pybiolib 1.2.211__tar.gz → 1.2.216__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 (124) hide show
  1. {pybiolib-1.2.211 → pybiolib-1.2.216}/PKG-INFO +1 -1
  2. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/executors/docker_executor.py +2 -2
  3. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/webserver/webserver.py +6 -2
  4. {pybiolib-1.2.211 → pybiolib-1.2.216}/pyproject.toml +1 -1
  5. {pybiolib-1.2.211 → pybiolib-1.2.216}/LICENSE +0 -0
  6. {pybiolib-1.2.211 → pybiolib-1.2.216}/PYPI_README.md +0 -0
  7. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/__init__.py +0 -0
  8. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_data_record/data_record.py +0 -0
  9. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/__init__.py +0 -0
  10. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/data_record/__init__.py +0 -0
  11. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/data_record/data_record.py +0 -0
  12. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/data_record/push_data.py +0 -0
  13. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
  14. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/file_utils.py +0 -0
  15. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/fuse_mount/__init__.py +0 -0
  16. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +0 -0
  17. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/http_client.py +0 -0
  18. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/lfs/__init__.py +0 -0
  19. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/lfs/cache.py +0 -0
  20. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/libs/__init__.py +0 -0
  21. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/libs/fusepy/__init__.py +0 -0
  22. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/push_application.py +0 -0
  23. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/runtime.py +0 -0
  24. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/__init__.py +0 -0
  25. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/app.py +0 -0
  26. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/data_record.py +0 -0
  27. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/experiment.py +0 -0
  28. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/file_node.py +0 -0
  29. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/resource.py +0 -0
  30. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/resource_version.py +0 -0
  31. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/types/typing.py +0 -0
  32. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/utils/__init__.py +0 -0
  33. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_internal/utils/multinode.py +0 -0
  34. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/_runtime/runtime.py +0 -0
  35. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/api/__init__.py +0 -0
  36. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/api/client.py +0 -0
  37. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/app/__init__.py +0 -0
  38. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/app/app.py +0 -0
  39. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/app/search_apps.py +0 -0
  40. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/__init__.py +0 -0
  41. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/api_client.py +0 -0
  42. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/app_types.py +0 -0
  43. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/auth.py +0 -0
  44. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  45. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  46. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/common_types.py +0 -0
  47. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/job_types.py +0 -0
  48. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/lfs_types.py +0 -0
  49. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_api_client/user_state.py +0 -0
  50. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/__init__.py +0 -0
  51. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  52. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/file_in_container.py +0 -0
  53. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/module_input.py +0 -0
  54. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/module_output_v2.py +0 -0
  55. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
  56. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
  57. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/saved_job.py +0 -0
  58. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  59. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/system_exception.py +0 -0
  60. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/system_status_update.py +0 -0
  61. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_binary_format/utils.py +0 -0
  62. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_docker_client/__init__.py +0 -0
  63. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_download_container.py +0 -0
  64. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_errors.py +0 -0
  65. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/biolib_logging.py +0 -0
  66. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/__init__.py +0 -0
  67. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/auth.py +0 -0
  68. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/data_record.py +0 -0
  69. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/download_container.py +0 -0
  70. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/init.py +0 -0
  71. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/lfs.py +0 -0
  72. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/push.py +0 -0
  73. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/run.py +0 -0
  74. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/runtime.py +0 -0
  75. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/start.py +0 -0
  76. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/.gitignore +0 -0
  77. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/__init__.py +0 -0
  78. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  79. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  80. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/__init__.py +0 -0
  81. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/cache_state.py +0 -0
  82. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/cache_types.py +0 -0
  83. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  84. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  85. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  86. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  87. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/executors/types.py +0 -0
  88. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  89. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  90. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/job_storage.py +0 -0
  91. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/job_worker.py +0 -0
  92. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  93. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/mappings.py +0 -0
  94. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
  95. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/utils.py +0 -0
  96. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/remote_host_proxy.py +0 -0
  97. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/socker_listener_thread.py +0 -0
  98. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/socket_sender_thread.py +0 -0
  99. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/utils.py +0 -0
  100. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/webserver/__init__.py +0 -0
  101. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  102. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/webserver/webserver_types.py +0 -0
  103. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  104. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/webserver/worker_thread.py +0 -0
  105. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/experiments/__init__.py +0 -0
  106. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/experiments/experiment.py +0 -0
  107. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/jobs/__init__.py +0 -0
  108. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/jobs/job.py +0 -0
  109. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/jobs/job_result.py +0 -0
  110. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/jobs/types.py +0 -0
  111. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/runtime/__init__.py +0 -0
  112. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/sdk/__init__.py +0 -0
  113. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/tables.py +0 -0
  114. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/templates/__init__.py +0 -0
  115. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/templates/example_app.py +0 -0
  116. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/typing_utils.py +0 -0
  117. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/user/__init__.py +0 -0
  118. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/user/sign_in.py +0 -0
  119. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/utils/__init__.py +0 -0
  120. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/utils/app_uri.py +0 -0
  121. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/utils/cache_state.py +0 -0
  122. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/utils/multipart_uploader.py +0 -0
  123. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/utils/seq_util.py +0 -0
  124. {pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/utils/zip/remote_zip.py +0 -0
{pybiolib-1.2.211 → pybiolib-1.2.216}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.1
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  Name: pybiolib
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- Version: 1.2.211
3
+ Version: 1.2.216
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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-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/job_worker/executors/docker_executor.py RENAMED
@@ -122,7 +122,7 @@ class DockerExecutor:
122
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  time.sleep(5 * retry_count)
123
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  try:
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  start_time = time.time()
125
- if utils.IS_RUNNING_IN_CLOUD and not self._options['job'].get('federated_job_uuid'):
125
+ if utils.IS_RUNNING_IN_CLOUD:
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  DockerImageCache().get(
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  image_uri=self._absolute_image_uri,
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  estimated_image_size_bytes=estimated_image_size_bytes,
@@ -133,7 +133,7 @@ class DockerExecutor:
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  try:
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  docker_client.images.get(self._absolute_image_uri)
135
135
  except ImageNotFound:
136
- job_uuid = self._options['job'].get('federated_job_uuid') or self._options['job']['public_id']
136
+ job_uuid = self._options['job']['public_id']
137
137
  docker_client.images.pull(
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  self._absolute_image_uri,
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139
  auth_config={'username': 'biolib', 'password': f',{job_uuid}'},
{pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/compute_node/webserver/webserver.py RENAMED
@@ -19,7 +19,11 @@ from biolib.typing_utils import Optional
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  app = Flask(__name__)
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- biolib_tmp_dir = tempfile.TemporaryDirectory()
22
+ if utils.IS_RUNNING_IN_CLOUD:
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+ _BIOLIB_TMP_DIR = '/biolib/tmp'
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+ os.makedirs(_BIOLIB_TMP_DIR, exist_ok=True)
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+ else:
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+ _BIOLIB_TMP_DIR = tempfile.TemporaryDirectory().name
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  @app.route('/hello/')
@@ -41,7 +45,7 @@ def save_job():
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  return jsonify({'job': 'Invalid job'}), 400
42
46
 
43
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  job_id = saved_job['job']['public_id']
44
- job_temporary_dir = os.path.join(biolib_tmp_dir.name, job_id)
48
+ job_temporary_dir = os.path.join(_BIOLIB_TMP_DIR, job_id)
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  os.makedirs(job_temporary_dir)
46
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  saved_job['BASE_URL'] = BiolibApiClient.get().base_url
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  saved_job['job_temporary_dir'] = job_temporary_dir
{pybiolib-1.2.211 → pybiolib-1.2.216}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "pybiolib"
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- version = "1.2.211"
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+ version = "1.2.216"
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  description = "BioLib Python Client"
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  readme = "PYPI_README.md"
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  license = "MIT"
{pybiolib-1.2.211 → pybiolib-1.2.216}/LICENSE RENAMED
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{pybiolib-1.2.211 → pybiolib-1.2.216}/PYPI_README.md RENAMED
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{pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/app/app.py RENAMED
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{pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/lfs.py RENAMED
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{pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/cli/run.py RENAMED
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{pybiolib-1.2.211 → pybiolib-1.2.216}/biolib/tables.py RENAMED
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