Add some missing parameter docstrings (#245)

* docstr typos, style nits

* add missing arg docstrs

Author: ryan-williams

python-spec/src/somacore/data.py

@@ -84,6 +84,11 @@ def create(
                 the minimum and maximum possible values for the column's
                 datatype.  This makes a dataframe growable.
 
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
+
+            context: Other implementation-specific configuration.
+
         Returns:
             The newly created dataframe, opened for writing.
 
@@ -326,6 +331,8 @@ def read(
                 a partitioned read, and which part of the data to include.
             result_order: the order to return results, specified as a
                 :class:`~options.ResultOrder` or its string value.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns: The data over the requested range as a tensor.
 
@@ -426,6 +433,8 @@ def read(
                 and which partition to include, if present.
             result_order: the order to return results, specified as a
                 :class:`~options.ResultOrder` or its string value.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns: The data that was requested in a :class:`SparseRead`,
             allowing access in any supported format.
@@ -479,6 +488,8 @@ def write(
 
                 Arrow table: a COO table, with columns named ``soma_dim_0``,
                     ..., ``soma_dim_N`` and ``soma_data``.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns: ``self``, to enable method chaining.
 

python-spec/src/somacore/query/axis.py

@@ -72,9 +72,9 @@ class AxisQuery:
 
         AxisQuery()  # all data
         AxisQuery(coords=())  # also all data
-        AxisQuery(coords=(slice(1,10),))  # 1D, slice
-        AxisQuery(coords=([0,1,2]))  # 1D, point indexing using array-like
-        AxisQuery(coords=(slice(None), numpy.array([0,88,1001])))  # 2D
+        AxisQuery(coords=(slice(1, 10),))  # 1D, slice
+        AxisQuery(coords=([0, 1, 2]))  # 1D, point indexing using array-like
+        AxisQuery(coords=(slice(None), numpy.array([0, 88, 1001])))  # 2D
         AxisQuery(value_filter="tissue == 'lung'")
         AxisQuery(coords=(slice(1,None),), value_filter="tissue == 'lung'")
 

python-spec/src/somacore/query/query.py

@@ -223,6 +223,8 @@ def X(
                 and which partition to include, if present.
             result_order: the order to return results, specified as a
                 :class:`~options.ResultOrder` or its string value.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Lifecycle: maturing
         """
@@ -539,7 +541,7 @@ def _read_axis_dataframe(
 
         # Do the actual query.
         arrow_table = axis_df.read(
-            axis_query.coords,
+            coords=axis_query.coords,
             value_filter=axis_query.value_filter,
             column_names=query_columns,
         ).concat()
@@ -679,7 +681,7 @@ class _AxisQueryResult:
     var: pd.DataFrame
     """Experiment.ms[...].var query slice, as a pandas DataFrame"""
     X: sparse.csr_matrix
-    """Experiment.ms[...].X[...] query slice, as an SciPy sparse.csr_matrix """
+    """Experiment.ms[...].X[...] query slice, as a SciPy sparse.csr_matrix """
     X_layers: Dict[str, sparse.csr_matrix] = attrs.field(factory=dict)
     """Any additional X layers requested, as SciPy sparse.csr_matrix(s)"""
     obsm: Dict[str, np.ndarray] = attrs.field(factory=dict)

python-spec/src/somacore/spatial.py

@@ -93,6 +93,9 @@ def create(
                 or if ``None`` in a given dimension, the corresponding index-column
                 domain will use the minimum and maximum possible values for the
                 column's datatype.  This makes a point cloud dataframe growable.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
+            context: Other implementation-specific configuration.
 
         Returns:
             The newly created geometry dataframe, opened for writing.
@@ -122,6 +125,8 @@ def read(
                 Defaults to ``()``, meaning no constraint -- all IDs.
             column_names: the named columns to read and return.
                 Defaults to ``None``, meaning no constraint -- all column names.
+            batch_size: The size of batches that should be returned from a read.
+                See :class:`options.BatchSize` for details.
             partitions: If present, specifies that this is part of
                 a partitioned read, and which part of the data to include.
             result_order: the order to return results, specified as a
@@ -130,6 +135,8 @@ def read(
                 The default of ``None`` represents no filter. Value filter
                 syntax is implementation-defined; see the documentation
                 for the particular SOMA implementation for details.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
         Returns:
             A :class:`ReadIter` of :class:`pa.Table`s.
 
@@ -177,6 +184,8 @@ def read_spatial_region(
                 The default of ``None`` represents no filter. Value filter
                 syntax is implementation-defined; see the documentation
                 for the particular SOMA implementation for details.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns:
             A :class:`SpatialRead` with :class:`ReadIter` of :class:`pa.Table`s data.
@@ -201,6 +210,8 @@ def write(
             values: An Arrow table containing all columns, including
                 the index columns. The schema for the values must match
                 the schema for the ``DataFrame``.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns: ``self``, to enable method chaining.
 
@@ -323,6 +334,9 @@ def create(
                 the corresponding index-column domain will use the minimum and maximum
                 possible values for the column's datatype.  This makes a dataframe
                 growable.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
+            context: Other implementation-specific configuration.
 
         Returns:
             The newly created geometry dataframe, opened for writing.
@@ -352,6 +366,8 @@ def read(
                 Defaults to ``()``, meaning no constraint -- all IDs.
             column_names: the named columns to read and return.
                 Defaults to ``None``, meaning no constraint -- all column names.
+            batch_size: The size of batches that should be returned from a read.
+                See :class:`options.BatchSize` for details.
             partitions: If present, specifies that this is part of
                 a partitioned read, and which part of the data to include.
             result_order: the order to return results, specified as a
@@ -360,6 +376,8 @@ def read(
                 The default of ``None`` represents no filter. Value filter
                 syntax is implementation-defined; see the documentation
                 for the particular SOMA implementation for details.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
         Returns:
             A :class:`ReadIter` of :class:`pa.Table`s.
 
@@ -407,6 +425,8 @@ def read_spatial_region(
                 The default of ``None`` represents no filter. Value filter
                 syntax is implementation-defined; see the documentation
                 for the particular SOMA implementation for details.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns:
             A :class:`SpatialRead` with :class:`ReadIter` of :class:`pa.Table`s data.
@@ -431,6 +451,8 @@ def write(
             values: An Arrow table containing all columns, including
                 the index columns. The schema for the values must match
                 the schema for the ``DataFrame``.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns: ``self``, to enable method chaining.
 
@@ -553,7 +575,7 @@ def create(
                 SOMADenseNDArray it must match have the shape provided by
                 ``level_shape`` and type specified in ``type. If set to ``None``, the
                 ``level_key`` will be used to construct a default child URI. For more
-                on URIs see :meth:`collection.Collection.add_new_collction`.
+                on URIs see :meth:`collection.Collection.add_new_collection`.
             coordinate_space: Either the coordinate space or the axis names for the
                 coordinate space the ``level=0`` image is defined on. This does not
                 include the channel dimension, only spatial dimensions.
@@ -562,6 +584,9 @@ def create(
                 axis is provided, this defaults to the channel axis followed by the
                 coordinate space axes in reverse order (e.g.
                 ``("soma_channel", "y", "x")`` if ``coordinate_space=("x", "y")``).
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
+            context: Other implementation-specific configuration.
 
         Returns:
             The newly created collection, opened for writing.
@@ -662,6 +687,8 @@ def read_spatial_region(
                 :class:`~options.ResultOrder` or its string value. This is the result
                 order the data is read from disk. It may be permuted if
                 ``data_axis_order`` is not the default order.
+            platform_config: platform-specific configuration; keys are SOMA
+                implementation names.
 
         Returns:
             The data bounding the requested region as a :class:`SpatialRead` with