Full Code of laminlabs/lamindb for AI

gitextract_xlz91t15/

├── .github/
│   ├── ISSUE_TEMPLATE/
│   │   ├── bug_report.yml
│   │   ├── config.yml
│   │   ├── enhancement.yml
│   │   └── usage_question.yml
│   └── workflows/
│       ├── build.yml
│       └── doc-changes.yml
├── .gitignore
├── .gitmodules
├── .pre-commit-config.yaml
├── CONTRIBUTING.md
├── LICENSE
├── README.md
├── docs/
│   ├── api.md
│   ├── arrays.md
│   ├── bionty.md
│   ├── changelog.md
│   ├── curate.md
│   ├── faq/
│   │   ├── acid.md
│   │   ├── curate-any.md
│   │   ├── idempotency.md
│   │   ├── import-modules.md
│   │   ├── keep-artifacts-local.md
│   │   ├── pydantic-pandera.md
│   │   ├── reference-field.md
│   │   ├── search.md
│   │   ├── symbol-mapping.md
│   │   ├── test_notebooks.py
│   │   ├── track-run-inputs.md
│   │   ├── trash-archive.md
│   │   └── validate-fields.md
│   ├── faq.md
│   ├── guide.md
│   ├── index.md
│   ├── lightning.md
│   ├── manage-changes.md
│   ├── manage-ontologies.md
│   ├── organize.md
│   ├── pertdb.md
│   ├── query-search.md
│   ├── registries.md
│   ├── scripts/
│   │   ├── curate_anndata_flexible.py
│   │   ├── curate_anndata_uns.py
│   │   ├── curate_dataframe_attrs.py
│   │   ├── curate_dataframe_external_features.py
│   │   ├── curate_dataframe_flexible.py
│   │   ├── curate_dataframe_minimal_errors.py
│   │   ├── curate_dataframe_union_features.py
│   │   ├── curate_mudata.py
│   │   ├── curate_soma_experiment.py
│   │   ├── curate_spatialdata.py
│   │   ├── define_schema_anndata_uns.py
│   │   ├── define_schema_df_metadata.py
│   │   ├── define_schema_spatialdata.py
│   │   ├── my_workflow.py
│   │   ├── my_workflow_with_click.py
│   │   ├── my_workflow_with_step.py
│   │   ├── run_script_with_step.py
│   │   ├── run_track_and_finish.py
│   │   ├── run_track_with_features_and_params.py
│   │   ├── run_track_with_params.py
│   │   └── synced_with_git.py
│   ├── storage/
│   │   ├── add-replace-cache.ipynb
│   │   ├── anndata-accessor.ipynb
│   │   ├── prepare-sync-local-to-cloud.ipynb
│   │   ├── sync-local-to-cloud.ipynb
│   │   ├── test-files/
│   │   │   └── iris.data
│   │   ├── test_notebooks.py
│   │   ├── upload.ipynb
│   │   └── vitessce.ipynb
│   ├── storage.md
│   ├── sync.md
│   ├── test_notebooks.py
│   └── track.md
├── lamindb/
│   ├── __init__.py
│   ├── _finish.py
│   ├── _secret_redaction.py
│   ├── _view.py
│   ├── base/
│   │   ├── __init__.py
│   │   ├── dtypes.py
│   │   ├── fields.py
│   │   ├── ids.py
│   │   ├── types.py
│   │   ├── uids.py
│   │   ├── users.py
│   │   └── utils.py
│   ├── core/
│   │   ├── __init__.py
│   │   ├── _compat.py
│   │   ├── _context.py
│   │   ├── _functions.py
│   │   ├── _mapped_collection.py
│   │   ├── _settings.py
│   │   ├── _sync_git.py
│   │   ├── _track_environment.py
│   │   ├── exceptions.py
│   │   ├── loaders.py
│   │   ├── storage/
│   │   │   ├── __init__.py
│   │   │   ├── _anndata_accessor.py
│   │   │   ├── _backed_access.py
│   │   │   ├── _polars_lazy_df.py
│   │   │   ├── _pyarrow_dataset.py
│   │   │   ├── _spatialdata_accessor.py
│   │   │   ├── _tiledbsoma.py
│   │   │   ├── _valid_suffixes.py
│   │   │   ├── _zarr.py
│   │   │   ├── objects.py
│   │   │   ├── paths.py
│   │   │   └── types.py
│   │   └── subsettings/
│   │       ├── __init__.py
│   │       ├── _annotation_settings.py
│   │       └── _creation_settings.py
│   ├── curators/
│   │   ├── __init__.py
│   │   └── core.py
│   ├── errors.py
│   ├── examples/
│   │   ├── __init__.py
│   │   ├── cellxgene/
│   │   │   ├── __init__.py
│   │   │   └── _cellxgene.py
│   │   ├── croissant/
│   │   │   ├── __init__.py
│   │   │   └── mini_immuno.anndata.zarr_metadata.json
│   │   ├── datasets/
│   │   │   ├── __init__.py
│   │   │   ├── _core.py
│   │   │   ├── _fake.py
│   │   │   ├── _small.py
│   │   │   ├── define_mini_immuno_features_labels.py
│   │   │   ├── define_mini_immuno_schema_flexible.py
│   │   │   ├── mini_immuno.py
│   │   │   └── save_mini_immuno_datasets.py
│   │   ├── fixtures/
│   │   │   ├── __init__.py
│   │   │   └── sheets.py
│   │   ├── mlflow/
│   │   │   └── __init__.py
│   │   ├── schemas/
│   │   │   ├── __init__.py
│   │   │   ├── _anndata.py
│   │   │   ├── _simple.py
│   │   │   ├── define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py
│   │   │   └── define_valid_features.py
│   │   └── wandb/
│   │       └── __init__.py
│   ├── integrations/
│   │   ├── __init__.py
│   │   ├── _croissant.py
│   │   ├── _vitessce.py
│   │   └── lightning.py
│   ├── migrations/
│   │   ├── 0177_squashed.py
│   │   ├── 0178_v2_2.py
│   │   ├── 0179_v2_2_part_2.py
│   │   ├── 0180_v2_2_part_3.py
│   │   ├── 0181_v2_2_part_4.py
│   │   ├── 0182_v2_2_part_5.py
│   │   ├── 0183_v2_2_part_6.py
│   │   ├── 0184_alter_transformrecord_feature.py
│   │   ├── 0185_alter_runrecord_feature.py
│   │   ├── 0186_v2_4.py
│   │   ├── 0187_squashed.py
│   │   ├── 0187_v2_4_part_2.py
│   │   ├── README.md
│   │   └── __init__.py
│   ├── models/
│   │   ├── __init__.py
│   │   ├── _describe.py
│   │   ├── _django.py
│   │   ├── _feature_manager.py
│   │   ├── _from_values.py
│   │   ├── _is_versioned.py
│   │   ├── _label_manager.py
│   │   ├── _relations.py
│   │   ├── _run_cleanup.py
│   │   ├── artifact.py
│   │   ├── artifact_set.py
│   │   ├── block.py
│   │   ├── can_curate.py
│   │   ├── collection.py
│   │   ├── feature.py
│   │   ├── has_parents.py
│   │   ├── project.py
│   │   ├── query_manager.py
│   │   ├── query_set.py
│   │   ├── record.py
│   │   ├── run.py
│   │   ├── save.py
│   │   ├── schema.py
│   │   ├── sqlrecord.py
│   │   ├── storage.py
│   │   ├── transform.py
│   │   └── ulabel.py
│   ├── py.typed
│   └── setup/
│       ├── __init__.py
│       ├── _merge.py
│       ├── _switch.py
│       ├── core/
│       │   └── __init__.py
│       ├── errors/
│       │   └── __init__.py
│       └── types/
│           └── __init__.py
├── lamindb_full.py
├── noxfile.py
├── pyproject.full.toml
├── pyproject.toml
├── scripts/
│   └── migrate_test_instances.py
└── tests/
    ├── core/
    │   ├── _dataset_fixtures.py
    │   ├── conftest.py
    │   ├── notebooks/
    │   │   ├── basic-r-notebook.Rmd.cleaned.html
    │   │   ├── basic-r-notebook.Rmd.html
    │   │   ├── duplicate/
    │   │   │   └── with-title-initialized-consecutive-finish.ipynb
    │   │   ├── load_schema.ipynb
    │   │   ├── no-title.ipynb
    │   │   ├── with-title-initialized-consecutive-finish-not-last-cell.ipynb
    │   │   └── with-title-initialized-consecutive-finish.ipynb
    │   ├── scripts/
    │   │   ├── duplicate1/
    │   │   │   └── script-to-test-versioning.py
    │   │   ├── duplicate2/
    │   │   │   └── script-to-test-versioning.py
    │   │   ├── duplicate3/
    │   │   │   └── script-to-test-versioning.py
    │   │   ├── duplicate4/
    │   │   │   └── script-to-test-versioning.py
    │   │   ├── duplicate5/
    │   │   │   └── script-to-test-versioning.py
    │   │   ├── script-to-test-filename-change.py
    │   │   └── script-to-test-versioning.py
    │   ├── test_artifact_anndata_with_curation.py
    │   ├── test_artifact_basics.py
    │   ├── test_artifact_dataframe_with_curation.py
    │   ├── test_artifact_describe_to_dataframe.py
    │   ├── test_artifact_features_annotations.py
    │   ├── test_artifact_parquet.py
    │   ├── test_blocks.py
    │   ├── test_branches.py
    │   ├── test_can_curate.py
    │   ├── test_collection.py
    │   ├── test_curator_basics.py
    │   ├── test_data_migrations.py
    │   ├── test_db.py
    │   ├── test_delete.py
    │   ├── test_feature.py
    │   ├── test_feature_dtype.py
    │   ├── test_from_values.py
    │   ├── test_has_parents.py
    │   ├── test_has_type.py
    │   ├── test_integrity.py
    │   ├── test_is_versioned.py
    │   ├── test_label_manager.py
    │   ├── test_load.py
    │   ├── test_manager.py
    │   ├── test_merge.py
    │   ├── test_nbconvert.py
    │   ├── test_notebooks.py
    │   ├── test_querydb.py
    │   ├── test_queryset.py
    │   ├── test_record_basics.py
    │   ├── test_record_sheet_examples.py
    │   ├── test_rename_features_labels.py
    │   ├── test_run.py
    │   ├── test_save.py
    │   ├── test_schema.py
    │   ├── test_search.py
    │   ├── test_settings.py
    │   ├── test_sqlrecord.py
    │   ├── test_storage.py
    │   ├── test_switch.py
    │   ├── test_track_flow.py
    │   ├── test_track_script_or_notebook.py
    │   ├── test_track_step.py
    │   ├── test_transform.py
    │   ├── test_transform_from_git.py
    │   └── test_view.py
    ├── curators/
    │   ├── conftest.py
    │   ├── test_cellxgene_curation.py
    │   ├── test_curate_from_croissant.py
    │   ├── test_curators_examples.py
    │   ├── test_curators_remote.py
    │   └── test_dataframe_curation.py
    ├── integrations/
    │   ├── conftest.py
    │   └── test_lightning.py
    ├── no_instance/
    │   ├── conftest.py
    │   ├── test_connect_dynamic_import.py
    │   ├── test_import_side_effects.py
    │   └── test_no_default_instance.py
    ├── permissions/
    │   ├── conftest.py
    │   ├── jwt_utils.py
    │   ├── scripts/
    │   │   ├── check_lamin_dev.py
    │   │   ├── setup_access.py
    │   │   └── setup_instance.py
    │   └── test_rls_dbwritelog.py
    ├── profiling/
    │   ├── import_lamindb.py
    │   ├── import_lamindb_and_connect.py
    │   ├── import_lamindb_core_storage.py
    │   └── import_records_from_dataframe.py
    ├── storage/
    │   ├── conftest.py
    │   ├── test_artifact_storage.py
    │   ├── test_artifact_zarr.py
    │   ├── test_cache.py
    │   ├── test_connect_reconnect.py
    │   ├── test_storage_lifecycle.py
    │   ├── test_streaming.py
    │   └── test_transfer.py
    └── tiledbsoma/
        ├── conftest.py
        ├── test_artifact_basics.py
        ├── test_curators.py
        └── test_storage.py

SYMBOL INDEX (1902 symbols across 176 files)

FILE: docs/faq/test_notebooks.py
  function test_notebooks (line 8) | def test_notebooks():

FILE: docs/scripts/my_workflow.py
  function ingest_dataset (line 5) | def ingest_dataset(key: str) -> ln.Artifact:

FILE: docs/scripts/my_workflow_with_click.py
  function main (line 8) | def main(key: str):

FILE: docs/scripts/my_workflow_with_step.py
  function subset_dataframe (line 5) | def subset_dataframe(
  function ingest_dataset (line 17) | def ingest_dataset(key: str, subset: bool = False) -> ln.Artifact:

FILE: docs/scripts/run_script_with_step.py
  function subset_dataframe (line 6) | def subset_dataframe(

FILE: docs/storage/test_notebooks.py
  function test_notebooks (line 8) | def test_notebooks():

FILE: docs/test_notebooks.py
  function test_tutorial (line 13) | def test_tutorial():
  function test_guide (line 18) | def test_guide():
  function test_tiledbsoma (line 23) | def test_tiledbsoma():
  function test_biology (line 28) | def test_biology():

FILE: lamindb/_finish.py
  function get_save_notebook_message (line 22) | def get_save_notebook_message() -> str:
  function get_save_notebook_message_retry (line 28) | def get_save_notebook_message_retry() -> str:
  function check_consecutiveness (line 33) | def check_consecutiveness(
  function get_shortcut (line 84) | def get_shortcut() -> str:
  function get_seconds_since_modified (line 90) | def get_seconds_since_modified(filepath) -> float:
  function save_run_logs (line 94) | def save_run_logs(run: Run, save_run: bool = False) -> None:
  function prepare_notebook (line 113) | def prepare_notebook(
  function notebook_to_report (line 139) | def notebook_to_report(notebook_path: Path, output_path: Path) -> None:
  function notebook_to_script (line 162) | def notebook_to_script(  # type: ignore
  function clean_r_notebook_html (line 180) | def clean_r_notebook_html(file_path: Path) -> tuple[str | None, Path]:
  function check_filepath_recently_saved (line 210) | def check_filepath_recently_saved(filepath: Path, is_finish_retry: bool)...
  function save_context_core (line 239) | def save_context_core(

FILE: lamindb/_secret_redaction.py
  function normalize_sensitive_key_name (line 52) | def normalize_sensitive_key_name(key: str) -> str:
  function is_sensitive_param_key (line 58) | def is_sensitive_param_key(key: str) -> bool:
  function is_sensitive_param_value (line 62) | def is_sensitive_param_value(value: object) -> bool:
  function _redact_assignment_match (line 68) | def _redact_assignment_match(match: re.Match[str]) -> str:
  function redact_secrets_in_source_code (line 87) | def redact_secrets_in_source_code(source_code: str) -> tuple[str, int]:

FILE: lamindb/_view.py
  function display_df_with_descriptions (line 22) | def display_df_with_descriptions(
  function view (line 96) | def view(

FILE: lamindb/base/dtypes.py
  function is_list_of_type (line 13) | def is_list_of_type(value: Any, expected_type: Any) -> bool:
  function check_dtype (line 21) | def check_dtype(expected_type: Any, nullable: bool) -> Callable:
  function is_valid_datetime_str (line 90) | def is_valid_datetime_str(date_string: str) -> bool | str:
  function is_iterable_of_sqlrecord (line 98) | def is_iterable_of_sqlrecord(value: Any):

FILE: lamindb/base/fields.py
  class CharField (line 33) | class CharField(models.CharField):
    method __init__ (line 39) | def __init__(self, max_length: int = 255, **kwargs):
  class TextField (line 46) | class TextField(models.TextField):
    method __init__ (line 52) | def __init__(self, *args, **kwargs):
  class ForeignKey (line 58) | class ForeignKey(models.ForeignKey):
    method __init__ (line 64) | def __init__(self, *args, **kwargs):
  class BooleanField (line 77) | class BooleanField(models.BooleanField):
    method __init__ (line 83) | def __init__(self, *args, **kwargs):
  class DateField (line 89) | class DateField(models.DateField):
    method __init__ (line 95) | def __init__(self, *args, **kwargs):
  class DateTimeField (line 100) | class DateTimeField(models.DateTimeField):
    method __init__ (line 106) | def __init__(self, *args, **kwargs):
  class BigIntegerField (line 111) | class BigIntegerField(models.BigIntegerField):
    method __init__ (line 117) | def __init__(self, *args, **kwargs):
  class IntegerField (line 123) | class IntegerField(models.IntegerField):
    method __init__ (line 129) | def __init__(self, *args, **kwargs):
  class OneToOneField (line 134) | class OneToOneField(models.OneToOneField):
    method __init__ (line 140) | def __init__(self, *args, **kwargs):
  class FloatField (line 145) | class FloatField(models.FloatField):
    method __init__ (line 151) | def __init__(self, *args, **kwargs):
  class DecimalField (line 156) | class DecimalField(models.DecimalField):
    method __init__ (line 162) | def __init__(self, *args, **kwargs):
  class JSONField (line 167) | class JSONField(models.JSONField):
    method __init__ (line 173) | def __init__(self, *args, **kwargs):
  class DurationField (line 178) | class DurationField(models.DurationField):
    method __init__ (line 184) | def __init__(self, *args, **kwargs):
  class URLField (line 189) | class URLField(models.URLField):
    method __init__ (line 195) | def __init__(self, *args, **kwargs):
  class EmailField (line 200) | class EmailField(models.EmailField):
    method __init__ (line 206) | def __init__(self, *args, **kwargs):
  class TimeField (line 211) | class TimeField(models.TimeField):
    method __init__ (line 217) | def __init__(self, *args, **kwargs):
  class SlugField (line 222) | class SlugField(models.SlugField):
    method __init__ (line 228) | def __init__(self, *args, **kwargs):
  class UUIDField (line 233) | class UUIDField(models.UUIDField):
    method __init__ (line 239) | def __init__(self, *args, **kwargs):
  class PositiveIntegerField (line 244) | class PositiveIntegerField(models.PositiveIntegerField):
    method __init__ (line 250) | def __init__(self, *args, **kwargs):
  class PositiveSmallIntegerField (line 255) | class PositiveSmallIntegerField(models.PositiveSmallIntegerField):
    method __init__ (line 261) | def __init__(self, *args, **kwargs):
  class SmallIntegerField (line 266) | class SmallIntegerField(models.SmallIntegerField):
    method __init__ (line 272) | def __init__(self, *args, **kwargs):
  class BinaryField (line 277) | class BinaryField(models.BinaryField):
    method __init__ (line 283) | def __init__(self, *args, **kwargs):
  class GenericIPAddressField (line 288) | class GenericIPAddressField(models.GenericIPAddressField):
    method __init__ (line 294) | def __init__(self, *args, **kwargs):

FILE: lamindb/base/uids.py
  function base64 (line 65) | def base64(n_char: int) -> str:
  function base62 (line 72) | def base62(n_char: int) -> str:
  function base26 (line 79) | def base26(n_char: int):
  function base62_4 (line 86) | def base62_4() -> str:
  function base62_8 (line 90) | def base62_8() -> str:
  function base62_12 (line 95) | def base62_12() -> str:
  function base62_16 (line 100) | def base62_16() -> str:
  function base62_20 (line 105) | def base62_20() -> str:
  function base62_24 (line 110) | def base62_24() -> str:

FILE: lamindb/base/users.py
  function _user_has_write_access (line 4) | def _user_has_write_access() -> bool:
  function current_user_id (line 17) | def current_user_id() -> int:

FILE: lamindb/base/utils.py
  class class_and_instance_method (line 16) | class class_and_instance_method:
    method __init__ (line 19) | def __init__(self, func):
    method __get__ (line 23) | def __get__(self, instance, owner):
  class strict_classmethod (line 32) | class strict_classmethod:
    method __init__ (line 35) | def __init__(self, func):
    method __get__ (line 39) | def __get__(self, instance, owner):

FILE: lamindb/core/__init__.py
  function __getattr__ (line 47) | def __getattr__(name: str):

FILE: lamindb/core/_compat.py
  function is_package_installed (line 7) | def is_package_installed(package_name: str) -> bool:
  function with_package (line 12) | def with_package(package_name: str, operation: Callable[[Any], T]) -> T:
  function with_package_obj (line 33) | def with_package_obj(

FILE: lamindb/core/_context.py
  function get_key_from_module (line 49) | def get_key_from_module(caller_module: str) -> str:
  function detect_and_process_source_code_file (line 57) | def detect_and_process_source_code_file(
  function get_uid_ext (line 123) | def get_uid_ext(version: str) -> str:
  function get_notebook_path (line 132) | def get_notebook_path() -> tuple[Path, str]:
  function get_notebook_key_colab (line 150) | def get_notebook_key_colab() -> str:
  function get_cli_call (line 167) | def get_cli_call() -> tuple[str, str] | None:
  function pretty_pypackages (line 178) | def pretty_pypackages(dependencies: dict) -> str:
  function last_non_empty_r_block (line 189) | def last_non_empty_r_block(line: str) -> str:
  class LogStreamHandler (line 196) | class LogStreamHandler:
    method __init__ (line 197) | def __init__(self, log_stream: TextIO, file: TextIO, use_buffer: bool):
    method write (line 204) | def write(self, data: str) -> int:
    method flush (line 227) | def flush(self):
    method isatty (line 235) | def isatty(self) -> bool:
    method flush_buffer (line 240) | def flush_buffer(self):
  class LogStreamTracker (line 247) | class LogStreamTracker:
    method __init__ (line 248) | def __init__(self):
    method start (line 268) | def start(self, run: Run):
    method finish (line 299) | def finish(self):
    method cleanup (line 310) | def cleanup(self, signo=None, frame=None):
    method handle_exception (line 347) | def handle_exception(self, exc_type, exc_value, exc_traceback):
  function serialize_params_to_json (line 364) | def serialize_params_to_json(params: dict) -> dict:
  class Context (line 402) | class Context:
    method __init__ (line 408) | def __init__(self, uid: str | None = None, path: Path | None = None):
    method transform (line 426) | def transform(self) -> Transform | None:
    method description (line 431) | def description(self) -> str | None:
    method description (line 436) | def description(self, value: str | None):
    method uid (line 440) | def uid(self) -> str | None:
    method uid (line 445) | def uid(self, value: str | None):
    method version (line 449) | def version(self) -> str | None:
    method version (line 454) | def version(self, value: str | None):
    method project (line 458) | def project(self) -> Project | None:
    method space (line 463) | def space(self) -> Space | None:
    method branch (line 468) | def branch(self) -> Branch | None:
    method run (line 473) | def run(self) -> Run | None:
    method _track (line 477) | def _track(
    method _track_notebook (line 842) | def _track_notebook(
    method _process_aux_transform (line 886) | def _process_aux_transform(
    method _create_or_load_transform (line 933) | def _create_or_load_transform(
    method _finish (line 1190) | def _finish(self, ignore_non_consecutive: None | bool = None) -> None:

FILE: lamindb/core/_functions.py
  function get_current_tracked_run (line 23) | def get_current_tracked_run() -> Run | None:
  function _create_tracked_decorator (line 31) | def _create_tracked_decorator(
  function flow (line 132) | def flow(
  function step (line 186) | def step(uid: str | None = None) -> Callable[[Callable[P, R]], Callable[...
  function tracked (line 202) | def tracked(uid: str | None = None) -> Callable[[Callable[P, R]], Callab...

FILE: lamindb/core/_mapped_collection.py
  class _Connect (line 27) | class _Connect:
    method __init__ (line 28) | def __init__(self, storage):
    method __enter__ (line 37) | def __enter__(self):
    method __exit__ (line 40) | def __exit__(self, exc_type, exc_val, exc_tb):
    method close (line 43) | def close(self):
  class MappedCollection (line 55) | class MappedCollection:
    method __init__ (line 107) | def __init__(
    method _make_connections (line 259) | def _make_connections(self, path_list: list, parallel: bool):
    method _cache_keys (line 273) | def _cache_keys(self):
    method _cache_categories (line 284) | def _cache_categories(self, obs_keys: list):
    method _make_encoders (line 300) | def _make_encoders(self, encode_labels: list):
    method _read_vars (line 314) | def _read_vars(self):
    method _make_join_vars (line 323) | def _make_join_vars(self):
    method check_vars_sorted (line 348) | def check_vars_sorted(self, ascending: bool = True) -> bool:
    method check_vars_non_aligned (line 358) | def check_vars_non_aligned(self, vars: pd.Index | list) -> list[int]:
    method _check_csc_raise_error (line 369) | def _check_csc_raise_error(
    method __len__ (line 381) | def __len__(self):
    method shape (line 385) | def shape(self) -> tuple[int, int]:
    method original_shapes (line 390) | def original_shapes(self) -> list[tuple[int, int]]:
    method __getitem__ (line 398) | def __getitem__(self, idx: int):
    method _get_lazy_data (line 438) | def _get_lazy_data(self, store: StorageType, layers_key: str, storage_...
    method _get_data_idx (line 449) | def _get_data_idx(
    method _get_obs_idx (line 490) | def _get_obs_idx(
    method get_label_weights (line 520) | def get_label_weights(
    method get_merged_labels (line 564) | def get_merged_labels(self, label_key: str):
    method get_merged_categories (line 577) | def get_merged_categories(self, label_key: str):
    method _get_categories (line 597) | def _get_categories(self, storage: StorageType, label_key: str):
    method _get_codes (line 628) | def _get_codes(self, storage: StorageType, label_key: str):
    method _get_labels (line 640) | def _get_labels(
    method close (line 661) | def close(self):
    method closed (line 675) | def closed(self) -> bool:
    method __enter__ (line 682) | def __enter__(self):
    method __exit__ (line 685) | def __exit__(self, exc_type, exc_val, exc_tb):
    method torch_worker_init_fn (line 689) | def torch_worker_init_fn(cls, worker_id):

FILE: lamindb/core/_settings.py
  function raise_if_storage_managed_by_other_instance (line 41) | def raise_if_storage_managed_by_other_instance(storage) -> None:
  class Settings (line 49) | class Settings:
    method __init__ (line 55) | def __init__(self):
    method __repr__ (line 59) | def __repr__(self) -> str:  # pragma: no cover
    method creation (line 93) | def creation(self) -> CreationSettings:
    method annotation (line 102) | def annotation(self) -> AnnotationSettings:
    method _using_key (line 126) | def _using_key(self) -> str | None:
    method _using_key (line 131) | def _using_key(self, value: str | None):
    method _storage_settings (line 136) | def _storage_settings(self) -> ln_setup.core.StorageSettings:
    method sync_git_repo (line 144) | def sync_git_repo(self) -> str | None:
    method sync_git_repo (line 171) | def sync_git_repo(self, value) -> None:
    method storage (line 177) | def storage(self) -> StorageSettings:
    method storage (line 207) | def storage(self, path_kwargs: AnyPathStr | tuple[AnyPathStr, Mapping]):
    method instance_uid (line 239) | def instance_uid(self) -> str:
    method cache_dir (line 244) | def cache_dir(self) -> UPath:
    method local_storage (line 249) | def local_storage(self) -> StorageSettings:
    method local_storage (line 259) | def local_storage(self, local_root: Path | str):
    method verbosity (line 277) | def verbosity(self) -> str:
    method verbosity (line 290) | def verbosity(self, verbosity: str | int):

FILE: lamindb/core/_sync_git.py
  function get_git_repo_from_remote (line 14) | def get_git_repo_from_remote(url: str | None = None, depth: int | None =...
  function check_local_git_repo (line 41) | def check_local_git_repo() -> bool:
  function get_git_commit_hash (line 62) | def get_git_commit_hash(blob_hash: str, repo_dir: Path | None = None) ->...
  function get_filepath_within_git_repo (line 128) | def get_filepath_within_git_repo(
  function get_transform_reference_from_git_repo (line 175) | def get_transform_reference_from_git_repo(path: Path) -> str:
  function get_and_validate_git_metadata (line 195) | def get_and_validate_git_metadata(

FILE: lamindb/core/_track_environment.py
  function track_python_environment (line 14) | def track_python_environment(run: Run) -> None:

FILE: lamindb/core/loaders.py
  function load_fcs (line 43) | def load_fcs(*args, **kwargs) -> AnnData:
  function load_csv (line 56) | def load_csv(path: Path | str, **kwargs) -> DataFrame:
  function load_parquet (line 64) | def load_parquet(path: Path | str, **kwargs) -> DataFrame:
  function load_tsv (line 72) | def load_tsv(path: Path | str, **kwargs) -> DataFrame:
  function load_h5ad (line 80) | def load_h5ad(filepath: AnyPathStr, **kwargs) -> AnnData:
  function load_h5mu (line 91) | def load_h5mu(filepath: Path | str, **kwargs) -> MuData:
  function load_zarr (line 99) | def load_zarr(storepath, **kwargs):  # type: ignore
  function load_html (line 107) | def load_html(path: Path | str) -> None | Path | str:
  function load_json (line 129) | def load_json(path: Path | str) -> dict[str, Any] | list[Any]:
  function load_yaml (line 139) | def load_yaml(path: Path | str) -> dict[str, Any] | list[Any]:
  function load_image (line 149) | def load_image(path: Path | str) -> None | Path | str:
  function load_svg (line 161) | def load_svg(path: Path | str) -> None | Path | str:
  function load_txt (line 173) | def load_txt(path: Path | str) -> str:
  function load_rds (line 179) | def load_rds(path: Path | str) -> Path | str:
  function load_to_memory (line 217) | def load_to_memory(

FILE: lamindb/core/storage/__init__.py
  function __getattr__ (line 55) | def __getattr__(name: str) -> Any:

FILE: lamindb/core/storage/_anndata_accessor.py
  class CSRDataset (line 55) | class CSRDataset(SparseDataset):
    method format_str (line 57) | def format_str(self) -> str:
  function sparse_dataset (line 60) | def sparse_dataset(group):
  function _check_group_format (line 75) | def _check_group_format(*args):
  function _subset_sparse (line 82) | def _subset_sparse(sparse_ds: CSRDataset | SparseDataset, indices):
  function get_module_name (line 92) | def get_module_name(obj):
  function _records_to_df (line 96) | def _records_to_df(obj):
  class AccessRegistry (line 117) | class AccessRegistry:
    method __init__ (line 118) | def __init__(self):
    method register_open (line 122) | def register_open(self, module: str):
    method open (line 129) | def open(self, module: str, *args, **kwargs):
    method register (line 135) | def register(self, module: str):
    method __getattr__ (line 145) | def __getattr__(self, func_name: str):
  function open (line 162) | def open(filepath: AnyPathStr, mode: str = "r", compression: str | None ...
  function read_dataframe (line 189) | def read_dataframe(elem: h5py.Dataset | h5py.Group):
  function safer_read_partial (line 197) | def safer_read_partial(elem, indices):
  function keys (line 266) | def keys(storage: h5py.File):
  function open (line 304) | def open(filepath: AnyPathStr, mode: Literal["r", "r+", "a", "w", "w-"] ...
  function read_dataframe (line 324) | def read_dataframe(elem: Union[zarr.Array, zarr.Group]):  # noqa
  function safer_read_partial (line 331) | def safer_read_partial(elem, indices):
  function keys (line 370) | def keys(storage: zarr.Group):
  function _to_memory (line 432) | def _to_memory(elem):
  function _try_backed_full (line 441) | def _try_backed_full(elem):
  function _to_index (line 458) | def _to_index(elem: np.ndarray):
  function _safer_read_index (line 464) | def _safer_read_index(elem):
  class _MapAccessor (line 483) | class _MapAccessor:
    method __init__ (line 484) | def __init__(self, elem, name, indices=None):
    method __getitem__ (line 489) | def __getitem__(self, key):
    method keys (line 495) | def keys(self):
    method __repr__ (line 498) | def __repr__(self):
  function _safer_read_df (line 505) | def _safer_read_df(elem, indices=None):
  class _AnnDataAttrsMixin (line 516) | class _AnnDataAttrsMixin:
    method obs (line 521) | def obs(self) -> pd.DataFrame | None:
    method var (line 531) | def var(self) -> pd.DataFrame | None:
    method uns (line 541) | def uns(self):
    method X (line 547) | def X(self):
    method obsm (line 555) | def obsm(self):
    method varm (line 564) | def varm(self):
    method obsp (line 573) | def obsp(self):
    method varp (line 582) | def varp(self):
    method layers (line 591) | def layers(self):
    method obs_names (line 598) | def obs_names(self):
    method var_names (line 602) | def var_names(self):
    method shape (line 606) | def shape(self):
    method to_dict (line 609) | def to_dict(self):
    method to_memory (line 633) | def to_memory(self):
  class AnnDataAccessorSubset (line 638) | class AnnDataAccessorSubset(_AnnDataAttrsMixin):
    method __init__ (line 639) | def __init__(self, storage, indices, attrs_keys, obs_names, var_names,...
    method __getitem__ (line 648) | def __getitem__(self, index: Index):
    method __repr__ (line 664) | def __repr__(self):
    method raw (line 673) | def raw(self):
  class AnnDataRawAccessor (line 691) | class AnnDataRawAccessor(AnnDataAccessorSubset):
    method __init__ (line 692) | def __init__(
    method raw (line 723) | def raw(self):
  class AnnDataAccessor (line 727) | class AnnDataAccessor(_AnnDataAttrsMixin):
    method __init__ (line 730) | def __init__(
    method close (line 754) | def close(self):
    method closed (line 787) | def closed(self):
    method __enter__ (line 790) | def __enter__(self):
    method __exit__ (line 795) | def __exit__(self, exc_type, exc_val, exc_tb):
    method __getitem__ (line 798) | def __getitem__(self, index: Index) -> AnnDataAccessorSubset:
    method __repr__ (line 811) | def __repr__(self):
    method raw (line 821) | def raw(self):
    method add_column (line 828) | def add_column(
  function _anndata_n_observations (line 859) | def _anndata_n_observations(object: AnyPathStr | AnnData) -> int | None:

FILE: lamindb/core/storage/_backed_access.py
  function _track_writes_factory (line 29) | def _track_writes_factory(obj: Any, finalize: Callable):
  class BackedAccessor (line 63) | class BackedAccessor:
  function backed_access (line 72) | def backed_access(
  function _non_gz_suffix (line 149) | def _non_gz_suffix(suffixes: list[str]) -> str:
  function _flat_suffixes (line 161) | def _flat_suffixes(paths: UPath | list[UPath]) -> set[str]:
  function _open_dataframe (line 177) | def _open_dataframe(

FILE: lamindb/core/storage/_polars_lazy_df.py
  function _polars_options (line 17) | def _polars_options(storepath: UPath) -> dict:
  function _open_polars_lazy_df (line 73) | def _open_polars_lazy_df(

FILE: lamindb/core/storage/_pyarrow_dataset.py
  function _open_pyarrow_dataset (line 16) | def _open_pyarrow_dataset(paths: UPath | list[UPath], **kwargs) -> PyArr...

FILE: lamindb/core/storage/_spatialdata_accessor.py
  class _TablesAccessor (line 14) | class _TablesAccessor:
    method __init__ (line 15) | def __init__(self, tables: Group, artifact: Artifact | None = None):
    method __getitem__ (line 20) | def __getitem__(self, key: str) -> AnnDataAccessor:
    method keys (line 28) | def keys(self) -> list[str]:
    method __repr__ (line 31) | def __repr__(self) -> str:
  class SpatialDataAccessor (line 39) | class SpatialDataAccessor:
    method __init__ (line 45) | def __init__(self, storage: Group, name: str, artifact: Artifact | Non...
    method tables (line 52) | def tables(self) -> _TablesAccessor:
    method __repr__ (line 56) | def __repr__(self):

FILE: lamindb/core/storage/_tiledbsoma.py
  function _load_h5ad_zarr (line 31) | def _load_h5ad_zarr(objpath: UPath):
  class SOMAS3ContextFactory (line 46) | class SOMAS3ContextFactory:
    method __init__ (line 57) | def __init__(self, storepath: UPath):
    method _extract_refreshable_credentials (line 106) | def _extract_refreshable_credentials(self) -> dict:
    method get_context (line 123) | def get_context(self) -> SOMATileDBContext:
  function _open_tiledbsoma (line 132) | def _open_tiledbsoma(
  function save_tiledbsoma_experiment (line 166) | def save_tiledbsoma_experiment(
  function _soma_store_n_observations (line 352) | def _soma_store_n_observations(obj) -> int:
  function _soma_n_observations (line 372) | def _soma_n_observations(objectpath: UPath) -> int:

FILE: lamindb/core/storage/_valid_suffixes.py
  class VALID_SUFFIXES (line 15) | class VALID_SUFFIXES:

FILE: lamindb/core/storage/_zarr.py
  function get_zarr_store (line 32) | def get_zarr_store(
  function _identify_zarr_type_from_storage (line 50) | def _identify_zarr_type_from_storage(
  function identify_zarr_type (line 66) | def identify_zarr_type(
  function load_zarr (line 89) | def load_zarr(

FILE: lamindb/core/storage/objects.py
  function infer_suffix (line 20) | def infer_suffix(
  function _infer_anndata_suffix (line 62) | def _infer_anndata_suffix(format: str | dict[str, Any] | None) -> str:
  function _infer_dataframe_suffix (line 76) | def _infer_dataframe_suffix(format: str | dict[str, Any] | None) -> str:
  function _infer_spatialdata_suffix (line 86) | def _infer_spatialdata_suffix(format: str | dict[str, Any] | None) -> str:
  function write_to_disk (line 102) | def write_to_disk(dmem: SupportedDataTypes, filepath: Path | str, **kwar...
  function _write_anndata (line 134) | def _write_anndata(dmem: Any, filepath: Path | str, **kwargs) -> None:
  function _write_dataframe (line 146) | def _write_dataframe(dmem: Any, filepath: Path | str, **kwargs) -> None:

FILE: lamindb/core/storage/paths.py
  function auto_storage_key_from_artifact (line 25) | def auto_storage_key_from_artifact(artifact: Artifact):
  function auto_storage_key_from_artifact_uid (line 36) | def auto_storage_key_from_artifact_uid(
  function check_path_is_child_of_root (line 48) | def check_path_is_child_of_root(path: AnyPathStr, root: AnyPathStr) -> b...
  function attempt_accessing_path (line 69) | def attempt_accessing_path(
  function filepath_from_artifact (line 100) | def filepath_from_artifact(
  function _cache_key_from_artifact_storage (line 114) | def _cache_key_from_artifact_storage(
  function filepath_cache_key_from_artifact (line 134) | def filepath_cache_key_from_artifact(
  function store_file_or_folder (line 144) | def store_file_or_folder(
  function delete_storage_using_key (line 183) | def delete_storage_using_key(
  function delete_storage (line 195) | def delete_storage(

FILE: lamindb/core/subsettings/_annotation_settings.py
  class AnnotationSettings (line 1) | class AnnotationSettings:

FILE: lamindb/core/subsettings/_creation_settings.py
  class CreationSettings (line 1) | class CreationSettings:

FILE: lamindb/curators/__init__.py
  function __getattr__ (line 44) | def __getattr__(name: str):

FILE: lamindb/curators/core.py
  function strip_ansi_codes (line 66) | def strip_ansi_codes(text):
  class CatLookup (line 72) | class CatLookup:
    method __init__ (line 87) | def __init__(
    method __getattr__ (line 104) | def __getattr__(self, name):
    method __getitem__ (line 115) | def __getitem__(self, name):
    method __repr__ (line 126) | def __repr__(self) -> str:
  class Curator (line 175) | class Curator:
    method __init__ (line 188) | def __init__(
    method validate (line 240) | def validate(self) -> bool | str:
    method save_artifact (line 245) | def save_artifact(
    method __repr__ (line 258) | def __repr__(self) -> str:
  class SlotsCurator (line 317) | class SlotsCurator(Curator):
    method __init__ (line 327) | def __init__(
    method slots (line 351) | def slots(self) -> dict[str, ComponentCurator]:
    method validate (line 356) | def validate(self) -> None:
    method save_artifact (line 382) | def save_artifact(
  function convert_dict_to_dataframe_for_validation (line 441) | def convert_dict_to_dataframe_for_validation(d: dict, schema: Schema) ->...
  class ComponentCurator (line 462) | class ComponentCurator(Curator):
    method __init__ (line 475) | def __init__(
    method cat (line 643) | def cat(self) -> DataFrameCatManager:
    method standardize (line 647) | def standardize(self) -> None:
    method _cat_manager_validate (line 696) | def _cat_manager_validate(self) -> None:
    method validate (line 706) | def validate(self) -> None:
  class DataFrameCurator (line 725) | class DataFrameCurator(SlotsCurator):
    method __init__ (line 760) | def __init__(
    method cat (line 810) | def cat(self) -> DataFrameCatManager:
    method standardize (line 814) | def standardize(self) -> None:
    method validate (line 825) | def validate(self) -> None:
    method save_artifact (line 832) | def save_artifact(
  class ExperimentalDictCurator (line 847) | class ExperimentalDictCurator(DataFrameCurator):
    method __init__ (line 850) | def __init__(
  function _resolve_schema_slot_path (line 870) | def _resolve_schema_slot_path(
  function _handle_dict_slots (line 907) | def _handle_dict_slots(
  class AnnDataCurator (line 968) | class AnnDataCurator(SlotsCurator):
    method __init__ (line 995) | def __init__(
  function _assign_var_fields_categoricals_multimodal (line 1036) | def _assign_var_fields_categoricals_multimodal(
  class MuDataCurator (line 1068) | class MuDataCurator(SlotsCurator):
    method __init__ (line 1086) | def __init__(
  class SpatialDataCurator (line 1151) | class SpatialDataCurator(SlotsCurator):
    method __init__ (line 1169) | def __init__(
  class TiledbsomaExperimentCurator (line 1245) | class TiledbsomaExperimentCurator(SlotsCurator):
    method __init__ (line 1264) | def __init__(
  class CatVector (line 1316) | class CatVector:
    method __init__ (line 1319) | def __init__(
    method values (line 1387) | def values(self):
    method values (line 1394) | def values(self, new_values):
    method is_validated (line 1403) | def is_validated(self) -> bool:
    method _replace_synonyms (line 1420) | def _replace_synonyms(self) -> list[str]:
    method __repr__ (line 1455) | def __repr__(self) -> str:
    method _add_validated (line 1469) | def _add_validated(self) -> tuple[list, list]:
    method _add_new (line 1631) | def _add_new(
    method _validate (line 1670) | def _validate(
    method validate (line 1759) | def validate(self) -> None:
    method standardize (line 1765) | def standardize(self) -> None:
    method add_new (line 1782) | def add_new(self, **create_kwargs) -> None:
  class DataFrameCatManager (line 1799) | class DataFrameCatManager:
    method __init__ (line 1810) | def __init__(
    method non_validated (line 1898) | def non_validated(self) -> dict[str, list[str]]:
    method categoricals (line 1909) | def categoricals(self) -> list[Feature]:
    method __repr__ (line 1913) | def __repr__(self) -> str:
    method lookup (line 1937) | def lookup(self, public: bool = False) -> CatLookup:
    method validate (line 1950) | def validate(self) -> bool:
    method standardize (line 1971) | def standardize(self, key: str) -> None:
    method add_new_from (line 1993) | def add_new_from(self, key: str, **kwargs):
  function get_current_filter_kwargs (line 2012) | def get_current_filter_kwargs(
  function annotate_artifact (line 2029) | def annotate_artifact(
  function _flatten_unique (line 2159) | def _flatten_unique(series: pd.Series[list[Any] | Any]) -> list[Any]:

FILE: lamindb/errors.py
  class ValidationError (line 51) | class ValidationError(Exception):
  class InvalidArgument (line 57) | class InvalidArgument(Exception):
  class TrackNotCalled (line 63) | class TrackNotCalled(Exception):
  class NotebookNotSaved (line 69) | class NotebookNotSaved(Exception):
  class UnknownStorageLocation (line 75) | class UnknownStorageLocation(Exception):
  class NoStorageLocationForSpace (line 81) | class NoStorageLocationForSpace(Exception):
  class InconsistentKey (line 87) | class InconsistentKey(Exception):
  class FieldValidationError (line 93) | class FieldValidationError(Exception):
  class IntegrityError (line 104) | class IntegrityError(Exception):
  class MissingContextUID (line 114) | class MissingContextUID(Exception):
  class UpdateContext (line 120) | class UpdateContext(Exception):
  class BlobHashNotFound (line 126) | class BlobHashNotFound(Exception):
  class NoWriteAccess (line 137) | class NoWriteAccess(Exception):
  class FileNotInDevDir (line 143) | class FileNotInDevDir(Exception):
  class BranchAlreadyExists (line 149) | class BranchAlreadyExists(Exception):

FILE: lamindb/examples/cellxgene/_cellxgene.py
  function save_cellxgene_defaults (line 21) | def save_cellxgene_defaults() -> None:
  function create_cellxgene_schema (line 99) | def create_cellxgene_schema(

FILE: lamindb/examples/croissant/__init__.py
  function mini_immuno (line 11) | def mini_immuno(

FILE: lamindb/examples/datasets/__init__.py
  function __getattr__ (line 101) | def __getattr__(name: str):

FILE: lamindb/examples/datasets/_core.py
  function file_fcs (line 19) | def file_fcs() -> Path:
  function file_fcs_alpert19 (line 28) | def file_fcs_alpert19(populate_registries: bool = False) -> Path:
  function file_jpg_paradisi05 (line 59) | def file_jpg_paradisi05() -> Path:
  function file_tsv_rnaseq_nfcore_salmon_merged_gene_counts (line 71) | def file_tsv_rnaseq_nfcore_salmon_merged_gene_counts(
  function file_fastq (line 97) | def file_fastq(in_storage_root=False) -> Path:
  function file_bam (line 106) | def file_bam(in_storage_root=False) -> Path:
  function file_mini_csv (line 115) | def file_mini_csv(in_storage_root=False) -> Path:
  function file_tiff_suo22 (line 124) | def file_tiff_suo22() -> Path:
  function dir_iris_images (line 138) | def dir_iris_images() -> UPath:
  function anndata_mouse_sc_lymph_node (line 155) | def anndata_mouse_sc_lymph_node(
  function anndata_pbmc68k_reduced (line 234) | def anndata_pbmc68k_reduced() -> ad.AnnData:
  function anndata_file_pbmc68k_test (line 262) | def anndata_file_pbmc68k_test() -> Path:
  function anndata_pbmc3k_processed (line 284) | def anndata_pbmc3k_processed() -> ad.AnnData:
  function anndata_human_immune_cells (line 294) | def anndata_human_immune_cells(
  function anndata_suo22_Visium10X (line 342) | def anndata_suo22_Visium10X():
  function mudata_papalexi21_subset (line 355) | def mudata_papalexi21_subset(with_uns: bool = False) -> MuData:
  function dict_cellxgene_uns (line 427) | def dict_cellxgene_uns() -> dict[str, Any]:
  function df_iris (line 459) | def df_iris() -> pd.DataFrame:
  function df_iris_in_meter (line 470) | def df_iris_in_meter() -> pd.DataFrame:
  function df_iris_in_meter_study1 (line 491) | def df_iris_in_meter_study1() -> pd.DataFrame:
  function df_iris_in_meter_study2 (line 497) | def df_iris_in_meter_study2() -> pd.DataFrame:
  function dir_scrnaseq_cellranger (line 503) | def dir_scrnaseq_cellranger(
  function schmidt22_crispra_gws_IFNG (line 555) | def schmidt22_crispra_gws_IFNG(basedir=".") -> Path:
  function schmidt22_perturbseq (line 567) | def schmidt22_perturbseq(basedir=".") -> Path:
  function anndata_visium_mouse_cellxgene (line 593) | def anndata_visium_mouse_cellxgene() -> ad.AnnData:
  function spatialdata_blobs (line 605) | def spatialdata_blobs() -> SpatialData:

FILE: lamindb/examples/datasets/_fake.py
  function fake_bio_notebook_titles (line 4) | def fake_bio_notebook_titles(n=100) -> list[str]:

FILE: lamindb/examples/datasets/_small.py
  function small_dataset3_cellxgene (line 10) | def small_dataset3_cellxgene(
  function anndata_with_obs (line 107) | def anndata_with_obs() -> ad.AnnData:

FILE: lamindb/examples/datasets/mini_immuno.py
  function define_features_labels (line 34) | def define_features_labels() -> None:
  function define_mini_immuno_schema_flexible (line 43) | def define_mini_immuno_schema_flexible() -> Schema:
  function save_mini_immuno_datasets (line 57) | def save_mini_immuno_datasets():
  function get_dataset1 (line 66) | def get_dataset1(
  function get_dataset2 (line 148) | def get_dataset2(

FILE: lamindb/examples/fixtures/sheets.py
  function populate_sheets_compound_treatment (line 9) | def populate_sheets_compound_treatment():
  function populate_nextflow_sheet_with_samples (line 160) | def populate_nextflow_sheet_with_samples():

FILE: lamindb/examples/mlflow/__init__.py
  function save_mlflow_features (line 9) | def save_mlflow_features():

FILE: lamindb/examples/schemas/_anndata.py
  function anndata_ensembl_gene_ids_and_valid_features_in_obs (line 10) | def anndata_ensembl_gene_ids_and_valid_features_in_obs() -> Schema:

FILE: lamindb/examples/schemas/_simple.py
  function valid_features (line 10) | def valid_features() -> Schema:

FILE: lamindb/examples/wandb/__init__.py
  function save_wandb_features (line 9) | def save_wandb_features():

FILE: lamindb/integrations/__init__.py
  function __getattr__ (line 31) | def __getattr__(name: str):

FILE: lamindb/integrations/_croissant.py
  function curate_from_croissant (line 17) | def curate_from_croissant(

FILE: lamindb/integrations/_vitessce.py
  function save_vitessce_config (line 21) | def save_vitessce_config(

FILE: lamindb/integrations/lightning.py
  class ArtifactEvent (line 77) | class ArtifactEvent:
  class ArtifactSavedEvent (line 91) | class ArtifactSavedEvent(ArtifactEvent):
  class ArtifactRemovedEvent (line 104) | class ArtifactRemovedEvent(ArtifactEvent):
  class ArtifactObserver (line 115) | class ArtifactObserver(Protocol):
    method on_artifact_saved (line 122) | def on_artifact_saved(self, event: ArtifactSavedEvent) -> None: ...
    method on_artifact_removed (line 124) | def on_artifact_removed(self, event: ArtifactRemovedEvent) -> None: ...
  class ArtifactPublisher (line 127) | class ArtifactPublisher(Protocol):
    method create_artifact (line 135) | def create_artifact(
    method storage_uri (line 146) | def storage_uri(self, artifact: Any) -> str: ...
  class LaminArtifactPublisher (line 149) | class LaminArtifactPublisher:
    method create_artifact (line 157) | def create_artifact(
    method storage_uri (line 180) | def storage_uri(self, artifact: ln.Artifact) -> str:
  function save_lightning_features (line 184) | def save_lightning_features() -> None:
  class FeatureAnnotator (line 256) | class FeatureAnnotator:
    method __init__ (line 272) | def __init__(
    method setup (line 287) | def setup(self, trainer: pl.Trainer, pl_module: pl.LightningModule) ->...
    method _attach_user_run_features (line 298) | def _attach_user_run_features(self) -> None:
    method _validate_user_features (line 303) | def _validate_user_features(self) -> None:
    method _discover_auto_features (line 319) | def _discover_auto_features(self) -> None:
    method _discover_hparam_features (line 334) | def _discover_hparam_features(
    method _collect_hparam_names (line 346) | def _collect_hparam_names(*sources: Any) -> set[str]:
    method get (line 354) | def get(self, name: str) -> ln.Feature | None:
    method _set (line 358) | def _set(self, target: dict[str | ln.Feature, Any], name: str, value: ...
    method save_run_features (line 363) | def save_run_features(
    method _collect_run_features (line 381) | def _collect_run_features(
    method _add_trainer_config_features (line 409) | def _add_trainer_config_features(
    method _add_hparam_features (line 425) | def _add_hparam_features(
    method collect_checkpoint_features (line 439) | def collect_checkpoint_features(
    method clear_best_model_flags (line 484) | def clear_best_model_flags(self, checkpoint_key_prefix: str) -> None:
    method clear_last_model_flags (line 488) | def clear_last_model_flags(self, checkpoint_key_prefix: str) -> None:
    method _clear_flagged_model_feature (line 492) | def _clear_flagged_model_feature(
    method update_model_ranks (line 519) | def update_model_ranks(self, checkpoint_key_prefix: str, mode: str) ->...
    method _get_artifact_feature_rows (line 543) | def _get_artifact_feature_rows(
  class ArtifactPublishingModelCheckpoint (line 580) | class ArtifactPublishingModelCheckpoint(ModelCheckpoint):
    method __init__ (line 599) | def __init__(
    method last_checkpoint_artifact (line 619) | def last_checkpoint_artifact(self) -> Any | None:
    method last_config_artifact (line 624) | def last_config_artifact(self) -> Any | None:
    method last_hparams_artifact (line 629) | def last_hparams_artifact(self) -> Any | None:
    method last_artifact_event (line 634) | def last_artifact_event(self) -> ArtifactSavedEvent | ArtifactRemovedE...
    method get_last_artifact (line 638) | def get_last_artifact(self, kind: ArtifactKind) -> Any | None:
    method add_artifact_observer (line 642) | def add_artifact_observer(self, observer: ArtifactObserver) -> None:
    method remove_artifact_observer (line 646) | def remove_artifact_observer(self, observer: ArtifactObserver) -> None:
    method resolve_artifact_storage_uri (line 650) | def resolve_artifact_storage_uri(self, artifact: Any) -> str:
    method resolve_artifact_key (line 654) | def resolve_artifact_key(
    method _notify_artifact_saved (line 663) | def _notify_artifact_saved(
    method _notify_artifact_removed (line 686) | def _notify_artifact_removed(
    method _notify_artifact_observers (line 711) | def _notify_artifact_observers(
    method on_artifact_saved (line 721) | def on_artifact_saved(self, event: ArtifactSavedEvent) -> None:
    method on_artifact_removed (line 725) | def on_artifact_removed(self, event: ArtifactRemovedEvent) -> None:
    method save_checkpoint_artifact (line 729) | def save_checkpoint_artifact(
    method save_config_artifact (line 740) | def save_config_artifact(self, trainer: pl.Trainer, config_path: Path ...
    method save_hparams_artifact (line 745) | def save_hparams_artifact(
  class Checkpoint (line 753) | class Checkpoint(ArtifactPublishingModelCheckpoint):
    method __init__ (line 883) | def __init__(
    method setup (line 926) | def setup(
    method _base_prefix (line 946) | def _base_prefix(self, trainer: pl.Trainer) -> str:
    method _active_run_uid (line 963) | def _active_run_uid(self) -> str | None:
    method _logger_prefix (line 969) | def _logger_prefix(self, trainer: pl.Trainer, run_uid: str | None) -> ...
    method base_prefix (line 983) | def base_prefix(self) -> str:
    method checkpoint_key_prefix (line 995) | def checkpoint_key_prefix(self) -> str:
    method resolve_artifact_storage_uri (line 1004) | def resolve_artifact_storage_uri(self, artifact: ln.Artifact) -> str:
    method resolve_artifact_key (line 1012) | def resolve_artifact_key(
    method _create_lamin_artifact (line 1028) | def _create_lamin_artifact(
    method save_checkpoint_artifact (line 1048) | def save_checkpoint_artifact(
    method save_config_artifact (line 1085) | def save_config_artifact(
    method save_hparams_artifact (line 1113) | def save_hparams_artifact(
    method _save_hparams_yaml (line 1143) | def _save_hparams_yaml(self, trainer: pl.Trainer) -> None:
    method _save_checkpoint (line 1159) | def _save_checkpoint(self, trainer: pl.Trainer, filepath: str) -> None:
    method _remove_checkpoint (line 1190) | def _remove_checkpoint(self, trainer: pl.Trainer, filepath: str) -> None:
  class SaveConfigCallback (line 1211) | class SaveConfigCallback(_SaveConfigCallback):
    method setup (line 1247) | def setup(
    method _config_path (line 1279) | def _config_path(self, trainer: pl.Trainer) -> Path:
    method _save_config (line 1306) | def _save_config(self, trainer: pl.Trainer, config_path: Path) -> None:
    method _get_artifact_checkpoint_callback (line 1318) | def _get_artifact_checkpoint_callback(
  class Callback (line 1331) | class Callback(pl.Callback):
    method __init__ (line 1343) | def __init__(
    method on_train_start (line 1358) | def on_train_start(
    method on_train_epoch_end (line 1374) | def on_train_epoch_end(

FILE: lamindb/migrations/0177_squashed.py
  function apply_constraints (line 169) | def apply_constraints(apps, schema_editor):
  class Migration (line 185) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0178_v2_2.py
  class Migration (line 10) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0179_v2_2_part_2.py
  class Migration (line 10) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0180_v2_2_part_3.py
  class Migration (line 9) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0181_v2_2_part_4.py
  class Migration (line 7) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0182_v2_2_part_5.py
  class Migration (line 10) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0183_v2_2_part_6.py
  class Migration (line 6) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0184_alter_transformrecord_feature.py
  class Migration (line 9) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0185_alter_runrecord_feature.py
  class Migration (line 9) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0186_v2_4.py
  class Migration (line 9) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0187_squashed.py
  function apply_constraints (line 169) | def apply_constraints(apps, schema_editor):
  class Migration (line 185) | class Migration(migrations.Migration):

FILE: lamindb/migrations/0187_v2_4_part_2.py
  class Migration (line 9) | class Migration(migrations.Migration):

FILE: lamindb/models/_describe.py
  function strip_ansi_from_string (line 31) | def strip_ansi_from_string(text: str) -> str:
  function format_rich_tree (line 37) | def format_rich_tree(
  function format_run_title (line 82) | def format_run_title(
  function format_title_with_version (line 105) | def format_title_with_version(
  function describe_header (line 119) | def describe_header(record: BaseSQLRecord) -> Tree:
  function format_bytes (line 160) | def format_bytes(bytes_value):
  function append_uid_run (line 174) | def append_uid_run(record: TracksRun, two_column_items: list, fk_data=No...
  function append_branch_space_created_at_created_by (line 192) | def append_branch_space_created_at_created_by(
  function add_two_column_items_to_tree (line 212) | def add_two_column_items_to_tree(tree: Tree, two_column_items: list) -> ...
  function describe_artifact (line 230) | def describe_artifact(
  function describe_collection (line 306) | def describe_collection(
  function display_text (line 322) | def display_text(
  function describe_run (line 340) | def describe_run(
  function describe_record (line 427) | def describe_record(
  function describe_transform (line 474) | def describe_transform(
  function describe_branch (line 499) | def describe_branch(record: Branch) -> Tree:
  function describe_schema (line 514) | def describe_schema(record: Schema, slot: str | None = None) -> Tree:
  function describe_postgres (line 597) | def describe_postgres(record):
  function describe_sqlite (line 639) | def describe_sqlite(record):
  function append_readme_blocks_to_tree (line 690) | def append_readme_blocks_to_tree(
  function describe_postgres_sqlite (line 724) | def describe_postgres_sqlite(

FILE: lamindb/models/_django.py
  function patch_many_to_many_descriptor (line 21) | def patch_many_to_many_descriptor() -> None:
  function get_related_model (line 65) | def get_related_model(model, field_name):
  function get_artifact_or_run_with_related (line 81) | def get_artifact_or_run_with_related(
  function get_collection_with_related (line 295) | def get_collection_with_related(
  function get_schema_m2m_relations (line 352) | def get_schema_m2m_relations(artifact: Artifact, slot_schema: dict, limi...

FILE: lamindb/models/_feature_manager.py
  function get_accessor_by_registry_ (line 72) | def get_accessor_by_registry_(host: Artifact | Collection) -> dict:
  function get_schema_by_slot_ (line 83) | def get_schema_by_slot_(host: Artifact) -> dict[str, Schema]:
  function get_label_links (line 101) | def get_label_links(
  function get_schema_links (line 113) | def get_schema_links(host: Artifact | Collection) -> BasicQuerySet:
  function get_link_attr (line 119) | def get_link_attr(
  function get_categorical_link_info (line 132) | def get_categorical_link_info(
  function strip_cat (line 190) | def strip_cat(feature_dtype: str) -> str:
  function format_dtype_for_display (line 201) | def format_dtype_for_display(dtype_str: str) -> str:
  class GroupConcat (line 242) | class GroupConcat(Aggregate):
  function custom_aggregate (line 247) | def custom_aggregate(field, using: str):
  function get_categoricals_postgres (line 254) | def get_categoricals_postgres(
  function get_categoricals_sqlite (line 329) | def get_categoricals_sqlite(
  function get_non_categoricals (line 362) | def get_non_categoricals(
  function create_feature_table (line 435) | def create_feature_table(
  function get_features_data (line 452) | def get_features_data(
  function describe_features (line 605) | def describe_features(
  function infer_convert_dtype_key_value (line 719) | def infer_convert_dtype_key_value(
  function _filter_one_feature_clause (line 793) | def _filter_one_feature_clause(
  function filter_with_feature_predicates (line 911) | def filter_with_feature_predicates(
  function filter_base (line 936) | def filter_base(
  function filter_with_features (line 970) | def filter_with_features(
  class FeatureManager (line 1024) | class FeatureManager:
    method __init__ (line 1027) | def __init__(self, sqlrecord: Artifact | Run | Record):
    method __repr__ (line 1034) | def __repr__(self) -> str:
    method describe (line 1037) | def describe(self, return_str: bool = False) -> str | None:
    method get_values (line 1050) | def get_values(self, external_only: bool = False) -> dict[str, Any]:
    method __getitem__ (line 1060) | def __getitem__(
    method slots (line 1164) | def slots(self) -> dict[str, Schema]:
    method _accessor_by_registry (line 1177) | def _accessor_by_registry(self):
    method _add_label_feature_links (line 1183) | def _add_label_feature_links(
    method _get_feature_objects (line 1215) | def _get_feature_objects(self, dictionary, feature_field):
    method _resolve_feature_value_dictionary (line 1251) | def _resolve_feature_value_dictionary(
    method _merge_feature_objects (line 1319) | def _merge_feature_objects(
    method _raise_not_validated_values (line 1336) | def _raise_not_validated_values(
    method _collect_record_feature_writes (line 1352) | def _collect_record_feature_writes(
    method add_values (line 1503) | def add_values(
    method _add_values (line 1617) | def _add_values(
    method set_values (line 1752) | def set_values(
    method _get_external_schema (line 1859) | def _get_external_schema(self) -> Schema | None:
    method remove_values (line 1867) | def remove_values(
    method _remove_values (line 1898) | def _remove_values(
    method _add_schema (line 2002) | def _add_schema(self, schema: Schema, slot: str) -> None:
    method _add_from (line 2033) | def _add_from(self, data: Artifact | Collection, transfer_logs: dict =...
  function bulk_set_features_in_records (line 2119) | def bulk_set_features_in_records(records: Iterable[Record]) -> None:

FILE: lamindb/models/_from_values.py
  function _from_values (line 17) | def _from_values(
  function get_existing_records (line 99) | def get_existing_records(
  function create_records_from_source (line 192) | def create_records_from_source(
  function index_iterable (line 307) | def index_iterable(iterable: ListLike) -> Index:
  function _format_values (line 317) | def _format_values(
  function _bulk_create_dicts_from_df (line 336) | def _bulk_create_dicts_from_df(
  function get_organism_record_from_field (line 357) | def get_organism_record_from_field(  # type: ignore

FILE: lamindb/models/_is_versioned.py
  class IsVersioned (line 21) | class IsVersioned(models.Model):
    class Meta (line 24) | class Meta:
    method __init__ (line 38) | def __init__(
    method stem_uid (line 47) | def stem_uid(self) -> str:
    method version (line 60) | def version(self) -> str:
    method version (line 70) | def version(self, value: str | None) -> None:
    method versions (line 74) | def versions(self) -> QuerySet:
    method _add_to_version_family (line 88) | def _add_to_version_family(
  function bump_version (line 120) | def bump_version(
  function set_version (line 165) | def set_version(version: str | None = None, previous_version: str | None...
  function create_uid (line 180) | def create_uid(
  function process_revises (line 219) | def process_revises(
  function _adjust_is_latest_when_deleting_is_versioned (line 239) | def _adjust_is_latest_when_deleting_is_versioned(
  function reconcile_is_latest_within_branch (line 294) | def reconcile_is_latest_within_branch(

FILE: lamindb/models/_label_manager.py
  function _get_labels (line 37) | def _get_labels(
  function _get_labels_postgres (line 63) | def _get_labels_postgres(
  function describe_labels (line 76) | def describe_labels(
  function _save_validated_records (line 129) | def _save_validated_records(
  function save_validated_records (line 162) | def save_validated_records(
  class LabelManager (line 174) | class LabelManager:
    method __init__ (line 182) | def __init__(self, sqlrecord: Artifact | Collection) -> None:
    method __repr__ (line 187) | def __repr__(self) -> str:
    method describe (line 190) | def describe(self, return_str=True) -> str:
    method add (line 195) | def add(
    method get (line 210) | def get(
    method add_from (line 227) | def add_from(self, data: Artifact | Collection, transfer_logs: dict = ...

FILE: lamindb/models/_relations.py
  function get_schema_modules (line 19) | def get_schema_modules(instance: str | None) -> set[str]:
  function dict_module_name_to_model_name (line 45) | def dict_module_name_to_model_name(
  function dict_related_model_to_related_name (line 66) | def dict_related_model_to_related_name(
  function get_related_name (line 100) | def get_related_name(features_type: type[SQLRecord]) -> str:

FILE: lamindb/models/_run_cleanup.py
  function main (line 14) | def main() -> None:

FILE: lamindb/models/artifact.py
  function _lazy_load_storage_module (line 79) | def _lazy_load_storage_module():
  function _s (line 114) | def _s():
  function _identify_zarr_type (line 126) | def _identify_zarr_type(storepath, *, check: bool = True):
  function process_pathlike (line 177) | def process_pathlike(
  function process_data (line 257) | def process_data(
  function get_stat_or_artifact (line 343) | def get_stat_or_artifact(
  function check_path_in_existing_storage (line 434) | def check_path_in_existing_storage(
  function get_relative_path_to_directory (line 452) | def get_relative_path_to_directory(
  function get_artifact_kwargs_from_data (line 469) | def get_artifact_kwargs_from_data(
  function log_storage_hint (line 610) | def log_storage_hint(
  function data_is_dataframe (line 640) | def data_is_dataframe(data: Any) -> bool:
  function data_is_scversedatastructure (line 646) | def data_is_scversedatastructure(
  function data_is_soma_experiment (line 704) | def data_is_soma_experiment(data: SOMAExperiment | AnyPathStr) -> bool:
  function check_otype_artifact (line 713) | def check_otype_artifact(
  function populate_subsequent_run (line 751) | def populate_subsequent_run(record: Artifact | Collection, run: Run | No...
  function get_run (line 762) | def get_run(run: Run | None) -> Run | None:
  function save_staged_schemas (line 780) | def save_staged_schemas(self: Artifact) -> None:
  function save_schema_links (line 804) | def save_schema_links(self: Artifact) -> None:
  function validate_feature (line 819) | def validate_feature(feature: Feature, records: list[SQLRecord]) -> None:
  function get_labels (line 830) | def get_labels(
  function add_labels (line 882) | def add_labels(
  function delete_permanently (line 990) | def delete_permanently(artifact: Artifact, storage: bool | None, using_k...
  class LazyArtifact (line 1048) | class LazyArtifact:
    method __init__ (line 1070) | def __init__(self, suffix: str, overwrite_versions: bool, **kwargs):
    method path (line 1090) | def path(self) -> UPath:
    method save (line 1093) | def save(self, upload: bool | None = None, **kwargs) -> Artifact:
    method __repr__ (line 1097) | def __repr__(self) -> str:  # pragma: no cover
  function _sqlrecord_or_id (line 1107) | def _sqlrecord_or_id(
  class Artifact (line 1129) | class Artifact(SQLRecord, IsVersioned, TracksRun, TracksUpdates):
    class Meta (line 1296) | class Meta(SQLRecord.Meta, IsVersioned.Meta, TracksRun.Meta, TracksUpd...
    method features (line 1328) | def features(self) -> FeatureManager:
    method labels (line 1370) | def labels(self) -> LabelManager:
    method __init__ (line 1570) | def __init__(
    method __init__ (line 1589) | def __init__(
    method __init__ (line 1594) | def __init__(
    method transform (line 1864) | def transform(self) -> Transform | None:
    method overwrite_versions (line 1869) | def overwrite_versions(self) -> bool:
    method _storage_ongoing (line 1881) | def _storage_ongoing(self) -> bool:
    method _storage_ongoing (line 1898) | def _storage_ongoing(self, value: bool | None) -> None:
    method feature_sets (line 1912) | def feature_sets(self):
    method path (line 1916) | def path(self) -> UPath:
    method _cache_path (line 1937) | def _cache_path(self) -> UPath:
    method get (line 1948) | def get(
    method filter (line 1990) | def filter(
    method from_lazy (line 2019) | def from_lazy(
    method from_dataframe (line 2065) | def from_dataframe(
    method from_df (line 2172) | def from_df(
    method from_anndata (line 2194) | def from_anndata(
    method from_mudata (line 2322) | def from_mudata(
    method from_spatialdata (line 2382) | def from_spatialdata(
    method from_tiledbsoma (line 2460) | def from_tiledbsoma(
    method from_dir (line 2516) | def from_dir(
    method replace (line 2627) | def replace(
    method open (line 2738) | def open(
    method load (line 2935) | def load(
    method cache (line 3012) | def cache(
    method delete (line 3047) | def delete(
    method save (line 3088) | def save(
  function _update_artifact_keys_with_suffix (line 3336) | def _update_artifact_keys_with_suffix(artifact: Artifact, suffix: str):
  function _confirm_artifact_move (line 3346) | def _confirm_artifact_move(source_path_str: str, target_path_str: str) -...
  function _handle_non_virtual_key_change_on_save (line 3359) | def _handle_non_virtual_key_change_on_save(
  function _handle_suffix_change_on_save (line 3382) | def _handle_suffix_change_on_save(artifact: Artifact) -> bool:
  function _sorted_sizes (line 3402) | def _sorted_sizes(fs: AbstractFileSystem, path: str) -> list[int]:
  function _rm_catch_error (line 3407) | def _rm_catch_error(fs: AbstractFileSystem, path: str) -> Exception | None:
  function _safe_move (line 3416) | def _safe_move(fs: AbstractFileSystem, source: str, target: str):
  function _move_artifact_to_storage (line 3446) | def _move_artifact_to_storage(
  function _synchronize_cleanup_on_error (line 3467) | def _synchronize_cleanup_on_error(
  function _delete_skip_storage (line 3488) | def _delete_skip_storage(artifact, *args, **kwargs) -> None:
  function _save_skip_storage (line 3492) | def _save_skip_storage(artifact, **kwargs) -> None:
  class ArtifactJsonValue (line 3498) | class ArtifactJsonValue(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 3504) | class Meta:
  class ArtifactUser (line 3509) | class ArtifactUser(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 3517) | class Meta:
  class ArtifactRun (line 3524) | class ArtifactRun(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 3533) | class Meta:
  class ArtifactArtifact (line 3540) | class ArtifactArtifact(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 3549) | class Meta:
  function track_run_input (line 3556) | def track_run_input(
  function migrate_save_completed_to_aux_postgres (line 3727) | def migrate_save_completed_to_aux_postgres(schema_editor) -> None:

FILE: lamindb/models/artifact_set.py
  class ArtifactSet (line 32) | class ArtifactSet(Iterable):
    method load (line 45) | def load(
    method open (line 62) | def open(
    method mapped (line 83) | def mapped(
  function artifacts_from_path (line 133) | def artifacts_from_path(artifacts: ArtifactSet, path: AnyPathStr) -> Art...

FILE: lamindb/models/block.py
  function _init_versioned_attached_block (line 50) | def _init_versioned_attached_block(
  class BaseBlock (line 166) | class BaseBlock(IsVersioned):
    class Meta (line 167) | class Meta:
  class Block (line 205) | class Block(BaseBlock, SQLRecord):
    class Meta (line 211) | class Meta:
    method __init__ (line 232) | def __init__(
    method __init__ (line 243) | def __init__(
    method __init__ (line 248) | def __init__(
  class HasBranch (line 367) | class HasBranch(models.Model):
    class Meta (line 368) | class Meta:
  class RecordBlock (line 389) | class RecordBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 392) | class Meta:
    method __init__ (line 398) | def __init__(self, *args, **kwargs):
  class ArtifactBlock (line 402) | class ArtifactBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 405) | class Meta:
    method __init__ (line 411) | def __init__(self, *args, **kwargs):
  class TransformBlock (line 415) | class TransformBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 418) | class Meta:
    method __init__ (line 428) | def __init__(self, *args, **kwargs):
  class RunBlock (line 434) | class RunBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 437) | class Meta:
    method __init__ (line 443) | def __init__(self, *args, **kwargs):
  class CollectionBlock (line 447) | class CollectionBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 450) | class Meta:
    method __init__ (line 458) | def __init__(self, *args, **kwargs):
  class SchemaBlock (line 462) | class SchemaBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 465) | class Meta:
    method __init__ (line 471) | def __init__(self, *args, **kwargs):
  class FeatureBlock (line 475) | class FeatureBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 478) | class Meta:
    method __init__ (line 484) | def __init__(self, *args, **kwargs):
  class ProjectBlock (line 488) | class ProjectBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 491) | class Meta:
    method __init__ (line 497) | def __init__(self, *args, **kwargs):
  class SpaceBlock (line 501) | class SpaceBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 504) | class Meta:
    method __init__ (line 510) | def __init__(self, *args, **kwargs):
  class ULabelBlock (line 514) | class ULabelBlock(BaseBlock, BaseSQLRecord, HasBranch):
    class Meta (line 517) | class Meta:
    method __init__ (line 523) | def __init__(self, *args, **kwargs):
  class BranchBlock (line 527) | class BranchBlock(BaseBlock, BaseSQLRecord):
    class Meta (line 530) | class Meta:
    method __init__ (line 536) | def __init__(self, *args, **kwargs):

FILE: lamindb/models/can_curate.py
  function _check_if_record_in_db (line 29) | def _check_if_record_in_db(record: str | SQLRecord | None, using_key: st...
  function _concat_lists (line 39) | def _concat_lists(values: ListLike | str) -> list[str]:
  function _inspect (line 56) | def _inspect(
  function _validate (line 159) | def _validate(
  function _standardize (line 218) | def _standardize(
  function _add_or_remove_synonyms (line 350) | def _add_or_remove_synonyms(
  function _check_synonyms_field_exist (line 430) | def _check_synonyms_field_exist(record: CanCurate):
  function _filter_queryset_with_organism (line 438) | def _filter_queryset_with_organism(
  class CanCurate (line 461) | class CanCurate:
    method inspect (line 465) | def inspect(
    method validate (line 521) | def validate(
    method from_values (line 575) | def from_values(
    method standardize (line 629) | def standardize(
    method add_synonym (line 710) | def add_synonym(
    method remove_synonym (line 746) | def remove_synonym(self, synonym: str | ListLike):
    method set_abbr (line 773) | def set_abbr(self, value: str):

FILE: lamindb/models/collection.py
  function _load_concat_artifacts (line 59) | def _load_concat_artifacts(
  class Collection (line 94) | class Collection(SQLRecord, IsVersioned, TracksRun, TracksUpdates):
    class Meta (line 124) | class Meta(SQLRecord.Meta, IsVersioned.Meta, TracksRun.Meta, TracksUpd...
    method __init__ (line 218) | def __init__(
    method __init__ (line 232) | def __init__(
    method __init__ (line 237) | def __init__(
    method get (line 341) | def get(
    method append (line 372) | def append(self, artifact: Artifact, run: Run | None = None) -> Collec...
    method open (line 399) | def open(
    method mapped (line 433) | def mapped(
    method cache (line 535) | def cache(self, is_run_input: bool | None = None) -> list[UPath]:
    method load (line 552) | def load(
    method save (line 569) | def save(self, using: str | None = None) -> Collection:
    method restore (line 599) | def restore(self) -> None:
    method transform (line 612) | def transform(self) -> Transform | None:
    method name (line 617) | def name(self) -> str:
    method ordered_artifacts (line 625) | def ordered_artifacts(self) -> QuerySet:
    method data_artifact (line 637) | def data_artifact(self) -> Artifact | None:
  function from_artifacts (line 650) | def from_artifacts(artifacts: Iterable[Artifact]) -> tuple[str, dict[str...
  class CollectionArtifact (line 668) | class CollectionArtifact(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 675) | class Meta:

FILE: lamindb/models/feature.py
  class FeaturePredicate (line 69) | class FeaturePredicate:
    method __bool__ (line 76) | def __bool__(self) -> bool:
  function parse_dtype (line 83) | def parse_dtype(
  function get_record_type_from_uid (line 127) | def get_record_type_from_uid(
  function get_record_type_from_nested_subtypes (line 144) | def get_record_type_from_nested_subtypes(
  function dtype_as_object (line 244) | def dtype_as_object(dtype_str: str, old_format: bool = False) -> type | ...
  function parse_cat_dtype (line 309) | def parse_cat_dtype(
  function parse_nested_brackets (line 394) | def parse_nested_brackets(dtype_str: str, old_format: bool = False) -> d...
  function extract_subtypes_and_filter (line 515) | def extract_subtypes_and_filter(subtype_str: str) -> dict[str, Any]:
  function serialize_dtype (line 578) | def serialize_dtype(
  function serialize_pandas_dtype (line 665) | def serialize_pandas_dtype(pandas_dtype: ExtensionDtype) -> str:
  function convert_to_pandas_dtype (line 689) | def convert_to_pandas_dtype(lamin_dtype: str) -> str | pd.CategoricalDtype:
  function parse_filter_string (line 713) | def parse_filter_string(filter_str: str) -> dict[str, tuple[str, str | N...
  function resolve_relation_filters (line 749) | def resolve_relation_filters(
  function migrate_dtype_to_uid_format (line 778) | def migrate_dtype_to_uid_format(connection, input_field: str = "_dtype_s...
  function process_init_feature_param (line 842) | def process_init_feature_param(args, kwargs):
  class Feature (line 931) | class Feature(SQLRecord, HasType, CanCurate, TracksRun, TracksUpdates):
    class Meta (line 1083) | class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
    method __init__ (line 1186) | def __init__(
    method __init__ (line 1202) | def __init__(
    method __init__ (line 1207) | def __init__(
    method __eq__ (line 1290) | def __eq__(self, other: object) -> bool:
    method __ne__ (line 1298) | def __ne__(self, other: object) -> bool:
    method __gt__ (line 1306) | def __gt__(self, value: Any) -> FeaturePredicate:
    method __ge__ (line 1309) | def __ge__(self, value: Any) -> FeaturePredicate:
    method __lt__ (line 1312) | def __lt__(self, value: Any) -> FeaturePredicate:
    method __le__ (line 1315) | def __le__(self, value: Any) -> FeaturePredicate:
    method query_features (line 1319) | def query_features(self) -> QuerySet:
    method from_dataframe (line 1328) | def from_dataframe(
    method from_df (line 1369) | def from_df(
    method from_dict (line 1375) | def from_dict(
    method save (line 1421) | def save(self, *args, **kwargs) -> Feature:
    method with_config (line 1426) | def with_config(self, optional: bool | None = None) -> tuple[Feature, ...
    method coerce_dtype (line 1434) | def coerce_dtype(self) -> bool | None:
    method coerce_dtype (line 1439) | def coerce_dtype(self, value: bool | None) -> None:
    method dtype (line 1444) | def dtype(self) -> str | None:
    method dtype_as_str (line 1464) | def dtype_as_str(self) -> DtypeStr | str | None:
    method dtype_as_object (line 1501) | def dtype_as_object(self) -> type | SQLRecord | FieldAttr | None:  # t...
  class JsonValue (line 1552) | class JsonValue(SQLRecord, TracksRun):
    class Meta (line 1584) | class Meta(BaseSQLRecord.Meta, TracksRun.Meta):
    method get_or_create (line 1589) | def get_or_create(cls, feature, value):
  function suggest_categorical_for_str_iterable (line 1604) | def suggest_categorical_for_str_iterable(
  function categoricals_from_df (line 1620) | def categoricals_from_df(df: pd.DataFrame) -> dict:

FILE: lamindb/models/has_parents.py
  function _query_relatives (line 34) | def _query_relatives(
  function keep_topmost_matches (line 74) | def keep_topmost_matches(records: list[HasType] | SQLRecordList) -> SQLR...
  function _query_ancestors_of_fk (line 135) | def _query_ancestors_of_fk(record: SQLRecord, attr: str) -> SQLRecordList:
  class HasParents (line 149) | class HasParents:
    method view_parents (line 152) | def view_parents(
    method view_children (line 187) | def view_children(
    method query_parents (line 220) | def query_parents(self) -> QuerySet:
    method query_children (line 224) | def query_children(self) -> QuerySet:
  function view_digraph (line 229) | def view_digraph(u: Digraph):
  function view_lineage (line 254) | def view_lineage(
  function view_parents (line 323) | def view_parents(
  function _get_parents (line 407) | def _get_parents(
  function _df_edges_from_parents (line 449) | def _df_edges_from_parents(
  function get_record_label (line 502) | def get_record_label(record: SQLRecord, field: str | None = None):
  function _get_all_parent_runs (line 527) | def _get_all_parent_runs(data: Artifact | Collection) -> list:
  function _get_all_child_runs (line 573) | def _get_all_child_runs(data: Artifact | Collection) -> list:
  function _df_edges_from_runs (line 634) | def _df_edges_from_runs(df_values: list):

FILE: lamindb/models/project.py
  class Reference (line 43) | class Reference(
    class Meta (line 65) | class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
    method __init__ (line 138) | def __init__(
    method __init__ (line 153) | def __init__(
    method __init__ (line 158) | def __init__(self, *args, **kwargs):
    method query_references (line 161) | def query_references(self) -> QuerySet:
  class Project (line 170) | class Project(SQLRecord, HasType, CanCurate, TracksRun, TracksUpdates, V...
    class Meta (line 187) | class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
    method __init__ (line 292) | def __init__(
    method __init__ (line 304) | def __init__(
    method __init__ (line 309) | def __init__(self, *args, **kwargs):
    method query_projects (line 312) | def query_projects(self) -> QuerySet:
  class ArtifactProject (line 321) | class ArtifactProject(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 333) | class Meta:
  class RunProject (line 339) | class RunProject(BaseSQLRecord, IsLink):
    class Meta (line 356) | class Meta:
  class BranchProject (line 361) | class BranchProject(BaseSQLRecord, IsLink):
    class Meta (line 366) | class Meta:
  class ProjectUser (line 371) | class ProjectUser(BaseSQLRecord, IsLink):
    class Meta (line 378) | class Meta:
  class TransformProject (line 383) | class TransformProject(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 388) | class Meta:
  class CollectionProject (line 393) | class CollectionProject(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 400) | class Meta:
  class ULabelProject (line 405) | class ULabelProject(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 410) | class Meta:
  class FeatureProject (line 415) | class FeatureProject(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 420) | class Meta:
  class SchemaProject (line 425) | class SchemaProject(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 430) | class Meta:
  class ReferenceRecord (line 436) | class ReferenceRecord(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 448) | class Meta:
  class RecordReference (line 453) | class RecordReference(BaseSQLRecord, IsLink):
    class Meta (line 461) | class Meta:
  class ProjectRecord (line 467) | class ProjectRecord(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 479) | class Meta:
  class RecordProject (line 484) | class RecordProject(BaseSQLRecord, IsLink):
    class Meta (line 490) | class Meta:
  class BlockProject (line 495) | class BlockProject(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 500) | class Meta:
  class ArtifactReference (line 505) | class ArtifactReference(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 517) | class Meta:
  class TransformReference (line 522) | class TransformReference(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 531) | class Meta:
  class CollectionReference (line 536) | class CollectionReference(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 545) | class Meta:

FILE: lamindb/models/query_manager.py
  function _search (line 34) | def _search(
  function _lookup (line 173) | def _lookup(
  class QueryManager (line 241) | class QueryManager(Manager):
    method to_list (line 264) | def to_list(self, field: str | None = None):
    method to_dataframe (line 271) | def to_dataframe(self, **kwargs):
    method df (line 279) | def df(self, **kwargs):
    method search (line 283) | def search(self, string: str, **kwargs):
    method lookup (line 288) | def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
    method get_queryset (line 292) | def get_queryset(self):
  class RelatedManager (line 302) | class RelatedManager(QueryManager):
    method add (line 333) | def add(self, *objs, bulk: bool = True) -> None:
    method set (line 337) | def set(self, objs, *, bulk: bool = True, clear: bool = False) -> None:
    method remove (line 341) | def remove(self, *objs, bulk: bool = True) -> None:
    method clear (line 345) | def clear(self) -> None:

FILE: lamindb/models/query_set.py
  function get_keys_from_df (line 84) | def get_keys_from_df(data: list, registry: SQLRecord) -> list[str]:
  function get_default_branch_ids (line 106) | def get_default_branch_ids(branch: Branch | None = None) -> list[int]:
  function one_helper (line 128) | def one_helper(
  function get_backward_compat_filter_kwargs (line 154) | def get_backward_compat_filter_kwargs(queryset, expressions):
  function process_expressions (line 251) | def process_expressions(queryset: QuerySet, queries: tuple, expressions:...
  function get (line 343) | def get(
  class SQLRecordList (line 404) | class SQLRecordList(UserList, Generic[T]):
    method __init__ (line 407) | def __init__(self, records: Iterable[T]):
    method to_dataframe (line 413) | def to_dataframe(self) -> pd.DataFrame:
    method df (line 421) | def df(self) -> pd.DataFrame:
    method to_list (line 424) | def to_list(
    method one (line 431) | def one(self) -> T:
    method save (line 435) | def save(self) -> SQLRecordList[T]:
  function get_basic_field_names (line 443) | def get_basic_field_names(
  function get_feature_annotate_kwargs (line 501) | def get_feature_annotate_kwargs(
  function analyze_lookup_cardinality (line 704) | def analyze_lookup_cardinality(
  function reorder_subset_columns_in_df (line 754) | def reorder_subset_columns_in_df(
  function encode_lamindb_fields_as_columns (line 765) | def encode_lamindb_fields_as_columns(
  function reshape_annotate_result (line 787) | def reshape_annotate_result(
  function process_links_features (line 982) | def process_links_features(
  function process_cols_from_include (line 1028) | def process_cols_from_include(
  function _queryset_class_factory (line 1047) | def _queryset_class_factory(
  class BasicQuerySet (line 1064) | class BasicQuerySet(models.QuerySet):
    method __new__ (line 1078) | def __new__(cls, model=None, query=None, using=None, hints=None):
    method _to_class (line 1082) | def _to_class(
    method _to_basic (line 1089) | def _to_basic(self, copy: bool = True) -> BasicQuerySet:
    method _to_non_basic (line 1093) | def _to_non_basic(self, copy: bool = True) -> QuerySet:
    method to_dataframe (line 1098) | def to_dataframe(
    method df (line 1228) | def df(
    method describe (line 1235) | def describe(self, return_str: bool = False) -> str | None:
    method delete (line 1239) | def delete(self, *args, permanent: bool | None = None, **kwargs):
    method to_list (line 1302) | def to_list(self, field: str | None = None) -> list[SQLRecord] | list[...
    method first (line 1318) | def first(self) -> SQLRecord | None:
    method one (line 1329) | def one(self) -> SQLRecord:
    method one_or_none (line 1333) | def one_or_none(self) -> SQLRecord | None:
    method search (line 1344) | def search(self, string: str, **kwargs):
    method lookup (line 1349) | def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
    method validate (line 1358) | def validate(self, values: ListLike, field: str | StrField | None = No...
    method inspect (line 1363) | def inspect(self, values: ListLike, field: str | StrField | None = Non...
    method standardize (line 1368) | def standardize(
  class QuerySet (line 1378) | class QuerySet(BasicQuerySet):
    method _handle_unknown_field (line 1394) | def _handle_unknown_field(self, error: FieldError) -> None:
    method get (line 1405) | def get(self, idlike: int | str | None = None, **expressions) -> SQLRe...
    method filter (line 1444) | def filter(self, *queries, **expressions) -> QuerySet:
  class NonInstantiableQuerySet (line 1512) | class NonInstantiableQuerySet:
    method __init__ (line 1515) | def __init__(self, qs: QuerySet, registry_name: str):
    method __repr__ (line 1519) | def __repr__(self) -> str:
    method __call__ (line 1522) | def __call__(self, *args, **kwargs):
    method __getattr__ (line 1528) | def __getattr__(self, attr):
  class ModuleNamespace (line 1532) | class ModuleNamespace:
    method __init__ (line 1540) | def __init__(self, query_db: DB, module_name: str):
    method __getattr__ (line 1545) | def __getattr__(self, name: str) -> NonInstantiableQuerySet:
    method __dir__ (line 1572) | def __dir__(self) -> list[str]:
  class BiontyDB (line 1589) | class BiontyDB(ModuleNamespace):
  class PertdbDB (line 1607) | class PertdbDB(ModuleNamespace):
  class DB (line 1619) | class DB:
    method __init__ (line 1681) | def __init__(self, instance: str):
    method __getattr__ (line 1694) | def __getattr__(self, name: str) -> NonInstantiableQuerySet | BiontyDB...
    method __repr__ (line 1741) | def __repr__(self) -> str:
    method __dir__ (line 1744) | def __dir__(self) -> list[str]:

FILE: lamindb/models/record.py
  class RecordBatch (line 56) | class RecordBatch:
    method __init__ (line 59) | def __init__(
    method __len__ (line 73) | def __len__(self) -> int:
    method type (line 77) | def type(self) -> Record:
    method _build_records (line 80) | def _build_records(self) -> list[Record]:
    method save (line 107) | def save(self) -> SQLRecordList[Record]:
  class Record (line 118) | class Record(SQLRecord, HasType, HasParents, CanCurate, TracksRun, Track...
    class Meta (line 225) | class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
    method __init__ (line 395) | def __init__(
    method __init__ (line 408) | def __init__(
    method __init__ (line 413) | def __init__(
    method save (line 463) | def save(self, *args, **kwargs) -> Record:
    method from_dataframe (line 472) | def from_dataframe(
    method features (line 560) | def features(self) -> FeatureManager:
    method is_sheet (line 570) | def is_sheet(self) -> bool:
    method query_parents (line 574) | def query_parents(self) -> QuerySet:
    method query_children (line 582) | def query_children(self) -> QuerySet:
    method query_records (line 590) | def query_records(self) -> QuerySet:
    method _set_export_run (line 598) | def _set_export_run(self, is_run_input: bool | Run | None = None) -> N...
    method to_dataframe (line 617) | def to_dataframe(
    method to_artifact (line 686) | def to_artifact(
  class RecordJson (line 722) | class RecordJson(BaseSQLRecord, IsLink):
    class Meta (line 728) | class Meta:
  class RecordRecord (line 736) | class RecordRecord(BaseSQLRecord, IsLink):
    class Meta (line 742) | class Meta:
  class RecordULabel (line 748) | class RecordULabel(BaseSQLRecord, IsLink):
    class Meta (line 754) | class Meta:
  class RecordUser (line 761) | class RecordUser(BaseSQLRecord, IsLink):
    class Meta (line 767) | class Meta:
  class RecordRun (line 774) | class RecordRun(BaseSQLRecord, IsLink):
    class Meta (line 780) | class Meta:
  class RunRecord (line 787) | class RunRecord(BaseSQLRecord, IsLink):
    class Meta (line 801) | class Meta:
  class RecordArtifact (line 807) | class RecordArtifact(BaseSQLRecord, IsLink):
    class Meta (line 813) | class Meta:
  class ArtifactRecord (line 819) | class ArtifactRecord(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 827) | class Meta:
  class RecordCollection (line 833) | class RecordCollection(BaseSQLRecord, IsLink):
    class Meta (line 841) | class Meta:
  class CollectionRecord (line 847) | class CollectionRecord(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 857) | class Meta:
  class RecordTransform (line 863) | class RecordTransform(BaseSQLRecord, IsLink):
    class Meta (line 871) | class Meta:
  class TransformRecord (line 877) | class TransformRecord(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 891) | class Meta:

FILE: lamindb/models/run.py
  function current_run (line 54) | def current_run() -> Run | None:
  class TracksRun (line 71) | class TracksRun(models.Model):
    class Meta (line 74) | class Meta:
  class TracksUpdates (line 95) | class TracksUpdates(models.Model):
    class Meta (line 98) | class Meta:
  class User (line 107) | class User(BaseSQLRecord, CanCurate):
    class Meta (line 121) | class Meta:
    method __init__ (line 163) | def __init__(
    method __init__ (line 171) | def __init__(
    method __init__ (line 176) | def __init__(
  class Run (line 184) | class Run(SQLRecord, TracksUpdates):
    class Meta (line 237) | class Meta:
    method __init__ (line 374) | def __init__(
    method __init__ (line 388) | def __init__(
    method __init__ (line 393) | def __init__(
    method status (line 438) | def status(self) -> RunStatus:
    method features (line 471) | def features(self) -> FeatureManager:
    method query_output_artifacts (line 480) | def query_output_artifacts(
    method filter (line 511) | def filter(
  function _permanent_delete_runs (line 539) | def _permanent_delete_runs(runs: Run | QuerySet) -> None:
  class RunJsonValue (line 587) | class RunJsonValue(BaseSQLRecord, IsLink):
    class Meta (line 601) | class Meta:
  class RunArtifact (line 608) | class RunArtifact(BaseSQLRecord, IsLink):
    class Meta (line 616) | class Meta:

FILE: lamindb/models/save.py
  function save (line 29) | def save(
  function bulk_create (line 128) | def bulk_create(
  function bulk_update (line 228) | def bulk_update(
  function check_and_attempt_upload (line 272) | def check_and_attempt_upload(
  function copy_or_move_to_cache (line 326) | def copy_or_move_to_cache(
  function check_and_attempt_clearing (line 380) | def check_and_attempt_clearing(
  function store_artifacts (line 410) | def store_artifacts(
  function prepare_error_message (line 472) | def prepare_error_message(records, stored_artifacts, exception) -> str:
  function upload_artifact (line 492) | def upload_artifact(

FILE: lamindb/models/schema.py
  function validate_features (line 67) | def validate_features(features: list[SQLRecord]) -> SQLRecord:
  function get_features_config (line 91) | def get_features_config(
  class SchemaOptionals (line 109) | class SchemaOptionals:
    method __init__ (line 112) | def __init__(self, schema) -> None:
    method get_uids (line 115) | def get_uids(self) -> list[str]:
    method get (line 129) | def get(self) -> QuerySet:
    method set (line 137) | def set(self, features: list[Feature]) -> None:
    method remove (line 147) | def remove(self, features: Feature | list[Feature]) -> None:
    method add (line 159) | def add(self, features: Feature | list[Feature]) -> None:
  class Schema (line 183) | class Schema(SQLRecord, HasType, CanCurate, TracksRun, TracksUpdates):
    class Meta (line 289) | class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
    method __init__ (line 412) | def __init__(
    method __init__ (line 437) | def __init__(
    method __init__ (line 442) | def __init__(
    method query_schemas (line 566) | def query_schemas(self) -> QuerySet:
    method _validate_kwargs_calculate_hash (line 574) | def _validate_kwargs_calculate_hash(
    method from_values (line 740) | def from_values(  # type: ignore
    method from_dataframe (line 819) | def from_dataframe(
    method from_df (line 864) | def from_df(
    method save (line 875) | def save(self, *args, **kwargs) -> Schema:
    method members (line 977) | def members(self) -> QuerySet:
    method dtype (line 1031) | def dtype(self) -> str | None:
    method dtype (line 1036) | def dtype(self, value: str | None) -> None:
    method coerce_dtype (line 1041) | def coerce_dtype(self) -> bool | None:
    method coerce_dtype (line 1046) | def coerce_dtype(self, value: bool | None) -> None:
    method n (line 1051) | def n(self) -> int | None:
    method n (line 1056) | def n(self, value: int | None) -> None:
    method index (line 1060) | def index(self) -> None | Feature:
    method index (line 1077) | def index(self, value: None | Feature) -> None:
    method _index_feature_uid (line 1087) | def _index_feature_uid(self) -> None | str:
    method _index_feature_uid (line 1095) | def _index_feature_uid(self, value: str | None) -> None:
    method slots (line 1103) | def slots(self) -> dict[str, Schema]:
    method optionals (line 1130) | def optionals(self) -> SchemaOptionals:
    method add_optional_features (line 1167) | def add_optional_features(self, features: list[Feature]) -> None:
    method remove_optional_features (line 1173) | def remove_optional_features(self, features: list[Feature]) -> None:
    method describe (line 1183) | def describe(cls_or_self, return_str: bool = False) -> None | str:
  function get_type_str (line 1195) | def get_type_str(dtype: str | None) -> str | None:
  function _get_related_name (line 1203) | def _get_related_name(self: Schema) -> str | None:
  class SchemaFeature (line 1213) | class SchemaFeature(BaseSQLRecord, IsLink):
    class Meta (line 1218) | class Meta:
  class ArtifactSchema (line 1223) | class ArtifactSchema(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 1230) | class Meta:
  class SchemaComponent (line 1235) | class SchemaComponent(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 1241) | class Meta:
  function migrate_auxiliary_fields_postgres (line 1253) | def migrate_auxiliary_fields_postgres(schema_editor) -> None:

FILE: lamindb/models/sqlrecord.py
  function _is_branch_sensitive_model (line 116) | def _is_branch_sensitive_model(model: type[BaseSQLRecord]) -> bool:
  class IsLink (line 160) | class IsLink:
  class HasType (line 164) | class HasType(models.Model):
    class Meta (line 178) | class Meta:
    method query_types (line 187) | def query_types(self) -> SQLRecordList:
  function deferred_attribute__repr__ (line 212) | def deferred_attribute__repr__(self):
  function unique_constraint_error_in_error_message (line 216) | def unique_constraint_error_in_error_message(error_msg: str) -> bool:
  function parse_violated_field_from_error_message (line 224) | def parse_violated_field_from_error_message(error_msg: str) -> list[str]...
  class ValidateFields (line 282) | class ValidateFields:
  function is_approx_pascal_case (line 286) | def is_approx_pascal_case(s: str) -> bool:
  function init_self_from_db (line 299) | def init_self_from_db(self: SQLRecord, existing_record: SQLRecord):
  function update_attributes (line 314) | def update_attributes(record: SQLRecord, attributes: dict[str, str]):
  function validate_literal_fields (line 331) | def validate_literal_fields(record: SQLRecord, kwargs) -> None:
  function validate_fields (line 377) | def validate_fields(record: SQLRecord, kwargs):
  function suggest_records_with_similar_names (line 436) | def suggest_records_with_similar_names(
  function delete_record (line 481) | def delete_record(record: BaseSQLRecord, is_soft: bool = True):
  function _synchronize_clone (line 529) | def _synchronize_clone(storage_root: str) -> str | None:
  class Registry (line 559) | class Registry(ModelBase):
    method __new__ (line 577) | def __new__(cls, name, bases, attrs, **kwargs):
    method __dir__ (line 584) | def __dir__(cls):
    method describe (line 615) | def describe(cls, return_str: bool = False) -> str | None:
    method lookup (line 631) | def lookup(
    method filter (line 640) | def filter(cls, *queries, **expressions) -> QuerySet:
    method get (line 663) | def get(
    method to_dataframe (line 692) | def to_dataframe(
    method df (line 743) | def df(
    method search (line 756) | def search(
    method using (line 774) | def using(
    method connect (line 782) | def connect(
    method __get_module_name__ (line 896) | def __get_module_name__(cls) -> str:
    method __get_name_with_module__ (line 903) | def __get_name_with_module__(cls) -> str:
    method __get_available_fields__ (line 911) | def __get_available_fields__(cls) -> set[str]:
  class BaseSQLRecord (line 926) | class BaseSQLRecord(models.Model, metaclass=Registry):
    class Meta (line 935) | class Meta:
    method __init__ (line 944) | def __init__(self, *args, **kwargs):
    method _populate_tracked_fields (line 1072) | def _populate_tracked_fields(self):
    method _field_changed (line 1090) | def _field_changed(self, field_name: str, check_is_saved: bool = True)...
    method save (line 1112) | def save(self: T, *args, **kwargs) -> T:
    method describe (line 1303) | def describe(
    method __repr__ (line 1324) | def __repr__(
    method __str__ (line 1384) | def __str__(self) -> str:
    method delete (line 1387) | def delete(self, permanent: bool | None = None):
  class Space (line 1406) | class Space(BaseSQLRecord):
    class Meta (line 1433) | class Meta:
    method __init__ (line 1465) | def __init__(
    method __init__ (line 1472) | def __init__(
    method __init__ (line 1477) | def __init__(
  class Branch (line 1500) | class Branch(BaseSQLRecord):
    class Meta (line 1616) | class Meta:
    method status (line 1689) | def status(self) -> BranchStatus:
    method status (line 1730) | def status(self, value: BranchStatus) -> None:
    method __init__ (line 1739) | def __init__(
    method __init__ (line 1746) | def __init__(
    method __init__ (line 1751) | def __init__(
  class BranchUser (line 1759) | class BranchUser(BaseSQLRecord, IsLink):
    class Meta (line 1760) | class Meta:
  class SQLRecord (line 1771) | class SQLRecord(BaseSQLRecord, metaclass=Registry):
    class Meta (line 1813) | class Meta:
    method restore (line 1816) | def restore(self) -> None:
    method delete (line 1824) | def delete(self, permanent: bool | None = None, **kwargs):
  function _format_django_validation_error (line 1911) | def _format_django_validation_error(record: SQLRecord, e: DjangoValidati...
  function _get_record_kwargs (line 1942) | def _get_record_kwargs(record_class) -> list[tuple[str, str]]:
  function get_name_field (line 1996) | def get_name_field(
  function add_db_connection (line 2039) | def add_db_connection(db: str, using: str):
  function update_fk_to_default_db (line 2052) | def update_fk_to_default_db(
  function transfer_fk_to_default_db_bulk (line 2103) | def transfer_fk_to_default_db_bulk(
  function get_transfer_run (line 2110) | def get_transfer_run(record) -> Run:
  function transfer_to_default_db (line 2151) | def transfer_to_default_db(
  function track_current_name_value (line 2204) | def track_current_name_value(record: SQLRecord):
  function check_name_change (line 2211) | def check_name_change(record: SQLRecord):
  function format_field_value (line 2277) | def format_field_value(value: datetime | str | Any, none: str = "None") ...
  class SQLRecordInfo (line 2294) | class SQLRecordInfo:
    method __init__ (line 2295) | def __init__(self, registry: Registry):
    method _get_type_for_field (line 2298) | def _get_type_for_field(self, field_name: str) -> str:
    method _get_base_class_fields (line 2307) | def _get_base_class_fields(self) -> list[str]:
    method _reorder_fields_by_class (line 2315) | def _reorder_fields_by_class(self, fields_to_order: list[Field]) -> li...
    method get_simple_fields (line 2329) | def get_simple_fields(self, return_str: bool = False) -> Any:
    method get_relational_fields (line 2356) | def get_relational_fields(self, return_str: bool = False):
  class Migration (line 2490) | class Migration(BaseSQLRecord):
    class Meta (line 2495) | class Meta:

FILE: lamindb/models/storage.py
  class Storage (line 41) | class Storage(SQLRecord, TracksRun, TracksUpdates):
    class Meta (line 158) | class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
    method __init__ (line 188) | def __init__(
    method __init__ (line 198) | def __init__(
    method __init__ (line 203) | def __init__(
    method host (line 314) | def host(self) -> str | None:
    method path (line 326) | def path(self) -> UPath:
    method save (line 334) | def save(self, *args, **kwargs):
    method delete (line 341) | def delete(self, permanent: bool | None = None) -> None:  # type: ignore

FILE: lamindb/models/transform.py
  class Transform (line 49) | class Transform(SQLRecord, IsVersioned):
    class Meta (line 131) | class Meta(SQLRecord.Meta, IsVersioned.Meta):
    method __init__ (line 229) | def __init__(
    method __init__ (line 243) | def __init__(
    method __init__ (line 248) | def __init__(
    method from_git (line 368) | def from_git(
    method latest_run (line 487) | def latest_run(self) -> Run:
    method type (line 493) | def type(self) -> TransformKind:
    method type (line 497) | def type(self, value: TransformKind):
    method view_lineage (line 500) | def view_lineage(self, with_successors: bool = False, distance: int = 5):
    method _update_source_code_from_path (line 517) | def _update_source_code_from_path(self, source_code_path: Path) -> Non...
  function _permanent_delete_transforms (line 548) | def _permanent_delete_transforms(transforms: Transform | QuerySet) -> None:
  class TransformTransform (line 570) | class TransformTransform(BaseSQLRecord, IsLink):
    class Meta (line 586) | class Meta:

FILE: lamindb/models/ulabel.py
  class ULabel (line 39) | class ULabel(SQLRecord, HasType, HasParents, CanCurate, TracksRun, Track...
    class Meta (line 83) | class Meta(SQLRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
    method __init__ (line 188) | def __init__(
    method __init__ (line 199) | def __init__(
    method __init__ (line 204) | def __init__(
    method query_ulabels (line 246) | def query_ulabels(self) -> QuerySet:
  class ArtifactULabel (line 255) | class ArtifactULabel(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 263) | class Meta:
  class TransformULabel (line 270) | class TransformULabel(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 275) | class Meta:
  class RunULabel (line 280) | class RunULabel(BaseSQLRecord, IsLink):
    class Meta (line 293) | class Meta:
  class BranchULabel (line 298) | class BranchULabel(BaseSQLRecord, IsLink):
    class Meta (line 305) | class Meta:
  class CollectionULabel (line 310) | class CollectionULabel(BaseSQLRecord, IsLink, TracksRun):
    class Meta (line 320) | class Meta:

FILE: lamindb/setup/_merge.py
  function merge (line 16) | def merge(branch: str | Branch) -> None:

FILE: lamindb/setup/_switch.py
  function switch (line 12) | def switch(target: str | Branch, *, space: bool = False, create: bool = ...

FILE: noxfile.py
  function lint (line 47) | def lint(session: nox.Session) -> None:
  function install (line 52) | def install(session):
  function install_ci (line 91) | def install_ci(session, group):
  function configure_coverage (line 194) | def configure_coverage(session) -> None:
  function prepare (line 227) | def prepare(session):
  function test (line 283) | def test(session, group):
  function clidocs (line 366) | def clidocs(session):
  function docs (line 452) | def docs(session):

FILE: scripts/migrate_test_instances.py
  function run (line 21) | def run(cmd: str) -> None:
  function main (line 27) | def main() -> None:

FILE: tests/core/_dataset_fixtures.py
  function get_small_adata (line 12) | def get_small_adata():
  function get_small_mdata (line 25) | def get_small_mdata():
  function get_small_sdata (line 48) | def get_small_sdata():
  function get_mini_csv (line 72) | def get_mini_csv() -> Generator[Path, None, None]:

FILE: tests/core/conftest.py
  function pytest_sessionstart (line 20) | def pytest_sessionstart():
  function pytest_sessionfinish (line 54) | def pytest_sessionfinish(session: pytest.Session):
  function ccaplog (line 64) | def ccaplog(caplog) -> pytest.LogCaptureFixture:
  function get_test_filepaths (line 87) | def get_test_filepaths(request):  # -> Tuple[bool, Path, Path, Path, str]
  function registered_storage_file_and_folder (line 125) | def registered_storage_file_and_folder():
  function example_dataframe (line 147) | def example_dataframe():
  function adata_file (line 152) | def adata_file():
  function tsv_file (line 166) | def tsv_file():
  function zip_file (line 174) | def zip_file():
  function yaml_file (line 182) | def yaml_file():
  function fcs_file (line 192) | def fcs_file():
  function mudata_file (line 199) | def mudata_file(get_small_mdata):
  function spatialdata_file (line 207) | def spatialdata_file(get_small_sdata):

FILE: tests/core/test_artifact_anndata_with_curation.py
  function test_create_anndata_with_curation (line 4) | def test_create_anndata_with_curation():

FILE: tests/core/test_artifact_basics.py
  function data (line 58) | def data(request):
  function test_basic_validation (line 70) | def test_basic_validation():
  function test_create_from_path_file (line 100) | def test_create_from_path_file(get_test_filepaths, key_is_virtual, key, ...
  function test_create_from_path_file_with_explicit_key_is_virtual (line 203) | def test_create_from_path_file_with_explicit_key_is_virtual(
  function test_create_from_empty_files_skips_hash_lookup (line 226) | def test_create_from_empty_files_skips_hash_lookup(tmp_path):
  function test_create_from_path_folder (line 247) | def test_create_from_path_folder(get_test_filepaths, key):
  function test_create_from_path_overwrite_versions_false (line 317) | def test_create_from_path_overwrite_versions_false(get_test_filepaths):
  function test_delete_permanently_from_trash_folder (line 344) | def test_delete_permanently_from_trash_folder(tmp_path):
  function test_create_from_path_set_branch (line 364) | def test_create_from_path_set_branch():
  function test_from_dir (line 376) | def test_from_dir(get_test_filepaths, key):
  function test_create_from_dataframe (line 402) | def test_create_from_dataframe(example_dataframe: pd.DataFrame):
  function test_dataframe_validate_suffix (line 522) | def test_dataframe_validate_suffix(example_dataframe: pd.DataFrame):
  function test_create_from_parquet_file_default_constructor (line 535) | def test_create_from_parquet_file_default_constructor(
  function test_create_from_anndata (line 545) | def test_create_from_anndata(get_small_adata, adata_file, example_datafr...
  function test_from_anndata_uses_h5ad_kwargs (line 567) | def test_from_anndata_uses_h5ad_kwargs(get_small_adata):
  function test_from_anndata_uses_zarr_kwargs (line 581) | def test_from_anndata_uses_zarr_kwargs(get_small_adata):
  function test_from_anndata_validate_suffix (line 596) | def test_from_anndata_validate_suffix(get_small_adata):
  function test_create_from_mudata (line 621) | def test_create_from_mudata(get_small_mdata, mudata_file, adata_file):
  function test_create_from_spatialdata (line 636) | def test_create_from_spatialdata(
  function test_create_from_anndata_in_storage (line 668) | def test_create_from_anndata_in_storage(data):
  function test_revise_recreate_artifact (line 685) | def test_revise_recreate_artifact(example_dataframe: pd.DataFrame, ccapl...
  function test_delete_and_restore_artifact (line 894) | def test_delete_and_restore_artifact(example_dataframe: pd.DataFrame):
  function test_delete_storage (line 925) | def test_delete_storage():
  function test_recreate_after_artifact_moved_in_storage (line 930) | def test_recreate_after_artifact_moved_in_storage(ccaplog):
  function test_move_artifact_exception_handling (line 948) | def test_move_artifact_exception_handling():
  function test_auto_storage_key_from_artifact_uid (line 1095) | def test_auto_storage_key_from_artifact_uid(suffix):
  function test_storage_root_upath_equivalence (line 1106) | def test_storage_root_upath_equivalence():
  function test_get_relative_path_to_directory (line 1112) | def test_get_relative_path_to_directory():
  function test_check_path_is_child_of_root (line 1150) | def test_check_path_is_child_of_root():
  function test_serialize_paths (line 1209) | def test_serialize_paths():
  function test_data_is_anndata_paths (line 1265) | def test_data_is_anndata_paths():
  function test_data_is_anndata_anndatacessor (line 1274) | def test_data_is_anndata_anndatacessor(get_small_adata):
  function test_data_is_mudata_paths (line 1283) | def test_data_is_mudata_paths():
  function test_data_is_spatialdata_paths (line 1288) | def test_data_is_spatialdata_paths():
  function test_data_is_scversedatastructure (line 1307) | def test_data_is_scversedatastructure(request, data, data_type, expected):
  function test_load_to_memory (line 1319) | def test_load_to_memory(tsv_file, zip_file, fcs_file, yaml_file):
  function test_bulk_delete (line 1341) | def test_bulk_delete():
  function test_no_unnecessary_imports (line 1387) | def test_no_unnecessary_imports(
  function test_artifact_get_tracking (line 1409) | def test_artifact_get_tracking(example_dataframe: pd.DataFrame):
  function test_get_by_path (line 1423) | def test_get_by_path(example_dataframe: pd.DataFrame):
  function test_update_suffix_for_registered_storage_with_real_key (line 1458) | def test_update_suffix_for_registered_storage_with_real_key(
  function test_update_suffix_for_registered_storage_folder_artifact (line 1486) | def test_update_suffix_for_registered_storage_folder_artifact(
  function test_update_non_virtual_key_for_registered_storage_file (line 1516) | def test_update_non_virtual_key_for_registered_storage_file(
  function test_update_non_virtual_key_for_registered_storage_file_invalid_suffix (line 1551) | def test_update_non_virtual_key_for_registered_storage_file_invalid_suffix(
  function test_update_key_to_none_raises_invalid_argument (line 1569) | def test_update_key_to_none_raises_invalid_argument(
  function test_update_non_virtual_key_before_save_raises_invalid_argument (line 1586) | def test_update_non_virtual_key_before_save_raises_invalid_argument(tsv_...
  function test_update_non_virtual_key_in_unmanaged_storage_raises_invalid_argument (line 1598) | def test_update_non_virtual_key_in_unmanaged_storage_raises_invalid_argu...
  function test_create_artifact_in_foreign_managed_storage_raises_value_error (line 1615) | def test_create_artifact_in_foreign_managed_storage_raises_value_error(t...
  function test_save_url_with_virtual_key_and_unmanaged_suffix_update_error (line 1629) | def test_save_url_with_virtual_key_and_unmanaged_suffix_update_error():
  function test_change_space_for_artifact_in_foreign_managed_storage_raises_value_error (line 1656) | def test_change_space_for_artifact_in_foreign_managed_storage_raises_val...
  function test_save_artifact_to_foreign_managed_storage_raises_value_error (line 1679) | def test_save_artifact_to_foreign_managed_storage_raises_value_error(tsv...
  function test_artifact_space_change (line 1693) | def test_artifact_space_change(tsv_file):
  function test_passing_foreign_keys_ids (line 1718) | def test_passing_foreign_keys_ids(tsv_file):

FILE: tests/core/test_artifact_dataframe_with_curation.py
  function two_internal_features (line 10) | def two_internal_features():
  function two_external_features (line 19) | def two_external_features():
  function test_create_artifact_with_external_feature_annotations (line 28) | def test_create_artifact_with_external_feature_annotations(
  function test_artifact_from_dataframe_with_schema (line 68) | def test_artifact_from_dataframe_with_schema(example_dataframe: pd.DataF...
  function test_artifact_dataframe_with_features (line 99) | def test_artifact_dataframe_with_features(example_dataframe: pd.DataFrame):
  function test_from_dataframe_with_external_schema (line 124) | def test_from_dataframe_with_external_schema(

FILE: tests/core/test_artifact_describe_to_dataframe.py
  function _check_df_equality (line 11) | def _check_df_equality(actual_df: pd.DataFrame, expected_df: pd.DataFram...
  function test_describe_to_dataframe_example_dataset (line 50) | def test_describe_to_dataframe_example_dataset():

FILE: tests/core/test_artifact_features_annotations.py
  function test_artifact_features_add_remove_query (line 13) | def test_artifact_features_add_remove_query():
  function test_features_name_duplicates_across_root_and_nested (line 383) | def test_features_name_duplicates_across_root_and_nested():
  function test_features_name_duplicates_across_equal_levels (line 399) | def test_features_name_duplicates_across_equal_levels():
  function test_feature_predicate_queries_safe_hybrid (line 440) | def test_feature_predicate_queries_safe_hybrid():
  function test_features_add_with_schema (line 505) | def test_features_add_with_schema():
  function test_artifact_feature_cat_filters_schema_end_to_end (line 527) | def test_artifact_feature_cat_filters_schema_end_to_end():
  function test_features_add_remove_error_behavior (line 575) | def test_features_add_remove_error_behavior():
  function test_add_remove_list_features (line 801) | def test_add_remove_list_features(ccaplog):
  function test_add_list_of_cat_features (line 837) | def test_add_list_of_cat_features():
  function test_artifact_features_accept_feature_object_keys (line 899) | def test_artifact_features_accept_feature_object_keys():

FILE: tests/core/test_artifact_parquet.py
  function test_parquet_kwargs (line 6) | def test_parquet_kwargs():

FILE: tests/core/test_blocks.py
  function test_block_recovery_based_on_hash (line 5) | def test_block_recovery_based_on_hash():
  function test_block_recovery_based_on_key (line 15) | def test_block_recovery_based_on_key():
  function test_readme_md_key_is_allowed_and_revises (line 25) | def test_readme_md_key_is_allowed_and_revises():
  function test_revise_blocks (line 39) | def test_revise_blocks():
  function test_record_block_readme_always_new_version (line 152) | def test_record_block_readme_always_new_version():
  function test_record_block_comment_always_new_block (line 165) | def test_record_block_comment_always_new_block():
  function test_record_block_recovery_based_on_record_and_kind (line 195) | def test_record_block_recovery_based_on_record_and_kind():
  function test_revise_record_blocks (line 206) | def test_revise_record_blocks():
  function test_record_block_filter_respects_default_branch_scope (line 271) | def test_record_block_filter_respects_default_branch_scope():

FILE: tests/core/test_branches.py
  function testbranch_id (line 4) | def testbranch_id():

FILE: tests/core/test_can_curate.py
  function test_inspect (line 8) | def test_inspect():
  function test_inspect_source (line 26) | def test_inspect_source():
  function test_standardize (line 55) | def test_standardize():
  function test_standardize_from_source (line 81) | def test_standardize_from_source():
  function test_add_remove_synonym (line 86) | def test_add_remove_synonym():
  function test_set_abbr (line 128) | def test_set_abbr():
  function test_validate_int (line 151) | def test_validate_int():
  function test_synonym_mapping (line 156) | def test_synonym_mapping():
  function test_validate_called_on_object_raises_error (line 173) | def test_validate_called_on_object_raises_error():
  function test_standardize_source (line 184) | def test_standardize_source():

FILE: tests/core/test_collection.py
  function df (line 13) | def df():
  function adata (line 18) | def adata():
  function adata2 (line 29) | def adata2():
  function test_from_single_artifact (line 38) | def test_from_single_artifact(adata):
  function test_edge_cases (line 68) | def test_edge_cases(df, ccaplog):
  function test_from_inconsistent_artifacts (line 96) | def test_from_inconsistent_artifacts(df, adata):
  function test_from_consistent_artifacts (line 126) | def test_from_consistent_artifacts(adata, adata2):
  function test_mapped (line 172) | def test_mapped(adata, adata2):
  function test_revise_collection (line 415) | def test_revise_collection(df, adata):
  function test_collection_append (line 477) | def test_collection_append(df, adata):
  function test_with_metadata (line 493) | def test_with_metadata(df, adata):
  function test_collection_get_tracking (line 510) | def test_collection_get_tracking(df):
  function test_describe_collection (line 527) | def test_describe_collection(adata, capsys):

FILE: tests/core/test_curator_basics.py
  function _strip_ansi (line 11) | def _strip_ansi(text: str) -> str:
  function df (line 18) | def df() -> pd.DataFrame:
  function df_missing_sample_type_column (line 29) | def df_missing_sample_type_column() -> pd.DataFrame:
  function df_missing_sample_name_column (line 39) | def df_missing_sample_name_column() -> pd.DataFrame:
  function df_changed_col_order (line 49) | def df_changed_col_order() -> pd.DataFrame:
  function df_extra_column (line 60) | def df_extra_column() -> pd.DataFrame:
  function df_disease (line 72) | def df_disease() -> pd.DataFrame:
  function disease_ontology_old (line 91) | def disease_ontology_old() -> bt.Source:
  function lists_df (line 100) | def lists_df():
  function cat_df (line 112) | def cat_df():
  function test_curator_df_multivalue (line 123) | def test_curator_df_multivalue(lists_df, cat_df):
  function test_curators_list_feature_nullable_empty_list (line 164) | def test_curators_list_feature_nullable_empty_list():
  function test_curator__repr__ (line 185) | def test_curator__repr__(df):
  function test_df_curator_typed_categorical (line 209) | def test_df_curator_typed_categorical(model_class):
  function test_df_curator_same_name_at_different_levels_involving_root (line 297) | def test_df_curator_same_name_at_different_levels_involving_root():
  function test_df_curator_same_name_at_different_levels_below_root (line 328) | def test_df_curator_same_name_at_different_levels_below_root():
  function test_df_curator_same_name_at_same_level (line 361) | def test_df_curator_same_name_at_same_level():
  function test_curator_schema_feature_mapping (line 397) | def test_curator_schema_feature_mapping():
  function test_dtypes_at_different_levels (line 416) | def test_dtypes_at_different_levels(ccaplog):
  function test_nullable (line 459) | def test_nullable():
  function test_pandera_dataframe_schema (line 483) | def test_pandera_dataframe_schema(
  function test_schema_not_saved (line 579) | def test_schema_not_saved(df):
  function test_schema_artifact_annotated (line 591) | def test_schema_artifact_annotated(df):
  function test_schema_optionals (line 610) | def test_schema_optionals():
  function test_schema_ordered_set (line 645) | def test_schema_ordered_set(df):
  function test_schema_minimal_set_var_allowed (line 670) | def test_schema_minimal_set_var_allowed(minimal_set):
  function test_schema_maximal_set_var (line 687) | def test_schema_maximal_set_var():
  function test_feature_dtype_path (line 707) | def test_feature_dtype_path():
  function test_cat_filters_specific_source_uid (line 786) | def test_cat_filters_specific_source_uid(df_disease, disease_ontology_old):
  function test_cat_filters_specific_source (line 806) | def test_cat_filters_specific_source(df_disease, disease_ontology_old):
  function test_cat_filters_multiple_relation_filters (line 827) | def test_cat_filters_multiple_relation_filters(df_disease, disease_ontol...
  function test_curate_columns (line 851) | def test_curate_columns(df):
  function test_wrong_datatype (line 879) | def test_wrong_datatype(df):
  function test_hash_index_feature (line 899) | def test_hash_index_feature(df):
  function test_add_new_from_subtype (line 942) | def test_add_new_from_subtype(df):
  function test_index_feature_exclusion_from_categoricals (line 975) | def test_index_feature_exclusion_from_categoricals(df):

FILE: tests/core/test_data_migrations.py
  function test_migrate_auxiliary_fields_postgres (line 13) | def test_migrate_auxiliary_fields_postgres():

FILE: tests/core/test_db.py
  function test_create_to_load (line 4) | def test_create_to_load():

FILE: tests/core/test_delete.py
  function test_delete_qs (line 7) | def test_delete_qs(permanent):
  function test_recreate_soft_deleted_record (line 22) | def test_recreate_soft_deleted_record():

FILE: tests/core/test_feature.py
  function dict_data (line 11) | def dict_data():
  function test_feature_init (line 23) | def test_feature_init():
  function test_cat_filters_empty_filter (line 106) | def test_cat_filters_empty_filter():
  function test_cat_filters_invalid_field_name (line 116) | def test_cat_filters_invalid_field_name():
  function test_cat_filters_artifact_schema_filter (line 134) | def test_cat_filters_artifact_schema_filter():
  function test_feature_from_df (line 149) | def test_feature_from_df():
  function test_feature_from_dict (line 204) | def test_feature_from_dict(dict_data):
  function test_feature_from_dict_type (line 226) | def test_feature_from_dict_type(dict_data):
  function test_feature_query_by_dtype (line 235) | def test_feature_query_by_dtype():

FILE: tests/core/test_feature_dtype.py
  function organism (line 19) | def organism():
  function test_serialize_basic_dtypes (line 31) | def test_serialize_basic_dtypes():
  function test_serialize_basic_list_dtypes (line 42) | def test_serialize_basic_list_dtypes():
  function test_seralize_pandas_numpy_dtypes (line 52) | def test_seralize_pandas_numpy_dtypes():
  function test_serialize_user (line 58) | def test_serialize_user(ccaplog):
  function test_serialize_record_objects (line 71) | def test_serialize_record_objects():
  function test_serialize_union_of_registries (line 114) | def test_serialize_union_of_registries():
  function test_serialize_with_field_information (line 121) | def test_serialize_with_field_information():
  function test_simple_record_with_subtype_and_field (line 133) | def test_simple_record_with_subtype_and_field():
  function test_multiple_records_with_subtypes_and_fields (line 150) | def test_multiple_records_with_subtypes_and_fields():
  function test_bionty_celltype_with_field (line 179) | def test_bionty_celltype_with_field():
  function test_bionty_perturbations_with_field (line 192) | def test_bionty_perturbations_with_field():
  function test_invalid_registry (line 212) | def test_invalid_registry():
  function test_empty_category (line 219) | def test_empty_category():
  function test_url_dtype_is_supported (line 225) | def test_url_dtype_is_supported():
  function test_malformed_categorical (line 231) | def test_malformed_categorical():
  function test_simple_registry_without_field (line 246) | def test_simple_registry_without_field():
  function test_registry_with_subtype_no_field (line 259) | def test_registry_with_subtype_no_field():
  function test_list_of_dtypes (line 276) | def test_list_of_dtypes():
  function test_registry_with_filter (line 295) | def test_registry_with_filter():
  function test_nested_cat_dtypes (line 308) | def test_nested_cat_dtypes():
  function test_nested_cat_with_filter (line 329) | def test_nested_cat_with_filter():
  function test_feature_dtype (line 357) | def test_feature_dtype():
  function test_cat_filters_incompatible_with_union_dtypes (line 379) | def test_cat_filters_incompatible_with_union_dtypes():
  function test_cat_filters_incompatible_with_nested_dtypes (line 392) | def test_cat_filters_incompatible_with_nested_dtypes():
  function test_parse_filter_string_basic (line 407) | def test_parse_filter_string_basic():
  function test_parse_filter_string_direct_fields (line 416) | def test_parse_filter_string_direct_fields():
  function test_parse_filter_string_empty (line 422) | def test_parse_filter_string_empty():
  function test_parse_filter_string_malformed (line 428) | def test_parse_filter_string_malformed():
  function test_parse_filter_string_missing_key (line 434) | def test_parse_filter_string_missing_key():
  function test_parse_filter_string_missing_value (line 440) | def test_parse_filter_string_missing_value():
  function test_resolve_direct_fields (line 446) | def test_resolve_direct_fields():
  function test_resolve_relation_filter_with_uid (line 452) | def test_resolve_relation_filter_with_uid():
  function test_resolve_relation_filter_with_name (line 469) | def test_resolve_relation_filter_with_name(organism):
  function test_resolve_multiple_relation_filters (line 476) | def test_resolve_multiple_relation_filters(organism):
  function test_resolve_nested_filter (line 496) | def test_resolve_nested_filter(organism):
  function test_resolve_relation_filter_failed_resolution (line 503) | def test_resolve_relation_filter_failed_resolution():
  function test_resolve_relation_filter_duplicate (line 509) | def test_resolve_relation_filter_duplicate():
  function test_convert_old_format_ulabel_string (line 523) | def test_convert_old_format_ulabel_string():
  function test_convert_old_format_record_string (line 539) | def test_convert_old_format_record_string():
  function test_convert_old_format_nested_record_string (line 555) | def test_convert_old_format_nested_record_string():
  function test_convert_old_format_list_string (line 573) | def test_convert_old_format_list_string():
  function test_feature_constructor_with_old_format_string (line 594) | def test_feature_constructor_with_old_format_string(ccaplog):
  function test_feature_constructor_with_old_format_nested_string (line 617) | def test_feature_constructor_with_old_format_nested_string(ccaplog):
  function test_bare_cat_dtype_backward_compatibility (line 643) | def test_bare_cat_dtype_backward_compatibility():
  function test_migrate_dtype_to_uid_format (line 655) | def test_migrate_dtype_to_uid_format():

FILE: tests/core/test_from_values.py
  function df (line 8) | def df():
  function test_from_values_name (line 19) | def test_from_values_name(df):
  function test_from_values_ontology_id (line 34) | def test_from_values_ontology_id(df):
  function test_from_values_multiple_match (line 43) | def test_from_values_multiple_match():
  function test_get_or_create_records (line 48) | def test_get_or_create_records():
  function test_from_values_synonyms_aware (line 57) | def test_from_values_synonyms_aware():
  function test_standardize (line 92) | def test_standardize():
  function test_from_values_no_source (line 105) | def test_from_values_no_source():

FILE: tests/core/test_has_parents.py
  function test_view_parents (line 5) | def test_view_parents():
  function test_query_parents_children (line 16) | def test_query_parents_children():
  function test_view_lineage_circular (line 33) | def test_view_lineage_circular():
  function test_view_parents_connected_instance (line 47) | def test_view_parents_connected_instance():
  function test_query_relatives_connected_instance (line 54) | def test_query_relatives_connected_instance():
  function test_view_lineage_connected_instance (line 65) | def test_view_lineage_connected_instance():

FILE: tests/core/test_has_type.py
  function test_invalid_type (line 19) | def test_invalid_type(model_class, extra_kwargs):
  function test_prevent_type_cycle (line 44) | def test_prevent_type_cycle(model_class):
  function test_query_sub_types_super_types_instances (line 73) | def test_query_sub_types_super_types_instances(model_class):

FILE: tests/core/test_integrity.py
  function test_migrate_check (line 4) | def test_migrate_check():
  function test_system_check (line 8) | def test_system_check():

FILE: tests/core/test_is_versioned.py
  function df1 (line 12) | def df1():
  function df2 (line 17) | def df2():
  function test_set_version (line 21) | def test_set_version():
  function test_bump_version (line 32) | def test_bump_version():
  function test_add_to_version_family (line 45) | def test_add_to_version_family(df1, df2):
  function test_transform_versioning_based_on_key (line 65) | def test_transform_versioning_based_on_key():
  function test_transform_versioning_based_on_revises (line 115) | def test_transform_versioning_based_on_revises():
  function test_transform_versioning_across_branches_preserves_main_latest (line 186) | def test_transform_versioning_across_branches_preserves_main_latest():
  function test_path_rename (line 228) | def test_path_rename():
  function test_version_backward_compatibility (line 243) | def test_version_backward_compatibility():
  function test_adjust_is_latest_when_deleting_is_versioned (line 300) | def test_adjust_is_latest_when_deleting_is_versioned():

FILE: tests/core/test_label_manager.py
  function adata (line 14) | def adata():
  function test_labels_add (line 22) | def test_labels_add(adata):
  function test_labels_add_using_anndata (line 99) | def test_labels_add_using_anndata(adata):
  function test_labels_get (line 261) | def test_labels_get(get_mini_csv: Path):  # noqa: F811
  function get_test_artifacts (line 279) | def get_test_artifacts():
  function test_add_from (line 293) | def test_add_from(get_test_artifacts):

FILE: tests/core/test_load.py
  function zip_file (line 13) | def zip_file():
  function html_filepath (line 22) | def html_filepath():
  function json_filepath (line 31) | def json_filepath():
  function csv_filepath (line 40) | def csv_filepath():
  function tsv_filepath (line 49) | def tsv_filepath():
  function parquet_filepath (line 58) | def parquet_filepath():
  function yaml_filepath (line 67) | def yaml_filepath():
  function image_filepath (line 76) | def image_filepath():
  function svg_filepath (line 85) | def svg_filepath():
  function rds_filepath (line 94) | def rds_filepath():
  function local_anndata_filepath (line 103) | def local_anndata_filepath():
  function adata (line 108) | def adata(local_anndata_filepath):
  function test_load_anndata (line 112) | def test_load_anndata(local_anndata_filepath, adata):
  function test_load_mudata (line 124) | def test_load_mudata(get_small_mdata):
  function test_load_spatialdata (line 131) | def test_load_spatialdata(get_small_sdata):
  function load_blobs__repr__ (line 138) | def load_blobs__repr__():
  function test_load_html (line 148) | def test_load_html(html_filepath):
  function test_load_json (line 153) | def test_load_json(json_filepath):
  function test_no_loader (line 159) | def test_no_loader(zip_file):
  function test_load_csv (line 165) | def test_load_csv(csv_filepath):
  function test_load_tsv (line 172) | def test_load_tsv(tsv_filepath):
  function test_load_parquet (line 179) | def test_load_parquet(parquet_filepath):
  function test_load_yaml (line 186) | def test_load_yaml(yaml_filepath):
  function test_load_image (line 193) | def test_load_image(image_filepath):
  function test_load_svg (line 199) | def test_load_svg(svg_filepath):
  function test_load_rds (line 205) | def test_load_rds(rds_filepath, ccaplog):

FILE: tests/core/test_manager.py
  function test_manager_list (line 4) | def test_manager_list():

FILE: tests/core/test_merge.py
  function test_merge_branch_into_main (line 7) | def test_merge_branch_into_main():
  function test_branch_status_values (line 44) | def test_branch_status_values():
  function test_draft_review_and_close_merge_request_status (line 70) | def test_draft_review_and_close_merge_request_status():
  function test_merge_nonexistent_branch_raises (line 92) | def test_merge_nonexistent_branch_raises():
  function test_merge_reconciles_is_latest_for_versioned_records (line 99) | def test_merge_reconciles_is_latest_for_versioned_records():
  function test_merge_updates_recordblock_branch (line 134) | def test_merge_updates_recordblock_branch():

FILE: tests/core/test_nbconvert.py
  function test_nbconvert (line 4) | def test_nbconvert():

FILE: tests/core/test_notebooks.py
  function test_all_notebooks (line 12) | def test_all_notebooks():
  function test_run_after_rename_no_uid (line 17) | def test_run_after_rename_no_uid():

FILE: tests/core/test_querydb.py
  function test_DB_multiple_instances (line 5) | def test_DB_multiple_instances():
  function test_DB_bionty (line 14) | def test_DB_bionty():
  function test_DB_missing_module (line 20) | def test_DB_missing_module():
  function test_DB_instantiate_class (line 33) | def test_DB_instantiate_class():
  function test_DB_rejects_invalid_attributes (line 52) | def test_DB_rejects_invalid_attributes(attr, expected_msg):
  function test_DB_cache (line 60) | def test_DB_cache():
  function test_queryset_caching (line 68) | def test_queryset_caching():
  function test_DB_dir (line 77) | def test_DB_dir():

FILE: tests/core/test_queryset.py
  function test_to_dataframe (line 15) | def test_to_dataframe():
  function test_complex_df_with_features (line 84) | def test_complex_df_with_features():
  function test_run_to_dataframe_includes_json_features (line 91) | def test_run_to_dataframe_includes_json_features():
  function test_one_first (line 107) | def test_one_first():
  function test_filter_related_field_name (line 129) | def test_filter_related_field_name():
  function test_filter_unknown_field (line 139) | def test_filter_unknown_field():
  function test_filter_status_field (line 145) | def test_filter_status_field():
  function test_get_id_type_error (line 168) | def test_get_id_type_error():
  function test_get_related_field_name (line 175) | def test_get_related_field_name():
  function test_get_unknown_field (line 185) | def test_get_unknown_field():
  function test_search (line 191) | def test_search():
  function test_lookup (line 202) | def test_lookup():
  function test_inspect (line 216) | def test_inspect():
  function test_validate (line 224) | def test_validate():
  function test_standardize (line 239) | def test_standardize():
  function test_get_doesnotexist_error (line 244) | def test_get_doesnotexist_error():
  function set_branch (line 259) | def set_branch(branch: ln.Branch):
  function test_get_filter_branch (line 268) | def test_get_filter_branch():
  function test_to_class (line 329) | def test_to_class():
  function test_queryset_soft_delete_error (line 348) | def test_queryset_soft_delete_error():
  function test_encode_lamindb_fields_as_columns (line 356) | def test_encode_lamindb_fields_as_columns():

FILE: tests/core/test_record_basics.py
  function test_record_docstring_examples (line 14) | def test_record_docstring_examples():
  function test_record_initialization (line 74) | def test_record_initialization():
  function test_record_lazy_features_on_save (line 88) | def test_record_lazy_features_on_save():
  function test_record_from_dataframe_bulk_save_paths (line 99) | def test_record_from_dataframe_bulk_save_paths():
  function test_record_from_dataframe_requires_named_type (line 133) | def test_record_from_dataframe_requires_named_type():
  function test_record_from_dataframe_with_string_type_creates_import_type (line 147) | def test_record_from_dataframe_with_string_type_creates_import_type():
  function test_record_from_dataframe_with_string_type_duplicate_name_errors (line 198) | def test_record_from_dataframe_with_string_type_duplicate_name_errors():
  function test_feature_manager_raise_not_validated_values (line 224) | def test_feature_manager_raise_not_validated_values():
  function test_name_lookup (line 248) | def test_name_lookup():
  function test_invalid_type_record_with_schema (line 266) | def test_invalid_type_record_with_schema():
  function test_record_features_add_remove_values (line 282) | def test_record_features_add_remove_values():
  function test_date_and_datetime_corruption (line 803) | def test_date_and_datetime_corruption():
  function test_only_list_type_features_and_field_qualifiers (line 847) | def test_only_list_type_features_and_field_qualifiers():
  function test_record_feature_predicate_query (line 921) | def test_record_feature_predicate_query():
  function test_record_features_accept_feature_object_keys (line 941) | def test_record_features_accept_feature_object_keys():

FILE: tests/core/test_record_sheet_examples.py
  function test_float_int_casting (line 9) | def test_float_int_casting():
  function test_record_example_compound_treatment (line 39) | def test_record_example_compound_treatment(
  function test_nextflow_sheet_with_samples (line 186) | def test_nextflow_sheet_with_samples(
  function test_record_soft_deleted_recreate (line 263) | def test_record_soft_deleted_recreate():
  function test_annotate_with_user_feature (line 282) | def test_annotate_with_user_feature():
  function test_to_artifact_exports_all_records (line 314) | def test_to_artifact_exports_all_records():
  function test_to_artifact_with_required_non_nullable_data_id_maximal_set_true (line 325) | def test_to_artifact_with_required_non_nullable_data_id_maximal_set_true():

FILE: tests/core/test_rename_features_labels.py
  function test_rename_feature (line 9) | def test_rename_feature(ccaplog):
  function test_rename_label (line 55) | def test_rename_label(model_class, ccaplog):

FILE: tests/core/test_run.py
  function test_run (line 7) | def test_run():
  function test_bulk_permanent_run_delete (line 58) | def test_bulk_permanent_run_delete(tmp_path):

FILE: tests/core/test_save.py
  function test_bulk_save_and_update (line 11) | def test_bulk_save_and_update():
  function test_prepare_error_message (line 24) | def test_prepare_error_message(get_mini_csv):
  function test_save_data_object (line 37) | def test_save_data_object(get_mini_csv):
  function test_store_artifacts_acid (line 44) | def test_store_artifacts_acid(get_mini_csv):
  function test_save_parents (line 60) | def test_save_parents():
  function test_save_batch_size (line 68) | def test_save_batch_size():
  function test_bulk_save_lazy_record_features (line 76) | def test_bulk_save_lazy_record_features():
  function test_bulk_save_lazy_record_features_requires_same_schema (line 119) | def test_bulk_save_lazy_record_features_requires_same_schema():
  function test_bulk_save_lazy_record_features_requires_schema (line 145) | def test_bulk_save_lazy_record_features_requires_schema():
  function test_bulk_resave_trashed_records (line 163) | def test_bulk_resave_trashed_records():

FILE: tests/core/test_schema.py
  function df (line 11) | def df():
  function test_schema_from_values (line 22) | def test_schema_from_values():
  function test_schema_from_records (line 68) | def test_schema_from_records(df):
  function test_schema_from_df (line 97) | def test_schema_from_df(df):
  function test_get_related_name (line 118) | def test_get_related_name():
  function test_validate_features (line 123) | def test_validate_features():
  function test_kwargs (line 138) | def test_kwargs():
  function test_edge_cases (line 143) | def test_edge_cases():
  function mini_immuno_schema_flexible (line 156) | def mini_immuno_schema_flexible():
  function test_schema_update_implicit_through_name_equality (line 169) | def test_schema_update_implicit_through_name_equality(
  function test_schema_update (line 249) | def test_schema_update(
  function test_schema_mutations_feature_removal (line 343) | def test_schema_mutations_feature_removal(
  function test_schema_add_remove_optional_features (line 368) | def test_schema_add_remove_optional_features(mini_immuno_schema_flexible...
  function test_schema_components (line 378) | def test_schema_components(mini_immuno_schema_flexible: ln.Schema):
  function test_mini_immuno_schema_flexible (line 425) | def test_mini_immuno_schema_flexible(mini_immuno_schema_flexible):
  function test_schema_recovery_based_on_hash (line 454) | def test_schema_recovery_based_on_hash(mini_immuno_schema_flexible: ln.S...
  function test_schemas_dataframe (line 466) | def test_schemas_dataframe():
  function test_schemas_anndata (line 487) | def test_schemas_anndata():
  function test_schema_already_saved_aux (line 534) | def test_schema_already_saved_aux():
  function test_schema_not_saved_describe (line 607) | def test_schema_not_saved_describe():
  function test_schema_is_type (line 614) | def test_schema_is_type():
  function test_composite_component (line 631) | def test_composite_component():
  function test_schema_describe_bracket_names (line 661) | def test_schema_describe_bracket_names():

FILE: tests/core/test_search.py
  function prepare_cell_type_registry (line 7) | def prepare_cell_type_registry():
  function test_search_synonyms (line 46) | def test_search_synonyms(prepare_cell_type_registry):
  function test_search_limit (line 51) | def test_search_limit(prepare_cell_type_registry):
  function test_search_case_sensitive (line 56) | def test_search_case_sensitive(prepare_cell_type_registry):
  function test_search_None (line 61) | def test_search_None():

FILE: tests/core/test_settings.py
  function test_settings_repr (line 5) | def test_settings_repr():
  function test_storage_setter_raises_on_foreign_managed_storage (line 18) | def test_storage_setter_raises_on_foreign_managed_storage(tmp_path):
  function test_local_storage_setter_raises_on_foreign_managed_storage (line 32) | def test_local_storage_setter_raises_on_foreign_managed_storage(tmp_path):

FILE: tests/core/test_sqlrecord.py
  function test_feature_describe (line 19) | def test_feature_describe():
  function test_artifact_describe (line 54) | def test_artifact_describe():
  function test_repr_describe (line 115) | def test_repr_describe():
  function test_record_describe_includes_features (line 121) | def test_record_describe_includes_features():
  function test_validate_literal_fields (line 135) | def test_validate_literal_fields():
  function test_init_with_args (line 141) | def test_init_with_args():
  function test_validate_required_fields (line 153) | def test_validate_required_fields():
  function get_search_test_filepaths (line 163) | def get_search_test_filepaths():
  function test_search_and_get (line 172) | def test_search_and_get(get_search_test_filepaths):
  function test_suggest_similar_names (line 238) | def test_suggest_similar_names():
  function test_pass_version (line 278) | def test_pass_version():
  function test_delete (line 296) | def test_delete():
  function test_get_name_field (line 315) | def test_get_name_field():
  function test_using (line 323) | def test_using():
  function test_get_record_kwargs (line 354) | def test_get_record_kwargs():
  function test_get_record_kwargs_empty (line 376) | def test_get_record_kwargs_empty():
  function test_soft_delete_error (line 389) | def test_soft_delete_error():
  function test_delete_return_value_permanent (line 397) | def test_delete_return_value_permanent():
  function test_unsaved_relationship_modification_attempts (line 415) | def test_unsaved_relationship_modification_attempts():
  function test_failed_connect (line 433) | def test_failed_connect():
  function test_unsaved_model_different_instance (line 441) | def test_unsaved_model_different_instance():
  function test_track_fields_with_deferred_columns (line 459) | def test_track_fields_with_deferred_columns(example_dataframe: pd.DataFr...
  function test_track_fields_must_exist_on_model (line 472) | def test_track_fields_must_exist_on_model(monkeypatch, example_dataframe...

FILE: tests/core/test_storage.py
  function test_reference_storage_location (line 9) | def test_reference_storage_location(ccaplog):
  function test_create_storage_locations_parallel (line 18) | def test_create_storage_locations_parallel():

FILE: tests/core/test_switch.py
  function test_switch_create_existing_branch_raises (line 7) | def test_switch_create_existing_branch_raises():

FILE: tests/core/test_track_flow.py
  function process_chunk (line 12) | def process_chunk(
  function test_flow (line 29) | def test_flow():
  function test_flow_track_arg_aliases_implicit (line 81) | def test_flow_track_arg_aliases_implicit():
  function test_flow_track_arg_aliases_false (line 96) | def test_flow_track_arg_aliases_false():

FILE: tests/core/test_track_script_or_notebook.py
  function test_serialize_params_to_json (line 27) | def test_serialize_params_to_json():
  function test_redact_secrets_in_source_code (line 68) | def test_redact_secrets_in_source_code():
  function test_redact_secrets_in_source_code_keeps_env_references (line 87) | def test_redact_secrets_in_source_code_keeps_env_references():
  function test_redact_secrets_in_source_code_ignores_annotations_and_forwarding (line 103) | def test_redact_secrets_in_source_code_ignores_annotations_and_forwardin...
  function test_serialize_params_to_json_redacts_provider_api_key_names (line 119) | def test_serialize_params_to_json_redacts_provider_api_key_names():
  function test_redact_secrets_in_source_code_redacts_provider_api_key_names (line 135) | def test_redact_secrets_in_source_code_redacts_provider_api_key_names():
  function test_track_basic_invocation (line 152) | def test_track_basic_invocation():
  function test_track_accepts_initiated_by_run_uid (line 240) | def test_track_accepts_initiated_by_run_uid():
  function test_track_uses_initiated_by_run_uid_from_env (line 272) | def test_track_uses_initiated_by_run_uid_from_env(monkeypatch: pytest.Mo...
  function test_track_with_plan_links_run (line 293) | def test_track_with_plan_links_run(tmp_path, pass_plan_as_key):
  function create_record (line 321) | def create_record():
  function test_track_input_record (line 344) | def test_track_input_record(create_record, kind):
  function test_track_notebook_colab (line 378) | def test_track_notebook_colab():
  function test_track_notebook_untitled (line 383) | def test_track_notebook_untitled():
  function test_detect_and_process_source_code_file_returns_key_from_module_for_package (line 393) | def test_detect_and_process_source_code_file_returns_key_from_module_for...
  function test_detect_and_process_source_code_file_returns_none_key_for_script (line 418) | def test_detect_and_process_source_code_file_returns_none_key_for_script():
  function test_finish_before_track (line 442) | def test_finish_before_track():
  function test_invalid_transform_kind (line 449) | def test_invalid_transform_kind():
  function test_create_or_load_transform (line 462) | def test_create_or_load_transform():
  function test_create_or_load_transform_warns_when_outside_dev_dir (line 500) | def test_create_or_load_transform_warns_when_outside_dev_dir(
  function test_run_scripts (line 527) | def test_run_scripts():
  function test_run_external_script (line 616) | def test_run_external_script():
  function test_track_notebook_or_script_manually (line 647) | def test_track_notebook_or_script_manually(type):
  function test_clean_r_notebook_html (line 657) | def test_clean_r_notebook_html():
  function test_notebook_to_script_notebooknode_metadata (line 672) | def test_notebook_to_script_notebooknode_metadata(tmp_path):
  class MockRun (line 691) | class MockRun:
    method __init__ (line 692) | def __init__(self, uid):
    method save (line 697) | def save(self):
  function test_logstream_tracker_multiple (line 701) | def test_logstream_tracker_multiple():
  function test_logstream_tracker_exception_handling (line 765) | def test_logstream_tracker_exception_handling():
  function test_logstream_tracker_cleanup_sigint_chains_to_keyboard_interrupt (line 805) | def test_logstream_tracker_cleanup_sigint_chains_to_keyboard_interrupt():

FILE: tests/core/test_track_step.py
  function process_chunk (line 11) | def process_chunk(
  function test_step_parallel (line 27) | def test_step_parallel():

FILE: tests/core/test_transform.py
  function test_transform_recovery_based_on_hash (line 8) | def test_transform_recovery_based_on_hash():
  function test_transform_recovery_based_on_key (line 18) | def test_transform_recovery_based_on_key():
  function test_revise_transforms (line 28) | def test_revise_transforms():
  function test_delete (line 159) | def test_delete():
  function test_successor_predecessor (line 195) | def test_successor_predecessor():
  function test_bulk_transform_permanent_delete (line 228) | def test_bulk_transform_permanent_delete(tmp_path):
  function test_single_transform_permanent_delete_delegates_to_queryset (line 263) | def test_single_transform_permanent_delete_delegates_to_queryset(tmp_path):
  function test_bulk_transform_soft_delete (line 291) | def test_bulk_transform_soft_delete():
  function test_bulk_transform_permanent_delete_promotes_previous_version (line 302) | def test_bulk_transform_permanent_delete_promotes_previous_version():
  function test_bulk_transform_soft_delete_promotes_previous_version (line 318) | def test_bulk_transform_soft_delete_promotes_previous_version():

FILE: tests/core/test_transform_from_git.py
  function test_transform_from_git (line 7) | def test_transform_from_git():
  function test_transform_from_git_with_entrypoint (line 51) | def test_transform_from_git_with_entrypoint():
  function test_transform_custom_key_and_hash_lookup (line 73) | def test_transform_custom_key_and_hash_lookup():
  function test_transform_from_git_failure_modes (line 92) | def test_transform_from_git_failure_modes():

FILE: tests/core/test_view.py
  function test_view (line 4) | def test_view():

FILE: tests/curators/conftest.py
  function pytest_sessionstart (line 8) | def pytest_sessionstart():
  function pytest_sessionfinish (line 15) | def pytest_sessionfinish(session: pytest.Session):
  function ccaplog (line 21) | def ccaplog(caplog):

FILE: tests/curators/test_cellxgene_curation.py
  function cellxgene_defaults (line 9) | def cellxgene_defaults() -> Generator:
  function test_cellxgene_curation (line 28) | def test_cellxgene_curation(cellxgene_defaults) -> None:

FILE: tests/curators/test_curate_from_croissant.py
  function test_curate_artifact_from_croissant (line 8) | def test_curate_artifact_from_croissant(filepath_prefix: str | None):
  function test_curate_collection_from_croissant (line 59) | def test_curate_collection_from_croissant():

FILE: tests/curators/test_curators_examples.py
  function mini_immuno_schema (line 17) | def mini_immuno_schema():
  function curator_params (line 62) | def curator_params():
  function mudata_papalexi21_subset_schema (line 75) | def mudata_papalexi21_subset_schema():
  function study_metadata_schema (line 147) | def study_metadata_schema():
  function anndata_uns_schema (line 157) | def anndata_uns_schema():
  function spatialdata_blobs_schema (line 167) | def spatialdata_blobs_schema():
  function test_dataframe_curator (line 189) | def test_dataframe_curator(mini_immuno_schema: ln.Schema):
  function test_dataframe_curator_index (line 292) | def test_dataframe_curator_index():
  function test_dataframe_curator_validate_all_annotate_cat (line 308) | def test_dataframe_curator_validate_all_annotate_cat(mini_immuno_schema):
  function test_same_name_different_type (line 334) | def test_same_name_different_type():
  function test_dataframe_curator_validate_all_annotate_cat2 (line 367) | def test_dataframe_curator_validate_all_annotate_cat2(mini_immuno_schema):
  function test_dataframe_attrs_validation (line 397) | def test_dataframe_attrs_validation(study_metadata_schema, include_attrs...
  function test_schema_new_genes (line 463) | def test_schema_new_genes(ccaplog):
  function test_schema_no_match_ensembl (line 493) | def test_schema_no_match_ensembl():
  function test_schema_mixed_ensembl_symbols (line 518) | def test_schema_mixed_ensembl_symbols(ccaplog):
  function test_schema_mixed_features (line 552) | def test_schema_mixed_features(ccaplog):
  function test_anndata_curator_different_components (line 579) | def test_anndata_curator_different_components(mini_immuno_schema: ln.Sch...
  function test_anndata_curator_varT_curation (line 656) | def test_anndata_curator_varT_curation():
  function test_anndata_curator_varT_curation_legacy (line 709) | def test_anndata_curator_varT_curation_legacy(ccaplog):
  function test_anndata_curator_nested_uns (line 753) | def test_anndata_curator_nested_uns(study_metadata_schema, anndata_uns_s...
  function test_anndata_curator_no_var (line 802) | def test_anndata_curator_no_var(mini_immuno_schema: ln.Schema):
  function test_mudata_curator (line 819) | def test_mudata_curator(
  function test_mudata_curator_nested_uns (line 860) | def test_mudata_curator_nested_uns(study_metadata_schema):
  function test_spatialdata_curator (line 907) | def test_spatialdata_curator(
  function test_specific_source (line 962) | def test_specific_source():

FILE: tests/curators/test_curators_remote.py
  function test_curator_remote (line 4) | def test_curator_remote():

FILE: tests/curators/test_dataframe_curation.py
  function transactions_schema (line 11) | def transactions_schema():
  function transactions_dataframe (line 68) | def transactions_dataframe():
  function test_schema_creation (line 92) | def test_schema_creation(transactions_schema):
  function test_data_curation (line 107) | def test_data_curation(
  function test_missing_required_feature (line 120) | def test_missing_required_feature(transactions_schema: ln.Schema):
  function test_invalid_label (line 139) | def test_invalid_label(transactions_schema: ln.Schema):
  function test_invalid_url_dtype (line 161) | def test_invalid_url_dtype(transactions_schema: ln.Schema):

FILE: tests/integrations/conftest.py
  function pytest_sessionstart (line 8) | def pytest_sessionstart():
  function pytest_sessionfinish (line 15) | def pytest_sessionfinish(session: pytest.Session):
  function ccaplog (line 21) | def ccaplog(caplog):

FILE: tests/integrations/test_lightning.py
  function cleanup_checkpoints (line 20) | def cleanup_checkpoints() -> Generator[None, None, None]:
  function cleanup_test_dir (line 29) | def cleanup_test_dir() -> Generator[None, None, None]:
  function simple_model (line 39) | def simple_model() -> pl.LightningModule:
  function dataloader (line 61) | def dataloader() -> DataLoader:
  function dirpath (line 68) | def dirpath(request: pytest.FixtureRequest) -> Generator[str, None, None]:
  function lightning_features (line 81) | def lightning_features() -> Generator[None, None, None]:
  function test_checkpoint_basic (line 99) | def test_checkpoint_basic(
  function test_checkpoint_with_features (line 121) | def test_checkpoint_with_features(
  function test_checkpoint_missing_features (line 159) | def test_checkpoint_missing_features(
  function test_checkpoint_auto_features (line 180) | def test_checkpoint_auto_features(
  function test_checkpoint_auto_features_with_duplicate_score_name (line 211) | def test_checkpoint_auto_features_with_duplicate_score_name(
  function test_checkpoint_best_model_with_duplicate_feature_names (line 237) | def test_checkpoint_best_model_with_duplicate_feature_names(
  function test_checkpoint_query_budget_scales_sublinearly_with_hparams (line 281) | def test_checkpoint_query_budget_scales_sublinearly_with_hparams(
  function test_model_rank_update_query_budget (line 319) | def test_model_rank_update_query_budget(
  function test_checkpoint_best_model_tracking (line 356) | def test_checkpoint_best_model_tracking(
  function test_checkpoint_model_rank (line 384) | def test_checkpoint_model_rank(
  function test_checkpoint_last_model_points_to_last_saved_artifact (line 414) | def test_checkpoint_last_model_points_to_last_saved_artifact(
  function test_checkpoint_semantic_paths (line 447) | def test_checkpoint_semantic_paths(
  function test_callback_deprecated (line 477) | def test_callback_deprecated(
  function test_checkpoint_overwrites_existing_artifact (line 505) | def test_checkpoint_overwrites_existing_artifact(
  function test_checkpoint_invalid_feature_keys (line 531) | def test_checkpoint_invalid_feature_keys(dirpath: str):
  function test_checkpoint_hparams (line 540) | def test_checkpoint_hparams(dataloader: DataLoader, dirpath: str, lightn...
  function test_checkpoint_datamodule_hparams (line 580) | def test_checkpoint_datamodule_hparams(
  function test_checkpoint_trainer_config (line 614) | def test_checkpoint_trainer_config(
  function test_checkpoint_hparams_yaml_with_hparams (line 661) | def test_checkpoint_hparams_yaml_with_hparams(
  function test_key_layout_matrix (line 726) | def test_key_layout_matrix(
  function test_run_uid_not_in_key_when_disabled (line 829) | def test_run_uid_not_in_key_when_disabled(
  function test_two_runs_same_logger_produce_different_keys (line 857) | def test_two_runs_same_logger_produce_different_keys(
  function test_checkpoint_artifact_key_prefix_matrix (line 898) | def test_checkpoint_artifact_key_prefix_matrix(
  function test_checkpoint_auto_features_without_dirpath (line 951) | def test_checkpoint_auto_features_without_dirpath(
  function test_save_config_artifact_key_matrix (line 1013) | def test_save_config_artifact_key_matrix(
  function test_save_config_artifact_tracked_as_run_input (line 1094) | def test_save_config_artifact_tracked_as_run_input(
  function test_checkpoint_subclass_receives_artifact_events (line 1149) | def test_checkpoint_subclass_receives_artifact_events(
  function test_checkpoint_artifact_observers_receive_shared_events (line 1245) | def test_checkpoint_artifact_observers_receive_shared_events(

FILE: tests/no_instance/conftest.py
  function ccaplog (line 5) | def ccaplog(caplog) -> pytest.LogCaptureFixture:

FILE: tests/no_instance/test_connect_dynamic_import.py
  function test_connect_dynamic_import (line 1) | def test_connect_dynamic_import(ccaplog):

FILE: tests/no_instance/test_import_side_effects.py
  function _probe_modules_loaded (line 73) | def _probe_modules_loaded(code: str) -> dict[str, bool]:
  function _assert_modules (line 104) | def _assert_modules(
  function test_storage_import_side_effects (line 120) | def test_storage_import_side_effects(

FILE: tests/no_instance/test_no_default_instance.py
  function test_no_read_only_warning (line 7) | def test_no_read_only_warning(ccaplog):
  function test_instance_not_connected (line 14) | def test_instance_not_connected():
  function test_query_artifacts_lamindata (line 21) | def test_query_artifacts_lamindata():
  function test_get_artifact_lamindata (line 28) | def test_get_artifact_lamindata():

FILE: tests/permissions/conftest.py
  function pytest_sessionstart (line 10) | def pytest_sessionstart():
  function pytest_sessionfinish (line 31) | def pytest_sessionfinish(session: pytest.Session):

FILE: tests/permissions/jwt_utils.py
  function sign_jwt (line 6) | def sign_jwt(db_url, payload: dict) -> str:

FILE: tests/permissions/scripts/check_lamin_dev.py
  function cleanup (line 9) | def cleanup(records):

FILE: tests/permissions/scripts/setup_access.py
  function create_jwt_user (line 21) | def create_jwt_user(dsn_admin: str, jwt_role_name: str):

FILE: tests/permissions/test_rls_dbwritelog.py
  function test_token_expiration (line 39) | def test_token_expiration():
  function test_authentication (line 56) | def test_authentication():
  function test_select_without_db_token (line 133) | def test_select_without_db_token():
  function test_fine_grained_permissions_account_and_dbwrite (line 178) | def test_fine_grained_permissions_account_and_dbwrite():
  function test_fine_grained_permissions_team (line 280) | def test_fine_grained_permissions_team():
  function test_fine_grained_permissions_single_records (line 285) | def test_fine_grained_permissions_single_records():
  function test_atomic (line 357) | def test_atomic():
  function test_utility_tables (line 371) | def test_utility_tables():
  function test_user_rls (line 392) | def test_user_rls():
  function test_write_role (line 415) | def test_write_role():
  function test_locking (line 441) | def test_locking():
  function test_tracking_error (line 449) | def test_tracking_error():
  function test_token_reset (line 494) | def test_token_reset():
  function test_dbwrite_uninstall (line 507) | def test_dbwrite_uninstall():
  function test_lamin_dev (line 537) | def test_lamin_dev():

FILE: tests/profiling/import_records_from_dataframe.py
  function generate_values (line 10) | def generate_values(dtype: str, n_rows: int, rng: Random):
  function main (line 26) | def main(n_rows: int):

FILE: tests/storage/conftest.py
  function create_test_instance (line 13) | def create_test_instance(pgurl: str):
  function pytest_sessionstart (line 29) | def pytest_sessionstart():
  function delete_test_instance (line 53) | def delete_test_instance():
  function pytest_sessionfinish (line 70) | def pytest_sessionfinish(session: pytest.Session):
  function ccaplog (line 76) | def ccaplog(caplog):

FILE: tests/storage/test_artifact_storage.py
  function test_create_from_anndata_in_existing_cloud_storage (line 11) | def test_create_from_anndata_in_existing_cloud_storage():
  function test_create_small_file_from_remote_path (line 30) | def test_create_small_file_from_remote_path(
  function test_versioning_arifact_from_existing_path (line 62) | def test_versioning_arifact_from_existing_path(ccaplog):
  function test_create_big_file_from_remote_path (line 74) | def test_create_big_file_from_remote_path():
  function test_delete_artifact_from_non_managed_storage (line 93) | def test_delete_artifact_from_non_managed_storage():
  function test_huggingface_paths (line 117) | def test_huggingface_paths():
  function test_gcp_paths (line 142) | def test_gcp_paths():
  function test_http_paths (line 162) | def test_http_paths():
  function test_folder_like_artifact_s3 (line 186) | def test_folder_like_artifact_s3():
  function test_single_file_directory_preserved (line 194) | def test_single_file_directory_preserved(tmp_path):

FILE: tests/storage/test_artifact_zarr.py
  function get_small_adata (line 16) | def get_small_adata():
  function test_zarr_upload_cache (line 25) | def test_zarr_upload_cache(get_small_adata):

FILE: tests/storage/test_cache.py
  function switch_storage (line 14) | def switch_storage():
  function test_local_cache (line 21) | def test_local_cache():
  function test_cloud_cache (line 69) | def test_cloud_cache(switch_storage):
  function test_cloud_cache_versions (line 141) | def test_cloud_cache_versions(switch_storage):
  function test_corrupted_cache_local (line 201) | def test_corrupted_cache_local():
  function test_corrupted_cache_cloud (line 217) | def test_corrupted_cache_cloud(switch_storage):

FILE: tests/storage/test_connect_reconnect.py
  function test_connect_reconnect (line 5) | def test_connect_reconnect():

FILE: tests/storage/test_storage_lifecycle.py
  function check_storage_location_on_hub_exists (line 8) | def check_storage_location_on_hub_exists(uid: str):
  function test_reference_storage_location (line 20) | def test_reference_storage_location(ccaplog):
  function test_switch_delete_storage_location (line 29) | def test_switch_delete_storage_location():

FILE: tests/storage/test_streaming.py
  function bad_adata_path (line 25) | def bad_adata_path():
  function test_anndata_io (line 51) | def test_anndata_io():
  function test_backed_access (line 67) | def test_backed_access(adata_format):
  function test_add_column (line 161) | def test_add_column():
  function test_to_index (line 195) | def test_to_index():
  function test_infer_suffix (line 205) | def test_infer_suffix():
  function test_write_to_disk (line 214) | def test_write_to_disk():
  function test_backed_bad_format (line 227) | def test_backed_bad_format(bad_adata_path):
  function test_backed_zarr_not_adata (line 248) | def test_backed_zarr_not_adata():
  function test_anndata_open_mode (line 262) | def test_anndata_open_mode():
  function test_from_lazy (line 277) | def test_from_lazy():
  function test_zarr_open_mode_overwrite_versions_false (line 303) | def test_zarr_open_mode_overwrite_versions_false():
  function test_from_lazy_cloud (line 317) | def test_from_lazy_cloud():
  function test_polars_options (line 333) | def test_polars_options():
  function test_open_dataframe_artifact (line 344) | def test_open_dataframe_artifact():
  function test_open_dataframe_collection (line 414) | def test_open_dataframe_collection():
  function test_backed_wrong_suffix (line 486) | def test_backed_wrong_suffix():
  function test_anndata_n_observations (line 498) | def test_anndata_n_observations(bad_adata_path):
  function _compress (line 524) | def _compress(input_filepath, output_filepath):
  function test_compressed (line 531) | def test_compressed(gz_suffix):

FILE: tests/storage/test_transfer.py
  function test_describe_artifact_from_remote_instance (line 9) | def test_describe_artifact_from_remote_instance(capsys):
  function test_transfer_from_remote_to_local (line 18) | def test_transfer_from_remote_to_local(ccaplog):
  function test_transfer_into_space (line 154) | def test_transfer_into_space():
  function test_using_record_organism (line 167) | def test_using_record_organism():
  function test_using_query_by_feature (line 215) | def test_using_query_by_feature():

FILE: tests/tiledbsoma/conftest.py
  function pytest_sessionstart (line 14) | def pytest_sessionstart():
  function pytest_sessionfinish (line 33) | def pytest_sessionfinish(session: pytest.Session):
  function adata_file (line 45) | def adata_file():
  function clean_soma_files (line 61) | def clean_soma_files(request):
  function soma_experiment_file (line 73) | def soma_experiment_file(clean_soma_files):

FILE: tests/tiledbsoma/test_artifact_basics.py
  function test_create_from_soma_experiment (line 6) | def test_create_from_soma_experiment(soma_experiment_file, adata_file):
  function test_data_is_soma_experiment_paths (line 21) | def test_data_is_soma_experiment_paths():
  function test_data_is_soma_experiment (line 26) | def test_data_is_soma_experiment(soma_experiment_file):

FILE: tests/tiledbsoma/test_curators.py
  function test_tiledbsoma_curator (line 10) | def test_tiledbsoma_curator(clean_soma_files):

FILE: tests/tiledbsoma/test_storage.py
  function test_write_read_tiledbsoma (line 19) | def test_write_read_tiledbsoma(storage):
  function test_from_tiledbsoma (line 182) | def test_from_tiledbsoma():
  function test_tiledb_config (line 211) | def test_tiledb_config():
  function test_tiledbsoma_in_managed_storage (line 220) | def test_tiledbsoma_in_managed_storage():

[
  {
    "path": ".github/ISSUE_TEMPLATE/bug_report.yml",
    "chars": 417,
    "preview": "name: Report a bug\ndescription: Report a bug.\nlabels:\n  - \":bug: bug\"\nbody:\n  - type: textarea\n    id: report\n    attrib"
  },
  {
    "path": ".github/ISSUE_TEMPLATE/config.yml",
    "chars": 347,
    "preview": "blank_issues_enabled: true\ncontact_links:\n    - name: LaminHub issues\n      url: https://github.com/laminlabs/laminhub-p"
  },
  {
    "path": ".github/ISSUE_TEMPLATE/enhancement.yml",
    "chars": 302,
    "preview": "name: Propose an enhancement\ndescription: Propose an enhancement.\nbody:\n  - type: textarea\n    id: description\n    attri"
  },
  {
    "path": ".github/ISSUE_TEMPLATE/usage_question.yml",
    "chars": 327,
    "preview": "name: Ask a usage question\ndescription: Ask a usage question.\nlabels:\n  - \"usage question\"\nbody:\n  - type: textarea\n    "
  },
  {
    "path": ".github/workflows/build.yml",
    "chars": 9618,
    "preview": "name: build\n\non:\n  push:\n    branches: [release]\n  pull_request:\n\njobs:\n  pre-filter:\n    runs-on: ubuntu-latest\n    out"
  },
  {
    "path": ".github/workflows/doc-changes.yml",
    "chars": 648,
    "preview": "name: doc-changes\n\non:\n  pull_request_target:\n    branches:\n      - main\n      - release\n    types:\n      - closed\n\njobs"
  },
  {
    "path": ".gitignore",
    "chars": 3755,
    "preview": "__MACOSX/\n\n# LaminDB\nREADME_stripped.md\ndocs/scripts/test_artifact_parquet.py\nREADME.ipynb\ndocs/sample.fasta\ndocs/faq/sa"
  },
  {
    "path": ".gitmodules",
    "chars": 496,
    "preview": "[submodule \"sub/lamindb-setup\"]\n\tpath = sub/lamindb-setup\n\turl = https://github.com/laminlabs/lamindb-setup\n[submodule \""
  },
  {
    "path": ".pre-commit-config.yaml",
    "chars": 2252,
    "preview": "fail_fast: false\ndefault_language_version:\n  python: python3\ndefault_stages:\n  - pre-commit\n  - pre-push\nminimum_pre_com"
  },
  {
    "path": "CONTRIBUTING.md",
    "chars": 3864,
    "preview": "# Contributing\n\nContributions are generally welcome. Please make an issue to discuss proposals.\n\n## Installation\n\n### Py"
  },
  {
    "path": "LICENSE",
    "chars": 11357,
    "preview": "                                 Apache License\n                           Version 2.0, January 2004\n                   "
  },
  {
    "path": "README.md",
    "chars": 19223,
    "preview": "[![docs](https://img.shields.io/badge/docs-yellow)](https://docs.lamin.ai) [![llms.txt](https://img.shields.io/badge/llm"
  },
  {
    "path": "docs/api.md",
    "chars": 229,
    "preview": "# API Reference\n\n<meta http-equiv=\"Refresh\" content=\"0; url=./lamindb.html\" />\n\n```{toctree}\n:maxdepth: 1\n:caption: CLI "
  },
  {
    "path": "docs/arrays.md",
    "chars": 4634,
    "preview": "---\nexecute_via: python\n---\n\n# Stream datasets from storage\n\nThis guide walks through streaming datasets from disk or cl"
  },
  {
    "path": "docs/bionty.md",
    "chars": 53,
    "preview": "# `bionty`\n\n```{eval-rst}\n.. automodule:: bionty\n```\n"
  },
  {
    "path": "docs/changelog.md",
    "chars": 43,
    "preview": "# Changelog\n\nActual content in lamin-docs.\n"
  },
  {
    "path": "docs/curate.md",
    "chars": 15017,
    "preview": "---\nexecute_via: python\n---\n\n# Validate & standardize datasets\n\nData curation with LaminDB ensures your datasets are **v"
  },
  {
    "path": "docs/faq/acid.md",
    "chars": 2666,
    "preview": "---\nexecute_via: python\n---\n\n# Will data & metadata stay in sync?\n\nHere, we walk through different errors that can occur"
  },
  {
    "path": "docs/faq/curate-any.md",
    "chars": 3670,
    "preview": "---\nexecute_via: python\n---\n\n# How do I validate & annotate arbitrary data structures?\n\nThis guide walks through the low"
  },
  {
    "path": "docs/faq/idempotency.md",
    "chars": 3311,
    "preview": "---\nexecute_via: python\n---\n\n# Will data get duplicated upon re-running code?\n\nLaminDB's operations are idempotent in th"
  },
  {
    "path": "docs/faq/import-modules.md",
    "chars": 534,
    "preview": "---\nexecute_via: python\n---\n\n# What happens if I import a schema module without lamindb?\n\n```python\n# !pip install 'lami"
  },
  {
    "path": "docs/faq/keep-artifacts-local.md",
    "chars": 4865,
    "preview": "---\nexecute_via: python\n---\n\n# Keep artifacts local in a cloud instance\n\nIf you want to default to keeping artifacts loc"
  },
  {
    "path": "docs/faq/pydantic-pandera.md",
    "chars": 15366,
    "preview": "---\nexecute_via: python\n---\n\n# Pydantic & Pandera vs. LaminDB\n\nThis doc explains conceptual differences between data val"
  },
  {
    "path": "docs/faq/reference-field.md",
    "chars": 828,
    "preview": "---\nexecute_via: python\n---\n\n# Where to store external links and IDs?\n\nWhen registering data in LaminDB, you might want "
  },
  {
    "path": "docs/faq/search.md",
    "chars": 1635,
    "preview": "---\nexecute_via: python\n---\n\n# How does search work?\n\n```python\nfrom laminci.db import setup_local_test_postgres\n\npgurl "
  },
  {
    "path": "docs/faq/symbol-mapping.md",
    "chars": 3629,
    "preview": "---\nexecute_via: python\n---\n\n# Why should I not index datasets with gene symbols?\n\nGene symbols are widely used for read"
  },
  {
    "path": "docs/faq/test_notebooks.py",
    "chars": 258,
    "preview": "from pathlib import Path\n\nimport nbproject_test as test\n\nimport lamindb as ln\n\n\ndef test_notebooks():\n    nbdir = Path(_"
  },
  {
    "path": "docs/faq/track-run-inputs.md",
    "chars": 2108,
    "preview": "---\nexecute_via: python\n---\n\n# Can I disable tracking run inputs?\n\nYes, if you switch {attr}`~lamindb.core.Settings.trac"
  },
  {
    "path": "docs/faq/trash-archive.md",
    "chars": 1386,
    "preview": "# How do I trash or archive objects?\n\nAny object in LaminDB has the following 3 levels of visibility through 3 default b"
  },
  {
    "path": "docs/faq/validate-fields.md",
    "chars": 568,
    "preview": "---\nexecute_via: python\n---\n\n# Django field validation\n\n[Django field validation](https://docs.djangoproject.com/en/5.1/"
  },
  {
    "path": "docs/faq.md",
    "chars": 252,
    "preview": "# FAQ\n\n```{toctree}\n:maxdepth: 1\n\nfaq/pydantic-pandera\nfaq/idempotency\nfaq/acid\nfaq/track-run-inputs\nfaq/curate-any\nfaq/"
  },
  {
    "path": "docs/guide.md",
    "chars": 298,
    "preview": "# Guide\n\n```{toctree}\n:hidden:\n:caption: \"Overview\"\n\nREADME\n```\n\n```{toctree}\n:hidden:\n:caption: \"How to\"\n\nquery-search\n"
  },
  {
    "path": "docs/index.md",
    "chars": 180,
    "preview": "```{include} ../README.md\n:start-line: 0\n:end-line: 5\n```\n\n<meta http-equiv=\"Refresh\" content=\"0; url=./guide.html\" />\n\n"
  },
  {
    "path": "docs/lightning.md",
    "chars": 12846,
    "preview": "# Lightning\n\nThis guide offers more context on the {class}`lamindb.integrations.lightning.Checkpoint` callback. For end-"
  },
  {
    "path": "docs/manage-changes.md",
    "chars": 230,
    "preview": "# Manage changes\n\nManaging changes in LaminDB is largely analogous to managing code changes via branching in git and Pul"
  },
  {
    "path": "docs/manage-ontologies.md",
    "chars": 9235,
    "preview": "---\nexecute_via: python\n---\n\n# Manage biological ontologies\n\nThis guide shows how to manage ontologies for basic biologi"
  },
  {
    "path": "docs/organize.md",
    "chars": 9434,
    "preview": "# Organize datasets\n\n```{toctree}\n:maxdepth: 1\n:hidden:\n\ncurate\n```\n\nThis guide walks through organizing datasets using "
  },
  {
    "path": "docs/pertdb.md",
    "chars": 53,
    "preview": "# `pertdb`\n\n```{eval-rst}\n.. automodule:: pertdb\n```\n"
  },
  {
    "path": "docs/query-search.md",
    "chars": 75,
    "preview": "# Query, search & stream\n\n```{toctree}\n:maxdepth: 1\n\nregistries\narrays\n```\n"
  },
  {
    "path": "docs/registries.md",
    "chars": 7542,
    "preview": "---\nexecute_via: python\n---\n\n# Query & search registries\n\nThis guide walks through different ways of querying & searchin"
  },
  {
    "path": "docs/scripts/curate_anndata_flexible.py",
    "chars": 322,
    "preview": "import lamindb as ln\n\nln.examples.datasets.mini_immuno.define_features_labels()\nadata = ln.examples.datasets.mini_immuno"
  },
  {
    "path": "docs/scripts/curate_anndata_uns.py",
    "chars": 325,
    "preview": "import lamindb as ln\n\nln.examples.datasets.mini_immuno.define_features_labels()\nadata = ln.examples.datasets.mini_immuno"
  },
  {
    "path": "docs/scripts/curate_dataframe_attrs.py",
    "chars": 486,
    "preview": "import lamindb as ln\n\nfrom .define_schema_df_metadata import study_metadata_schema\n\ndf = ln.examples.datasets.mini_immun"
  },
  {
    "path": "docs/scripts/curate_dataframe_external_features.py",
    "chars": 799,
    "preview": "import lamindb as ln\nfrom datetime import date\n\ndf = ln.examples.datasets.mini_immuno.get_dataset1(otype=\"DataFrame\")\n\nt"
  },
  {
    "path": "docs/scripts/curate_dataframe_flexible.py",
    "chars": 283,
    "preview": "import lamindb as ln\n\nln.examples.datasets.mini_immuno.define_features_labels()\ndf = ln.examples.datasets.mini_immuno.ge"
  },
  {
    "path": "docs/scripts/curate_dataframe_minimal_errors.py",
    "chars": 418,
    "preview": "import lamindb as ln\n\nschema = ln.examples.datasets.mini_immuno.define_mini_immuno_schema_flexible()\ndf = ln.examples.da"
  },
  {
    "path": "docs/scripts/curate_dataframe_union_features.py",
    "chars": 398,
    "preview": "import lamindb as ln\nimport pandas as pd\n\nunion_feature = ln.Feature(\n    name=\"mixed_feature\",\n    dtype=\"cat[bionty.Ti"
  },
  {
    "path": "docs/scripts/curate_mudata.py",
    "chars": 2287,
    "preview": "import lamindb as ln\nimport bionty as bt\n\nfrom docs.scripts.define_schema_df_metadata import study_metadata_schema\n\n# de"
  },
  {
    "path": "docs/scripts/curate_soma_experiment.py",
    "chars": 1210,
    "preview": "import lamindb as ln\nimport bionty as bt\nimport tiledbsoma as soma\nimport tiledbsoma.io\n\nadata = ln.examples.datasets.mi"
  },
  {
    "path": "docs/scripts/curate_spatialdata.py",
    "chars": 548,
    "preview": "import lamindb as ln\n\nspatialdata = ln.examples.datasets.spatialdata_blobs()\nsdata_schema = ln.Schema.get(name=\"spatiald"
  },
  {
    "path": "docs/scripts/define_schema_anndata_uns.py",
    "chars": 217,
    "preview": "import lamindb as ln\n\nfrom define_schema_df_metadata import study_metadata_schema\n\nanndata_uns_schema = ln.Schema(\n    o"
  },
  {
    "path": "docs/scripts/define_schema_df_metadata.py",
    "chars": 239,
    "preview": "import lamindb as ln\n\nstudy_metadata_schema = ln.Schema(\n    name=\"Study metadata schema\",\n    features=[\n        ln.Fea"
  },
  {
    "path": "docs/scripts/define_schema_spatialdata.py",
    "chars": 1438,
    "preview": "import lamindb as ln\nimport bionty as bt\n\n# a very comprehensive schema for different slots of a SpatialData object\n\n# d"
  },
  {
    "path": "docs/scripts/my_workflow.py",
    "chars": 301,
    "preview": "import lamindb as ln\n\n\n@ln.flow()\ndef ingest_dataset(key: str) -> ln.Artifact:\n    df = ln.examples.datasets.mini_immuno"
  },
  {
    "path": "docs/scripts/my_workflow_with_click.py",
    "chars": 270,
    "preview": "import click\nimport lamindb as ln\n\n\n@click.command()\n@click.option(\"--key\", required=True)\n@ln.flow()\ndef main(key: str)"
  },
  {
    "path": "docs/scripts/my_workflow_with_step.py",
    "chars": 742,
    "preview": "import lamindb as ln\n\n\n@ln.step()\ndef subset_dataframe(\n    artifact: ln.Artifact,\n    subset_rows: int = 2,\n    subset_"
  },
  {
    "path": "docs/scripts/run_script_with_step.py",
    "chars": 945,
    "preview": "import argparse\nimport lamindb as ln\n\n\n@ln.step()\ndef subset_dataframe(\n    artifact: ln.Artifact,\n    subset_rows: int "
  },
  {
    "path": "docs/scripts/run_track_and_finish.py",
    "chars": 213,
    "preview": "import lamindb as ln\n\nln.track()  # initiate a tracked notebook/script run\n\n# your code automatically tracks inputs & ou"
  },
  {
    "path": "docs/scripts/run_track_with_features_and_params.py",
    "chars": 410,
    "preview": "import argparse\nimport lamindb as ln\n\n\nif __name__ == \"__main__\":\n    p = argparse.ArgumentParser()\n    p.add_argument(\""
  },
  {
    "path": "docs/scripts/run_track_with_params.py",
    "chars": 570,
    "preview": "import argparse\nimport lamindb as ln\n\nif __name__ == \"__main__\":\n    p = argparse.ArgumentParser()\n    p.add_argument(\"-"
  },
  {
    "path": "docs/scripts/synced_with_git.py",
    "chars": 110,
    "preview": "import lamindb as ln\n\nln.settings.sync_git_repo = \"https://github.com/...\"\nln.track()\n# your code\nln.finish()\n"
  },
  {
    "path": "docs/storage/add-replace-cache.ipynb",
    "chars": 18914,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"id\": \"0\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Add, replace, cache"
  },
  {
    "path": "docs/storage/anndata-accessor.ipynb",
    "chars": 6555,
    "preview": "{\n \"cells\": [\n  {\n   \"attachments\": {},\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Test `AnnDa"
  },
  {
    "path": "docs/storage/prepare-sync-local-to-cloud.ipynb",
    "chars": 2197,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Prepare sync artifacts from a loc"
  },
  {
    "path": "docs/storage/sync-local-to-cloud.ipynb",
    "chars": 2582,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Sync artifacts from a local insta"
  },
  {
    "path": "docs/storage/test-files/iris.data",
    "chars": 182,
    "preview": "5.1,3.5,1.4,0.2,Iris-setosa\n4.9,3.0,1.4,0.2,Iris-setosa\n7.0,3.2,4.7,1.4,Iris-versicolor\n6.4,3.2,4.5,1.5,Iris-versicolor\n"
  },
  {
    "path": "docs/storage/test_notebooks.py",
    "chars": 214,
    "preview": "from pathlib import Path\n\nimport nbproject_test as test\n\nimport lamindb as ln\n\n\ndef test_notebooks():\n    nbdir = Path(_"
  },
  {
    "path": "docs/storage/upload.ipynb",
    "chars": 7492,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"id\": \"0\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Track artifacts, in"
  },
  {
    "path": "docs/storage/vitessce.ipynb",
    "chars": 4532,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# Vitessce integration\"\n   ]\n  },\n "
  },
  {
    "path": "docs/storage.md",
    "chars": 189,
    "preview": "# Storage\n\n```{toctree}\n:maxdepth: 1\n\nstorage/upload\nstorage/add-replace-cache\nstorage/anndata-accessor\nstorage/prepare-"
  },
  {
    "path": "docs/sync.md",
    "chars": 2557,
    "preview": "---\nexecute_via: python\n---\n\n# Sync data across databases\n\nThis guide shows how to sync objects from a source database t"
  },
  {
    "path": "docs/test_notebooks.py",
    "chars": 711,
    "preview": "import sys\nfrom pathlib import Path\n\nimport nbproject_test as test\n\nsys.path[:0] = [str(Path(__file__).parent.parent)]\n\n"
  },
  {
    "path": "docs/track.md",
    "chars": 14325,
    "preview": "---\nexecute_via: python\n---\n\n# Track notebooks, scripts & workflows\n\nThis guide walks from tracking data lineage in a no"
  },
  {
    "path": "lamindb/__init__.py",
    "chars": 4417,
    "preview": "\"\"\"A data framework for biology.\n\nInstallation::\n\n   pip install lamindb\n\nIf you just want to *read* data from a LaminDB"
  },
  {
    "path": "lamindb/_finish.py",
    "chars": 21121,
    "preview": "from __future__ import annotations\n\nimport builtins\nimport re\nfrom datetime import datetime, timezone\nfrom time import s"
  },
  {
    "path": "lamindb/_secret_redaction.py",
    "chars": 3829,
    "preview": "from __future__ import annotations\n\nimport re\n\nREDACTED_SECRET_VALUE = \"***REDACTED***\"  # noqa: S105\nSENSITIVE_PARAM_KE"
  },
  {
    "path": "lamindb/_view.py",
    "chars": 4900,
    "preview": "from __future__ import annotations\n\nimport builtins\nimport importlib\nimport inspect\nfrom typing import TYPE_CHECKING\n\nfr"
  },
  {
    "path": "lamindb/base/__init__.py",
    "chars": 313,
    "preview": "\"\"\"Base library.\n\nIs available also when no instance is setup.\n\nModules\n-------\n\n.. autosummary::\n   :toctree: .\n\n   uid"
  },
  {
    "path": "lamindb/base/dtypes.py",
    "chars": 4298,
    "preview": "\"\"\"Dtype utils.\n\n.. autofunction:: check_dtype\n\n\"\"\"\n\nfrom datetime import datetime\nfrom typing import Any, Callable, Ite"
  },
  {
    "path": "lamindb/base/fields.py",
    "chars": 8367,
    "preview": "\"\"\"Fields.\n\nDjango fields with modified default arguments.\n\n.. autoclass:: CharField\n.. autoclass:: TextField\n.. autocla"
  },
  {
    "path": "lamindb/base/ids.py",
    "chars": 34,
    "preview": "from .uids import *  # noqa: F403\n"
  },
  {
    "path": "lamindb/base/types.py",
    "chars": 5995,
    "preview": "\"\"\"Base types.\n\nCentral object types\n--------------------\n\n.. autoclass:: ArtifactKind\n.. autoclass:: TransformKind\n.. a"
  },
  {
    "path": "lamindb/base/uids.py",
    "chars": 2183,
    "preview": "\"\"\"Universal IDs.\n\nBase generators\n===============\n\n.. autofunction:: base26\n.. autofunction:: base62\n.. autofunction:: "
  },
  {
    "path": "lamindb/base/users.py",
    "chars": 2116,
    "preview": "user_id_cache = {}\n\n\ndef _user_has_write_access() -> bool:\n    from django.db import connection\n\n    with connection.cur"
  },
  {
    "path": "lamindb/base/utils.py",
    "chars": 1480,
    "preview": "\"\"\"Utilities.\n\n.. autodecorator:: doc_args\n.. autodecorator:: deprecated\n.. autodecorator:: class_and_instance_method\n.."
  },
  {
    "path": "lamindb/core/__init__.py",
    "chars": 1392,
    "preview": "\"\"\"Core library.\n\nSettings & context:\n\n.. autosummary::\n   :toctree: .\n\n   Settings\n   subsettings\n   Context\n\nArtifact "
  },
  {
    "path": "lamindb/core/_compat.py",
    "chars": 2017,
    "preview": "import importlib.util\nfrom typing import Any, Callable, TypeVar\n\nT = TypeVar(\"T\")\n\n\ndef is_package_installed(package_nam"
  },
  {
    "path": "lamindb/core/_context.py",
    "chars": 54364,
    "preview": "from __future__ import annotations\n\nimport builtins\nimport hashlib\nimport os\nimport signal\nimport sys\nimport threading\ni"
  },
  {
    "path": "lamindb/core/_functions.py",
    "chars": 7860,
    "preview": "import functools\nimport inspect\nfrom contextvars import ContextVar\nfrom datetime import datetime, timezone\nfrom pathlib "
  },
  {
    "path": "lamindb/core/_mapped_collection.py",
    "chars": 28485,
    "preview": "from __future__ import annotations\n\nfrom collections import Counter\nfrom functools import reduce\nfrom typing import TYPE"
  },
  {
    "path": "lamindb/core/_settings.py",
    "chars": 10509,
    "preview": "from __future__ import annotations\n\nimport os\nimport sys\nfrom typing import TYPE_CHECKING\n\nimport lamindb_setup as ln_se"
  },
  {
    "path": "lamindb/core/_sync_git.py",
    "chars": 9650,
    "preview": "from __future__ import annotations\n\nimport subprocess\nfrom pathlib import Path\n\nfrom lamin_utils import logger\nfrom lami"
  },
  {
    "path": "lamindb/core/_track_environment.py",
    "chars": 974,
    "preview": "from __future__ import annotations\n\nimport subprocess\nimport sys\nfrom typing import TYPE_CHECKING\n\nimport lamindb_setup "
  },
  {
    "path": "lamindb/core/exceptions.py",
    "chars": 53,
    "preview": "from ..errors import *  # noqa: F403 backward compat\n"
  },
  {
    "path": "lamindb/core/loaders.py",
    "chars": 6744,
    "preview": "\"\"\"Loaders in :class:`lamindb.Artifact.load`.\n\n.. autodata:: SUPPORTED_SUFFIXES\n.. autofunction:: load_fcs\n.. autofuncti"
  },
  {
    "path": "lamindb/core/storage/__init__.py",
    "chars": 1913,
    "preview": "\"\"\"Storage API.\n\nValid suffixes.\n\n.. autodata:: VALID_SUFFIXES\n\nArray accessors.\n\n.. autoclass:: AnnDataAccessor\n.. auto"
  },
  {
    "path": "lamindb/core/storage/_anndata_accessor.py",
    "chars": 29854,
    "preview": "from __future__ import annotations\n\nimport inspect\nfrom functools import cached_property\nfrom importlib.metadata import "
  },
  {
    "path": "lamindb/core/storage/_backed_access.py",
    "chars": 8409,
    "preview": "from __future__ import annotations\n\nfrom dataclasses import dataclass\nfrom typing import TYPE_CHECKING, Any, Callable, L"
  },
  {
    "path": "lamindb/core/storage/_polars_lazy_df.py",
    "chars": 3916,
    "preview": "from __future__ import annotations\n\nfrom contextlib import contextmanager\nfrom typing import TYPE_CHECKING\n\nfrom lamindb"
  },
  {
    "path": "lamindb/core/storage/_pyarrow_dataset.py",
    "chars": 1398,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING\n\nimport pyarrow.dataset\nfrom lamindb_setup.core.upa"
  },
  {
    "path": "lamindb/core/storage/_spatialdata_accessor.py",
    "chars": 1718,
    "preview": "from __future__ import annotations\n\nfrom functools import cached_property\nfrom typing import TYPE_CHECKING\n\nfrom ._annda"
  },
  {
    "path": "lamindb/core/storage/_tiledbsoma.py",
    "chars": 14553,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Literal\nfrom urllib.parse import urlparse\n\nimport "
  },
  {
    "path": "lamindb/core/storage/_valid_suffixes.py",
    "chars": 501,
    "preview": "from __future__ import annotations\n\nfrom lamindb_setup.core.upath import VALID_COMPOSITE_SUFFIXES, VALID_SIMPLE_SUFFIXES"
  },
  {
    "path": "lamindb/core/storage/_zarr.py",
    "chars": 4459,
    "preview": "from __future__ import annotations\n\nfrom importlib.metadata import version as get_version\nfrom typing import TYPE_CHECKI"
  },
  {
    "path": "lamindb/core/storage/objects.py",
    "chars": 4212,
    "preview": "from __future__ import annotations\n\nfrom pathlib import Path\nfrom typing import TYPE_CHECKING, Any, TypeAlias\n\nfrom lami"
  },
  {
    "path": "lamindb/core/storage/paths.py",
    "chars": 7340,
    "preview": "from __future__ import annotations\n\nimport shutil\nfrom typing import TYPE_CHECKING\n\nimport fsspec\nfrom lamindb_setup.cor"
  },
  {
    "path": "lamindb/core/storage/types.py",
    "chars": 424,
    "preview": "\"\"\"Storage-related type definitions.\"\"\"\n\nfrom __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Any\n\nif T"
  },
  {
    "path": "lamindb/core/subsettings/__init__.py",
    "chars": 192,
    "preview": "\"\"\"Sub settings.\n\n.. autoclass:: CreationSettings\n.. autoclass:: AnnotationSettings\n\n\"\"\"\n\nfrom ._annotation_settings imp"
  },
  {
    "path": "lamindb/core/subsettings/_annotation_settings.py",
    "chars": 370,
    "preview": "class AnnotationSettings:\n    n_max_records: int = 1000\n    \"\"\"Maximal number of records to annotate with during automat"
  },
  {
    "path": "lamindb/core/subsettings/_creation_settings.py",
    "chars": 906,
    "preview": "class CreationSettings:\n    search_names: bool = True\n    \"\"\"Switch off to speed up creating records (default `True`).\n\n"
  },
  {
    "path": "lamindb/curators/__init__.py",
    "chars": 1040,
    "preview": "\"\"\"Curators.\n\nHigh-level curators\n-------------------\n\n.. autoclass:: DataFrameCurator\n.. autoclass:: AnnDataCurator\n.. "
  },
  {
    "path": "lamindb/curators/core.py",
    "chars": 86644,
    "preview": "\"\"\"Curator utilities.\n\n.. autoclass:: Curator\n.. autoclass:: SlotsCurator\n.. autoclass:: ComponentCurator\n.. autoclass::"
  },
  {
    "path": "lamindb/errors.py",
    "chars": 3446,
    "preview": "\"\"\"Errors.\n\nDjango.\n\n.. autoexception:: ObjectDoesNotExist\n.. autoexception:: MultipleObjectsReturned\n\nLaminDB.\n\n.. auto"
  },
  {
    "path": "lamindb/examples/__init__.py",
    "chars": 213,
    "preview": "\"\"\"Examples.\n\n.. autosummary::\n   :toctree: .\n\n   schemas\n   datasets\n   cellxgene\n   croissant\n   mlflow\n   wandb\n\n\"\"\"\n"
  },
  {
    "path": "lamindb/examples/cellxgene/__init__.py",
    "chars": 201,
    "preview": "\"\"\"CELLxGENE utilities.\n\n.. autofunction:: save_cellxgene_defaults\n.. autofunction:: create_cellxgene_schema\n\n\"\"\"\n\nfrom "
  },
  {
    "path": "lamindb/examples/cellxgene/_cellxgene.py",
    "chars": 11086,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Collection, Literal, NamedTuple\n\nif TYPE_CHECKING:"
  },
  {
    "path": "lamindb/examples/croissant/__init__.py",
    "chars": 2292,
    "preview": "\"\"\"Examples for MLCommons Croissant files, which are used to store metadata about datasets.\n\n.. autofunction:: mini_immu"
  },
  {
    "path": "lamindb/examples/croissant/mini_immuno.anndata.zarr_metadata.json",
    "chars": 2921,
    "preview": "{\n  \"@context\": {\n    \"@vocab\": \"https://schema.org/\",\n    \"cr\": \"https://mlcommons.org/croissant/\",\n    \"ml\": \"http://m"
  },
  {
    "path": "lamindb/examples/datasets/__init__.py",
    "chars": 5966,
    "preview": "\"\"\"Example datasets.\n\nThe mini immuno dataset\n-----------------------\n\n.. autosummary::\n   :toctree: .\n\n   mini_immuno\n\n"
  },
  {
    "path": "lamindb/examples/datasets/_core.py",
    "chars": 21666,
    "preview": "from __future__ import annotations\n\nfrom pathlib import Path\nfrom typing import TYPE_CHECKING, Any\nfrom urllib.request i"
  },
  {
    "path": "lamindb/examples/datasets/_fake.py",
    "chars": 953,
    "preview": "from __future__ import annotations\n\n\ndef fake_bio_notebook_titles(n=100) -> list[str]:\n    \"\"\"A fake collection of study"
  },
  {
    "path": "lamindb/examples/datasets/_small.py",
    "chars": 4852,
    "preview": "from __future__ import annotations\n\nfrom typing import Any, Literal\n\nimport anndata as ad\nimport numpy as np\nimport pand"
  },
  {
    "path": "lamindb/examples/datasets/define_mini_immuno_features_labels.py",
    "chars": 878,
    "preview": "import bionty as bt\n\nimport lamindb as ln\n\n# define valid labels\nperturbation_type = ln.Record(name=\"Perturbation\", is_t"
  },
  {
    "path": "lamindb/examples/datasets/define_mini_immuno_schema_flexible.py",
    "chars": 459,
    "preview": "import lamindb as ln\n\nschema = ln.Schema(\n    name=\"Mini immuno schema\",\n    features=[\n        ln.Feature.get(name=\"per"
  },
  {
    "path": "lamindb/examples/datasets/mini_immuno.py",
    "chars": 6004,
    "preview": "\"\"\"Two \"mini immuno\" datasets.\n\nDatasets\n--------\n\n.. autofunction:: get_dataset1\n.. autofunction:: get_dataset2\n\nSchema"
  },
  {
    "path": "lamindb/examples/datasets/save_mini_immuno_datasets.py",
    "chars": 1704,
    "preview": "from datetime import date\n\nimport bionty as bt\n\nimport lamindb as ln\n\n## define valid labels\nln.Record.from_values([\"DMS"
  },
  {
    "path": "lamindb/examples/fixtures/__init__.py",
    "chars": 0,
    "preview": ""
  },
  {
    "path": "lamindb/examples/fixtures/sheets.py",
    "chars": 12195,
    "preview": "import bionty as bt\nimport pandas as pd\nimport pytest\n\nimport lamindb as ln\n\n\n@pytest.fixture(scope=\"module\")\ndef popula"
  },
  {
    "path": "lamindb/examples/mlflow/__init__.py",
    "chars": 1314,
    "preview": "\"\"\"Examples and utilities for Mlflow.\n\n.. autofunction:: save_mlflow_features\n\"\"\"\n\nimport lamindb as ln\n\n\ndef save_mlflo"
  },
  {
    "path": "lamindb/examples/schemas/__init__.py",
    "chars": 238,
    "preview": "\"\"\"Example schemas.\n\n.. autofunction:: valid_features\n.. autofunction:: anndata_ensembl_gene_ids_and_valid_features_in_o"
  },
  {
    "path": "lamindb/examples/schemas/_anndata.py",
    "chars": 1021,
    "preview": "from __future__ import annotations\n\nimport importlib\nfrom typing import TYPE_CHECKING\n\nif TYPE_CHECKING:\n    from ... im"
  },
  {
    "path": "lamindb/examples/schemas/_simple.py",
    "chars": 722,
    "preview": "from __future__ import annotations\n\nimport importlib\nfrom typing import TYPE_CHECKING\n\nif TYPE_CHECKING:\n    from ... im"
  },
  {
    "path": "lamindb/examples/schemas/define_schema_anndata_ensembl_gene_ids_and_valid_features_in_obs.py",
    "chars": 358,
    "preview": "import bionty as bt\n\nimport lamindb as ln\n\nobs_schema = ln.examples.schemas.valid_features()\nvarT_schema = ln.Schema(\n  "
  },
  {
    "path": "lamindb/examples/schemas/define_valid_features.py",
    "chars": 89,
    "preview": "import lamindb as ln\n\nschema = ln.Schema(name=\"valid_features\", itype=ln.Feature).save()\n"
  },
  {
    "path": "lamindb/examples/wandb/__init__.py",
    "chars": 1322,
    "preview": "\"\"\"Examples and utilities for Weights & Biases.\n\n.. autofunction:: save_wandb_features\n\"\"\"\n\nimport lamindb as ln\n\n\ndef s"
  },
  {
    "path": "lamindb/integrations/__init__.py",
    "chars": 800,
    "preview": "\"\"\"Integrations.\n\nModules\n-------\n\n.. autosummary::\n   :toctree: .\n\n   lightning\n\nFunctions\n---------\n\n.. autofunction::"
  },
  {
    "path": "lamindb/integrations/_croissant.py",
    "chars": 5296,
    "preview": "from __future__ import annotations\n\nimport json\nfrom pathlib import Path\nfrom typing import TYPE_CHECKING, Any\n\nimport l"
  },
  {
    "path": "lamindb/integrations/_vitessce.py",
    "chars": 4032,
    "preview": "from __future__ import annotations\n\nimport json\nfrom datetime import datetime, timezone\nfrom typing import TYPE_CHECKING"
  },
  {
    "path": "lamindb/integrations/lightning.py",
    "chars": 54260,
    "preview": "\"\"\"PyTorch Lightning integration for LaminDB.\n\nThe public API has two layers:\n\n- :class:`Checkpoint` is the concrete Lam"
  },
  {
    "path": "lamindb/migrations/0177_squashed.py",
    "chars": 224328,
    "preview": "# Generated by Django 5.2 on 2026-01-10 23:06\n\nimport django.core.validators\nimport django.db.models.deletion\nimport dja"
  },
  {
    "path": "lamindb/migrations/0178_v2_2.py",
    "chars": 20145,
    "preview": "# Generated by Django 5.2 on 2026-02-15 11:25\n\nimport django.db.models.deletion\nfrom django.db import migrations, models"
  },
  {
    "path": "lamindb/migrations/0179_v2_2_part_2.py",
    "chars": 1840,
    "preview": "# Generated by Django 5.2 on 2026-02-15 14:12\n\nimport django.db.models.deletion\nfrom django.db import migrations, models"
  },
  {
    "path": "lamindb/migrations/0180_v2_2_part_3.py",
    "chars": 963,
    "preview": "# Generated by Django 5.2 on 2026-02-15 14:29\n\nimport django.db.models.deletion\nfrom django.db import migrations\n\nimport"
  },
  {
    "path": "lamindb/migrations/0181_v2_2_part_4.py",
    "chars": 749,
    "preview": "# Generated by Django 5.2 on 2026-02-15 15:43\n\nimport django.db.models.deletion\nfrom django.db import migrations, models"
  },
  {
    "path": "lamindb/migrations/0182_v2_2_part_5.py",
    "chars": 10910,
    "preview": "# Generated by Django 5.2 on 2026-02-17 16:33\n\nimport django.db.models.deletion\nfrom django.db import migrations, models"
  },
  {
    "path": "lamindb/migrations/0183_v2_2_part_6.py",
    "chars": 399,
    "preview": "# Generated by Django 5.2 on 2026-02-17 23:04\n\nfrom django.db import migrations\n\n\nclass Migration(migrations.Migration):"
  },
  {
    "path": "lamindb/migrations/0184_alter_transformrecord_feature.py",
    "chars": 661,
    "preview": "# Generated by Django 5.2 on 2026-03-07 12:16\n\nimport django.db.models.deletion\nfrom django.db import migrations\n\nimport"
  },
  {
    "path": "lamindb/migrations/0185_alter_runrecord_feature.py",
    "chars": 667,
    "preview": "# Generated by Django 5.2 on 2026-04-05 14:32\n\nimport django.db.models.deletion\nfrom django.db import migrations\n\nimport"
  },
  {
    "path": "lamindb/migrations/0186_v2_4.py",
    "chars": 8539,
    "preview": "# Generated by Django 5.2 on 2026-04-12 18:49\n\nimport django.db.models.deletion\nfrom django.db import migrations, models"
  },
  {
    "path": "lamindb/migrations/0187_squashed.py",
    "chars": 248028,
    "preview": "# Generated by Django 5.2 on 2026-04-16 06:44\n\nimport django.core.validators\nimport django.db.models.deletion\nimport dja"
  },
  {
    "path": "lamindb/migrations/0187_v2_4_part_2.py",
    "chars": 1151,
    "preview": "# Generated by Django 5.2 on 2026-04-16 06:38\n\nimport django.db.models.deletion\nfrom django.db import migrations\n\nimport"
  },
  {
    "path": "lamindb/migrations/README.md",
    "chars": 191,
    "preview": "# Attention\n\nRemember that lamindb schema changes that do not work on old databases (like adding columns or tables) cann"
  },
  {
    "path": "lamindb/migrations/__init__.py",
    "chars": 0,
    "preview": ""
  },
  {
    "path": "lamindb/models/__init__.py",
    "chars": 5369,
    "preview": "\"\"\"Auxiliary models & database library.\n\nRegistry basics\n---------------\n\n.. autoclass:: BaseSQLRecord\n.. autoclass:: SQ"
  },
  {
    "path": "lamindb/models/_describe.py",
    "chars": 25667,
    "preview": "from __future__ import annotations\n\nimport re\nfrom types import SimpleNamespace\nfrom typing import TYPE_CHECKING, Litera"
  },
  {
    "path": "lamindb/models/_django.py",
    "chars": 15199,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Any\n\nfrom django.contrib.postgres.aggregates impor"
  },
  {
    "path": "lamindb/models/_feature_manager.py",
    "chars": 95302,
    "preview": "# ruff: noqa: TC004\nfrom __future__ import annotations\n\nfrom collections import defaultdict\nfrom collections.abc import "
  },
  {
    "path": "lamindb/models/_from_values.py",
    "chars": 14762,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING\n\nfrom lamin_utils import colors, logger\n\nif TYPE_CH"
  },
  {
    "path": "lamindb/models/_is_versioned.py",
    "chars": 11451,
    "preview": "from __future__ import annotations\n\nfrom pathlib import PurePosixPath\nfrom typing import TYPE_CHECKING, Any, Iterable, L"
  },
  {
    "path": "lamindb/models/_label_manager.py",
    "chars": 11468,
    "preview": "from __future__ import annotations\n\nfrom collections import defaultdict\nfrom typing import TYPE_CHECKING\n\nfrom django.db"
  },
  {
    "path": "lamindb/models/_relations.py",
    "chars": 4004,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING\n\nimport lamindb_setup as ln_setup\nfrom django.db.mo"
  },
  {
    "path": "lamindb/models/_run_cleanup.py",
    "chars": 1624,
    "preview": "\"\"\"Background cleanup of report/environment artifacts after Run bulk delete.\n\nRunnable as: python -m lamindb.models._run"
  },
  {
    "path": "lamindb/models/artifact.py",
    "chars": 155481,
    "preview": "# ruff: noqa: TC004\nfrom __future__ import annotations\n\nimport shutil\nimport types\nimport warnings\nfrom collections impo"
  },
  {
    "path": "lamindb/models/artifact_set.py",
    "chars": 6015,
    "preview": "from __future__ import annotations\n\nfrom collections.abc import Iterable, Iterator\nfrom typing import TYPE_CHECKING, Lit"
  },
  {
    "path": "lamindb/models/block.py",
    "chars": 17610,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Any, Literal, get_args, overload\n\nfrom django.db i"
  },
  {
    "path": "lamindb/models/can_curate.py",
    "chars": 29648,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Iterable, Literal, Union\n\nimport numpy as np\nfrom "
  },
  {
    "path": "lamindb/models/collection.py",
    "chars": 26745,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Any, Literal, overload\n\nfrom django.db import mode"
  },
  {
    "path": "lamindb/models/feature.py",
    "chars": 64115,
    "preview": "from __future__ import annotations\n\nimport importlib\nimport warnings\nfrom dataclasses import dataclass\nfrom typing impor"
  },
  {
    "path": "lamindb/models/has_parents.py",
    "chars": 21853,
    "preview": "# ruff: noqa: TC004\nfrom __future__ import annotations\n\nimport builtins\nfrom typing import TYPE_CHECKING, Literal\n\nimpor"
  },
  {
    "path": "lamindb/models/project.py",
    "chars": 20221,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, overload\n\nfrom django.core.validators import Regex"
  },
  {
    "path": "lamindb/models/query_manager.py",
    "chars": 11216,
    "preview": "from __future__ import annotations\n\nimport re\nfrom functools import reduce\nfrom typing import TYPE_CHECKING, Literal, Na"
  },
  {
    "path": "lamindb/models/query_set.py",
    "chars": 67359,
    "preview": "from __future__ import annotations\n\nimport ast\nimport re\nimport warnings\nfrom collections import UserList, defaultdict\nf"
  },
  {
    "path": "lamindb/models/record.py",
    "chars": 37129,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Any, overload\n\nimport pgtrigger\nfrom django.conf i"
  },
  {
    "path": "lamindb/models/run.py",
    "chars": 22288,
    "preview": "from __future__ import annotations\n\nimport os\nimport subprocess\nimport sys\nfrom typing import TYPE_CHECKING, overload\n\nf"
  },
  {
    "path": "lamindb/models/save.py",
    "chars": 20915,
    "preview": "# ruff: noqa: TC004\nfrom __future__ import annotations\n\nimport os\nimport shutil\nimport traceback\nfrom collections import"
  },
  {
    "path": "lamindb/models/schema.py",
    "chars": 55222,
    "preview": "from __future__ import annotations\n\nimport warnings\nfrom typing import TYPE_CHECKING, Any, Type, overload\n\nimport numpy "
  },
  {
    "path": "lamindb/models/sqlrecord.py",
    "chars": 98341,
    "preview": "from __future__ import annotations\n\nimport builtins\nimport gzip\nimport inspect\nimport os\nimport re\nimport shutil\nimport "
  },
  {
    "path": "lamindb/models/storage.py",
    "chars": 16193,
    "preview": "from __future__ import annotations\n\nfrom typing import (\n    TYPE_CHECKING,\n    overload,\n)\nfrom uuid import UUID\n\nfrom "
  },
  {
    "path": "lamindb/models/transform.py",
    "chars": 23042,
    "preview": "from __future__ import annotations\n\nimport warnings\nfrom typing import TYPE_CHECKING, overload\n\nfrom django.db import mo"
  },
  {
    "path": "lamindb/models/ulabel.py",
    "chars": 12278,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, overload\n\nimport pgtrigger\nfrom django.conf import"
  },
  {
    "path": "lamindb/py.typed",
    "chars": 0,
    "preview": ""
  },
  {
    "path": "lamindb/setup/__init__.py",
    "chars": 507,
    "preview": "import lamindb_setup as _lamindb_setup\nfrom lamindb_setup import *  # noqa: F403\nfrom lamindb_setup import (\n    connect"
  },
  {
    "path": "lamindb/setup/_merge.py",
    "chars": 3723,
    "preview": "# Tested in lamin-cli (tests/core/test_create_switch_delete_list_settings.py::test_merge*).\nfrom __future__ import annot"
  },
  {
    "path": "lamindb/setup/_switch.py",
    "chars": 1263,
    "preview": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING\n\nfrom lamin_utils import logger\nfrom lamindb_setup "
  },
  {
    "path": "lamindb/setup/core/__init__.py",
    "chars": 167,
    "preview": "import lamindb_setup as _lamindb_setup\nfrom lamindb_setup.core import *  # noqa: F403\n\n__doc__ = _lamindb_setup.core.__d"
  },
  {
    "path": "lamindb/setup/errors/__init__.py",
    "chars": 171,
    "preview": "import lamindb_setup as _lamindb_setup\nfrom lamindb_setup.errors import *  # noqa: F403\n\n__doc__ = _lamindb_setup.errors"
  },
  {
    "path": "lamindb/setup/types/__init__.py",
    "chars": 169,
    "preview": "import lamindb_setup as _lamindb_setup\nfrom lamindb_setup.types import *  # noqa: F403\n\n__doc__ = _lamindb_setup.types._"
  },
  {
    "path": "lamindb_full.py",
    "chars": 397,
    "preview": "\"\"\"Full/meta-package module for the `lamindb` distribution.\"\"\"\n\nfrom __future__ import annotations\n\nimport re\nfrom pathl"
  },
  {
    "path": "noxfile.py",
    "chars": 16112,
    "preview": "import os\nimport shutil\nfrom pathlib import Path\n\nimport nox\nfrom laminci import convert_executable_md_files, upload_doc"
  },
  {
    "path": "pyproject.full.toml",
    "chars": 1237,
    "preview": "[build-system]\nrequires = [\"flit_core >=3.2,<4\"]\nbuild-backend = \"flit_core.buildapi\"\n\n[project]\nname = \"lamindb\"\nrequir"
  },
  {
    "path": "pyproject.toml",
    "chars": 7784,
    "preview": "[build-system]\nrequires = [\"flit_core >=3.2,<4\"]\nbuild-backend = \"flit_core.buildapi\"\n\n[project]\nname = \"lamindb-core\"\nr"
  },
  {
    "path": "scripts/migrate_test_instances.py",
    "chars": 911,
    "preview": "#!/usr/bin/env python3\n\"\"\"Migrate all LaminDB instances used in lamindb tests.\n\nFor each instance: connect, run migratio"
  },
  {
    "path": "tests/core/_dataset_fixtures.py",
    "chars": 1977,
    "preview": "from pathlib import Path\nfrom typing import Generator\n\nimport lamindb as ln\nimport numpy as np\nimport pandas as pd\nimpor"
  },
  {
    "path": "tests/core/conftest.py",
    "chars": 6635,
    "preview": "import os\nimport shutil\nfrom pathlib import Path\nfrom subprocess import DEVNULL, run\nfrom time import perf_counter\n\nimpo"
  },
  {
    "path": "tests/core/notebooks/basic-r-notebook.Rmd.cleaned.html",
    "chars": 2771,
    "preview": "<!doctype html>\n<html>\n  <meta charset=\"utf-8\" />\n  \n  \n\n  <!-- rnb-text-begin -->\n  <!-- rnb-text-end -->\n  <!-- rnb-ch"
  },
  {
    "path": "tests/core/notebooks/basic-r-notebook.Rmd.html",
    "chars": 2943,
    "preview": "<!doctype html>\n<html>\n  <meta charset=\"utf-8\" />\n  <title>My exemplary R analysis</title>\n  <h1 class=\"title toc-ignore"
  },
  {
    "path": "tests/core/notebooks/duplicate/with-title-initialized-consecutive-finish.ipynb",
    "chars": 927,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# My duplicated test notebook (cons"
  },
  {
    "path": "tests/core/notebooks/load_schema.ipynb",
    "chars": 1007,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"code\",\n   \"execution_count\": null,\n   \"id\": \"0\",\n   \"metadata\": {},\n   \"outputs\": [],"
  },
  {
    "path": "tests/core/notebooks/no-title.ipynb",
    "chars": 1336,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"id\": \"0\",\n   \"metadata\": {},\n   \"source\": [\n    \"A notebook without ti"
  },
  {
    "path": "tests/core/notebooks/with-title-initialized-consecutive-finish-not-last-cell.ipynb",
    "chars": 1382,
    "preview": "{\n \"cells\": [\n  {\n   \"cell_type\": \"markdown\",\n   \"metadata\": {},\n   \"source\": [\n    \"# My test notebook (consecutive) wi"
  }
]

// ... and 88 more files (download for full content)