Merge branch 'main' into ig/fill_val_0_nonint

Author: d-v-b

.github/PULL_REQUEST_TEMPLATE.md

@@ -3,7 +3,7 @@
 TODO:
 * [ ] Add unit tests and/or doctests in docstrings
 * [ ] Add docstrings and API docs for any new/modified user-facing classes and functions
-* [ ] New/modified features documented in `docs/user-guide/*.rst`
+* [ ] New/modified features documented in `docs/user-guide/*.md`
 * [ ] Changes documented as a new file in `changes/`
 * [ ] GitHub Actions have all passed
 * [ ] Test coverage is 100% (Codecov passes)

.github/labeler.yml

@@ -1,4 +1,4 @@
 needs release notes:
   - all:
     - changed-files:
-      - all-globs-to-all-files: '!changes/*.rst'
+      - all-globs-to-all-files: '!changes/*.md'

.github/workflows/check_changelogs.yml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
 
       - name: Install uv
-        uses: astral-sh/setup-uv@e92bafb6253dcd438e0484186d7669ea7a8ca1cc # v6.4.3
+        uses: astral-sh/setup-uv@b75a909f75acd358c2196fb9a5f1299a9a8868a4 # v6.7.0
 
       - name: Check changelog entries
         run: uv run --no-sync python ci/check_changelog_entries.py

.github/workflows/gpu_test.yml

@@ -29,7 +29,9 @@ jobs:
         dependency-set: ["minimal"]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0  # grab all branches and tags
     # - name: cuda-toolkit
     #   uses: Jimver/cuda-toolkit@v0.2.16
     #   id: cuda-toolkit
@@ -49,7 +51,7 @@ jobs:
         echo $LD_LIBRARY_PATH
         nvcc -V
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'

.github/workflows/hypothesis.yaml

@@ -28,7 +28,7 @@ jobs:
         dependency-set: ["optional"]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set HYPOTHESIS_PROFILE based on trigger
       run: |
         if [[ "${{ github.event_name }}" == "schedule" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then
@@ -37,7 +37,7 @@ jobs:
           echo "HYPOTHESIS_PROFILE=ci" >> $GITHUB_ENV
         fi
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'

.github/workflows/needs_release_notes.yml

@@ -11,7 +11,7 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@8558fd74291d67161a8a78ce36a881fa63b766a9  # v5.0.0
+    - uses: actions/labeler@634933edcd8ababfe52f92936142cc22ac488b1b  # v6.0.1
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         sync-labels: true

.github/workflows/nightly_wheels.yml

@@ -0,0 +1,37 @@
+name: Nightly Wheels
+
+on:
+  schedule:
+    # Run nightly at 2 AM UTC
+    - cron: '0 2 * * *'
+  workflow_dispatch:
+
+jobs:
+  build_and_upload_nightly:
+    name: Build and upload nightly wheels
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v6
+        name: Install Python
+        with:
+          python-version: '3.13'
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+
+      - name: Build wheel and sdist
+        run: hatch build
+
+      - name: Upload nightly wheels
+        uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf
+        with:
+          artifacts_path: dist
+          anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }}

.github/workflows/releases.yml

@@ -11,12 +11,12 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5.2.0
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: '3.11'
@@ -55,7 +55,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.12.4
+      - uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/test.yml

@@ -44,11 +44,11 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0  # grab all branches and tags
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -86,11 +86,11 @@ jobs:
           - python-version: "3.11"
             dependency-set: upstream
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -115,11 +115,11 @@ jobs:
     name: doctests
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.13'
         cache: 'pip'
@@ -129,11 +129,10 @@ jobs:
         pip install hatch
     - name: Set Up Hatch Env
       run: |
-        hatch env create doctest
-        hatch env run -e doctest list-env
+        hatch run doctest:pip list
     - name: Run Tests
       run: |
-        hatch env run --env doctest run
+        hatch run doctest:test
 
   test-complete:
     name: Test complete

.gitignore

@@ -49,9 +49,9 @@ coverage.xml
 # Django stuff:
 *.log
 
-# Sphinx documentation
+# Documentation
+site/
 docs/_build/
-docs/api
 docs/data
 data
 data.zip
@@ -90,3 +90,4 @@ tests/.hypothesis
 .hypothesis/
 
 zarr/version.py
+zarr.egg-info/