Merge branch 'main' into ak-array-views

.azure-pipelines.yml

@@ -4,7 +4,7 @@ trigger:
 variables:
   PIP_CACHE_DIR: $(Pipeline.Workspace)/.pip
   RUN_COVERAGE: no
-  PYTEST_ADDOPTS: --color=yes --junitxml=junit/test-results.xml
+  PYTEST_ADDOPTS: --color=yes --junitxml=test-data/test-results.xml
   PRERELEASE_DEPENDENCIES: no
 
 jobs:
@@ -37,15 +37,13 @@ jobs:
         displayName: Cache pip packages
 
       - script: |
-          python -m pip install --upgrade pip
-          pip install pytest-cov wheel
+          python -m pip install --upgrade pip wheel
           pip install .[dev,test]
         displayName: "Install dependencies"
         condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'no')
 
       - script: |
-          python -m pip install --pre --upgrade pip
-          pip install --pre pytest-cov wheel
+          python -m pip install --pre --upgrade pip wheel
           pip install --pre .[dev,test]
         displayName: "Install dependencies release candidates"
         condition: eq(variables['PRERELEASE_DEPENDENCIES'], 'yes')
@@ -67,14 +65,14 @@ jobs:
       - task: PublishCodeCoverageResults@1
         inputs:
           codeCoverageTool: Cobertura
-          summaryFileLocation: "$(System.DefaultWorkingDirectory)/**/coverage.xml"
-          reportDirectory: "$(System.DefaultWorkingDirectory)/**/htmlcov"
+          summaryFileLocation: "test-data/coverage.xml"
         condition: eq(variables['RUN_COVERAGE'], 'yes')
 
       - task: PublishTestResults@2
         condition: succeededOrFailed()
         inputs:
-          testResultsFiles: "junit/test-*.xml"
+          testResultsFiles: "test-data/test-results.xml"
+          testResultsFormat: JUnit
           testRunTitle: "Publish test results for Python $(python.version)"
 
       - script: bash <(curl -s https://codecov.io/bash)

.gitignore

@@ -2,26 +2,21 @@
 .DS_Store
 *~
 
-# Compiled files
+# Caches for compiled and downloaded files
 __pycache__/
+/*cache/
+/data/
 
 # Distribution / packaging
-/build/
 /dist/
 /anndata/_version.py
-/*.egg-info/
 /requirements*.lock
 /.python-version
 /hatch.toml
 
-# Tests and coverage
-/*cache/
-/data/
-/tmp.zarr/
-test.h5ad
-test.loom
-test.zarr
-.coverage
+# Test results (nunit/junit) and coverage
+/test-data/
+/*coverage*
 
 # jupyter
 .ipynb_checkpoints

.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/compat/__init__.py

@@ -1,8 +1,13 @@
 from __future__ import annotations
 
+from contextlib import AbstractContextManager
+from dataclasses import dataclass, field
+
 from functools import singledispatch, wraps
 from codecs import decode
 from inspect import signature, Parameter
+import os
+from pathlib import Path
 from typing import Any, Tuple, Union, Mapping, Optional
 from warnings import warn
 
@@ -24,7 +29,31 @@ class Empty:
 H5Array = h5py.Dataset
 
 
-# try importing zarr, dask, and zappy
+#############################
+# stdlib
+#############################
+
+
+try:
+    from contextlib import chdir
+except ImportError:  # Python < 3.11
+
+    @dataclass
+    class chdir(AbstractContextManager):
+        path: Path
+        _old_cwd: list[Path] = field(default_factory=list)
+
+        def __enter__(self) -> None:
+            self._old_cwd.append(Path())
+            os.chdir(self.path)
+
+        def __exit__(self, *_exc_info) -> None:
+            os.chdir(self._old_cwd.pop())
+
+
+#############################
+# Optional deps
+#############################
 
 try:
     from zarr.core import Array as ZarrArray
@@ -105,6 +134,11 @@ def __repr__():
             return "mock cupy.ndarray"
 
 
+#############################
+# IO helpers
+#############################
+
+
 @singledispatch
 def _read_attr(attrs: Mapping, name: str, default: Optional[Any] = Empty):
     if default is Empty:

conftest.py

@@ -1,15 +1,37 @@
-# This file exists just to allow ignoring warnings without test collection failing on CI
-# TODO: Fix that
+# This file exists
+# 1. to allow ignoring warnings without test collection failing on CI
+# 2. as a pytest plugin/config that applies to doctests as well
+# TODO: Fix that, e.g. with the `pytest -p anndata.testing._pytest` pattern.
+
+from pathlib import Path
+
 import pytest
 
+from anndata.compat import chdir
+
+
+doctest_marker = pytest.mark.usefixtures("doctest_env")
+
+
+@pytest.fixture
+def doctest_env(cache: pytest.Cache, tmp_path: Path) -> None:
+    from scanpy import settings
+
+    old_dd, settings.datasetdir = settings.datasetdir, cache.mkdir("scanpy-data")
+    with chdir(tmp_path):
+        yield
+    settings.datasetdir = old_dd
+
 
 def pytest_itemcollected(item):
-    """Defining behavior of pytest.mark.gpu"""
+    """Define behavior of pytest.mark.gpu and doctests."""
     from importlib.util import find_spec
 
-    gpu = len([mark for mark in item.iter_markers(name="gpu")]) > 0
-
-    if gpu:
+    is_gpu = len([mark for mark in item.iter_markers(name="gpu")]) > 0
+    if is_gpu:
         item.add_marker(
             pytest.mark.skipif(not find_spec("cupy"), reason="Cupy not installed.")
         )
+
+    if isinstance(item, pytest.DoctestItem):
+        item.add_marker(doctest_marker)