From 03af4a591094ea9a9690e4acacc217e32c84fe2b Mon Sep 17 00:00:00 2001
From: Julia Dark <24235303+jp-dark@users.noreply.github.com>
Date: Mon, 18 Nov 2024 15:37:13 -0500
Subject: [PATCH] Remove ``index_column`` as an option for the spatial
 dataframes (#248)

We may add the option to specify additional index columns back to the
API in the future, but for the alpha release we would like to constain
the spatial dataframes to only be index by spatial indices.
---
 python-spec/src/somacore/spatial.py | 32 +++++++++++------------------
 1 file changed, 12 insertions(+), 20 deletions(-)

diff --git a/python-spec/src/somacore/spatial.py b/python-spec/src/somacore/spatial.py
index c196595..25b5a2e 100644
--- a/python-spec/src/somacore/spatial.py
+++ b/python-spec/src/somacore/spatial.py
@@ -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,
@@ -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.
@@ -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,
@@ -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,
@@ -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.
@@ -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