update dependencies

Author: pattonw

.github/workflows/publish-docs.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/test.yml

@@ -0,0 +1,31 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - "*"
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.10", "3.11", "3.12" ]
+        platform: [ ubuntu-latest ]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Run tests
+        run: uv run --python=${{ matrix.python-version }} --group dev pytest -v --color
+          yes --cov gunpowder --cov-report xml
+
+      - uses: codecov/codecov-action@v3

pyproject.toml

@@ -38,32 +38,12 @@ dependencies = [
     "augment-nd>=0.1.3",
     "tqdm",
     "funlib.geometry>=0.3",
-    "zarr>=2,<3",
+    "zarr>=3",
     "networkx>=3.1",
     "funlib.persistence>=0.7",
 ]
 
 [project.optional-dependencies]
-dev = [
-    "pytest",
-    "pytest-cov",
-    "flake8",
-    "mypy",
-    "types-requests",
-    "types-tqdm",
-    "black>=26",
-    "ruff",
-]
-docs = [
-    "sphinx",
-    "sphinx_rtd_theme",
-    "sphinx_togglebutton",
-    "tomli",
-    "jupyter_sphinx",
-    "ipykernel",
-    "matplotlib",
-    "torch",
-]
 pytorch = ['torch']
 tensorflow = [
     # TF doesn't provide <2.0 wheels for py>=3.8 on pypi