diff --git a/lamindb/_curate.py b/lamindb/_curate.py index d40012793..5787928f9 100644 --- a/lamindb/_curate.py +++ b/lamindb/_curate.py @@ -140,10 +140,10 @@ def save_artifact( """Save the dataset as artifact. Args: - description: `str | None = None` A description of the DataFrame object. - key: `str | None = None` A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. - revises: `Artifact | None = None` Previous version of the artifact. Triggers a revision. - run: `Run | None = None` The run that creates the artifact. + description: A description of the DataFrame object. + key: A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. + revises: Previous version of the artifact. Triggers a revision. + run: The run that creates the artifact. Returns: A saved artifact record. @@ -157,14 +157,14 @@ class DataFrameCurator(BaseCurator): See also :class:`~lamindb.Curator`. Args: - df: `pd.DataFrame` The DataFrame object to curate. - columns: `FieldAttr=Feature.name` The field attribute for the feature column. - categoricals: `dict[str, FieldAttr] | None = None` A dictionary mapping column names to registry_field. - using_key: `str | None = None` The reference instance containing registries to validate against. - verbosity: `str = "hint"` The verbosity level. - organism: `str | None = None` The organism name. - sources: `dict[str, Record] | None = None` A dictionary mapping column names to Source records. - exclude: `dict | None = None` A dictionary mapping column names to values to exclude. + df: The DataFrame object to curate. + columns: The field attribute for the feature column. + categoricals: A dictionary mapping column names to registry_field. + using_key: The reference instance containing registries to validate against. + verbosity: The verbosity level. + organism: The organism name. + sources: A dictionary mapping column names to Source records. + exclude: A dictionary mapping column names to values to exclude. Returns: A curator object. @@ -440,10 +440,10 @@ def save_artifact( """Save the validated DataFrame and metadata. Args: - description: `str | None = None` Description of the DataFrame object. - key: `str | None = None` A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. - revises: `Artifact | None = None` Previous version of the artifact. Triggers a revision. - run: `Run | None = None` The run that creates the artifact. + description: Description of the DataFrame object. + key: A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. + revises: Previous version of the artifact. Triggers a revision. + run: The run that creates the artifact. Returns: A saved artifact record. @@ -494,15 +494,15 @@ class AnnDataCurator(DataFrameCurator): See :doc:`docs:cellxgene-curate` for instructions on how to curate against a specific cellxgene schema version. Args: - data: `ad.AnnData | UPathStr` The AnnData object or an AnnData-like path. - var_index: `FieldAttr` The registry field for mapping the ``.var`` index. - categoricals: `dict[str, FieldAttr] | None = None` A dictionary mapping ``.obs.columns`` to a registry field. - obs_columns: `FieldAttr` The registry field for mapping the ``.obs.columns``. - using_key: `str | None = None` A reference LaminDB instance. - verbosity: `str = "hint"` The verbosity level. - organism: `str | None = None` The organism name. - sources: `dict[str, Record] | None = None` A dictionary mapping ``.obs.columns`` to Source records. - exclude: `dict | None = None` A dictionary mapping column names to values to exclude. + data: The AnnData object or an AnnData-like path. + var_index: The registry field for mapping the ``.var`` index. + categoricals: A dictionary mapping ``.obs.columns`` to a registry field. + obs_columns: The registry field for mapping the ``.obs.columns``. + using_key: A reference LaminDB instance. + verbosity: The verbosity level. + organism: The organism name. + sources: A dictionary mapping ``.obs.columns`` to Source records. + exclude: A dictionary mapping column names to values to exclude. Examples: >>> import bionty as bt @@ -709,10 +709,10 @@ def save_artifact( """Save the validated ``AnnData`` and metadata. Args: - description: `str | None = None` A description of the ``AnnData`` object. - key: `str | None = None` A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. - revises: `Artifact | None = None` Previous version of the artifact. Triggers a revision. - run: `Run | None = None` The run that creates the artifact. + description: A description of the ``AnnData`` object. + key: A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. + revises: Previous version of the artifact. Triggers a revision. + run: The run that creates the artifact. Returns: A saved artifact record. @@ -751,17 +751,17 @@ class MuDataCurator: the object should be recreated using :meth:`~lamindb.Curator.from_mudata`. Args: - mdata: `MuData` The MuData object to curate. - var_index: `dict[str, dict[str, FieldAttr]]` The registry field for mapping the ``.var`` index for each modality. + mdata: The MuData object to curate. + var_index: The registry field for mapping the ``.var`` index for each modality. For example: ``{"modality_1": bt.Gene.ensembl_gene_id, "modality_2": ln.CellMarker.name}`` - categoricals: `dict[str, FieldAttr] | None = None` A dictionary mapping ``.obs.columns`` to a registry field. + categoricals: A dictionary mapping ``.obs.columns`` to a registry field. Use modality keys to specify categoricals for MuData slots such as `"rna:cell_type": bt.CellType.name"`. - using_key: `str | None = None` A reference LaminDB instance. - verbosity: `str = "hint"` The verbosity level. - organism: `str | None = None` The organism name. - sources: `dict[str, Record] | None = None` A dictionary mapping ``.obs.columns`` to Source records. - exclude: `dict | None = None` A dictionary mapping column names to values to exclude. + using_key: A reference LaminDB instance. + verbosity: The verbosity level. + organism: The organism name. + sources: A dictionary mapping ``.obs.columns`` to Source records. + exclude: A dictionary mapping column names to values to exclude. Examples: >>> import bionty as bt @@ -1004,8 +1004,8 @@ def standardize(self, key: str, modality: str | None = None): """Replace synonyms with standardized values. Args: - key: `str` The key referencing the slot in the `MuData`. - modality: `str | None = None` The modality name. + key: The key referencing the slot in the `MuData`. + modality: The modality name. Inplace modification of the dataset. """ @@ -1026,10 +1026,10 @@ def save_artifact( """Save the validated ``MuData`` and metadata. Args: - description: `str | None = None` A description of the ``MuData`` object. - key: `str | None = None` A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. - revises: `Artifact | None = None` Previous version of the artifact. Triggers a revision. - run: `Run | None = None` The run that creates the artifact. + description: A description of the ``MuData`` object. + key: A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. + revises: Previous version of the artifact. Triggers a revision. + run: The run that creates the artifact. Returns: A saved artifact record. @@ -1437,10 +1437,10 @@ def save_artifact( description: A description of the artifact. organism: The organism name. adata: The AnnData object to save and get n_observations, must be provided if data is a path. - type: `Literal["dataset", "model"] | None = None` The artifact type. - key: `str | None = None` A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. - revises: `Artifact | None = None` Previous version of the artifact. Triggers a revision. - run: `Run | None = None` The run that creates the artifact. + type: The artifact type. + key: A path-like key to reference artifact in default storage, e.g., `"myfolder/myfile.fcs"`. Artifacts with the same key form a revision family. + revises: Previous version of the artifact. Triggers a revision. + run: The run that creates the artifact. Returns: The saved Artifact.