pybiolib 1.1.1984__tar.gz → 1.1.1986__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 (113) hide show
  1. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/PKG-INFO +1 -1
  2. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +8 -5
  3. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/experiments/experiment.py +2 -2
  4. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/pyproject.toml +1 -1
  5. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/LICENSE +0 -0
  6. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/README.md +0 -0
  7. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/__init__.py +0 -0
  8. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/__init__.py +0 -0
  9. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/data_record/__init__.py +0 -0
  10. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/data_record/data_record.py +0 -0
  11. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
  12. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/fuse_mount/__init__.py +0 -0
  13. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/http_client.py +0 -0
  14. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/libs/__init__.py +0 -0
  15. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/libs/fusepy/__init__.py +0 -0
  16. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/push_application.py +0 -0
  17. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/runtime.py +0 -0
  18. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/_internal/utils/__init__.py +0 -0
  19. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/api/__init__.py +0 -0
  20. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/api/client.py +0 -0
  21. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/app/__init__.py +0 -0
  22. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/app/app.py +0 -0
  23. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/app/search_apps.py +0 -0
  24. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/__init__.py +0 -0
  25. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/api_client.py +0 -0
  26. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/app_types.py +0 -0
  27. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/auth.py +0 -0
  28. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  29. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  30. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/common_types.py +0 -0
  31. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/job_types.py +0 -0
  32. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/lfs_types.py +0 -0
  33. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_api_client/user_state.py +0 -0
  34. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/__init__.py +0 -0
  35. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  36. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/file_in_container.py +0 -0
  37. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/module_input.py +0 -0
  38. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/module_output_v2.py +0 -0
  39. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
  40. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
  41. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/saved_job.py +0 -0
  42. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  43. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/system_exception.py +0 -0
  44. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/system_status_update.py +0 -0
  45. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_binary_format/utils.py +0 -0
  46. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_docker_client/__init__.py +0 -0
  47. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_download_container.py +0 -0
  48. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_errors.py +0 -0
  49. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/biolib_logging.py +0 -0
  50. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/__init__.py +0 -0
  51. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/auth.py +0 -0
  52. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/data_record.py +0 -0
  53. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/download_container.py +0 -0
  54. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/init.py +0 -0
  55. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/lfs.py +0 -0
  56. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/push.py +0 -0
  57. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/run.py +0 -0
  58. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/runtime.py +0 -0
  59. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/cli/start.py +0 -0
  60. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/.gitignore +0 -0
  61. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/__init__.py +0 -0
  62. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  63. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  64. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/__init__.py +0 -0
  65. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/cache_state.py +0 -0
  66. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/cache_types.py +0 -0
  67. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  68. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  69. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
  70. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  71. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  72. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/executors/types.py +0 -0
  73. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  74. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  75. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/job_storage.py +0 -0
  76. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/job_worker.py +0 -0
  77. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  78. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/mappings.py +0 -0
  79. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
  80. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/job_worker/utils.py +0 -0
  81. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/remote_host_proxy.py +0 -0
  82. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/socker_listener_thread.py +0 -0
  83. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/socket_sender_thread.py +0 -0
  84. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/utils.py +0 -0
  85. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/webserver/__init__.py +0 -0
  86. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  87. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/webserver/webserver.py +0 -0
  88. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/webserver/webserver_types.py +0 -0
  89. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  90. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/compute_node/webserver/worker_thread.py +0 -0
  91. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/experiments/__init__.py +0 -0
  92. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/experiments/types.py +0 -0
  93. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/jobs/__init__.py +0 -0
  94. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/jobs/job.py +0 -0
  95. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/jobs/job_result.py +0 -0
  96. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/jobs/types.py +0 -0
  97. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/lfs/__init__.py +0 -0
  98. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/lfs/cache.py +0 -0
  99. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/lfs/utils.py +0 -0
  100. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/runtime/__init__.py +0 -0
  101. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/sdk/__init__.py +0 -0
  102. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/tables.py +0 -0
  103. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/templates/__init__.py +0 -0
  104. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/templates/example_app.py +0 -0
  105. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/typing_utils.py +0 -0
  106. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/user/__init__.py +0 -0
  107. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/user/sign_in.py +0 -0
  108. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/utils/__init__.py +0 -0
  109. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/utils/app_uri.py +0 -0
  110. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/utils/cache_state.py +0 -0
  111. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/utils/multipart_uploader.py +0 -0
  112. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/utils/seq_util.py +0 -0
  113. {pybiolib-1.1.1984 → pybiolib-1.1.1986}/biolib/utils/zip/remote_zip.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: pybiolib
3
- Version: 1.1.1984
3
+ Version: 1.1.1986
4
4
  Summary: BioLib Python Client
5
5
  Home-page: https://github.com/biolib
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  License: MIT
@@ -29,10 +29,10 @@ class ExperimentFuseMount(Operations):
29
29
  self._mounted_at_epoch_seconds: int = int(time())
30
30
 
31
31
  @staticmethod
32
- def mount(experiment, path: str) -> None:
32
+ def mount_experiment(experiment, mount_path: str) -> None:
33
33
  FUSE(
34
34
  operations=ExperimentFuseMount(experiment),
35
- mountpoint=path,
35
+ mountpoint=mount_path,
36
36
  nothreads=True,
37
37
  foreground=True,
38
38
  allow_other=False,
@@ -108,6 +108,12 @@ class ExperimentFuseMount(Operations):
108
108
 
109
109
  return file.get_data(start=offset, length=size)
110
110
 
111
+ def release(self, path: str, fh: int) -> int:
112
+ return 0
113
+
114
+ def releasedir(self, path: str, fh: int) -> int:
115
+ return 0
116
+
111
117
  @staticmethod
112
118
  def _get_directory_attributes(timestamp_epoch_seconds: int) -> _AttributeDict:
113
119
  return _AttributeDict(
@@ -196,8 +202,5 @@ class ExperimentFuseMount(Operations):
196
202
  def flush(self, path, fh):
197
203
  raise FuseOSError(errno.EACCES)
198
204
 
199
- def release(self, path, fh):
200
- raise FuseOSError(errno.EACCES)
201
-
202
205
  def fsync(self, path, datasync, fh):
203
206
  raise FuseOSError(errno.EACCES)
@@ -73,7 +73,7 @@ class Experiment:
73
73
  def add_job(self, job_id: str) -> None:
74
74
  api.client.patch(path=f'/jobs/{job_id}/', data={'experiment_uuid': self.uuid})
75
75
 
76
- def mount_files(self, path: str) -> None:
76
+ def mount_files(self, mount_path: str) -> None:
77
77
  try:
78
78
  # Only attempt to import FUSE dependencies when strictly necessary
79
79
  from biolib._internal.fuse_mount import ( # pylint: disable=import-outside-toplevel
@@ -84,7 +84,7 @@ class Experiment:
84
84
  'Failed to import FUSE mounting utils. Please ensure FUSE is installed on your system.'
85
85
  ) from error
86
86
 
87
- _ExperimentFuseMount.mount(experiment=self, path=path)
87
+ _ExperimentFuseMount.mount_experiment(experiment=self, mount_path=mount_path)
88
88
 
89
89
  def export_job_list(self, export_format='dicts'):
90
90
  valid_formats = ('dicts', 'dataframe')
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "pybiolib"
3
- version = "1.1.1984"
3
+ version = "1.1.1986"
4
4
  description = "BioLib Python Client"
5
5
  readme = "README.md"
6
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  license = "MIT"
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