pybiolib 1.2.871__tar.gz → 1.2.874__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 (146) hide show
  1. {pybiolib-1.2.871 → pybiolib-1.2.874}/PKG-INFO +1 -1
  2. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/push_application.py +19 -1
  3. {pybiolib-1.2.871 → pybiolib-1.2.874}/pyproject.toml +1 -1
  4. {pybiolib-1.2.871 → pybiolib-1.2.874}/LICENSE +0 -0
  5. {pybiolib-1.2.871 → pybiolib-1.2.874}/PYPI_README.md +0 -0
  6. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/__init__.py +0 -0
  7. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_data_record/data_record.py +0 -0
  8. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/__init__.py +0 -0
  9. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/add_copilot_prompts.py +0 -0
  10. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/data_record/__init__.py +0 -0
  11. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/data_record/data_record.py +0 -0
  12. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/data_record/push_data.py +0 -0
  13. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
  14. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/file_utils.py +0 -0
  15. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/fuse_mount/__init__.py +0 -0
  16. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +0 -0
  17. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/http_client.py +0 -0
  18. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/lfs/__init__.py +0 -0
  19. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/lfs/cache.py +0 -0
  20. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/libs/__init__.py +0 -0
  21. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/libs/fusepy/__init__.py +0 -0
  22. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/llm_instructions/.github/instructions/general-app-knowledge.instructions.md +0 -0
  23. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/llm_instructions/.github/instructions/style-general.instructions.md +0 -0
  24. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/llm_instructions/.github/instructions/style-python.instructions.md +0 -0
  25. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/llm_instructions/.github/instructions/style-react-ts.instructions.md +0 -0
  26. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/llm_instructions/.github/prompts/biolib_app_inputs.prompt.md +0 -0
  27. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/llm_instructions/.github/prompts/biolib_run_apps.prompt.md +0 -0
  28. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/llm_instructions/__init__.py +0 -0
  29. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/runtime.py +0 -0
  30. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/__init__.py +0 -0
  31. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/init_template/.biolib/config.yml +0 -0
  32. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/init_template/.github/workflows/biolib.yml +0 -0
  33. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/init_template/.gitignore +0 -0
  34. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/init_template/Dockerfile +0 -0
  35. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/init_template/requirements.txt +0 -0
  36. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/init_template/run.py +0 -0
  37. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/init_template/run.sh +0 -0
  38. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/templates/templates.py +0 -0
  39. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/tree_utils.py +0 -0
  40. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/__init__.py +0 -0
  41. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/app.py +0 -0
  42. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/data_record.py +0 -0
  43. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/experiment.py +0 -0
  44. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/file_node.py +0 -0
  45. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/push.py +0 -0
  46. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/resource.py +0 -0
  47. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/resource_permission.py +0 -0
  48. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/resource_version.py +0 -0
  49. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/result.py +0 -0
  50. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/types/typing.py +0 -0
  51. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/utils/__init__.py +0 -0
  52. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_internal/utils/multinode.py +0 -0
  53. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_runtime/runtime.py +0 -0
  54. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/_session/session.py +0 -0
  55. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/api/__init__.py +0 -0
  56. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/api/client.py +0 -0
  57. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/app/__init__.py +0 -0
  58. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/app/app.py +0 -0
  59. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/app/search_apps.py +0 -0
  60. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/__init__.py +0 -0
  61. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/api_client.py +0 -0
  62. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/app_types.py +0 -0
  63. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/auth.py +0 -0
  64. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  65. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  66. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/common_types.py +0 -0
  67. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/job_types.py +0 -0
  68. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/lfs_types.py +0 -0
  69. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_api_client/user_state.py +0 -0
  70. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/__init__.py +0 -0
  71. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  72. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/file_in_container.py +0 -0
  73. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/module_input.py +0 -0
  74. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/module_output_v2.py +0 -0
  75. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
  76. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
  77. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/saved_job.py +0 -0
  78. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  79. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/system_exception.py +0 -0
  80. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/system_status_update.py +0 -0
  81. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_binary_format/utils.py +0 -0
  82. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_docker_client/__init__.py +0 -0
  83. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_download_container.py +0 -0
  84. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_errors.py +0 -0
  85. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/biolib_logging.py +0 -0
  86. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/__init__.py +0 -0
  87. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/auth.py +0 -0
  88. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/data_record.py +0 -0
  89. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/download_container.py +0 -0
  90. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/init.py +0 -0
  91. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/lfs.py +0 -0
  92. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/push.py +0 -0
  93. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/run.py +0 -0
  94. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/runtime.py +0 -0
  95. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/sdk.py +0 -0
  96. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/cli/start.py +0 -0
  97. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/.gitignore +0 -0
  98. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/__init__.py +0 -0
  99. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  100. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  101. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/__init__.py +0 -0
  102. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/cache_state.py +0 -0
  103. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/cache_types.py +0 -0
  104. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  105. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  106. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
  107. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  108. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  109. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/executors/types.py +0 -0
  110. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  111. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  112. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/job_storage.py +0 -0
  113. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/job_worker.py +0 -0
  114. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  115. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/mappings.py +0 -0
  116. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
  117. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/job_worker/utils.py +0 -0
  118. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/remote_host_proxy.py +0 -0
  119. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/socker_listener_thread.py +0 -0
  120. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/socket_sender_thread.py +0 -0
  121. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/utils.py +0 -0
  122. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/webserver/__init__.py +0 -0
  123. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  124. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/webserver/webserver.py +0 -0
  125. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/webserver/webserver_types.py +0 -0
  126. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  127. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/compute_node/webserver/worker_thread.py +0 -0
  128. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/experiments/__init__.py +0 -0
  129. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/experiments/experiment.py +0 -0
  130. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/jobs/__init__.py +0 -0
  131. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/jobs/job.py +0 -0
  132. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/jobs/job_result.py +0 -0
  133. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/jobs/types.py +0 -0
  134. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/py.typed +0 -0
  135. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/runtime/__init__.py +0 -0
  136. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/sdk/__init__.py +0 -0
  137. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/tables.py +0 -0
  138. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/typing_utils.py +0 -0
  139. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/user/__init__.py +0 -0
  140. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/user/sign_in.py +0 -0
  141. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/utils/__init__.py +0 -0
  142. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/utils/app_uri.py +0 -0
  143. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/utils/cache_state.py +0 -0
  144. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/utils/multipart_uploader.py +0 -0
  145. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/utils/seq_util.py +0 -0
  146. {pybiolib-1.2.871 → pybiolib-1.2.874}/biolib/utils/zip/remote_zip.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: pybiolib
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- Version: 1.2.871
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+ Version: 1.2.874
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  Summary: BioLib Python Client
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  License: MIT
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  Keywords: biolib
@@ -1,9 +1,11 @@
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  import os
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  import re
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+ import sys
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  from pathlib import Path
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  import rich.progress
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  import yaml
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+ from rich.console import Console
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  from biolib import api, utils
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  from biolib._internal.data_record.push_data import (
@@ -36,7 +38,9 @@ class DockerStatusUpdate(TypedDict, total=False):
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  def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate], action: str) -> None:
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- with rich.progress.Progress() as progress:
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+ console = Console(force_terminal=True, force_interactive=True, legacy_windows=False)
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+
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+ with rich.progress.Progress(console=console, refresh_per_second=20, transient=False) as progress:
40
44
  layer_id_to_task_id = {}
41
45
  overall_task_id = progress.add_task(description=f'[bold blue]{action} Docker image', total=None)
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@@ -54,12 +58,16 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
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  completed=progress_detail['current'],
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  total=progress_detail['total'],
56
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  )
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+ progress.refresh()
62
+ sys.stdout.flush()
57
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  elif update['status'] == 'Layer already exists':
58
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  progress.update(
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  completed=100,
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  task_id=layer_id_to_task_id[layer_id],
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  total=100,
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  )
69
+ progress.refresh()
70
+ sys.stdout.flush()
63
71
  elif 'status' in update and 'id' in update:
64
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  layer_id = update['id']
65
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  status = update['status']
@@ -71,10 +79,14 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
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  progress.update(
72
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  task_id=layer_id_to_task_id[layer_id], description=f'[yellow]{status} layer {layer_id}'
73
81
  )
82
+ progress.refresh()
83
+ sys.stdout.flush()
74
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  elif status in ['Pushing', 'Uploading']:
75
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  progress.update(
76
86
  task_id=layer_id_to_task_id[layer_id], description=f'[cyan]{status} layer {layer_id}'
77
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  )
88
+ progress.refresh()
89
+ sys.stdout.flush()
78
90
  elif status in ['Pushed', 'Uploaded']:
79
91
  progress.update(
80
92
  task_id=layer_id_to_task_id[layer_id],
@@ -82,6 +94,8 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
82
94
  completed=100,
83
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  total=100,
84
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  )
97
+ progress.refresh()
98
+ sys.stdout.flush()
85
99
  elif status == 'Layer already exists':
86
100
  progress.update(
87
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  task_id=layer_id_to_task_id[layer_id],
@@ -89,10 +103,14 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
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  completed=100,
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  total=100,
91
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  )
106
+ progress.refresh()
107
+ sys.stdout.flush()
92
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  elif 'status' in update and update['status']:
93
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  status = update['status']
94
110
  if status not in ['Preparing', 'Pushing', 'Pushed', 'Waiting', 'Layer already exists']:
95
111
  progress.update(task_id=overall_task_id, description=f'[bold blue]{action} Docker image - {status}')
112
+ progress.refresh()
113
+ sys.stdout.flush()
96
114
  elif 'status' not in update and 'progressDetail' not in update:
97
115
  print(update)
98
116
 
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "pybiolib"
3
- version = "1.2.871"
3
+ version = "1.2.874"
4
4
  description = "BioLib Python Client"
5
5
  readme = "PYPI_README.md"
6
6
  license = "MIT"
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