0 -0
  53. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  54. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/system_exception.py +0 -0
  55. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/system_status_update.py +0 -0
  56. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_binary_format/utils.py +0 -0
  57. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_docker_client/__init__.py +0 -0
  58. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_download_container.py +0 -0
  59. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_errors.py +0 -0
  60. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/biolib_logging.py +0 -0
  61. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/__init__.py +0 -0
  62. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/auth.py +0 -0
  63. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/data_record.py +0 -0
  64. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/download_container.py +0 -0
  65. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/init.py +0 -0
  66. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/lfs.py +0 -0
  67. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/push.py +0 -0
  68. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/run.py +0 -0
  69. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/runtime.py +0 -0
  70. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/cli/start.py +0 -0
  71. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/.gitignore +0 -0
  72. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/__init__.py +0 -0
  73. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  74. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  75. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/__init__.py +0 -0
  76. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/cache_state.py +0 -0
  77. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/cache_types.py +0 -0
  78. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  79. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  80. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
  81. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  82. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  83. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/executors/types.py +0 -0
  84. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  85. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  86. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/job_worker.py +0 -0
  87. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  88. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/mappings.py +0 -0
  89. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
  90. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/utils.py +0 -0
  91. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/remote_host_proxy.py +0 -0
  92. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/socker_listener_thread.py +0 -0
  93. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/socket_sender_thread.py +0 -0
  94. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/utils.py +0 -0
  95. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/webserver/__init__.py +0 -0
  96. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  97. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/webserver/webserver.py +0 -0
  98. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/webserver/webserver_types.py +0 -0
  99. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  100. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/webserver/worker_thread.py +0 -0
  101. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/experiments/__init__.py +0 -0
  102. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/experiments/experiment.py +0 -0
  103. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/jobs/__init__.py +0 -0
  104. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/jobs/job.py +0 -0
  105. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/jobs/job_result.py +0 -0
  106. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/jobs/types.py +0 -0
  107. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/runtime/__init__.py +0 -0
  108. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/sdk/__init__.py +0 -0
  109. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/tables.py +0 -0
  110. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/templates/__init__.py +0 -0
  111. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/templates/example_app.py +0 -0
  112. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/typing_utils.py +0 -0
  113. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/user/__init__.py +0 -0
  114. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/user/sign_in.py +0 -0
  115. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/utils/__init__.py +0 -0
  116. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/utils/app_uri.py +0 -0
  117. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/utils/cache_state.py +0 -0
  118. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/utils/multipart_uploader.py +0 -0
  119. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/utils/seq_util.py +0 -0
  120. {pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/utils/zip/remote_zip.py +0 -0
{pybiolib-1.1.2204 → pybiolib-1.1.2208}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: pybiolib
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- Version: 1.1.2204
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+ Version: 1.1.2208
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  Summary: BioLib Python Client
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  Home-page: https://github.com/biolib
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  License: MIT
{pybiolib-1.1.2204 → pybiolib-1.1.2208}/biolib/compute_node/job_worker/job_storage.py RENAMED
@@ -47,8 +47,21 @@ class JobStorage:
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  module_output_path = os.path.join(job_temporary_dir, JobStorage.module_output_file_name)
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  module_output_size = os.path.getsize(module_output_path)
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+ # Calculate chunk size based on max chunk count of 10_000, using 9_000 to be on the safe side
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+ max_chunk_count = 9_000
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+ min_chunk_size_bytes = 50_000_000
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+ chunk_size_in_bytes = max(min_chunk_size_bytes, module_output_size // max_chunk_count)
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+
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+ logger_no_user_data.debug(
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+ f'Job "{job_uuid}" uploading result of size {module_output_size} bytes '
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+ f'with chunk size of {chunk_size_in_bytes} bytes...'
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+ )
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+
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  with open(module_output_path, mode='rb') as module_output_file:
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- module_output_iterator = get_chunk_iterator_from_file_object(module_output_file)
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+ module_output_iterator = get_chunk_iterator_from_file_object(
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+ file_object=module_output_file,
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+ chunk_size_in_bytes=chunk_size_in_bytes,
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+ )
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  multipart_uploader = JobStorage._get_module_output_uploader(job_uuid)
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  multipart_uploader.upload(
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  payload_iterator=module_output_iterator,
{pybiolib-1.1.2204 → pybiolib-1.1.2208}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "pybiolib"
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- version = "1.1.2204"
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+ version = "1.1.2208"
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  description = "BioLib Python Client"
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  readme = "README.md"
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  license = "MIT"
{pybiolib-1.1.2204 → pybiolib-1.1.2208}/LICENSE RENAMED
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{pybiolib-1.1.2204 → pybiolib-1.1.2208}/README.md RENAMED
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