Merge branch 'main' into partial-reading

Author: LucaMarconato

.github/ISSUE_TEMPLATE/bug_report.md

@@ -46,8 +46,8 @@ If applicable, add screenshots to help explain your problem.
 
 **Desktop (optional):**
 
--   OS: [e.g. macOS, Windows, Linux]
--   Version [e.g. 22]
+- OS: [e.g. macOS, Windows, Linux]
+- Version [e.g. 22]
 
 **Additional context**
 Add any other context about the problem here.

.github/release.yml

@@ -0,0 +1,22 @@
+changelog:
+    exclude:
+        labels:
+            - release-ignore
+        authors:
+            - pre-commit-ci
+    categories:
+        - title: Major
+          labels:
+              - "release-major"
+        - title: Minor
+          labels:
+              - "release-minor"
+        - title: Changed
+          labels:
+              - "release-changed"
+        - title: Fixed
+          labels:
+              - "release-fixed"
+        - title: Other Changes
+          labels:
+              - "*"

.github/workflows/build.yaml

@@ -5,26 +5,26 @@ on:
         types: [published]
 
 jobs:
-    release:
-        # requires that you have put your twine API key in your
-        # github secrets (see readme for details)
+    package_and_release:
         runs-on: ubuntu-latest
-        if: contains(github.ref, 'tags')
+        if: startsWith(github.ref, 'refs/tags/v')
         steps:
-            - name: Checkout code
-              uses: actions/checkout@v3
-
+            - uses: actions/checkout@v3
             - name: Set up Python 3.12
               uses: actions/setup-python@v4
               with:
                   python-version: "3.12"
-
+                  cache: pip
+            - name: Install build dependencies
+              run: python -m pip install --upgrade pip wheel twine build
+            - name: Build package
+              run: python -m build
+            - name: Check package
+              run: twine check --strict dist/*.whl
             - name: Install hatch
               run: pip install hatch
-
             - name: Build project for distribution
               run: hatch build
-
             - name: Publish a Python distribution to PyPI
               uses: pypa/gh-action-pypi-publish@release/v1
               with:

.github/workflows/release.yaml

@@ -18,11 +18,11 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python: ["3.9", "3.12"]
+                python: ["3.10", "3.12"]
                 os: [ubuntu-latest]
                 include:
                     - os: macos-latest
-                      python: "3.9"
+                      python: "3.10"
                     - os: macos-latest
                       python: "3.12"
                       pip-flags: "--pre"

.github/workflows/test.yaml

@@ -17,7 +17,9 @@ __pycache__/
 /data/
 
 # docs
-/docs
+docs/_build
+!docs/api/.md
+docs/**/generated
 
 # IDEs
 /.idea/
@@ -29,8 +31,6 @@ __pycache__/
 # temp files
 temp/
 
-# rst generated from myst
-docs/generated
 
 # symlinks (luca) for extending the refactoring to satellite projects
 napari-spatialdata
@@ -47,3 +47,5 @@ _version.py
 
 # other
 node_modules/
+
+.asv/

.gitignore

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.9
+python_version = 3.10
 plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False

.mypy.ini

@@ -2,32 +2,32 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 ci:
     skip: []
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.8.0
+      rev: 24.10.0
       hooks:
           - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.8
+    - repo: https://github.com/rbubley/mirrors-prettier
+      rev: v3.4.2
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.18.0
+      rev: 1.19.1
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.11.2
+      rev: v1.14.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.6.8
+      rev: v0.9.1
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]