From 24a137a3ee9b43f668509e0e9d56e2e985179c39 Mon Sep 17 00:00:00 2001 From: keviny2 Date: Fri, 16 May 2025 08:59:14 -0700 Subject: [PATCH 1/3] Add more detail to docstring for to_anndata() --- src/spatialfeatureexperiment/sfe.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/src/spatialfeatureexperiment/sfe.py b/src/spatialfeatureexperiment/sfe.py index 90acfb1..088e072 100644 --- a/src/spatialfeatureexperiment/sfe.py +++ b/src/spatialfeatureexperiment/sfe.py @@ -790,15 +790,24 @@ def set_column_data( ######>> AnnData interop <<##### ################################ - def to_anndata(self, include_alternative_experiments: bool = False) -> "anndata.AnnData": + def to_anndata(self, include_alternative_experiments: bool = False) -> Tuple["anndata.AnnData", Dict[str, "anndata.AnnData"]]: """Transform :py:class:`~SpatialFeatureExperiment`-like into a :py:class:`~anndata.AnnData` representation. + This method extends the :py:meth:`~SpatialExperiment.to_anndata` method from the parent class + by adding SpatialFeatureExperiment-specific elements to the AnnData object's `uns["spatial"]` + dictionary. The additional elements include: + - `col_geometries` + - `row_geometries` + - `annot_geometries` + - `spatial_graphs` + - `unit` + Args: include_alternative_experiments: Whether to transform alternative experiments. Returns: - An ``AnnData`` representation of the experiment. + A tuple containing an ``AnnData`` object with spatial information and a list of alternative experiments. """ obj, alt_exps = super().to_anndata(include_alternative_experiments=include_alternative_experiments) From f4c5c956b15c76588109ff3ee912b09c4b784ddc Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 16 May 2025 16:00:17 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/spatialfeatureexperiment/sfe.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/spatialfeatureexperiment/sfe.py b/src/spatialfeatureexperiment/sfe.py index 088e072..fc0e04f 100644 --- a/src/spatialfeatureexperiment/sfe.py +++ b/src/spatialfeatureexperiment/sfe.py @@ -790,11 +790,13 @@ def set_column_data( ######>> AnnData interop <<##### ################################ - def to_anndata(self, include_alternative_experiments: bool = False) -> Tuple["anndata.AnnData", Dict[str, "anndata.AnnData"]]: + def to_anndata( + self, include_alternative_experiments: bool = False + ) -> Tuple["anndata.AnnData", Dict[str, "anndata.AnnData"]]: """Transform :py:class:`~SpatialFeatureExperiment`-like into a :py:class:`~anndata.AnnData` representation. This method extends the :py:meth:`~SpatialExperiment.to_anndata` method from the parent class - by adding SpatialFeatureExperiment-specific elements to the AnnData object's `uns["spatial"]` + by adding SpatialFeatureExperiment-specific elements to the AnnData object's `uns["spatial"]` dictionary. The additional elements include: - `col_geometries` - `row_geometries` From 73657a43f8b13f66a449dc235e5c86d7bcbc8bdd Mon Sep 17 00:00:00 2001 From: keviny2 Date: Fri, 16 May 2025 09:02:51 -0700 Subject: [PATCH 3/3] Add import for Tuple --- CHANGELOG.md | 2 +- src/spatialfeatureexperiment/sfe.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c4d77d2..30e2f15 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## Version 0.0.4 +## Version 0.0.4-0.0.5 - Implement `to_anndata()` to convert from spatial feature experiment to AnnData diff --git a/src/spatialfeatureexperiment/sfe.py b/src/spatialfeatureexperiment/sfe.py index 088e072..2d88f80 100644 --- a/src/spatialfeatureexperiment/sfe.py +++ b/src/spatialfeatureexperiment/sfe.py @@ -1,4 +1,4 @@ -from typing import Any, Dict, List, Optional, Union +from typing import Any, Dict, List, Optional, Union, Tuple from warnings import warn import biocutils as ut