diff --git a/apis/python/src/tiledbsoma/__init__.py b/apis/python/src/tiledbsoma/__init__.py
index 07180e1ea6..460d783a75 100644
--- a/apis/python/src/tiledbsoma/__init__.py
+++ b/apis/python/src/tiledbsoma/__init__.py
@@ -83,7 +83,6 @@
- :class:`NotImplementedError` will be raised when the requested function or method
is unsupported.
- :class:`SOMAError` is a base class for all SOMA-specific errors.
-- ``TileDBError`` will be raised for many TileDB-specific errors.
Most errors will raise an appropriate Python error, e.g., ::class:`TypeError` or
:class:`ValueError`.
diff --git a/apis/python/src/tiledbsoma/_common_nd_array.py b/apis/python/src/tiledbsoma/_common_nd_array.py
index 83853ab082..885cc8f136 100644
--- a/apis/python/src/tiledbsoma/_common_nd_array.py
+++ b/apis/python/src/tiledbsoma/_common_nd_array.py
@@ -88,7 +88,7 @@ def create(
def shape(self) -> Tuple[int, ...]:
"""Returns capacity of each dimension, always a list of length ``ndim``.
This will not necessarily match the bounds of occupied cells within the array.
- Rather, it is the bounds outside of which no data may be written.
+ Rather, it is the bounds outside of which no data may be read or written.
Lifecycle:
Maturing.
diff --git a/apis/python/src/tiledbsoma/_dataframe.py b/apis/python/src/tiledbsoma/_dataframe.py
index 094c853a54..a15b5292a1 100644
--- a/apis/python/src/tiledbsoma/_dataframe.py
+++ b/apis/python/src/tiledbsoma/_dataframe.py
@@ -428,7 +428,7 @@ def _maybe_soma_joinid_maxshape(self) -> Optional[int]:
def tiledbsoma_has_upgraded_domain(self) -> bool:
"""Returns true if the array has the upgraded resizeable domain feature
from TileDB-SOMA 1.15: the array was created with this support, or it has
- had ``.tiledbsoma_upgrade_domain`` applied to it.
+ had ``tiledbsoma_upgrade_domain`` applied to it.
Lifecycle:
Maturing.
diff --git a/apis/python/src/tiledbsoma/_indexer.py b/apis/python/src/tiledbsoma/_indexer.py
index bf289d6777..4f39b0b042 100644
--- a/apis/python/src/tiledbsoma/_indexer.py
+++ b/apis/python/src/tiledbsoma/_indexer.py
@@ -29,15 +29,15 @@
def tiledbsoma_build_index(
data: IndexerDataType, *, context: Optional["SOMATileDBContext"] = None
) -> IndexLike:
- """Initialize re-indexer for provided indices.
+ """Initialize re-indexer for provided indices (deprecated).
- Deprecated. Provides the same functionality as the``IntIndexer`` class.
+ Provides the same functionality as the``IntIndexer`` class.
Args:
data:
Integer keys used to build the index (hash) table.
context:
- ``SOMATileDBContext`` object containing concurrecy level.
+ ``SOMATileDBContext`` object containing concurrency level.
Lifecycle:
Deprecated.
@@ -62,7 +62,7 @@ def __init__(
data:
Integer keys used to build the index (hash) table.
context:
- ``SOMATileDBContext`` object containing concurrecy level.
+ ``SOMATileDBContext`` object containing concurrency level.
Lifecycle:
Maturing.
diff --git a/apis/python/src/tiledbsoma/_sparse_nd_array.py b/apis/python/src/tiledbsoma/_sparse_nd_array.py
index f48747f3ca..b3e9a157ec 100644
--- a/apis/python/src/tiledbsoma/_sparse_nd_array.py
+++ b/apis/python/src/tiledbsoma/_sparse_nd_array.py
@@ -528,7 +528,7 @@ def _dim_capacity_and_extent(
def used_shape(self) -> Tuple[Tuple[int, int], ...]:
"""
- Retrieve the range of indexes for a dimension that were explicitly written.
+ Retrieve the range of indexes for a dimension that were explicitly written (deprecated).
Compare this to ``shape`` which returns the available/writable capacity.
This method is deprecated as of TileDB-SOMA 1.13, and will be removed in TileDB-SOMA 1.15.
diff --git a/apis/python/src/tiledbsoma/io/ingest.py b/apis/python/src/tiledbsoma/io/ingest.py
index cfe2ec9c9c..465e7d058f 100644
--- a/apis/python/src/tiledbsoma/io/ingest.py
+++ b/apis/python/src/tiledbsoma/io/ingest.py
@@ -279,7 +279,7 @@ def from_h5ad(
``obs`` / ``var``.
NOTE: it is not necessary for this column to be the index-column
- name in the input AnnData objects ``obs``/``var``.
+ name in the input AnnData object's ``obs``/``var``.
X_layer_name: SOMA array name for the AnnData's ``X`` matrix.
@@ -759,7 +759,7 @@ def append_obs(
Writes new rows to an existing ``obs`` dataframe. (This is distinct from ``update_obs``
which mutates the entirety of the ``obs`` dataframe, e.g. to add/remove columns.)
- Example:
+ Example::
rd = tiledbsoma.io.register_anndatas(
exp_uri,
@@ -817,7 +817,7 @@ def append_var(
Writes new rows to an existing ``var`` dataframe. (This is distinct from ``update_var``
which mutates the entirety of the ``var`` dataframe, e.g. to add/remove columns.)
- Example:
+ Example::
rd = tiledbsoma.io.register_anndatas(
exp_uri,
@@ -886,7 +886,7 @@ def append_X(
with ``update_obs`` and ``update_var``, as an itemized alternative to doing
``from_anndata`` with a registration mapping supplied.
- Example:
+ Example::
rd = tiledbsoma.io.register_anndatas(
exp_uri,
@@ -1413,18 +1413,17 @@ def update_obs(
type for the column, the entire update will raise a ``ValueError`` exception.
Args:
- exp: The :class:`SOMAExperiment` whose ``obs`` is to be updated. Must
- be opened for write.
+ exp: The :class:`SOMAExperiment` whose ``obs`` is to be updated. Must be opened for write.
new_data: a Pandas dataframe with the desired contents.
context: Optional :class:`SOMATileDBContext` containing storage parameters, etc.
- platform_config: Platform-specific options used to update this array, provided
- in the form ``{"tiledb": {"create": {"dataframe_dim_zstd_level": 7}}}``
+ platform_config: Platform-specific options used to update this array, provided in the form
+ ``{"tiledb": {"create": {"dataframe_dim_zstd_level": 7}}}``
- default_index_name: What to call the ``new_data`` index column if it is
- nameless in Pandas, or has name ``"index"``.
+ default_index_name: What to call the ``new_data`` index column if it is nameless in Pandas,
+ or has name ``"index"``.
Returns:
None
@@ -1473,11 +1472,11 @@ def update_var(
context: Optional :class:`SOMATileDBContext` containing storage parameters, etc.
- platform_config: Platform-specific options used to update this array, provided
- in the form ``{"tiledb": {"create": {"dataframe_dim_zstd_level": 7}}}``
+ platform_config: Platform-specific options used to update this array, provided in the form
+ ``{"tiledb": {"create": {"dataframe_dim_zstd_level": 7}}}``
- default_index_name: What to call the ``new_data`` index column if it is
- nameless in Pandas, or has name ``"index"``.
+ default_index_name: What to call the ``new_data`` index column if it is nameless in Pandas,
+ or has name ``"index"``.
Returns:
None
@@ -1615,7 +1614,7 @@ def update_matrix(
intended shape of written contents of the array match those of the existing
data. The intended use-case is to replace updated numerical values.
- Example:
+ Example::
with tiledbsoma.Experiment.open(uri, "w") as exp:
tiledbsoma.io.update_matrix(
@@ -1633,7 +1632,7 @@ def update_matrix(
context: Optional :class:`SOMATileDBContext` containing storage parameters, etc.
platform_config: Platform-specific options used to update this array, provided
- in the form ``{"tiledb": {"create": {"dataframe_dim_zstd_level": 7}}}``
+ in the form ``{"tiledb": {"create": {"dataframe_dim_zstd_level": 7}}}``
Returns:
None
@@ -1740,8 +1739,7 @@ def add_matrix_to_collection(
context: Optional[SOMATileDBContext] = None,
) -> None:
"""This is useful for adding X/obsp/varm/etc data, for example from
- `Scanpy `_'s ``scanpy.pp.normalize_total``,
- ``scanpy.pp.log1p``, etc.
+ Scanpy's ``scanpy.pp.normalize_total``, ``scanpy.pp.log1p``, etc.
Use ``ingest_mode="resume"`` to not error out if the schema already exists.
diff --git a/apis/python/src/tiledbsoma/io/outgest.py b/apis/python/src/tiledbsoma/io/outgest.py
index 0775b7c7e3..922f4c05f5 100644
--- a/apis/python/src/tiledbsoma/io/outgest.py
+++ b/apis/python/src/tiledbsoma/io/outgest.py
@@ -69,8 +69,7 @@ def to_h5ad(
obsm_varm_width_hints: Optional[Dict[str, Dict[str, int]]] = None,
uns_keys: Optional[Sequence[str]] = None,
) -> None:
- """Converts the experiment group to `AnnData `_
- format and writes it to the specified ``.h5ad`` file.
+ """Converts the experiment group to AnnData format and writes it to the specified ``.h5ad`` file.
Arguments are as in ``to_anndata``.
@@ -203,14 +202,14 @@ def to_anndata(
obsm_varm_width_hints: Optional[Dict[str, Dict[str, int]]] = None,
uns_keys: Optional[Sequence[str]] = None,
) -> ad.AnnData:
- """Converts the experiment group to `AnnData `_
- format. Choice of matrix formats is following what we often see in input
- ``.h5ad`` files:
+ """Converts the experiment group to AnnData format.
+
+ The choice of matrix formats is following what we often see in input ``.h5ad`` files:
* ``X`` as ``scipy.sparse.csr_matrix``
- * ``obs``,``var`` as ``pandas.dataframe``
- * ``obsm``,``varm`` arrays as ``numpy.ndarray``
- * ``obsp``,``varp`` arrays as ``scipy.sparse.csr_matrix``
+ * ``obs``, ``var`` as ``pandas.dataframe``
+ * ``obsm``, ``varm`` arrays as ``numpy.ndarray``
+ * ``obsp``, ``varp`` arrays as ``scipy.sparse.csr_matrix``
The ``X_layer_name`` is the name of the TileDB-SOMA measurement's ``X``
collection which will be outgested to the resulting AnnData object's
diff --git a/apis/python/src/tiledbsoma/io/shaping.py b/apis/python/src/tiledbsoma/io/shaping.py
index ddd5e30eac..00371e2dc9 100644
--- a/apis/python/src/tiledbsoma/io/shaping.py
+++ b/apis/python/src/tiledbsoma/io/shaping.py
@@ -118,7 +118,7 @@ def resize_experiment(
output_handle: Printable = cast(Printable, sys.stdout),
) -> bool:
"""For each dataframe contained within the SOMA ``Experiment`` pointed to by
- the given URI, resizes the ``domain`` for the ``soma_joinid index column
+ the given URI, resizes the ``domain`` for the ``soma_joinid`` index column
(if it is an indexed column) to match the desired new value.
The desired new value may be the same size as at present, or bigger, but not
@@ -137,10 +137,10 @@ def resize_experiment(
given dimension, or bigger, but not exceeding ``maxshape`` for the given
dimension.
- If any array has not been upgraded, then its resize will fail.
+ If any array has not been upgraded, then the experiment's ``resize`` will fail.
Args:
- uri: The URI of a SOMA :class:`Experiment``.
+ uri: The URI of a SOMA :class:`Experiment`.
nobs: The desired new shape of the experiment's ``obs`` dataframe.
nvars: The desired new shapes of the experiment's ``var`` dataframes.
This should be a dict from measurement name to shape, e.g.
diff --git a/apis/python/src/tiledbsoma/stats.py b/apis/python/src/tiledbsoma/stats.py
index 0462753a5d..4cb0c0c9c5 100644
--- a/apis/python/src/tiledbsoma/stats.py
+++ b/apis/python/src/tiledbsoma/stats.py
@@ -11,12 +11,12 @@
def tiledbsoma_stats_json() -> str:
- """Returns tiledbsoma stats as a JSON string"""
+ """Returns tiledbsoma stats as a JSON string."""
# cast is needed for pybind11 things
return cast(str, tiledbsoma_stats_string())
def tiledbsoma_stats_as_py() -> ParsedStats:
- """Returns tiledbsoma stats as a Python dict"""
+ """Returns tiledbsoma stats as a Python dict."""
# cast is needed for pybind11 things
return cast(ParsedStats, json.loads(tiledbsoma_stats_string()))