lamindb 1.11a1__py3-none-any.whl → 1.11.1__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.
- lamindb/__init__.py +1 -1
- lamindb/_finish.py +3 -3
- lamindb/core/_context.py +4 -2
- lamindb/curators/core.py +13 -5
- lamindb/errors.py +6 -0
- lamindb/examples/cellxgene/_cellxgene.py +1 -1
- lamindb/examples/croissant/__init__.py +20 -4
- lamindb/examples/datasets/_core.py +8 -1
- lamindb/examples/datasets/mini_immuno.py +0 -1
- lamindb/examples/fixtures/sheets.py +8 -2
- lamindb/integrations/_croissant.py +34 -11
- lamindb/migrations/0121_recorduser.py +7 -0
- lamindb/models/__init__.py +1 -0
- lamindb/models/_feature_manager.py +78 -18
- lamindb/models/artifact.py +71 -65
- lamindb/models/artifact_set.py +12 -3
- lamindb/models/query_set.py +146 -58
- lamindb/models/record.py +5 -1
- lamindb/models/run.py +2 -27
- lamindb/models/save.py +6 -8
- lamindb/models/sqlrecord.py +47 -33
- {lamindb-1.11a1.dist-info → lamindb-1.11.1.dist-info}/METADATA +12 -17
- {lamindb-1.11a1.dist-info → lamindb-1.11.1.dist-info}/RECORD +25 -25
- {lamindb-1.11a1.dist-info → lamindb-1.11.1.dist-info}/LICENSE +0 -0
- {lamindb-1.11a1.dist-info → lamindb-1.11.1.dist-info}/WHEEL +0 -0
lamindb/models/save.py
CHANGED
@@ -47,11 +47,10 @@ def save(
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Args:
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records: Multiple :class:`~lamindb.models.SQLRecord` objects.
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ignore_conflicts: If
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batch_size: Number of records to process in each batch. Defaults to 10000.
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ignore_conflicts: If `True`, do not error if some records violate a unique or another constraint.
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However, it won't inplace update the id fields of records.
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If you need records with ids, you need to query them from the database.
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batch_size: Number of records to process in each batch.
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Large batch sizes can improve performance but may lead to memory issues.
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Examples:
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@@ -130,7 +129,7 @@ def bulk_create(
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Args:
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records: Iterable of SQLRecord objects to create
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ignore_conflicts: Whether to ignore conflicts during creation
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batch_size: Number of records to process in each batch.
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batch_size: Number of records to process in each batch.
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"""
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records_by_orm = defaultdict(list)
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for record in records:
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@@ -332,8 +331,7 @@ def store_artifacts(
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from .artifact import Artifact
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exception: Exception | None = None
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# because uploads might fail, we need to maintain a new list
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# of the succeeded uploads
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# because uploads might fail, we need to maintain a new list of the succeeded uploads
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stored_artifacts = []
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# upload new local artifacts
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lamindb/models/sqlrecord.py
CHANGED
@@ -319,6 +319,43 @@ def suggest_records_with_similar_names(
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return None
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def delete_record(record: BaseSQLRecord, is_soft: bool = True):
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def delete():
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if is_soft:
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record.branch_id = -1
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record.save()
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else:
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super(BaseSQLRecord, record).delete()
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# deal with versioned records
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# if _ovewrite_version = True, there is only a single version and
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# no need to set the new latest version because all versions are deleted
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# when deleting the latest version
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if (
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isinstance(record, IsVersioned)
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and record.is_latest
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and not getattr(record, "_overwrite_versions", False)
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):
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new_latest = (
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record.__class__.objects.using(record._state.db)
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.filter(is_latest=False, uid__startswith=record.stem_uid)
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.exclude(branch_id=-1) # exclude candidates in the trash
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.order_by("-created_at")
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.first()
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)
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if new_latest is not None:
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new_latest.is_latest = True
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if is_soft:
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record.is_latest = False
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with transaction.atomic():
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new_latest.save()
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delete()
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logger.warning(f"new latest version is: {new_latest}")
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return None
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# deal with all other cases of the nested if condition now
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delete()
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RECORD_REGISTRY_EXAMPLE = """Example::
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from lamindb import SQLRecord, fields
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# this just retrives the full connection string from iresult
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db = update_db_using_local(iresult, settings_file)
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cache_using_filepath.write_text(
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f"{iresult['lnid']}\n{iresult['schema_str']}"
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f"{iresult['lnid']}\n{iresult['schema_str']}", encoding="utf-8"
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)
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# need to set the token if it is a fine_grained_access and the user is jwt (not public)
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is_fine_grained_access = (
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source_modules = isettings.modules
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db = isettings.db
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cache_using_filepath.write_text(
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f"{isettings.uid}\n{','.join(source_modules)}"
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f"{isettings.uid}\n{','.join(source_modules)}", encoding="utf-8"
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)
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# need to set the token if it is a fine_grained_access and the user is jwt (not public)
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is_fine_grained_access = (
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):
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raise NoWriteAccess(
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f"You’re not allowed to write to the space '{self.space.name}'.\n"
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"Please contact
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"Please contact administrators of the space if you need write access."
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) from None
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else:
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raise
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def delete(self) -> None:
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"""Delete."""
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-
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# _overwrite_versions is set to True for folder artifacts
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# no need to set the new latest version becase all versions are deleted
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# when deleting the latest version of a folder artifact
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if (
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isinstance(self, IsVersioned)
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and self.is_latest
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and not getattr(self, "_overwrite_versions", False)
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):
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new_latest = (
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self.__class__.objects.using(self._state.db)
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.filter(is_latest=False, uid__startswith=self.stem_uid)
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.order_by("-created_at")
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.first()
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)
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if new_latest is not None:
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new_latest.is_latest = True
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with transaction.atomic():
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new_latest.save()
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super().delete() # type: ignore
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logger.warning(f"new latest version is: {new_latest}")
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return None
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super().delete()
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delete_record(self, is_soft=False)
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class Space(BaseSQLRecord):
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*args,
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**kwargs,
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):
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if "uid" not in kwargs:
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if not args and "uid" not in kwargs:
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warn = False
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msg = ""
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isettings = setup_settings.instance
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# change branch_id to trash
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trash_branch_id = -1
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if self.branch_id > trash_branch_id and permanent is not True:
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self
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logger.warning(f"moved record to trash (`branch_id = -1`): {self}")
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delete_record(self, is_soft=True)
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logger.warning(f"moved record to trash (branch_id = -1): {self}")
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return
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# permanent delete
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f"Record {self.uid} is already in trash! Are you sure you want to delete it from your"
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" database? You can't undo this action. (y/n) "
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)
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confirm_delete = response == "y"
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confirm_delete = permanent
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if
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if confirm_delete:
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if name_with_module == "Run":
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from .run import delete_run_artifacts
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.3
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Name: lamindb
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Version: 1.
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Version: 1.11.1
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Summary: A data framework for biology.
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Author-email: Lamin Labs <open-source@lamin.ai>
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Requires-Python: >=3.10,<3.14
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Requires-Dist: lamin_utils==0.15.0
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Requires-Dist: lamin_cli==1.7.
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Requires-Dist: lamindb_setup[aws]==1.10.
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Requires-Dist: lamin_cli==1.7.1
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Requires-Dist: lamindb_setup[aws]==1.10.1
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Requires-Dist: bionty>=1.7a1
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Requires-Dist: wetlab>=1.5a1
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Requires-Dist: nbproject==0.11.1
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Requires-Dist: jupytext
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Requires-Dist: nbconvert>=7.2.1
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Requires-Dist: mistune!=3.1.0
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Requires-Dist: pyyaml
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Requires-Dist: pyarrow
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Requires-Dist: pandera>=0.24.0
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Requires-Dist: fsspec
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Requires-Dist: graphviz
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Requires-Dist: psycopg2-binary
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Requires-Dist: bionty>=1.6.1rc1 ; extra == "bionty"
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Requires-Dist: clinicore>=1.2.1 ; extra == "clinicore"
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Requires-Dist: tomlkit ; extra == "dev"
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Requires-Dist: line_profiler ; extra == "dev"
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Requires-Dist: pre-commit ; extra == "dev"
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Requires-Dist: laminci>=0.3 ; extra == "dev"
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Requires-Dist: pytest>=6.0 ; extra == "dev"
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Requires-Dist: coverage ; extra == "dev"
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Requires-Dist: pytest-cov ; extra == "dev"
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Requires-Dist: pytest-cov<7.0.0 ; extra == "dev"
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Requires-Dist: mudata ; extra == "dev"
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Requires-Dist: nbproject_test>=0.6.0 ; extra == "dev"
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Requires-Dist: faker-biology ; extra == "dev"
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Requires-Dist: pronto ; extra == "dev"
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Requires-Dist: readfcs>=2.0.1 ; extra == "fcs"
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Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
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Requires-Dist: nbproject==0.11.1 ; extra == "jupyter"
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Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"
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Requires-Dist: wetlab>=1.3.1 ; extra == "wetlab"
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Requires-Dist: numcodecs<0.16.0 ; extra == "zarr"
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Requires-Dist: zarr>=2.16.0,<3.0.0a0 ; extra == "zarr"
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Project-URL: Home, https://github.com/laminlabs/lamindb
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Provides-Extra: bionty
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Provides-Extra: clinicore
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Provides-Extra: dev
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Provides-Extra: fcs
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[](https://github.com/laminlabs/lamindb)
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Install the `lamindb` Python package:
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```shell
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pip install
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pip install lamindb
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```
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Create a LaminDB instance:
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@@ -134,7 +129,7 @@ Conversely, you can query artifacts by the script that created them.
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ln.Artifact.get(transform__key="create-fasta.py") # query artifact by transform key
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```
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Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/
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Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/9K1dteZ6Qx0EXK8g).
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<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480001.png" width="850">
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@@ -1,8 +1,8 @@
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lamindb/__init__.py,sha256=
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lamindb/_finish.py,sha256=
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lamindb/__init__.py,sha256=jO-XCxfKHm4hUoqFpHDOPFPoKbknvdkm0oImBWGod8A,3241
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lamindb/_finish.py,sha256=4KkFyb9d-GEGjDw_zDrnGt_bq3auQ_OQu0hV-2U73AQ,21355
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lamindb/_tracked.py,sha256=fls9yd7EEGO9Ni51kA_pcBkeLpzm2HZrWtwYGQequNE,4395
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lamindb/_view.py,sha256=GOKTfwnEaly9fdeWo9SlhYRc3UWEyLDmTlIUzjFXMYY,4960
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lamindb/errors.py,sha256=
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lamindb/errors.py,sha256=kHKRWXPGQPnzTo0D0vQxJjY_8bGH_Xx1IGFgM-dYN3E,2277
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lamindb/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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lamindb/base/__init__.py,sha256=u623ZDoNCwwyLLt_Jhtp3KDeum0LOg6cwAqn5TEgz_E,313
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lamindb/base/dtypes.py,sha256=Bfrca8Slb3vIAIMLd-mjG4_9bTHz-LlThSIUHvfNmhA,3189
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lamindb/base/users.py,sha256=8MSmAvCKoUF15YsDE6BGLBXsFWpfoEEg8iDTKZ7kD48,848
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lamindb/core/__init__.py,sha256=I9F-GugBMZwFLpUPb1MXyLfccIVAj021Gb_00h_18MY,633
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lamindb/core/_compat.py,sha256=NLnKk1qk4xdgMV-QwFDnBnbio02ujjlF86icvhpdv4c,2029
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lamindb/core/_context.py,sha256=
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lamindb/core/_context.py,sha256=wPRNcQ0tPrwvYkYbHxZz0VzdxeBZEuorWOIqpucnbFk,40444
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lamindb/core/_mapped_collection.py,sha256=osquwC6ee0wJ_I6O-8AZwnQUa_r9zqa0MN82Q-nBI3Y,25746
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lamindb/core/_settings.py,sha256=519bOSopRb7_nE874KDJB263v1xFlk4TOqhBNNeO4yw,10992
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lamindb/core/_sync_git.py,sha256=Z7keuyS5X7CAj285sEbZIFExZF9mtjGH8DzKwz3xhHw,5881
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@@ -37,25 +37,25 @@ lamindb/core/subsettings/_annotation_settings.py,sha256=o-yTYw-NmjFmtehbKU8qnf7t
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lamindb/core/subsettings/_creation_settings.py,sha256=NGHWKqCFSzVNBxAr2VnmdYguiFdW29XUK7T9wRsVshg,906
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lamindb/curators/__init__.py,sha256=WLnaVxrhQGZxGB3pjg-SM4oUu6DaKA78S_J3BfVKLEg,496
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lamindb/curators/_legacy.py,sha256=Ay2nd4u2OPL59aYC6rKNE9YpfVTC-MMPvnyzS3fM6xg,55172
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lamindb/curators/core.py,sha256=
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lamindb-1.11.1.dist-info/WHEEL,sha256=CpUCUxeHQbRN5UGRQHYRJorO5Af-Qy_fHMctcQ8DSGI,82
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lamindb-1.11.1.dist-info/METADATA,sha256=rrGmUwB5UIBBj-3k8HznNPlWCsAf2mHkQEK5aMSinUY,4865
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