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Remove index_column as an option for the spatial dataframes #248

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Nov 18, 2024
Merged

Remove index_column as an option for the spatial dataframes #248

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32 changes: 12 additions & 20 deletions python-spec/src/somacore/spatial.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,6 @@ def create(
"x",
"y",
),
index_column_names: Optional[Sequence[str]] = None,
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
context: Optional[Any] = None,
Expand All @@ -69,10 +68,14 @@ def create(

The schema of the created point cloud will include a column named
``soma_joinid`` of type ``pyarrow.int64``, with negative values disallowed, and
at least one axis with numeric type. If a ``soma_joinid`` column is
present in the provided schema, it must be of the correct type. If the
``soma_joinid`` column is not provided, one will be added. The ``soma_joinid``
may be an index column. The axis columns must be index columns.
at least one axis with numeric type. If a ``soma_joinid`` column is present in
the provided schema, it must be of the correct type. If the ``soma_joinid``
column is not provided, one will be added.


The schema of the created point cloud must contain columns for the axes in the
``coordinate_space``. These columns will be index columns for the point cloud
dataframe.

Args:
uri: The URI where the dataframe will be created.
Expand All @@ -82,11 +85,6 @@ def create(
implementation, an error will be raised.
coordinate_space: Either the coordinate space or the axis names for the
coordinate space the point cloud is defined on.
index_column_names: A list of column names to use as user-defined index
columns (e.g., ``['x', 'y']``). Must include the axis names for all
axes in the coordinate space. May include the ``soma_joinid``.
Defaults to ``None`` which sets the index column names to be the
``soma_joinid`` followed by the axis names for the coordinate space.
domain: An optional sequence of tuples specifying the domain of each
index column. Each tuple should be a pair consisting of the minimum
and maximum values storable in the index column. If omitted entirely,
Expand Down Expand Up @@ -295,10 +293,6 @@ def create(
"x",
"y",
),
index_column_names: Sequence[str] = (
options.SOMA_JOINID,
options.SOMA_GEOMETRY,
),
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
context: Optional[Any] = None,
Expand All @@ -311,8 +305,10 @@ def create(
``pyarrow.large_binary``. If a ``soma_joinid`` column or ``soma_geometry``
are present in the provided schema, they must be of the correct type. If
either the ``soma_joinid`` column or ``soma_geometry`` column are not provided,
one will be added. The ``soma_joinid`` may be an index column. The
``soma_geometry`` column must be an index column.
one will be added.

The geometry dataframe will be indexed using a spatial index for the
``soma_geometry`` column.

Args:
uri: The URI where the dataframe will be created.
Expand All @@ -322,10 +318,6 @@ def create(
implementation, an error will be raised.
coordinate_space: Either the coordinate space or the axis names for the
coordinate space the point cloud is defined on.
index_column_names: A list of column names to use as user-defined
index columns (e.g., ``['cell_type', 'tissue_type']``).
All named columns must exist in the schema, and at least one
index column name is required.
domain: An optional sequence of tuples specifying the domain of each
index column. Two tuples must be provided for the ``soma_geometry``
column which store the width followed by the height. Each tuple should
Expand Down
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