Merge pull request #233 from funkelab/zarr3

Zarr3

Author: pattonw

.claude/settings.local.json

@@ -0,0 +1,7 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(uv run *)"
+    ]
+  }
+}

.github/workflows/black.yaml

@@ -32,7 +32,7 @@ jobs:
       - name: Install package and dependencies
         run: |
           pip install git+https://github.com/funkelab/funlib.learn.torch
-          python -m pip install -e .[docs]
+          python -m pip install --group docs -e .
 
       - name: Build documentation
         run: sphinx-build docs/source docs/build/html -b html

.github/workflows/mypy.yaml

@@ -6,29 +6,15 @@ on:
 
 jobs:
   build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    name: Build and publish to PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v3
-        with:
-          python-version: "3.10"
-      - name: Install pypa/build
-        run: >-
-          python -m
-          pip install
-          build
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
-      - name: Publish distribution 📦 to PyPI
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - name: Build
+        run: uv build
+      - name: Publish to PyPI
         if: startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/publish-docs.yaml

@@ -0,0 +1,12 @@
+name: ruff
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - run: uv run --dev ruff check gunpowder tests

.github/workflows/publish.yaml

@@ -3,7 +3,7 @@ name: Tests
 on:
   push:
     branches:
-    - "*"
+      - "*"
   pull_request:
     branches:
       - master
@@ -15,8 +15,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
-        platform: [ubuntu-latest]
+        python-version: [ "3.12", "3.13" ]
+        platform: [ ubuntu-latest ]
 
     steps:
       - uses: actions/checkout@v3
@@ -25,6 +25,7 @@ jobs:
         uses: astral-sh/setup-uv@v7
 
       - name: Run tests
-        run: uv run --python=${{ matrix.python-version }} --extra dev pytest -v --color yes --cov gunpowder --cov-report xml
+        run: uv run --python=${{ matrix.python-version }} --group dev pytest -v --color
+          yes --cov gunpowder --cov-report xml
 
       - uses: codecov/codecov-action@v3

.github/workflows/ruff.yaml

@@ -0,0 +1,12 @@
+name: ty
+
+on: [push, pull_request]
+
+jobs:
+  typecheck:
+    name: Type Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - run: uv run --dev ty check

.github/workflows/test.yml

@@ -11,6 +11,7 @@ net_iter*
 *.hdf
 *.h5
 docs/_build/
+uv.lock
 
 # Byte-compiled / optimized / DLL files
 __pycache__/