Enable syntax highlighting in the markdown docs

mkdocs.yaml had no markdown_extensions block, so the fenced blocks in index.md,
workflow.md, api.md and basicusage.md rendered as unstyled <pre>: mkdocs' builtin
fenced_code marks a block up but nothing colours it. Add pymdownx.highlight and
superfences (plus admonition/attr_list/details, matching iscc) and label the one
unlabelled fence, the pip install in index.md, as bash.

Verified in the built HTML rather than just a passing build: 25 highlight blocks
across the four pages, and workflow.md's tables still render (toc/tables/
fenced_code are mkdocs builtins and survive an explicit extensions block).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Author: pedrofale

docs/index.md

@@ -12,7 +12,7 @@ Deep exponential families for single-cell data. scDEF learns hierarchies of cell
 ## Installation
 scDEF is available through [PyPI](https://pypi.org/project/scdef):
 
-```
+```bash
 pip install scdef
 ```
 

mkdocs.yaml

@@ -29,6 +29,25 @@ theme:
   custom_dir: docs/overrides/
 
 
+# Without pymdownx.highlight the fenced blocks in the .md pages render as plain
+# unstyled <pre> -- mkdocs' builtin `fenced_code` marks up the block but nothing
+# colours it. `toc` and `tables` are mkdocs builtins and stay enabled whether or
+# not they appear here; `toc` is repeated below only to set `permalink`.
+markdown_extensions:
+  - admonition
+  - attr_list
+  - tables
+  - pymdownx.details
+  - pymdownx.highlight:
+      anchor_linenums: true
+  # Highlights inline code carrying a shebang hint, e.g. `#!python model.fit()`.
+  - pymdownx.inlinehilite
+  # Superset of `fenced_code`; also what lets a fence sit inside a list item or
+  # an admonition without breaking out of it.
+  - pymdownx.superfences
+  - toc:
+      permalink: true
+
 plugins:
   - search
   - mkdocs-jupyter: