Extend linting

.gitignore

@@ -1,50 +1,22 @@
-_build/
-data*
-results*
-logs*
-_issues.ipynb
-*/figures/*
-figures/*
-data/*
-write/*
-
-*.egg-info/
-.pytest_cache/
-.coverage
-cache/
-coverage.xml
-test.h5ad
-test_compr.h5ad
-test_no_compr.h5ad
-docs/_build
-archive/
-data/
-README.html
-scripts/
-test_notebooks.txt
-upload_to_pypi.sh
+/_build/
+/dist/
+*.h5ad
+*.zip
 
-# Ignore biomart file
-.pybiomart.sqlite
+/cache/
+/archive/
+/data/
+/write/
+/figures/
+/scripts/
 
-# always-ignore extensions
+# caches
 *~
-
-# Python / Byte-compiled / optimized / DLL
 __pycache__/
-*.py[cod]
-*.so
-.cache
+.ipynb_checkpoints/
+.*cache/
 
 # OS or Editor files and folders
 .DS_Store
 Thumbs.db
-.ipynb_checkpoints/
 .directory
-/.idea/
-/.vscode/
-/hatch.toml
-
-# always-ignore directories
-/dist/
-/build/

.pre-commit-config.yaml

@@ -15,15 +15,14 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.12.12
     hooks:
-      - id: ruff
-        types_or: [python, pyi, jupyter]
+      - id: ruff-check
         args: ["--fix"]
       - id: ruff-format
-        types_or: [python, pyi, jupyter]
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.6.0
     hooks:
-      - id: prettier
-        exclude_types:
-          - markdown
-        language_version: 21.5.0
+      - id: pyproject-fmt
+  - repo: https://github.com/biomejs/pre-commit
+    rev: v2.2.3
+    hooks:
+      - id: biome-format

.vscode/launch.json

@@ -0,0 +1,14 @@
+{
+	// https://go.microsoft.com/fwlink/?linkid=830387
+	"version": "0.2.0",
+	"configurations": [
+		{
+			"name": "Build docs",
+			"type": "debugpy",
+			"request": "launch",
+			"module": "sphinx",
+			"args": ["-M", "html", ".", "_build"],
+			"console": "internalConsole",
+		},
+	],
+}

.vscode/settings.json

@@ -0,0 +1,13 @@
+{
+	"[python]": {
+		"editor.formatOnSave": true,
+		"editor.defaultFormatter": "charliermarsh.ruff",
+		"editor.codeActionsOnSave": {
+			"source.fixAll": "always",
+			"source.organizeImports": "always",
+		},
+	},
+	"notebook.formatOnSave.enabled": true,
+	"python.terminal.activateEnvironment": true,
+	"python.analysis.typeCheckingMode": "basic",
+}

_static/css/custom.css

@@ -1,15 +1,15 @@
 body {
-  background-image: repeating-linear-gradient(
-    45deg,
-    var(--pst-color-danger-bg) 0,
-    var(--pst-color-danger-bg) 20px,
-    transparent 20px,
-    transparent 40px
-  );
+	background-image: repeating-linear-gradient(
+		45deg,
+		var(--pst-color-danger-bg) 0,
+		var(--pst-color-danger-bg) 20px,
+		transparent 20px,
+		transparent 40px
+	);
 }
 
 .bd-sidebar-primary,
 .bd-sidebar-secondary,
 body:not(.scrolled) .bd-header-article {
-  background-color: initial !important;
+	background-color: initial !important;
 }

basic-scrna-tutorial.ipynb

@@ -25,11 +25,13 @@
    "outputs": [],
    "source": [
     "# Core scverse libraries\n",
-    "import scanpy as sc\n",
+    "from __future__ import annotations\n",
+    "\n",
     "import anndata as ad\n",
     "\n",
     "# Data retrieval\n",
-    "import pooch"
+    "import pooch\n",
+    "import scanpy as sc"
    ]
   },
   {
@@ -185,9 +187,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.pp.calculate_qc_metrics(\n",
-    "    adata, qc_vars=[\"mt\", \"ribo\", \"hb\"], inplace=True, log1p=True\n",
-    ")"
+    "sc.pp.calculate_qc_metrics(adata, qc_vars=[\"mt\", \"ribo\", \"hb\"], inplace=True, log1p=True)"
    ]
   },
   {
@@ -604,12 +604,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": null,
    "id": "11bb19be-3df1-4a17-ad84-16b50a9348ea",
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Using the igraph implementation and a fixed number of iterations can be significantly faster, especially for larger datasets\n",
+    "# Using the igraph implementation and a fixed number of iterations can be significantly faster,\n",
+    "# especially for larger datasets\n",
     "sc.tl.leiden(adata, flavor=\"igraph\", n_iterations=2)"
    ]
   },
@@ -764,9 +765,7 @@
    "outputs": [],
    "source": [
     "for res in [0.02, 0.5, 2.0]:\n",
-    "    sc.tl.leiden(\n",
-    "        adata, key_added=f\"leiden_res_{res:4.2f}\", resolution=res, flavor=\"igraph\"\n",
-    "    )"
+    "    sc.tl.leiden(adata, key_added=f\"leiden_res_{res:4.2f}\", resolution=res, flavor=\"igraph\")"
    ]
   },
   {
@@ -1052,9 +1051,7 @@
     }
    ],
    "source": [
-    "sc.pl.rank_genes_groups_dotplot(\n",
-    "    adata, groupby=\"leiden_res_0.50\", standard_scale=\"var\", n_genes=5\n",
-    ")"
+    "sc.pl.rank_genes_groups_dotplot(adata, groupby=\"leiden_res_0.50\", standard_scale=\"var\", n_genes=5)"
    ]
   },
   {
@@ -1214,7 +1211,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "notebook",
    "language": "python",
    "name": "python3"
   },
@@ -1228,7 +1225,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.13.7"
   },
   "mystnb": {
    "execution_mode": "off"

biome.jsonc

@@ -0,0 +1,18 @@
+{
+	"$schema": "https://biomejs.dev/schemas/2.1.1/schema.json",
+	"formatter": { "useEditorconfig": true },
+	"overrides": [
+		{
+			"includes": ["./.vscode/*.json", "**/*.jsonc", "**/asv.conf.json"],
+			"json": {
+				"formatter": {
+					"trailingCommas": "all",
+				},
+				"parser": {
+					"allowComments": true,
+					"allowTrailingCommas": true,
+				},
+			},
+		},
+	],
+}

conf.py

@@ -1,8 +1,9 @@
-from collections.abc import Mapping
-from datetime import datetime
+from __future__ import annotations
+
+from datetime import UTC, datetime
 from importlib.metadata import metadata
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Sequence
+from typing import TYPE_CHECKING, ClassVar
 
 from docutils import nodes
 from sphinx import addnodes
@@ -11,7 +12,10 @@
 from sphinx.ext.intersphinx import resolve_reference_in_inventory
 from sphinx.util.docutils import SphinxDirective
 
+
 if TYPE_CHECKING:
+    from collections.abc import Mapping, Sequence
+
     from docutils.parsers.rst.states import Inliner
     from sphinx.application import Sphinx
     from sphinx.environment import BuildEnvironment
@@ -20,7 +24,7 @@
 meta = metadata("scanpy-tutorials")
 project = meta["Name"]
 author = meta["Author"]
-copyright = f"{datetime.now():%Y}, {author}"
+copyright = f"{datetime.now(UTC):%Y}, {author}"  # noqa: A001
 release = version = meta["Version"]
 
 extensions = [
@@ -48,7 +52,6 @@
     anndata=("https://anndata.readthedocs.io/en/stable/", None),
     scanpy=("https://scanpy.readthedocs.io/en/stable/", None),
 )
-# TODO: move images here from scanpy
 suppress_warnings = ["image.not_readable"]
 
 # -- Options for HTML output ----------------------------------------------
@@ -88,6 +91,7 @@ def fake_cite(
     options: Mapping[str, object] = MappingProxyType({}),
     content: Sequence[str] = (),
 ) -> tuple[list[nodes.Node], list[str]]:
+    del name, lineno, options, content
     msg = f"cite:{text}"
     return [
         inliner.document.reporter.info(msg),
@@ -96,16 +100,15 @@ def fake_cite(
 
 
 class FakeDomain(Domain):
-    name = "cite"
-    roles = dict(p=fake_cite, t=fake_cite)
+    name: ClassVar = "cite"
+    roles: ClassVar = dict(p=fake_cite, t=fake_cite)
 
 
 # Role linking to the canonical location in scanpy’s docs
 
 
 MSG = (
-    "Please access this document in its canonical location "
-    "as the currently accessed page may not be rendered correctly"
+    "Please access this document in its canonical location as the currently accessed page may not be rendered correctly"
 )
 
 
@@ -144,6 +147,7 @@ def missing_reference(
     node: addnodes.pending_xref,
     contnode: nodes.TextElement,
 ) -> nodes.Node | None:
+    del app, env, contnode
     # ignore known scanpy labels
     if node["reftarget"] in {
         "external-data-integration",