feat: add the zarr-indexing package (TensorStore-style index transforms, ndsel wire format)

.github/workflows/check_changelogs.yml

@@ -29,3 +29,6 @@ jobs:
 
       - name: Check zarr-metadata changelog entries
         run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-metadata/changes
+
+      - name: Check zarr-indexing changelog entries
+        run: uv run --no-sync python ci/check_changelog_entries.py packages/zarr-indexing/changes

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

@@ -0,0 +1,117 @@
+name: zarr-indexing release
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - 'zarr_indexing-v*'
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build wheel and sdist
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+        working-directory: packages/zarr-indexing
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+        with:
+          persist-credentials: false
+          fetch-depth: 0          # hatch-vcs needs full history + tags
+
+      - name: Install Hatch
+        uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+        with:
+          version: '1.16.5'
+
+      - name: Build
+        run: hatch build
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: zarr-indexing-dist
+          path: packages/zarr-indexing/dist
+
+  test_artifacts:
+    name: Test built artifacts
+    needs: [build]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: zarr-indexing-dist
+          path: dist
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
+        with:
+          enable-cache: false
+
+      - name: Set up Python
+        run: uv python install 3.12
+
+      - name: Install built wheel and run import smoke test
+        run: |
+          wheel=$(ls dist/*.whl)
+          uv run --with "${wheel}" --python 3.12 --no-project \
+            python -c "import zarr_indexing; print('zarr_indexing', zarr_indexing.__version__)"
+
+  upload_pypi:
+    name: Upload to PyPI
+    needs: [build, test_artifacts]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/zarr_indexing-v')
+    runs-on: ubuntu-latest
+    environment:
+      name: zarr-indexing-releases
+      url: https://pypi.org/p/zarr-indexing
+    permissions:
+      id-token: write          # required for OIDC trusted publishing
+      attestations: write      # required for artifact attestations
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: zarr-indexing-dist
+          path: dist
+
+      - name: Generate artifact attestation
+        uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0
+        with:
+          subject-path: dist/*
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
+
+  upload_testpypi:
+    name: Upload to TestPyPI
+    needs: [build, test_artifacts]
+    if: github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    environment:
+      name: zarr-indexing-releases-test
+      url: https://test.pypi.org/p/zarr-indexing
+    permissions:
+      id-token: write
+      attestations: write
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: zarr-indexing-dist
+          path: dist
+
+      - name: Generate artifact attestation
+        uses: actions/attest@f7c74d28b9d84cb8768d0b8ca14a4bac6ef463e6 # v4.2.0
+        with:
+          subject-path: dist/*
+
+      - name: Publish package to TestPyPI
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
+        with:
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/zarr-indexing.yml

@@ -0,0 +1,102 @@
+name: zarr-indexing
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'packages/zarr-indexing/**'
+      - '.github/workflows/zarr-indexing.yml'
+  pull_request:
+    paths:
+      - 'packages/zarr-indexing/**'
+      - '.github/workflows/zarr-indexing.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: pytest py=${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.12', '3.13', '3.14']
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+        with:
+          persist-credentials: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        with:
+          enable-cache: true
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+      # The transform tests exercise chunk resolution against zarr's ChunkGrid,
+      # so they run from the repo root against the full workspace (which installs
+      # both `zarr` and the `zarr-indexing` workspace member) rather than in
+      # package isolation.
+      - name: Sync test dependency group
+        run: uv sync --all-packages --group test --python ${{ matrix.python-version }}
+      - name: Run pytest
+        run: uv run --no-sync --group test pytest packages/zarr-indexing/tests
+
+  ruff:
+    name: ruff
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+        working-directory: packages/zarr-indexing
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+        with:
+          persist-credentials: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+      - name: Run ruff
+        run: uvx ruff check .
+
+  pyright:
+    name: pyright
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+        working-directory: packages/zarr-indexing
+    steps:
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
+        with:
+          persist-credentials: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        with:
+          enable-cache: true
+      - name: Set up Python
+        run: uv python install 3.12
+      - name: Sync test dependency group
+        run: uv sync --group test --python 3.12
+      - name: Run pyright
+        run: uv run --group test --with pyright pyright src
+
+  zarr-indexing-complete:
+    name: zarr-indexing complete
+    needs: [test, ruff, pyright]
+    if: always()
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check failure
+        if: |
+          contains(needs.*.result, 'failure') ||
+          contains(needs.*.result, 'cancelled')
+        run: exit 1
+      - name: Success
+        run: echo Success!

packages/zarr-indexing/CHANGELOG.md

@@ -0,0 +1,3 @@
+# Release notes
+
+<!-- towncrier release notes start -->

packages/zarr-indexing/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2015-2025 Zarr Developers <https://github.com/zarr-developers>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

packages/zarr-indexing/README.md

@@ -0,0 +1,30 @@
+# zarr-indexing
+
+Composable, lazy coordinate transforms for Zarr array indexing.
+
+This package implements TensorStore-inspired index transforms. The core idea:
+every indexing operation (slicing, fancy indexing, etc.) produces a coordinate
+mapping from user space to storage space. These mappings compose lazily — no
+I/O until you explicitly read or write.
+
+Key types:
+
+- `IndexDomain` — a rectangular region of integer coordinates
+- `IndexTransform` — maps input coordinates to storage coordinates
+- `ConstantMap`, `DimensionMap`, `ArrayMap` — the three ways a single output
+  dimension can depend on the input
+- `compose` — chain two transforms into one
+
+The package depends only on NumPy and the standard library; it does not import
+`zarr`. It is developed in the [zarr-python](https://github.com/zarr-developers/zarr-python)
+repository and consumed by `zarr` to resolve array indexing operations.
+
+## Installation
+
+```bash
+pip install zarr-indexing
+```
+
+## License
+
+MIT

packages/zarr-indexing/changes/3906.feature.md

@@ -0,0 +1 @@
+Reworked the JSON layer to conform to the [ndsel](https://github.com/d-v-b/ndsel) draft wire format, which adapts TensorStore's `IndexTransform`. A new `zarr_indexing.messages` module (`parse_ndsel`, `normalize_ndsel`, `NdselError`) is a pure JSON-to-JSON layer that accepts all five message kinds (`point`/`box`/`slice`/`points`/`transform`) and normalizes them to the canonical transform body, enforcing the full ndsel error taxonomy. The package is checked against the vendored, language-agnostic ndsel conformance corpus. `index_transform_to_json`/`index_transform_from_json` (and the domain variants) now produce and consume the canonical body. On serialization, orthogonal (`oindex`) `index_array` maps no longer emit `input_dimension` alongside `index_array` (a combination both ndsel and TensorStore reject), and degenerate all-singleton index arrays collapse to constant maps; the in-memory `input_dimension` is reconstructed from the array's dependency axes on load.

packages/zarr-indexing/changes/README.md

@@ -0,0 +1,25 @@
+Writing a changelog entry for `zarr-indexing`
+-----------------------------------------------
+
+Fragments in **this** directory are release notes for the `zarr-indexing`
+package only — kept separate from the parent zarr-python `changes/`
+directory so a PR touching only `packages/zarr-indexing/` produces a
+release note for this package only.
+
+Please put a new file in this directory named `xxxx.<type>.md`, where
+
+- `xxxx` is the pull request number associated with this entry
+- `<type>` is one of:
+  - feature
+  - bugfix
+  - doc
+  - removal
+  - misc
+
+Inside the file, please write a short description of what you have
+changed, and how it impacts users of `zarr-indexing`.
+
+A `zarr-indexing` release runs `towncrier build` in `packages/zarr-indexing/`,
+which consumes the fragments here and updates `CHANGELOG.md`. Fragments
+that describe parent zarr-python changes (not the transforms package)
+belong in the top-level `changes/` directory, not here.