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🏷️ Remove duplicated typing in Curator #2232

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Nov 29, 2024
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🏷️ Remove duplicated typing in Curator #2232

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94 changes: 47 additions & 47 deletions lamindb/_curate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand All @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.
"""
Expand All @@ -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.
Expand Down Expand Up @@ -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.
Expand Down