fix(store): copy buffers on write in MemoryStore

.github/ISSUE_TEMPLATE/release-checklist.md

@@ -18,8 +18,8 @@ assignees: ''
 
 - [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/#support-window) to see if the minimum supported version of Python or NumPy needs bumping.
 - [ ] Verify that the latest CI workflows on `main` are passing: [Tests](https://github.com/zarr-developers/zarr-python/actions/workflows/test.yml), [GPU Tests](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml), [Hypothesis](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml), [Docs](https://github.com/zarr-developers/zarr-python/actions/workflows/docs.yml), [Lint](https://github.com/zarr-developers/zarr-python/actions/workflows/lint.yml), [Wheels](https://github.com/zarr-developers/zarr-python/actions/workflows/releases.yml).
-- [ ] Run the ["Prepare release" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/prepare_release.yml) with the target version. This will build the changelog and open a release PR with the `run-downstream` label.
-- [ ] Verify that the [downstream tests](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) (triggered automatically by the `run-downstream` label) pass on the release PR.
+- [ ] Run the [downstream tests](https://github.com/zarr-developers/zarr-python/actions/workflows/downstream.yml) against `main`: go to the workflow page, click "Run workflow", and select the `main` branch. Verify that the Xarray and numcodecs integration tests pass.
+- [ ] Open a release PR with the changelog entries for the upcoming release, generated with `uv run --only-group release towncrier build --version x.y.z`.
 - [ ] Review the release PR and verify the changelog in `docs/release-notes.md` looks correct.
 - [ ] Merge the release PR.
 
@@ -45,7 +45,8 @@ In rare cases (e.g. patch releases for an older minor version), you may need to
 
 - Create the release branch from the appropriate tag if it doesn't already exist.
 - Cherry-pick or backport the necessary commits onto the branch.
-- Run `towncrier build --version x.y.z` and commit the result to the release branch instead of `main`.
+- Run `towncrier build --version x.y.z` and open the release PR against the release branch instead of `main`.
+- Run the downstream tests against the release branch instead of `main`.
 - When drafting the GitHub Release, set the target to the release branch instead of `main`.
 - After the release, ensure any relevant changelog updates are also reflected on `main`.
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,7 @@
 
 - [ ] I am a human, these are my changes, and I have reviewed and understood every change and can explain why each is correct.
 
-AI coding assistance is welcome, but a human must be the author and is responsible for the contents of the PR. The description and any review responses must be in your own words. Please read [AI-assisted contributions](https://zarr.readthedocs.io/en/stable/contributing/#ai-assisted-contributions) before opening.
+<!-- AI coding assistance is welcome, but a human must be the author and is responsible for the contents of the PR. The description and any review responses must be in your own words. Please read [AI-assisted contributions](https://zarr.readthedocs.io/en/stable/contributing/#ai-assisted-contributions) before opening. -->
 
 ## TODO
 

.github/workflows/check_changelogs.yml

@@ -22,7 +22,7 @@ jobs:
           persist-credentials: false
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Check zarr-python changelog entries
         run: uv run --no-sync python ci/check_changelog_entries.py

.github/workflows/codspeed.yml

@@ -32,7 +32,7 @@ jobs:
       with:
         version: '1.16.5'
     - name: Run the benchmarks
-      uses: CodSpeedHQ/action@a4a36bb07c0638b0b4ca52bf1f3dad1b4289e52f # v4.18.1
+      uses: CodSpeedHQ/action@f99becdce5e5d51fd556489ebef684f4ecfd6286 # v4.18.5
       with:
           mode: walltime
           run: hatch run test.py3.12-minimal:pytest tests/benchmarks --codspeed

.github/workflows/docs.yml

@@ -22,8 +22,13 @@ jobs:
       - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
         with:
           persist-credentials: false
-      - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      - uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
       - run: uv sync --group docs
+      # Fast source-level guards that need no built site, so they run before the (slower)
+      # build for a quick failure: every public export is in the API reference, and no
+      # docstring/Markdown carries reStructuredText markup that MkDocs won't render.
+      - run: uv run python ci/check_documented_exports.py docs/api
+      - run: uv run python ci/lint_docs.py
       # --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)
       # fails CI instead of merging as a silent warning.

.github/workflows/downstream.yml

@@ -45,7 +45,7 @@ jobs:
           python-version: '3.13'
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Install xarray and test dependencies
         working-directory: xarray
@@ -102,7 +102,7 @@ jobs:
           python-version: '3.13'
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: Install numcodecs with test-zarr-main group
         working-directory: numcodecs

.github/workflows/gpu_test.yml

@@ -62,7 +62,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
     - name: Install Hatch
       uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
       with:

.github/workflows/hypothesis.yaml

@@ -57,7 +57,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
     - name: Install Hatch
       uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
       with:

.github/workflows/issue-metrics.yml

@@ -33,7 +33,7 @@ jobs:
         echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
 
     - name: Run issue-metrics tool
-      uses: github-community-projects/issue-metrics@44173f9e0a3b2144a777a10a340e4c09a25ac9f8 # v4.2.8
+      uses: github-community-projects/issue-metrics@df8c49d20958f9345281fa2124858bd0ad227e1f # v5.0.0
       env:
         GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"'

.github/workflows/links.yml

@@ -0,0 +1,32 @@
+name: Check links
+
+on:
+  repository_dispatch:
+  workflow_dispatch:
+  # pull_request:
+  schedule:
+    - cron: "00 18 * * *"
+
+jobs:
+  linkChecker:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write # required for peter-evans/create-issue-from-file
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+        with:
+          persist-credentials: false
+
+      - name: Link Checker
+        id: lychee
+        uses: lycheeverse/lychee-action@e7477775783ea5526144ba13e8db5eec57747ce8 # v2.9.0
+        with:
+          fail: false
+
+      - name: Create Issue From File
+        if: steps.lychee.outputs.exit_code != 0
+        uses: peter-evans/create-issue-from-file@fca9117c27cdc29c6c4db3b86c48e4115a786710 # v6.0.0
+        with:
+          title: Link Checker Report
+          content-filepath: ./lychee/out.md
+          labels: report, automated issue

.github/workflows/lint.yml

@@ -27,7 +27,7 @@ jobs:
         with:
           python-version: "3.12"
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
       - uses: j178/prek-action@e98a699c41eb69ab013a45817a0406469a748f8d # v2.0.5

.github/workflows/needs_release_notes.yml

@@ -21,7 +21,7 @@ jobs:
       pull-requests: write # Required to add labels to PRs
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@f27b608878404679385c85cfa523b85ccb86e213  # v6.1.0
+    - uses: actions/labeler@b8dd2d9be0f68b860e7dae5dae7d772984eacd6d  # v6.2.0
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         sync-labels: true

.github/workflows/test.yml

@@ -66,7 +66,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
     - name: Install Hatch
       run: python -m pip install hatch==1.16.5
     - name: Set Up Hatch Env
@@ -115,7 +115,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
     - name: Install Hatch
       run: python -m pip install hatch==1.16.5
     - name: Set Up Hatch Env
@@ -150,7 +150,7 @@ jobs:
         python-version: '3.13'
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
     - name: Install Hatch
       run: python -m pip install hatch==1.16.5
     - name: Set Up Hatch Env
@@ -174,7 +174,7 @@ jobs:
         python-version: '3.13'
         cache: 'pip'
     - name: Install uv
-      uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
     - name: Install Hatch
       run: python -m pip install hatch==1.16.5
     - name: Run Benchmarks

.github/workflows/zarr-metadata-release.yml

@@ -51,7 +51,7 @@ jobs:
           path: dist
 
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: false
 

.github/workflows/zarr-metadata.yml

@@ -36,7 +36,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
       - name: Set up Python ${{ matrix.python-version }}
@@ -58,7 +58,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
       - name: Run ruff
         run: uvx ruff check .
 
@@ -74,7 +74,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Install uv
-        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
       - name: Set up Python

.markdownlint-cli2.jsonc

@@ -0,0 +1,54 @@
+// markdownlint-cli2 configuration for zarr-python docs.
+//
+// We keep the rules that catch real rendering/structure problems and disable those that
+// are pure style, conflict with house conventions, or fire false positives against our
+// MkDocs/mkdocstrings + pymdownx toolchain. Complementary, not overlapping, with
+// ci/lint_docs.py (RST residue + list-breaking fences) and `mkdocs build --strict`.
+{
+  "config": {
+    "default": true,
+
+    // House style: Markdown paragraphs are single unwrapped lines, so line length is not
+    // a meaningful constraint.
+    "MD013": false,
+
+    // Purely stylistic marker/emphasis choices -- not worth the churn across existing docs.
+    "MD004": false, // ul bullet style (-, *, +)
+    "MD007": false, // ul indentation width
+    "MD050": false, // strong (bold) style
+    "MD035": false, // hr style
+
+    // False positives from our toolchain:
+    // mkdocstrings cross-refs `[`X`][zarr.X]` read as undefined reference links (MD052);
+    // pymdownx.magiclink auto-links bare URLs (MD034);
+    // md_in_html lets us embed intentional raw HTML (MD033);
+    // generated/included files (api stubs, snippets) need not open with an H1 (MD041).
+    "MD052": false,
+    "MD034": false,
+    "MD033": false,
+    "MD041": false,
+
+    // Duplicate headings are legitimate under different sections (e.g. repeated
+    // "Documentation"); only flag true sibling duplicates.
+    "MD024": { "siblings_only": true },
+
+    // Opinionated table/link/command rules with low value for these docs.
+    "MD055": false, // table pipe style
+    "MD060": false, // table column style
+    "MD059": false, // "descriptive" link text (no "click here")
+    "MD014": false, // $ before commands without shown output
+
+    // markdownlint does not understand MkDocs `!!!` admonitions, so it reads their
+    // 4-space-indented bodies as indented code blocks and flags them (and, via inferred
+    // file style, flags real fenced blocks too). Cannot coexist with our admonitions.
+    "MD046": false // code block style (fenced vs indented)
+    // Kept on (structural / real rendering bugs): MD012 (multiple blanks), MD022/MD031/MD032
+    // (blanks around headings/fences/lists), MD025 (single H1), MD029 (ordered-list prefix),
+    // MD040 (fenced code language), MD042 (empty links),
+    // MD047 (trailing newline), MD056 (table column count), among others.
+  },
+  "globs": ["docs/**/*.md"],
+  "ignores": [
+    "docs/api/**" // mkdocstrings stubs (`::: zarr.X`)
+  ]
+}

.pre-commit-config.yaml

@@ -31,6 +31,16 @@ repos:
       - id: check-yaml
         exclude: mkdocs.yml
       - id: trailing-whitespace
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.22.1
+    hooks:
+      # Markdown structure/hygiene. Rule selection and ignores are in
+      # .markdownlint-cli2.jsonc; complements ci/lint_docs.py (RST residue,
+      # list-breaking fences) and `mkdocs build --strict`. Scoped to docs/ to
+      # match the config's globs (pre-commit passes filenames, which would
+      # otherwise override that scoping and lint all repo Markdown).
+      - id: markdownlint-cli2
+        files: ^docs/
   - repo: local
     hooks:
       - id: mypy

TEAM.md

@@ -11,6 +11,7 @@
 - @dcherian (Deepak Cherian)
 - @TomAugspurger (Tom Augspurger)
 - @maxrjones (Max Jones)
+- @ilan-gold (Ilan Gold)
 
 ## Emeritus core-developers
 - @alimanfoo (Alistair Miles)