Bump python version

Author: grst

.github/workflows/make-tutorials-json.yml

@@ -31,7 +31,7 @@ jobs:
           cache-dependency-glob: pyproject.toml
       - name: Execute validation script and create output directory
         run: |
-          uv run validate --outdir=build
+          uvx hatch run registry:validate
 
       - name: Upload GitHub Pages artifact
         uses: actions/upload-pages-artifact@v3

docs/extensions/typed_returns.py

@@ -9,7 +9,7 @@
 from sphinx.ext.napoleon import NumpyDocstring
 
 
-def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
+def _process_return(lines: Iterable[str]) -> Generator[str]:
     for line in lines:
         if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
             yield f"-{m['param']} (:class:`~{m['type']}`)"

pyproject.toml

@@ -8,19 +8,12 @@ version = "0.0.1"
 description = "Tutorials for single-cell analysis with scverse packages"
 readme = "README.md"
 license = "BSD-3-Clause"
-maintainers = [
-  { name = "scverse team", email = "core-team@scverse.org" },
-]
-authors = [
-  { name = "scverse team" },
-]
-requires-python = ">=3.10"
+maintainers = [ { name = "scverse team", email = "core-team@scverse.org" } ]
+authors = [ { name = "scverse team" } ]
+requires-python = ">=3.13"
 classifiers = [
   "Private :: Do Not Upload",                    # Prevent uploading to PyPI
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
 ]
@@ -39,12 +32,7 @@ optional-dependencies.docs = [
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
-optional-dependencies.registry = [
-  "httpx",
-  "jsonschema",
-  "pillow",
-  "pyyaml",
-]
+optional-dependencies.registry = [ "httpx", "jsonschema", "pillow", "pyyaml" ]
 urls.Documentation = "https://scverse.org/scverse-tutorials"
 urls.Home-page = "https://github.com/scverse/scverse-tutorials"
 urls.Source = "https://github.com/scverse/scverse-tutorials"

tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml

@@ -2,7 +2,7 @@ name: Pseudo-bulk differential expression and functional analysis
 description: |
   This notebook showcases decoupler for pathway and TF enrichment on ~5k
   Blood myeloid cells from healthy and COVID-19 infected patients.
-link: https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html
+link: https://decoupler.readthedocs.io/en/latest/notebooks/scell/rna_psbk.html
 image: icon.png
 primary_category: scRNA-seq
 order: 30

tutorial-registry/tutorials/plotting-in-scanpy/meta.yaml

@@ -2,7 +2,7 @@ name: Plotting in scanpy
 description: |
   This tutorial explores the visualization possibilities of scanpy, including
   embeddings and the visualization of marker genes and differentially expressed genes.
-link: https://scanpy-tutorials.readthedocs.io/en/latest/plotting/core.html
+link: https://scanpy.readthedocs.io/en/stable/tutorials/plotting/core.html
 image: icon.png
 primary_category: Tips & Tricks
 order: 10

tutorial-registry/validate.py

@@ -5,6 +5,7 @@
 
 import argparse
 import json
+import logging
 import shutil
 import sys
 from pathlib import Path
@@ -16,13 +17,19 @@
 import yaml
 from PIL import Image
 
+logger = logging.getLogger(__name__)
+
 if TYPE_CHECKING:
     from collections.abc import Generator, Iterable, Mapping
 
 HERE = Path(__file__).absolute().parent
 
 
 def _check_url_exists(url: str) -> None:
+    logger.info(f"Testing URL: {url}")
+    import time
+
+    time.sleep(0.5)
     response = httpx.head(url, follow_redirects=True)
     if response.status_code != 200:
         raise ValueError(f"URL {url} is not reachable (error {response.status_code}). ")
@@ -47,7 +54,7 @@ def _check_image(img_path: Path) -> None:
         )
 
 
-def validate_tutorials(schema_file: Path, tutorials_dir: Path) -> Generator[dict, None, None]:
+def validate_tutorials(schema_file: Path, tutorials_dir: Path) -> Generator[dict]:
     """Find all tutorial `meta.yaml` files in the tutorials dir and yield tutorial records."""
     schema = json.loads(schema_file.read_bytes())
     known_links = set()
@@ -143,6 +150,8 @@ def main(schema_file: Path, meta_dir: Path, categories_file: Path, *, outdir: Pa
 
 
 if __name__ == "__main__":
+    logging.basicConfig(level=logging.INFO, format="%(message)s")
+
     parser = argparse.ArgumentParser(
         prog="validate.py",
         description="Validate tutorials' meta.yaml and generate an output directory with json/images to be uploaded on github pages.",