Merge branch 'main' into docs/document-load-vs-open

Author: SAY-5

.github/workflows/check_changelogs.yml

@@ -17,12 +17,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Check zarr-python changelog entries
         run: uv run --no-sync python ci/check_changelog_entries.py

.github/workflows/codspeed.yml

@@ -23,7 +23,7 @@ jobs:
       github.event_name == 'workflow_dispatch' ||
       (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark'))
     steps:
-    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+    - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
       with:
         fetch-depth: 0
         persist-credentials: false
@@ -32,7 +32,7 @@ jobs:
       with:
         version: '1.16.5'
     - name: Run the benchmarks
-      uses: CodSpeedHQ/action@3194d9a39c4d46684cb44bf7207fc56626aad8fd # v4.15.1
+      uses: CodSpeedHQ/action@9d332c4d90b43981c3e55ae8e38e68709996240f # v4.17.0
       with:
           mode: walltime
           run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed

.github/workflows/docs.yml

@@ -19,10 +19,10 @@ jobs:
     name: Check docs
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           persist-credentials: false
-      - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+      - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
       - run: uv sync --group docs
       # --strict turns warnings into errors, so a docs code block that fails to execute
       # at build time (e.g. a non-exec python fence disrupting a later exec="true" block)

.github/workflows/downstream.yml

@@ -21,39 +21,56 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out zarr-python
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           fetch-depth: 0
           persist-credentials: false
 
       - name: Check out xarray
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           repository: pydata/xarray
           path: xarray
           persist-credentials: false
 
-      - name: Set up pixi
-        uses: prefix-dev/setup-pixi@5185adfbffb4bd703da3010310260805d89ebb11 # v0.9.6
+      # We install xarray with plain pip/uv rather than pixi. pixi solves
+      # xarray's entire manifest (it has no committed lockfile), which drags in
+      # the `mypy-upstream` environment; that environment sources numcodecs from
+      # git and fails to build under newer pixi with
+      # `meson-python: error: Unknown option "pixi-conda-environment"`, breaking
+      # the job before any test runs. Tests that need a backend we don't install
+      # are skipped via xarray's `requires_*` markers, not failed.
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
-          manifest-path: xarray/pixi.toml
+          python-version: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
-      - name: Install zarr-python from branch
+      - name: Install xarray and test dependencies
         working-directory: xarray
-        run: pixi run -e test-py313 -- pip install --no-deps ..
+        run: |
+          uv venv
+          # xarray's pytest tooling lives in the PEP 735 `dev` dependency group;
+          # the zarr-relevant backends come from the `io` and `parallel` extras.
+          uv pip install --group dev ".[io,parallel,accel]"
+
+      - name: Override zarr-python with branch version
+        working-directory: xarray
+        run: uv pip install --no-deps ..
 
       - name: Show versions
         working-directory: xarray
         run: |
-          pixi run -e test-py313 -- python -c "
+          uv run python -c "
           import zarr; print(f'zarr {zarr.__version__}')
           import xarray; print(f'xarray {xarray.__version__}')
           "
 
       - name: Run xarray zarr backend tests
         working-directory: xarray
         run: |
-          pixi run -e test-py313 -- python -m pytest --no-header -q \
+          uv run python -m pytest --no-header -q \
             xarray/tests/test_backends.py \
             xarray/tests/test_backends_api.py \
             xarray/tests/test_backends_datatree.py
@@ -66,13 +83,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out zarr-python
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           fetch-depth: 0
           persist-credentials: false
 
       - name: Check out numcodecs
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           repository: zarr-developers/numcodecs
           fetch-depth: 0
@@ -85,7 +102,7 @@ jobs:
           python-version: '3.13'
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
 
       - name: Install numcodecs with test-zarr-main group
         working-directory: numcodecs

.github/workflows/gpu_test.yml

@@ -34,7 +34,7 @@ jobs:
         python-version: ['3.12']
 
     steps:
-    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+    - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
       with:
         fetch-depth: 0  # grab all branches and tags
         persist-credentials: false
@@ -62,7 +62,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
     - name: Install Hatch
       uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
       with:

.github/workflows/hypothesis.yaml

@@ -39,7 +39,7 @@ jobs:
         dependency-set: ["optional"]
 
     steps:
-    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+    - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
       with:
         persist-credentials: false
     - name: Set HYPOTHESIS_PROFILE based on trigger
@@ -57,7 +57,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
     - name: Install Hatch
       uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
       with:

.github/workflows/lint.yml

@@ -19,15 +19,15 @@ jobs:
     name: Lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           persist-credentials: false
       - name: Set up Python
         uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: "3.12"
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
         with:
           enable-cache: true
       - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4

.github/workflows/nightly_wheels.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           submodules: true
           fetch-depth: 0

.github/workflows/prepare_release.yml

@@ -36,7 +36,7 @@ jobs:
           VERSION: ${{ inputs.version }}
           TARGET_BRANCH: ${{ inputs.target_branch }}
 
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           ref: ${{ inputs.target_branch }}
           fetch-depth: 0

.github/workflows/releases.yml

@@ -26,7 +26,7 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
         with:
           submodules: true
           fetch-depth: 0