Merge branch 'main' into ig/refactor_base_class

.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:
@@ -16,8 +16,8 @@ jobs:
         Python3.11:
           python.version: "3.11"
           RUN_COVERAGE: yes
-        Python3.8:
-          python.version: "3.8"
+        Python3.9:
+          python.version: "3.9"
         PreRelease:
           python.version: "3.11"
           PRERELEASE_DEPENDENCIES: yes
@@ -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)

.cirun.yml

@@ -7,6 +7,5 @@ runners:
     preemptible:
       - true
       - false
-    workflow: .github/workflows/test-gpu.yml
     labels:
       - cirun-aws-gpu

.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

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.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

@@ -1,20 +1,20 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.285"
+    rev: "v0.0.292"
     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
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -26,3 +26,10 @@ repos:
       - id: detect-private-key
       - id: no-commit-to-branch
         args: ["--branch=main"]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli

anndata/__init__.py

@@ -1,4 +1,5 @@
 """Annotated multivariate observation data."""
+from __future__ import annotations
 
 try:  # See https://github.com/maresb/hatch-vcs-footgun-example
     from setuptools_scm import get_version
@@ -34,15 +35,26 @@
     read_zarr,
 )
 from ._warnings import (
+    ExperimentalFeatureWarning,
+    ImplicitModificationWarning,
     OldFormatWarning,
     WriteWarning,
-    ImplicitModificationWarning,
-    ExperimentalFeatureWarning,
 )
-from . import experimental
 
-# backwards compat / shortcut for default format
-read = read_h5ad
+# Experimental needs to be imported last
+from . import experimental  # isort: skip
+
+
+def read(*args, **kwargs):
+    import warnings
+
+    warnings.warn(
+        "`anndata.read` is deprecated, use `anndata.read_h5ad` instead. "
+        "`ad.read` will be removed in mid 2024.",
+        FutureWarning,
+    )
+    return read_h5ad(*args, **kwargs)
+
 
 __all__ = [
     "__version__",

anndata/_core/access.py

@@ -1,13 +1,16 @@
+from __future__ import annotations
+
 from functools import reduce
-from typing import NamedTuple, Tuple
+from typing import TYPE_CHECKING, NamedTuple
 
-from . import anndata
+if TYPE_CHECKING:
+    from anndata import AnnData
 
 
 class ElementRef(NamedTuple):
-    parent: "anndata.AnnData"
+    parent: AnnData
     attrname: str
-    keys: Tuple[str, ...] = ()
+    keys: tuple[str, ...] = ()
 
     def __str__(self) -> str:
         return f".{self.attrname}" + "".join(map(lambda x: f"['{x}']", self.keys))