Update template to v0.6.0 (#241)

scverse-bot · flying-sheep · grst · web-flow · commit 6387a35074dd · 2025-09-30T11:53:58.000+02:00
Co-authored-by: Phil Schaf &lt;flying-sheep@web.de&gt;
Co-authored-by: Gregor Sturm &lt;mail@gregor-sturm.de&gt;
diff --git a/.cruft.json b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
-  "checkout": "v0.4.0",
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
   "context": {
     "cookiecutter": {
       "project_name": "scverse-tutorials",
@@ -10,19 +10,32 @@
       "author_full_name": "scverse team",
       "author_email": "core-team@scverse.org",
       "github_user": "scverse",
-      "project_repo": "https://github.com/scverse/scverse-tutorials",
+      "github_repo": "scverse-tutorials",
       "license": "BSD 3-Clause License",
+      "ide_integration": true,
       "_copy_without_render": [
         ".github/workflows/build.yaml",
         ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
+      "_exclude_on_template_update": [
+        ".github/ISSUE_TEMPLATE/**",
+        "environment.yml",
+        "*.md",
+        "src/**",
+        "docs/*.md",
+        "docs/notebooks/**",
+        "docs/references.bib",
+        "tests/**",
+        "tutorial-registry/**"
+      ],
       "_render_devdocs": false,
       "_jinja2_env_vars": {
         "lstrip_blocks": true,
         "trim_blocks": true
       },
-      "_template": "https://github.com/scverse/cookiecutter-scverse"
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
     }
   },
   "directory": null
diff --git a/.editorconfig b/.editorconfig
@@ -8,10 +8,7 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[*.{yml,yaml}]
-indent_size = 2
-
-[.cruft.json]
+[{*.{yml,yaml,toml},.cruft.json}]
 indent_size = 2
 
 [Makefile]
diff --git a/.github/workflows/execute-nbs.yaml b/.github/workflows/execute-nbs.yaml
@@ -83,6 +83,6 @@ jobs:
             jcache notebook merge $f $f
           done
 
-      - uses: stefanzweifel/git-auto-commit-action@v4
+      - uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: Render notebooks
diff --git a/.gitignore b/.gitignore
@@ -1,25 +1,22 @@
-# Caches
-/.*cache/
-/node_modules/
-/data/
-.ipynb_checkpoints/
-__pycache__/
-
 # Temp files
 .DS_Store
 *~
+buck-out/
 
-# Virtual environments
+# Compiled files
 .venv/
+__pycache__/
+.ipynb_checkpoints/
+.*cache/
 
-# Build artifacts
+# Distribution / packaging
 /dist/
-/docs/generated/
-/docs/_build/
 
-# User configuration
-/hatch.toml
+# Tests and coverage
+/data/
+/node_modules/
+/.coverage*
 
-# IDEs
-/.idea/
-/.vscode/
+# docs
+/docs/generated/
+/docs/_build/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,14 +6,19 @@ default_stages:
   - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.6.2
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v2.2.4
     hooks:
-      - id: prettier
+      - id: biome-format
+        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.6.0
+    hooks:
+      - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.1
+    rev: v0.13.2
     hooks:
-      - id: ruff
+      - id: ruff-check
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
@@ -31,23 +36,14 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
-  - repo: local
-    hooks:
-      - id: forbid-to-commit
-        name: Don't commit rej files
-        entry: |
-          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-          Fix the merge conflicts manually and remove the .rej files.
-        language: fail
-        files: '.*\.rej$'
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.34.0
+    rev: '0.34.0'
     hooks:
       - id: check-jsonschema
         files: "tutorial-registry/schema.json"
         args: ["--check-metaschema"]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.34.0
+    rev: '0.34.0'
     hooks:
       - id: check-jsonschema
         files: "tutorial-registry/tutorials/.*/meta.yaml"
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,16 +1,15 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.12"
-sphinx:
-  configuration: docs/conf.py
-  fail_on_warning: true
-python:
-  install:
-    - requirements: docs/patched-deps.txt
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+    build:
+      html:
+        - uvx hatch run docs:build
+        - mv docs/_build $READTHEDOCS_OUTPUT
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -0,0 +1,18 @@
+{
+    "recommendations": [
+        // GitHub integration
+        "github.vscode-github-actions",
+        "github.vscode-pull-request-github",
+        // Language support
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+        "ms-toolsai.jupyter",
+        "tamasfe.even-better-toml",
+        // Dependency management
+        "ninoseki.vscode-mogami",
+        // Linting and formatting
+        "editorconfig.editorconfig",
+        "charliermarsh.ruff",
+        "biomejs.biome",
+    ],
+}
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -0,0 +1,18 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Build Documentation",
+            "type": "debugpy",
+            "request": "launch",
+            "module": "sphinx",
+            "args": ["-M", "html", ".", "_build"],
+            "cwd": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+    ],
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,16 @@
+{
+    "[python][json][jsonc]": {
+        "editor.formatOnSave": true,
+    },
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "always",
+            "source.organizeImports": "always",
+        },
+    },
+    "[json][jsonc]": {
+        "editor.defaultFormatter": "biomejs.biome",
+    },
+    "python.analysis.typeCheckingMode": "basic",
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/biome.jsonc b/biome.jsonc
@@ -0,0 +1,17 @@
+{
+    "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+    "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "includes": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": { "trailingCommas": "all" },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -9,11 +9,11 @@
 {% block attributes %}
 {% if attributes %}
 Attributes table
-~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~
 
 .. autosummary::
 {% for item in attributes %}
-    ~{{ fullname }}.{{ item }}
+    ~{{ name }}.{{ item }}
 {%- endfor %}
 {% endif %}
 {% endblock %}
@@ -26,7 +26,7 @@ Methods table
 .. autosummary::
 {% for item in methods %}
     {%- if item != '__init__' %}
-    ~{{ fullname }}.{{ item }}
+    ~{{ name }}.{{ item }}
     {%- endif -%}
 {%- endfor %}
 {% endif %}
@@ -35,7 +35,7 @@ Methods table
 {% block attributes_documentation %}
 {% if attributes %}
 Attributes
-~~~~~~~~~~~
+~~~~~~~~~~
 
 {% for item in attributes %}
 
diff --git a/docs/conf.py b/docs/conf.py
@@ -35,7 +35,7 @@
 needs_sphinx = "4.0"
 
 html_context = {
-    "display_github": True,
+    "display_github": True,  # Integrate GitHub
     "github_user": "scverse",
     "github_repo": project_name,
     "github_version": "main",
@@ -56,6 +56,7 @@
     "sphinx_issues",
     "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
+    "sphinx_tabs.tabs",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
@@ -85,7 +86,11 @@
 nb_merge_streams = True
 typehints_defaults = "braces"
 
-source_suffix = {".rst": "restructuredtext", ".ipynb": "myst-nb", ".myst": "myst-nb"}
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".ipynb": "myst-nb",
+    ".myst": "myst-nb",
+}
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
@@ -117,14 +122,9 @@
 
 html_theme_options = {
     "repository_url": repository_url,
-    "repository_branch": "main",
+    "use_repository_button": True,
     "path_to_docs": "docs/",
     "navigation_with_keys": False,
-    "use_repository_button": True,
-    "launch_buttons": {
-        "binderhub_url": "https://mybinder.org",
-        # "colab_url": "https://colab.research.google.com",
-    },
 }
 
 pygments_style = "default"
diff --git a/docs/patched-deps.txt b/docs/patched-deps.txt
diff --git a/pyproject.toml b/pyproject.toml
