Check links with HEAD request (#249)

grst · flying-sheep · web-flow · commit 4f98426901ae · 2025-11-13T19:32:28.000+01:00
Co-authored-by: Phil Schaf &lt;flying-sheep@web.de&gt;
Co-authored-by: flying-sheep &lt;291575+flying-sheep@users.noreply.github.com&gt;
diff --git a/.github/workflows/make-tutorials-json.yml b/.github/workflows/make-tutorials-json.yml
@@ -25,15 +25,11 @@ jobs:
           filter: blob:none
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-          cache: "pip" # caching pip dependencies
-      - name: Install dependencies for validation script
-        run: pip install .[registry]
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
       - name: Execute validation script and create output directory
         run: |
-          ./tutorial-registry/validate.py --outdir=build
+          uvx hatch run registry:validate --outdir build
 
       - name: Upload GitHub Pages artifact
         uses: actions/upload-pages-artifact@v3
diff --git a/docs/extensions/typed_returns.py b/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']}`)"
diff --git a/docs/notebooks/anndata_getting_started.ipynb b/docs/notebooks/anndata_getting_started.ipynb
diff --git a/docs/notebooks/basic-scrna-tutorial.ipynb b/docs/notebooks/basic-scrna-tutorial.ipynb
diff --git a/docs/notebooks/scverse_data_backed.ipynb b/docs/notebooks/scverse_data_backed.ipynb
diff --git a/docs/notebooks/scverse_data_interoperability.ipynb b/docs/notebooks/scverse_data_interoperability.ipynb
@@ -121,7 +121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,
diff --git a/docs/notebooks/tutorial_axes_anndata_mudata.ipynb b/docs/notebooks/tutorial_axes_anndata_mudata.ipynb
diff --git a/docs/notebooks/tutorial_concatenation_anndata_mudata.ipynb b/docs/notebooks/tutorial_concatenation_anndata_mudata.ipynb
@@ -119,9 +119,9 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1793: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1798: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
       "  utils.warn_names_duplicates(\"var\")\n",
-      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1793: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
+      "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/anndata/_core/anndata.py:1798: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.\n",
       "  utils.warn_names_duplicates(\"var\")\n",
       "/home/runner/miniconda3/envs/tutorials/lib/python3.12/site-packages/mudata/_core/mudata.py:947: UserWarning: var_names are not unique. To make them unique, call `.var_names_make_unique`.\n",
       "  warnings.warn(\n"
@@ -948,7 +948,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.12.12"
   },
   "vscode": {
    "interpreter": {
diff --git a/pyproject.toml b/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"
diff --git a/tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml b/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
diff --git a/tutorial-registry/tutorials/plotting-in-scanpy/meta.yaml b/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
diff --git a/tutorial-registry/validate.py b/tutorial-registry/validate.py
@@ -5,6 +5,7 @@
 
 import argparse
 import json
+import logging
 import shutil
 import sys
 from pathlib import Path
@@ -16,14 +17,17 @@
 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:
-    response = httpx.get(url)
+    logger.info(f"Testing URL: {url}")
+    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 +51,7 @@ 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 +147,8 @@ 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.",

Original file line number	Diff line number	Diff line change
`@@ -121,7 +121,7 @@`
`121`	`121`	`"name": "python",`
`122`	`122`	`"nbconvert_exporter": "python",`
`123`	`123`	`"pygments_lexer": "ipython3",`
`124`		`- "version": "3.12.11"`
	`124`	`+ "version": "3.12.12"`
`125`	`125`	`}`
`126`	`126`	`},`
`127`	`127`	`"nbformat": 4,`