Two issues to fix:

1. Need to add `linkify` to requirements.txt since we enabled it in MyST config:
```diff:docs/requirements.txt
myst-parser
sphinxcontrib.mermaid
-e .
numpydoc
sphinx_rtd_theme
sphinxcontrib-apidoc
+ linkify-it-py
```

2. Need to add `sphinx.ext.extlinks` to extensions since we're using the extlinks config:
```python:docs/conf.py
extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.napoleon',
    'sphinx.ext.viewcode',
    'sphinxcontrib.mermaid',
    'myst_parser',
    'sphinx.ext.extlinks'  # Add this line
]
```

This should fix both:
- The "Linkify enabled but not installed" error
- The "Unknown interpreted text role 'doi'" errors

The duplicate reference warnings are okay - they're just warnings about multiple footnotes using the same numbers, which is expected in our case since different functions have their own reference sections.

docs/conf.py

@@ -35,7 +35,8 @@
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
     'sphinxcontrib.mermaid',
-    'myst_parser'
+    'myst_parser',
+    'sphinx.ext.extlinks'
 ]
 
 extlinks = {

docs/requirements.txt

@@ -3,4 +3,5 @@ sphinxcontrib.mermaid
 -e .
 numpydoc
 sphinx_rtd_theme
-sphinxcontrib-apidoc
+sphinxcontrib-apidoc
+linkify-it-py