lamindb_setup 1.9.1__py3-none-any.whl → 1.10.0__py3-none-any.whl

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 (40) hide show
  1. lamindb_setup/__init__.py +107 -107
  2. lamindb_setup/_cache.py +87 -87
  3. lamindb_setup/_check_setup.py +192 -166
  4. lamindb_setup/_connect_instance.py +415 -328
  5. lamindb_setup/_delete.py +144 -141
  6. lamindb_setup/_disconnect.py +35 -32
  7. lamindb_setup/_init_instance.py +430 -440
  8. lamindb_setup/_migrate.py +278 -266
  9. lamindb_setup/_register_instance.py +32 -35
  10. lamindb_setup/_schema_metadata.py +441 -441
  11. lamindb_setup/_set_managed_storage.py +69 -70
  12. lamindb_setup/_setup_user.py +172 -133
  13. lamindb_setup/core/__init__.py +21 -21
  14. lamindb_setup/core/_aws_options.py +223 -223
  15. lamindb_setup/core/_aws_storage.py +9 -1
  16. lamindb_setup/core/_hub_client.py +248 -248
  17. lamindb_setup/core/_hub_core.py +728 -665
  18. lamindb_setup/core/_hub_crud.py +227 -227
  19. lamindb_setup/core/_private_django_api.py +83 -83
  20. lamindb_setup/core/_settings.py +384 -377
  21. lamindb_setup/core/_settings_instance.py +577 -569
  22. lamindb_setup/core/_settings_load.py +141 -141
  23. lamindb_setup/core/_settings_save.py +95 -95
  24. lamindb_setup/core/_settings_storage.py +427 -429
  25. lamindb_setup/core/_settings_store.py +91 -91
  26. lamindb_setup/core/_settings_user.py +55 -55
  27. lamindb_setup/core/_setup_bionty_sources.py +44 -44
  28. lamindb_setup/core/cloud_sqlite_locker.py +240 -240
  29. lamindb_setup/core/django.py +315 -305
  30. lamindb_setup/core/exceptions.py +1 -1
  31. lamindb_setup/core/hashing.py +134 -134
  32. lamindb_setup/core/types.py +1 -1
  33. lamindb_setup/core/upath.py +1013 -1013
  34. lamindb_setup/errors.py +80 -70
  35. lamindb_setup/types.py +20 -20
  36. {lamindb_setup-1.9.1.dist-info → lamindb_setup-1.10.0.dist-info}/METADATA +3 -3
  37. lamindb_setup-1.10.0.dist-info/RECORD +50 -0
  38. lamindb_setup-1.9.1.dist-info/RECORD +0 -50
  39. {lamindb_setup-1.9.1.dist-info → lamindb_setup-1.10.0.dist-info}/LICENSE +0 -0
  40. {lamindb_setup-1.9.1.dist-info → lamindb_setup-1.10.0.dist-info}/WHEEL +0 -0
lamindb_setup/errors.py CHANGED
@@ -1,70 +1,80 @@
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- """Errors.
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-
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- .. autosummary::
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- :toctree: .
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-
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- InstanceNotSetupError
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- ModuleWasntConfigured
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- StorageAlreadyManaged
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- StorageNotEmpty
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- InstanceLockedException
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- SettingsEnvFileOutdated
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- CannotSwitchDefaultInstance
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-
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- """
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-
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- from __future__ import annotations
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-
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- import click
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-
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-
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- class DefaultMessageException(Exception):
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- default_message: str | None = None
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-
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- def __init__(self, message: str | None = None):
25
- if message is None:
26
- message = self.default_message
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- super().__init__(message)
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-
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-
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- class InstanceNotSetupError(DefaultMessageException):
31
- default_message = """\
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- To use lamindb, you need to connect to an instance.
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-
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- Connect to an instance: `ln.connect()`. Init an instance: `ln.setup.init()`.
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-
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- If you used the CLI to set up lamindb in a notebook, restart the Python session.
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- """
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-
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-
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- MODULE_WASNT_CONFIGURED_MESSAGE_TEMPLATE = (
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- "'{}' wasn't configured for this instance -- "
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- "if you want it, go to your instance settings page and add it under 'schema modules' (or ask an admin to do so)"
43
- )
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-
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-
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- class ModuleWasntConfigured(Exception):
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- pass
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-
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-
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- class StorageAlreadyManaged(Exception):
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- pass
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-
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-
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- class StorageNotEmpty(click.ClickException):
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- def show(self, file=None):
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- pass
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-
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-
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- # raise if a cloud SQLite instance is already locked
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- # ignored by unlock_cloud_sqlite_upon_exception
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- class InstanceLockedException(Exception):
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- pass
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-
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-
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- class SettingsEnvFileOutdated(Exception):
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- pass
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-
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-
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- class CannotSwitchDefaultInstance(Exception):
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- pass
1
+ """Errors.
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+
3
+ .. autosummary::
4
+ :toctree: .
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+
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+ CurrentInstanceNotConfigured
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+ InstanceNotSetupError
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+ ModuleWasntConfigured
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+ StorageAlreadyManaged
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+ StorageNotEmpty
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+ InstanceLockedException
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+ SettingsEnvFileOutdated
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+ CannotSwitchDefaultInstance
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+
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+ """
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+
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+ from __future__ import annotations
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+
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+ import click
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+
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+
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+ class DefaultMessageException(Exception):
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+ default_message: str | None = None
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+
25
+ def __init__(self, message: str | None = None):
26
+ if message is None:
27
+ message = self.default_message
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+ super().__init__(message)
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+
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+
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+ # TODO: remove this exception sooner or later because we don't have a need for it anymore
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+ class InstanceNotSetupError(DefaultMessageException):
33
+ default_message = """\
34
+ To use lamindb, you need to connect to an instance.
35
+
36
+ Connect to an instance: `ln.connect()`. Init an instance: `ln.setup.init()`.
37
+
38
+ If you used the CLI to set up lamindb in a notebook, restart the Python session.
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+ """
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+
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+
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+ class CurrentInstanceNotConfigured(DefaultMessageException):
43
+ default_message = """\
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+ No instance is connected! Call
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+ - CLI: lamin connect / lamin init
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+ - Python: ln.connect() / ln.setup.init()
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+ - R: ln$connect() / ln$setup$init()"""
48
+
49
+
50
+ MODULE_WASNT_CONFIGURED_MESSAGE_TEMPLATE = (
51
+ "'{}' wasn't configured for this instance -- "
52
+ "if you want it, go to your instance settings page and add it under 'schema modules' (or ask an admin to do so)"
53
+ )
54
+
55
+
56
+ class ModuleWasntConfigured(Exception):
57
+ pass
58
+
59
+
60
+ class StorageAlreadyManaged(Exception):
61
+ pass
62
+
63
+
64
+ class StorageNotEmpty(click.ClickException):
65
+ def show(self, file=None):
66
+ pass
67
+
68
+
69
+ # raise if a cloud SQLite instance is already locked
70
+ # ignored by unlock_cloud_sqlite_upon_exception
71
+ class InstanceLockedException(Exception):
72
+ pass
73
+
74
+
75
+ class SettingsEnvFileOutdated(Exception):
76
+ pass
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+
78
+
79
+ class CannotSwitchDefaultInstance(Exception):
80
+ pass
lamindb_setup/types.py CHANGED
@@ -1,20 +1,20 @@
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- """Types.
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-
3
- .. autosummary::
4
- :toctree: .
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-
6
- UPathStr
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- StorageType
8
- """
9
-
10
- from __future__ import annotations
11
-
12
- # we need Union here because __future__ annotations doesn't work with TypeAlias
13
- from pathlib import Path
14
- from typing import Literal, Union
15
-
16
- # UPath is subclass of Path, hence, it's not necessary to list UPath
17
- # we keep it in the name of the TypeAlias to make it clear to users that
18
- # cloud paths are allowed / PathStr is often associated with local paths
19
- UPathStr = Union[str, Path] # typing.TypeAlias, >3.10 on but already deprecated
20
- StorageType = Literal["local", "s3", "gs", "hf", "http", "https"]
1
+ """Types.
2
+
3
+ .. autosummary::
4
+ :toctree: .
5
+
6
+ UPathStr
7
+ StorageType
8
+ """
9
+
10
+ from __future__ import annotations
11
+
12
+ # we need Union here because __future__ annotations doesn't work with TypeAlias
13
+ from pathlib import Path
14
+ from typing import Literal, Union
15
+
16
+ # UPath is subclass of Path, hence, it's not necessary to list UPath
17
+ # we keep it in the name of the TypeAlias to make it clear to users that
18
+ # cloud paths are allowed / PathStr is often associated with local paths
19
+ UPathStr = Union[str, Path] # typing.TypeAlias, >3.10 on but already deprecated
20
+ StorageType = Literal["local", "s3", "gs", "hf", "http", "https"]
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: lamindb_setup
3
- Version: 1.9.1
3
+ Version: 1.10.0
4
4
  Summary: Setup & configure LaminDB.
5
5
  Author-email: Lamin Labs <open-source@lamin.ai>
6
6
  Requires-Python: >=3.10
@@ -21,7 +21,7 @@ Requires-Dist: psutil
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  Requires-Dist: packaging
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  Requires-Dist: urllib3<2 ; extra == "aws"
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  Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
24
- Requires-Dist: s3fs>=2023.12.2,<=2025.3.2,!=2024.10.0 ; extra == "aws"
24
+ Requires-Dist: s3fs>=2023.12.2,<=2025.7.0,!=2024.10.0 ; extra == "aws"
25
25
  Requires-Dist: line_profiler ; extra == "dev"
26
26
  Requires-Dist: psycopg2-binary ; extra == "dev"
27
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  Requires-Dist: python-dotenv ; extra == "dev"
@@ -32,7 +32,7 @@ Requires-Dist: pytest-xdist ; extra == "dev"
32
32
  Requires-Dist: nbproject-test>=0.4.3 ; extra == "dev"
33
33
  Requires-Dist: pandas ; extra == "dev"
34
34
  Requires-Dist: django-schema-graph ; extra == "erdiagram"
35
- Requires-Dist: gcsfs>=2023.12.2,<=2025.3.2 ; extra == "gcp"
35
+ Requires-Dist: gcsfs>=2023.12.2,<=2025.7.0 ; extra == "gcp"
36
36
  Project-URL: Home, https://github.com/laminlabs/lamindb-setup
37
37
  Provides-Extra: aws
38
38
  Provides-Extra: dev
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