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Add some missing parameter docstrings #245

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merged 2 commits into from
Nov 8, 2024
Merged

Add some missing parameter docstrings #245

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20a819e
docstr typos, style nits
ryan-williams Nov 5, 2024
ec287df
add missing arg docstrs
ryan-williams Nov 8, 2024
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11 changes: 11 additions & 0 deletions python-spec/src/somacore/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down Expand Up @@ -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.

Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.

Expand Down
6 changes: 3 additions & 3 deletions python-spec/src/somacore/query/axis.py
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Expand Up @@ -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'")

Expand Down
6 changes: 4 additions & 2 deletions python-spec/src/somacore/query/query.py
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Expand Up @@ -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
"""
Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -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)
Expand Down
29 changes: 28 additions & 1 deletion python-spec/src/somacore/spatial.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand All @@ -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.

Expand Down Expand Up @@ -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.
Expand All @@ -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.

Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand All @@ -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.

Expand Down Expand Up @@ -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.
Expand All @@ -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.

Expand Down Expand Up @@ -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.
Expand All @@ -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.
Expand Down Expand Up @@ -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
Expand Down
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