Merge branch 'main' into creation-from-other-zarr

# Conflicts:
#	tests/test_array.py

Author: brokkoli71

.github/workflows/test.yml

@@ -94,13 +94,38 @@ jobs:
       run: |
         hatch env run --env ${{ matrix.dependency-set }} run
 
+  doctests:
+    name: doctests
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.13'
+        cache: 'pip'
+    - name: Install Hatch
+      run: |
+        python -m pip install --upgrade pip
+        pip install hatch
+    - name: Set Up Hatch Env
+      run: |
+        hatch env create doctest
+        hatch env run -e doctest list-env
+    - name: Run Tests
+      run: |
+        hatch env run --env doctest run
+
   test-complete:
     name: Test complete
 
     needs:
       [
         test,
         test-upstream-and-min-deps,
+        doctests
       ]
     if: always()
     runs-on: ubuntu-latest
@@ -111,4 +136,4 @@ jobs:
           contains(needs.*.result, 'cancelled')
         run: exit 1
       - name: Success
-        run: echo Success!
+        run: echo Success!

.gitignore

@@ -51,7 +51,10 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
-docs/_autoapi
+docs/api
+docs/data
+data
+data.zip
 
 # PyBuilder
 target/

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.2
+    rev: v0.8.6
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
@@ -22,7 +22,7 @@ repos:
     - id: check-yaml
     - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
       - id: mypy
         files: src|tests

data/donotdelete

@@ -52,7 +52,7 @@ help:
 .PHONY: clean
 clean:
 	rm -rf $(BUILDDIR)/*
-	rm -rf $(BUILDDIR)/../_autoapi
+	rm -rf $(BUILDDIR)/../api
 
 .PHONY: html
 html:

docs/Makefile

@@ -0,0 +1,24 @@
+About
+=====
+
+Zarr is a format for the storage of chunked, compressed, N-dimensional arrays
+inspired by `HDF5 <https://www.hdfgroup.org/HDF5/>`_, `h5py
+<https://www.h5py.org/>`_ and `bcolz <https://bcolz.readthedocs.io/>`_.
+
+These documents describe the Zarr-Python implementation. More information
+about the Zarr format can be found on the `main website <https://zarr.dev>`_.
+
+Projects using Zarr
+-------------------
+
+If you are using Zarr-Python, we would `love to hear about it
+<https://github.com/zarr-developers/community/issues/19>`_.
+
+Funding
+-------
+The project is fiscally sponsored by `NumFOCUS <https://numfocus.org/>`_, a US
+501(c)(3) public charity, and development is supported by the
+`MRC Centre for Genomics and Global Health <https://www.cggh.org>`_
+and the `Chan Zuckerberg Initiative <https://chanzuckerberg.com/>`_.
+
+.. _NumCodecs: https://numcodecs.readthedocs.io/

docs/about.rst

@@ -17,6 +17,7 @@
 import sys
 from typing import Any
 
+import sphinx
 import sphinx.application
 
 from importlib.metadata import version as get_version
@@ -56,10 +57,24 @@
 autoapi_add_toctree_entry = False
 autoapi_generate_api_docs = True
 autoapi_member_order = "groupwise"
-autoapi_root = "_autoapi"
+autoapi_root = "api"
 autoapi_keep_files = True
 autoapi_options = [ 'members', 'undoc-members', 'show-inheritance', 'show-module-summary', 'imported-members', ]
 
+def skip_submodules(
+        app: sphinx.application.Sphinx,
+        what: str,
+        name: str,
+        obj: object,
+        skip: bool,
+        options: dict[str, Any]
+      ) -> bool:
+    # Skip documenting zarr.codecs submodules
+    # codecs are documented in the main zarr.codecs namespace
+    if what == "module" and name.startswith("zarr.codecs."):
+        skip = True
+    return skip
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -87,7 +102,13 @@
      "spec/v1": 'https://zarr-specs.readthedocs.io/en/latest/v1/v1.0.html',
      "spec/v2": "https://zarr-specs.readthedocs.io/en/latest/v2/v2.0.html",
      "spec/v3": "https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html",
-     "license": "https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt"
+     "license": "https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt",
+     "tutorial": "user-guide",
+     "getting-started": "quickstart",
+     "release": "developers/release.html",
+     "roadmap": "developers/roadmap.html",
+     "installation": "user-guide/installation.html",
+     "api": "api/zarr/index"
 }
 
 # The language for content autogenerated by Sphinx. Refer to documentation
@@ -179,6 +200,7 @@
 
 def setup(app: sphinx.application.Sphinx) -> None:
     app.add_css_file("custom.css")
+    app.connect("autoapi-skip-member", skip_submodules)
 
 
 # The name of an image file (relative to this directory) to use as a favicon of