Update instance repo (PR 443 -- feat: runnable bug repots)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-  "commit": "a370e73f7e342f377fee8e902111bbe2bca30b3b",
+  "commit": "ca6fc800653f9b1dc1f2025b5b2637c4db7e6167",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -36,7 +36,7 @@
         "trim_blocks": true
       },
       "_template": "/home/runner/work/cookiecutter-scverse/cookiecutter-scverse",
-      "_commit": "a370e73f7e342f377fee8e902111bbe2bca30b3b"
+      "_commit": "ca6fc800653f9b1dc1f2025b5b2637c4db7e6167"
     }
   },
   "directory": null

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,6 +1,6 @@
 name: Bug report
 description: Report something that is broken or incorrect
-labels: bug
+type: Bug
 body:
   - type: markdown
     attributes:
@@ -9,8 +9,7 @@ body:
         detailing how to provide the necessary information for us to reproduce your bug. In brief:
           * Please provide exact steps how to reproduce the bug in a clean Python environment.
           * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
-          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
-            available datasets or to share a subset of your data.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
 
   - type: textarea
     id: report
@@ -20,6 +19,31 @@ body:
     validations:
       required: true
 
+  - type: textarea
+    id: code
+    attributes:
+      label: Minimal code sample
+      description: |
+        Reproducible code sample. Must list dependencies in [inline script metadata][]. When put in a file named `issue.py` using [uv run][] i.e., `uv run issue.py`, should show the issue.
+
+        [uv run]: https://docs.astral.sh/uv/guides/scripts/#running-a-script-with-dependencies
+        [inline script metadata]: https://packaging.python.org/en/latest/specifications/inline-script-metadata/#example
+      render: python
+      value: |
+        ```python
+        # /// script
+        # requires-python = ">=3.12"
+        # dependencies = [
+        #   "cookiecutter_scverse_instance@git+https://github.com/scverse/cookiecutter-scverse-instance.git@main",
+        # ]
+        # ///
+        #
+        # This script automatically imports the development branch of cookiecutter_scverse_instance to check for issues
+
+        import cookiecutter_scverse_instance
+        # your reproducer code
+          ```
+
   - type: textarea
     id: versions
     attributes:

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,6 +1,6 @@
 name: Feature request
 description: Propose a new feature for cookiecutter-scverse-instance
-labels: enhancement
+type: Enhancement
 body:
   - type: textarea
     id: description

.github/workflows/test.yaml

@@ -55,6 +55,7 @@ jobs:
 
     name: ${{ matrix.env.label }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ contains(matrix.env.name, 'pre') }}  # make "all-green" pass even if pre-release job fails
 
     steps:
       - uses: actions/checkout@v5

.readthedocs.yaml

@@ -4,6 +4,7 @@ build:
   os: ubuntu-24.04
   tools:
     python: "3.13"
+    nodejs: latest
   jobs:
     create_environment:
       - asdf plugin add uv

docs/conf.py

@@ -5,11 +5,14 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Path setup --------------------------------------------------------------
+import shutil
 import sys
 from datetime import datetime
 from importlib.metadata import metadata
 from pathlib import Path
 
+from sphinxcontrib import katex
+
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE / "extensions"))
 
@@ -54,9 +57,9 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinxcontrib.bibtex",
+    "sphinxcontrib.katex",
     "sphinx_autodoc_typehints",
     "sphinx_tabs.tabs",
-    "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
     "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
@@ -124,6 +127,7 @@
 }
 
 pygments_style = "default"
+katex_prerender = shutil.which(katex.NODEJS_BINARY) is not None
 
 nitpick_ignore = [
     # If building the documentation fails because of a missing link that is outside your control,

pyproject.toml

@@ -27,42 +27,42 @@ dependencies = [
   # for debug logging (referenced from the issue template)
   "session-info2",
 ]
-optional-dependencies.dev = [
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Documentation = "https://cookiecutter-scverse-instance.readthedocs.io/"
+urls.Homepage = "https://github.com/scverse/cookiecutter-scverse-instance"
+urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
+
+[dependency-groups]
+dev = [
   "pre-commit",
   "twine>=4.0.2",
 ]
-optional-dependencies.doc = [
-  "docutils>=0.8,!=0.18.*,!=0.19.*",
+test = [
+  "coverage>=7.10",
+  "pytest",
+  "pytest-cov",     # For VS Code’s coverage functionality
+]
+doc = [
   "ipykernel",
   "ipython",
   "myst-nb>=1.1",
   "pandas",
-  # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
-  "setuptools",
   "sphinx>=8.1",
   "sphinx-autodoc-typehints",
   "sphinx-book-theme>=1",
   "sphinx-copybutton",
   "sphinx-tabs",
   "sphinxcontrib-bibtex>=1",
+  "sphinxcontrib-katex",
   "sphinxext-opengraph",
 ]
-optional-dependencies.test = [
-  "coverage>=7.10",
-  "pytest",
-  "pytest-cov",     # For VS Code’s coverage functionality
-]
-# https://docs.pypi.org/project_metadata/#project-urls
-urls.Documentation = "https://cookiecutter-scverse-instance.readthedocs.io/"
-urls.Homepage = "https://github.com/scverse/cookiecutter-scverse-instance"
-urls.Source = "https://github.com/scverse/cookiecutter-scverse-instance"
 
 [tool.hatch.envs.default]
 installer = "uv"
-features = [ "dev" ]
+dependency-groups = [ "dev" ]
 
 [tool.hatch.envs.docs]
-features = [ "doc" ]
+dependency-groups = [ "doc" ]
 scripts.build = "sphinx-build -M html docs docs/_build -W {args}"
 scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
 scripts.clean = "git clean -fdX -- {args:docs}"
@@ -78,7 +78,7 @@ deps = [ "pre" ]
 python = [ "3.14" ]
 
 [tool.hatch.envs.hatch-test]
-features = [ "dev", "test" ]
+dependency-groups = [ "dev", "test" ]
 
 [tool.hatch.envs.hatch-test.overrides]
 # If the matrix variable `deps` is set to "pre",
@@ -127,9 +127,9 @@ lint.per-file-ignores."docs/*" = [ "I" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.pydocstyle.convention = "numpy"
 
-[tool.pytest.ini_options]
+[tool.pytest]
+strict = true
 testpaths = [ "tests" ]
-xfail_strict = true
 addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]

src/cookiecutter_scverse_instance/pp/basic.py

@@ -29,18 +29,25 @@ def basic_preproc(adata: AnnData) -> int:
 def elaborate_example(
     items: Iterable[ScverseDataStructures],
     transform: Callable[[Any], str],
-    *,  # functions after the asterix are key word only arguments
+    *,  # functions after the asterix are keyword-only arguments
     layer_key: str | None = None,
-    mudata_mod: str | None = "rna",  # Only specify defaults in the signature, not the docstring!
+    # Only specify defaults and types in the signature, not the docstring!
+    mudata_mod: str | None = "rna",
     sdata_table_key: str | None = "table1",
     max_items: int = 100,
 ) -> list[str]:
-    """A method with a more complex docstring.
+    r"""A method with a more complex docstring.
 
     This is where you add more details.
     Try to support general container classes such as Sequence, Mapping, or Collection
     where possible to ensure that your functions can be widely used.
 
+    Data science means there’s lots of math too:
+
+    ..  math::
+
+        x = \frac{-b \pm \sqrt{b^2-4ac}}{2a}
+
     Parameters
     ----------
     items
@@ -77,10 +84,11 @@ def elaborate_example(
         elif isinstance(item, SpatialData):
             matrix = item.tables[sdata_table_key].X if not layer_key else item.tables[sdata_table_key].layers[layer_key]
         else:
-            raise ValueError(f"Item {item} must be of type AnnData, MuData, or SpatialData but is {item.__class__}.")
-
+            msg = f"Item {item} must be of type AnnData, MuData, or SpatialData but is {item.__class__}."
+            raise ValueError(msg)
         if not isinstance(matrix, np.ndarray):
-            raise ValueError(f"Item {item} matrix is not a Numpy matrix but of type {matrix.__class__}")
+            msg = f"Item {item} matrix is not a Numpy matrix but of type {matrix.__class__}"
+            raise ValueError(msg)
 
         result.append(transform(matrix.flatten()))