From c7c28d9dfa9d24ba806363efe55b468d23d26870 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Wed, 14 Feb 2024 08:39:24 -0800
Subject: [PATCH] Support for delayed and file-backed array when coercing to
 anndata (#34).

Also update tests.
---
 setup.cfg                                     |  2 ++
 .../SingleCellExperiment.py                   | 28 ++++++-------------
 tests/test_sce_io.py                          |  2 ++
 3 files changed, 12 insertions(+), 20 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index edce69a..44aa670 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -63,6 +63,7 @@ optional =
     anndata
     h5py
     mudata
+    delayedarray
 
 # Add here test requirements (semicolon/line-separated)
 testing =
@@ -72,6 +73,7 @@ testing =
     anndata
     h5py
     mudata
+    delayedarray
 
 [options.entry_points]
 # Add here console scripts like:
diff --git a/src/singlecellexperiment/SingleCellExperiment.py b/src/singlecellexperiment/SingleCellExperiment.py
index aac38cb..0df4ff9 100644
--- a/src/singlecellexperiment/SingleCellExperiment.py
+++ b/src/singlecellexperiment/SingleCellExperiment.py
@@ -4,7 +4,6 @@
 
 import biocframe
 import biocutils as ut
-from genomicranges import GenomicRanges
 from summarizedexperiment._combineutils import (
     check_assays_are_equal,
     merge_assays,
@@ -984,25 +983,16 @@ def to_anndata(self, include_alternative_experiments: bool = False):
         Returns:
             A tuple with ``AnnData`` main experiment and a list of alternative experiments.
         """
-        from anndata import AnnData
+        obj = super().to_anndata()
 
-        layers = OrderedDict()
-        for asy, mat in self.assays.items():
-            layers[asy] = mat.transpose()
+        if self.reduced_dims is not None:
+            obj.obsm = self.reduced_dims
 
-        trows = self.row_data
-        if isinstance(self.row_data, GenomicRanges):
-            trows = self.row_data.to_pandas()
-
-        obj = AnnData(
-            obs=self.col_data,
-            var=trows,
-            uns=self.metadata,
-            obsm=self.reduced_dims,
-            layers=layers,
-            varp=self.row_pairs,
-            obsp=self.column_pairs,
-        )
+        if self.row_pairs is not None:
+            obj.varp = self.row_pairs
+
+        if self.column_pairs is not None:
+            obj.obsp = self.column_pairs
 
         if include_alternative_experiments is True:
             adatas = None
@@ -1014,8 +1004,6 @@ def to_anndata(self, include_alternative_experiments: bool = False):
                 ) in self.alternative_experiments.items():
                     adatas[alt_name] = alternative_experiment.to_anndata()
 
-            return obj, adatas
-
         return obj, None
 
     @classmethod
diff --git a/tests/test_sce_io.py b/tests/test_sce_io.py
index 8a2c102..75bd505 100644
--- a/tests/test_sce_io.py
+++ b/tests/test_sce_io.py
@@ -61,6 +61,8 @@ def test_SCE_to_anndata():
     adata = tse.to_anndata()
     assert adata is not None
     assert isinstance(adata[0], anndata.AnnData)
+    assert adata[0].shape[0] == counts.shape[1]
+    assert adata[0].shape[1] == counts.shape[0]
 
 
 def test_SCE_fromH5AD():