Switch to (testing.)fast-array-utils

.github/workflows/test-cpu.yml

@@ -8,7 +8,7 @@ on:
   pull_request:
 
 env:
-  PYTEST_ADDOPTS: "-v --color=yes"
+  PYTEST_ADDOPTS: "-v --color=yes -n auto --instafail"
   FORCE_COLOR: "1"
 
 defaults:
@@ -19,7 +19,7 @@ defaults:
 # https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false  # TODO: set to `true` again
 
 jobs:
   pytest:
@@ -34,9 +34,9 @@ jobs:
           - python-version: '3.13'
             dependencies-version: pre-release
             test-type: strict-warning
-          - python-version: '3.11'
-            dependencies-version: minimum
-            test-type: coverage
+          #- python-version: '3.11'
+          #  dependencies-version: minimum
+          #  test-type: coverage
     steps:
       - uses: actions/checkout@v4
         with:
@@ -74,15 +74,15 @@ jobs:
 
       - name: Run Pytest
         if: matrix.test-type == 'standard'
-        run: pytest -n auto
+        run: pytest
 
       - name: Run Pytest (coverage)
         if: matrix.test-type == 'coverage'
-        run: coverage run -m pytest -n auto --cov --cov-report=xml
+        run: coverage run -m pytest --cov --cov-report=xml
 
       - name: Run Pytest (treat warnings as errors)
         if: matrix.test-type == 'strict-warning'
-        run: pytest --strict-warnings -n auto
+        run: pytest --strict-warnings
 
       - uses: codecov/codecov-action@v4
         if: matrix.test-type == 'coverage'

ci/constraints.txt

@@ -1 +1,2 @@
 numba>=0.56
+fast-array-utils @ git+https://github.com/scverse/fast-array-utils.git

hatch.toml

@@ -16,7 +16,7 @@ scripts.clean = "git restore --source=HEAD --staged --worktree -- docs/release-n
 [envs.hatch-test]
 default-args = [  ]
 features = [ "dev", "test" ]
-extra-dependencies = [ "ipykernel" ]
+extra-dependencies = [ "ipykernel", "fast-array-utils @ git+https://github.com/scverse/fast-array-utils.git" ]
 env-vars.UV_CONSTRAINT = "ci/constraints.txt"
 overrides.matrix.deps.env-vars = [
     { if = [ "pre" ], key = "UV_PRERELEASE", value = "allow" },

pyproject.toml

@@ -46,6 +46,7 @@ dependencies = [
     "packaging>=24.2",
     # array-api-compat 1.5 has https://github.com/scverse/anndata/issues/1410
     "array_api_compat>1.4,!=1.5",
+    "fast-array-utils",
     "legacy-api-wrap",
     "zarr >=2.15.0, !=3.0.0, !=3.0.1, !=3.0.2, !=3.0.3",
 ]
@@ -85,25 +86,27 @@ doc = [
 dev-doc = [ "towncrier>=24.8.0" ] # release notes tool
 test-full = [ "anndata[test,lazy]" ]
 test = [
-    "loompy>=3.0.5",
     "pytest>=8.2,<8.3.4",
     "pytest-cov",
     "pytest-randomly",
     "pytest-memray",
     "pytest-mock",
+    "pytest-instafail",
+    "fast-array-utils[testing]",
     "pytest-xdist[psutil]",
     "filelock",
     "matplotlib",
     "scikit-learn",
+    "loompy>=3.0.5",
     "openpyxl",
     "joblib",
     "boltons",
     "scanpy>=1.10",
-    "httpx",                # For data downloading
+    "httpx",                     # For data downloading
     "dask[distributed]",
     "awkward>=2.3",
     "pyarrow",
-    "anndata[dask]",
+    "anndata[dask,lazy]",
 ]
 gpu = [ "cupy" ]
 cu12 = [ "cupy-cuda12x" ]

src/anndata/_core/merge.py

@@ -32,7 +32,7 @@
     DaskArray,
     _map_cat_to_str,
 )
-from ..utils import asarray, axis_len, warn_once
+from ..utils import axis_len, warn_once
 from .anndata import AnnData
 from .index import _subset, make_slice
 
@@ -115,8 +115,8 @@ def not_missing(v) -> bool:
 # TODO: Hopefully this will stop being an issue in the future and this code can be removed.
 @singledispatch
 def equal(a, b) -> bool:
-    a = asarray(a)
-    b = asarray(b)
+    a = np.asarray(a)
+    b = np.asarray(b)
     if a.ndim == b.ndim == 0:
         return bool(a == b)
     return np.array_equal(a, b)
@@ -150,7 +150,7 @@ def equal_dask_array(a, b) -> bool:
 def equal_array(a, b) -> bool:
     # Reshaping allows us to compare inputs with >2 dimensions
     # We cast to pandas since it will still work with non-numeric types
-    b = asarray(b)
+    b = np.asarray(b)
     if a.shape != b.shape:
         return False
 

src/anndata/compat/__init__.py

@@ -12,7 +12,7 @@
 import h5py
 import numpy as np
 import pandas as pd
-import scipy
+import scipy.sparse
 from packaging.version import Version
 from zarr import Array as ZarrArray  # noqa: F401
 from zarr import Group as ZarrGroup