Merge branch 'v3' into hypothesis-tests

* v3: (22 commits)
  [v3] `Buffer` ensure correct subclass based on the `BufferPrototype` argument (zarr-developers#1974)
  Fix doc build (zarr-developers#1987)
  Fix doc build warnings (zarr-developers#1985)
  Automatically generate API reference docs (zarr-developers#1918)
  Update `RemoteStore.__str__` and add UPath tests (zarr-developers#1964)
  [v3] Elevate codec pipeline (zarr-developers#1932)
  0 dim arrays: indexing (zarr-developers#1980)
  `parse_shapelike` allows 0 (zarr-developers#1979)
  Clean up typing and docs for indexing (zarr-developers#1961)
  add json indentation to config (zarr-developers#1952)
  chore: update pre-commit hooks (zarr-developers#1973)
  Bump pypa/gh-action-pypi-publish in the actions group (zarr-developers#1969)
  chore: update pre-commit hooks (zarr-developers#1957)
  Update release.rst (zarr-developers#1960)
  doc: update release notes for 3.0.0.alpha (zarr-developers#1959)
  Basic working FsspecStore (zarr-developers#1785)
  Feature: Top level V3 API (zarr-developers#1884)
  Buffer Prototype Argument (zarr-developers#1910)
  Create issue-metrics.yml
  fixes bug in transpose (zarr-developers#1949)
  ...

Author: dcherian

.github/workflows/issue-metrics.yml

@@ -0,0 +1,42 @@
+name: Monthly issue metrics
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '3 2 1 * *'
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: issue metrics
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
+    steps:
+    - name: Get dates for last month
+      shell: bash
+      run: |
+        # Calculate the first day of the previous month
+        first_day=$(date -d "last month" +%Y-%m-01)
+
+        # Calculate the last day of the previous month
+        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+
+        #Set an environment variable with the date range
+        echo "$first_day..$last_day"
+        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+
+    - name: Run issue-metrics tool
+      uses: github/issue-metrics@v3
+      env:
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"'
+
+    - name: Create issue
+      uses: peter-evans/create-issue-from-file@v5
+      with:
+        title: Monthly issue metrics report
+        token: ${{ secrets.GITHUB_TOKEN }}
+        content-filepath: ./issue_metrics.md

.github/workflows/releases.yml

@@ -55,7 +55,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.8.14
+      - uses: pypa/gh-action-pypi-publish@v1.9.0
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.gitignore

@@ -51,7 +51,6 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
-docs/_autoapi/
 
 # PyBuilder
 target/

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.4.5'
+    rev: 'v0.4.9'
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

docs/api.rst

@@ -0,0 +1,7 @@
+API Reference
+=============
+
+.. toctree::
+    :maxdepth: 1
+
+    zarr

docs/api/attrs.rst

@@ -0,0 +1,5 @@
+zarr
+====
+
+.. autoapimodule:: zarr
+    :members:

docs/api/codecs.rst

@@ -15,13 +15,17 @@
 
 import os
 import sys
+from typing import Any
+
+import sphinx.application
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
 import zarr
+import sphinx
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -42,19 +46,21 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
-    "sphinx_automodapi.automodapi",
+    'autoapi.extension',
     "numpydoc",
     "sphinx_issues",
     "sphinx_copybutton",
     "sphinx_design",
 ]
 
-numpydoc_show_class_members = False
-numpydoc_class_members_toctree = False
 issues_github_path = "zarr-developers/zarr-python"
 
-automodapi_inheritance_diagram = False
-automodapi_toctreedirnm = "_autoapi"
+autoapi_dirs = ['../src/zarr']
+autoapi_add_toctree_entry = False
+autoapi_generate_api_docs = False
+autoapi_member_order = "groupwise"
+autoapi_root = "api"
+
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -166,8 +172,7 @@
 html_logo = "_static/logo1.png"
 
 
-# Add custom css
-def setup(app):
+def setup(app: sphinx.application.Sphinx) -> None:
     app.add_css_file("custom.css")
 
 

docs/api/convenience.rst

@@ -10,7 +10,7 @@ Zarr-Python
 
     getting_started
     tutorial
-    api
+    api/index
     spec
     release
     license
@@ -80,7 +80,7 @@ Zarr is a file storage format for chunked, compressed, N-dimensional arrays base
 
         +++
 
-        .. button-ref:: api
+        .. button-ref:: api/index
             :expand:
             :color: dark
             :click-parent: