Fix links in score-genes how-to (#199)

Author: flying-sheep

conf.py

@@ -40,18 +40,12 @@
 source_suffix = ".rst"
 master_doc = "index"
 language = "en"
-exclude_patterns = [
-    "_build",
-    "Thumbs.db",
-    ".DS_Store",
-    "**.ipynb_checkpoints",
-    "scanpy_workshop/*",
-]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "scanpy_workshop", ".*cache"]
 pygments_style = "sphinx"
 
 intersphinx_mapping = dict(
     anndata=("https://anndata.readthedocs.io/en/stable/", None),
-    scanpy=("https://scanpy.readthedocs.io/en/stable/", None),
+    scanpy=("https://scanpy.readthedocs.io/en/latest/", None),
 )
 suppress_warnings = ["image.not_readable"]
 
@@ -137,7 +131,7 @@ def run(self) -> list[nodes.Node]:
         )
         if ref is None:
             msg = f"Reference to scanpy:{text} not found"
-            raise AssertionError(msg)
+            raise self.warning(msg)
         desc = nodes.inline("", f"{MSG}: ")
         banner = nodes.danger(
             text,

how-to/cell-cycle.ipynb

@@ -495,8 +495,8 @@
    "metadata": {},
    "source": [
     "We here perform cell cycle scoring.\n",
-    "The function is actually a wrapper to {func}`scanpy.tl.score_gene_list`, which is launched twice, to score separately S and G2M phases.\n",
-    "Both {func}`scanpy.tl.score_gene_list` and {func}`scanpy.tl.score_cell_cycle_genes` are a port from _Seurat_ and are supposed to work in a very similar way. \n",
+    "The function is actually a wrapper to {func}`scanpy.tl.score_genes`, which is launched twice, to score separately S and G2M phases.\n",
+    "Both {func}`scanpy.tl.score_genes` and {func}`scanpy.tl.score_genes_cell_cycle` are a port from _Seurat_ and are supposed to work in a very similar way. \n",
     "To score a gene list, the algorithm calculates the difference of mean expression of the given list and the mean expression of reference genes.\n",
     "To build the reference, the function randomly chooses a bunch of genes matching the distribution of the expression of the given list.\n",
     "Cell cycle scoring adds three slots in data, a score for S phase, a score for G2M phase and the predicted cell cycle phase."