Update template to v0.5.0

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "87a407a65408d75a949c0b54b19fd287475a56f8",
-  "checkout": "v0.4.0",
+  "commit": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1",
+  "checkout": "v0.5.0",
   "context": {
     "cookiecutter": {
       "project_name": "scverse-tutorials",
@@ -10,19 +10,33 @@
       "author_full_name": "scverse team",
       "author_email": "[email protected]",
       "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": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
       "_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": "94ef9fb6f9ad8cfe65a3d9575679c03c80c49cd1"
     }
   },
   "directory": null

.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]

.github/workflows/execute-nbs.yaml

@@ -48,7 +48,7 @@ jobs:
           activate-environment: tutorials
           channel-priority: flexible
           environment-file: environment.yml
-          miniforge-variant: Mambaforge
+          miniforge-variant: Miniforge3
           miniforge-version: latest
           use-mamba: true
           # some important packages are not available as .tar.bz2 anymore
@@ -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

.gitignore

@@ -8,18 +8,21 @@ __pycache__/
 # Temp files
 .DS_Store
 *~
+buck-out/
 
-# Virtual environments
+# Compiled files
 .venv/
 
-# Build artifacts
+# Distribution / packaging
 /dist/
+
+# Tests and coverage
+/data/
+/node_modules/
+
+# docs
 /docs/generated/
 /docs/_build/
 
 # User configuration
 /hatch.toml
-
-# IDEs
-/.idea/
-/.vscode/

.pre-commit-config.yaml

@@ -6,10 +6,15 @@ default_stages:
   - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.5.3
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v1.9.4
     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: v2.5.1
+    hooks:
+      - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.11.5
     hooks:

.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",
+    ],
+}

.vscode/launch.json

@@ -0,0 +1,33 @@
+{
+    // 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": "${workspaceFolder}/docs",
+            "console": "internalConsole",
+            "justMyCode": false,
+        },
+        {
+            "name": "Python: Debug Test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": ["debug-test"],
+            "console": "internalConsole",
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--color=yes",
+            },
+            "presentation": {
+                "hidden": true,
+            },
+        },
+    ],
+}

.vscode/settings.json

@@ -0,0 +1,18 @@
+{
+    "[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",
+    "python.testing.pytestEnabled": true,
+    "python.testing.pytestArgs": ["-vv", "--color=yes"],
+}

biome.jsonc

@@ -0,0 +1,16 @@
+{
+    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "formatter": { "useEditorconfig": true },
+    "overrides": [
+        {
+            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "json": {
+                "formatter": { "trailingCommas": "all" },
+                "parser": {
+                    "allowComments": true,
+                    "allowTrailingCommas": true,
+                },
+            },
+        },
+    ],
+}

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 %}
 

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",
@@ -89,14 +89,20 @@
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
     "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
 }
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", ".jupyter_cache"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "**.ipynb_checkpoints",
+    ".jupyter_cache",
+]
 
 
 # -- Options for HTML output -------------------------------------------------