Merge branch 'main' into zarr-sparse-array

.github/workflows/check-pr-milestoned.yml

@@ -20,12 +20,16 @@ on:
       - synchronize
 
 env:
-  LABELS: ${{ join( github.event.pull_request.labels.*.name, '|' ) }}
+  LABELS: ${{ join(github.event.pull_request.labels.*.name, '|') }}
 
 jobs:
   check-milestone:
     name: "Triage: Check Milestone"
     runs-on: ubuntu-latest
     steps:
-      - if: github.event.pull_request.milestone == null && contains( env.LABELS, 'no milestone' ) == false
+      - name: Check if merging isn’t blocked
+        if: contains(env.LABELS, 'DON’T MERGE')
+        run: exit 1
+      - name: Check if a milestone is necessary and exists
+        if: github.event.pull_request.milestone == null && contains(env.LABELS, 'no milestone') == false
         run: exit 1

.pre-commit-config.yaml

@@ -5,12 +5,12 @@ repos:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.286"
+    rev: "v0.0.287"
     hooks:
       - id: ruff
         args: ["--fix"]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.2
+    rev: v3.0.3
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks

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

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)