From 1eaa56cc8611ef5961176f63979b1f08262a5cb5 Mon Sep 17 00:00:00 2001
From: Severin Dicks <37635888+Intron7@users.noreply.github.com>
Date: Tue, 29 Aug 2023 13:44:43 +0200
Subject: [PATCH] forces Raw move to CPU (#1107)

* forces move to CPU

* added raw GPU test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Use qualified function names, plus avoid future scipy deprecations

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Isaac Virshup <ivirshup@gmail.com>
---
 anndata/_core/raw.py      |  6 +++++-
 anndata/tests/test_gpu.py | 27 +++++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/anndata/_core/raw.py b/anndata/_core/raw.py
index f18f75bf8..f248b99be 100644
--- a/anndata/_core/raw.py
+++ b/anndata/_core/raw.py
@@ -29,7 +29,11 @@ def __init__(
         self._n_obs = adata.n_obs
         # construct manually
         if adata.isbacked == (X is None):
-            self._X = X
+            # Move from GPU to CPU since it's large and not always used
+            if isinstance(X, (CupyArray, CupySparseMatrix)):
+                self._X = X.get()
+            else:
+                self._X = X
             self._var = _gen_dataframe(var, self.X.shape[1], ["var_names"])
             self._varm = AxisArrays(self, 1, varm)
         elif X is None:  # construct from adata
diff --git a/anndata/tests/test_gpu.py b/anndata/tests/test_gpu.py
index a5f820bd8..434567ca8 100644
--- a/anndata/tests/test_gpu.py
+++ b/anndata/tests/test_gpu.py
@@ -1,4 +1,7 @@
 import pytest
+from scipy import sparse
+
+from anndata import AnnData, Raw
 
 
 @pytest.mark.gpu
@@ -9,3 +12,27 @@ def test_gpu():
     import cupy  # This test shouldn't run if cupy isn't installed
 
     cupy.ones(1)
+
+
+@pytest.mark.gpu
+def test_adata_raw_gpu():
+    from cupyx.scipy import sparse as cupy_sparse
+    import cupy as cp
+
+    adata = AnnData(
+        X=cupy_sparse.random(500, 50, density=0.01, format="csr", dtype=cp.float32)
+    )
+    adata.raw = adata
+    assert isinstance(adata.raw.X, sparse.csr_matrix)
+
+
+@pytest.mark.gpu
+def test_raw_gpu():
+    from cupyx.scipy import sparse as cupy_sparse
+    import cupy as cp
+
+    adata = AnnData(
+        X=cupy_sparse.random(500, 50, density=0.01, format="csr", dtype=cp.float32)
+    )
+    araw = Raw(adata)
+    assert isinstance(araw.X, sparse.csr_matrix)