update docs to zarr3

Author: pattonw

.github/workflows/publish-docs.yaml

@@ -24,15 +24,13 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           mamba-version: "*"
           channels: conda-forge
           channel-priority: true
 
       - name: Install package and dependencies
-        run: |
-          pip install git+https://github.com/funkelab/funlib.learn.torch
-          python -m pip install --group docs -e .
+        run: python -m pip install --group docs -e .
 
       - name: Build documentation
         run: sphinx-build docs/source docs/build/html -b html

docs/source/conf.py

@@ -17,14 +17,13 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 
+import tomllib
 from datetime import datetime
 
-import tomli  # ty: ignore[unresolved-import]
-
 import gunpowder
 
 with open("../../pyproject.toml", "rb") as fh:
-    project = tomli.load(fh)["project"]
+    project = tomllib.load(fh)["project"]
 
 author_list = ", ".join([author["name"] for author in project["authors"]])
 

docs/source/tutorial_simple_pipeline.rst

@@ -681,7 +681,7 @@ node with its equivalent :class:`torch.Predict`.
 
     # prepare the zarr dataset to write to
     f = zarr.open('sample_data.zarr')
-    ds = f.create_dataset('prediction', shape=(1, 1, 512, 512))
+    ds = f.create_array('prediction', shape=(1, 1, 512, 512), dtype='float32')
     ds.attrs['resolution'] = (1, 1)
     ds.attrs['offset'] = (0, 0)
 

pyproject.toml

@@ -79,8 +79,8 @@ docs = [
     "sphinx>=7.4.7",
     "sphinx-rtd-theme>=3.1.0",
     "sphinx-togglebutton>=0.4.4",
-    "tomli>=2.4.0",
     "torch>=2.8.0",
+    "funlib.learn.torch @ git+https://github.com/funkelab/funlib.learn.torch",
 ]