From d699792ac14170a446e23a132cab7dff76e9d440 Mon Sep 17 00:00:00 2001
From: Jonathan Taylor <jonathan.taylor@stanford.edu>
Date: Tue, 27 Oct 2026 11:07:43 -0700
Subject: [PATCH] Docs: build with uv, without conda or R

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 .github/workflows/build_docs.yml | 26 +++++++++++++++++---------
 CHANGELOG.md                     |  8 ++++++++
 docs/make_notebooks.py           | 17 ++++++++++-------
 docs/requirements.txt            |  1 -
 4 files changed, 35 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index 1a69807..9ebd94b 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -21,17 +21,23 @@ jobs: # This workflow contains a single
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v7
-      - uses: actions/setup-python@v7
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v10.3.0
         with:
-          python-version: '3.12'
-          cache: 'pip'
-      # Install
-      - name: Install dependencies 
+          enable-cache: true
+          cache-dependency-glob: |
+            **/pyproject.toml
+            docs/requirements.txt
+
+      # a virtual environment, on the PATH of the later steps (no R: no page
+      # or lab runs it)
+      - name: Install dependencies
         run: |
-          sudo apt-get update
-          sudo apt-get install -y r-base libtirpc-dev
-          pip install -r docs/requirements.txt
-          pip install .
+          uv venv --python 3.12
+          echo "$PWD/.venv/bin" >> "$GITHUB_PATH"
+          uv pip install -r docs/requirements.txt
+          uv pip install .
 
       # Checkout labs
       - name: Checkout version of labs
@@ -60,6 +66,8 @@ jobs: # This workflow contains a single
   deploy:
     runs-on: ubuntu-latest
     needs: build
+    # (a run on another branch only builds, to try it)
+    if: github.ref == 'refs/heads/main'
 
     # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
     permissions:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index c76caa3..730dd39 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,14 @@
 [modelmatrix](https://github.com/intro-stat-learning/modelmatrix), which
 ISLP now depends on (`modelmatrix>=0.3`).
 
+### Documentation
+
+- **The docs build with uv, without conda or R**: the docs workflow
+  installs with uv, and `docs/make_notebooks.py` runs a lab in a uv
+  virtual environment (Python 3.12 by default) instead of a conda
+  environment. R and `rpy2` are no longer installed: no page or lab runs R.
+  A run of the workflow on a branch other than main only builds.
+
 ### Breaking changes
 
 - **`ModelSpec`'s `intercept` defaults to `False`**, as 0.6.0 announced. Pass
diff --git a/docs/make_notebooks.py b/docs/make_notebooks.py
index cfea244..57897c7 100644
--- a/docs/make_notebooks.py
+++ b/docs/make_notebooks.py
@@ -1,10 +1,12 @@
 '''
 Run notebooks in an isolated environment specified by a requirements.txt file
+(a virtual environment made with uv, https://docs.astral.sh/uv/)
 '''
 
 from hashlib import md5
 import tempfile
 import os
+import shutil
 from argparse import ArgumentParser
 
 
@@ -16,7 +18,7 @@
                     type=str,
                     nargs='+')
 parser.add_argument('--python',
-                    default='3.10')
+                    default='3.12')
 parser.add_argument('--tarball',
                     default=None,
                     dest='tarball')
@@ -36,7 +38,7 @@ def make_notebooks(requirements='requirements.txt',
                    tarball='',
                    inplace=False,
                    tmpdir='',
-                   python='3.10',
+                   python='3.12',
                    timeout=5000, # should be enough for Ch10
                    env_tag='',
                    ):
@@ -48,11 +50,12 @@ def make_notebooks(requirements='requirements.txt',
     md5_.update(open(requirements, 'rb').read());
     hash_ = md5_.hexdigest()[:8]
 
-    env_name = f'isolated_env_{hash_}' + env_tag
+    env_dir = os.path.join(tempfile.gettempdir(), f'isolated_env_{hash_}' + env_tag)
+    env_bin = os.path.join(env_dir, 'bin')
 
     setup_cmd = f'''
-    conda create -n {env_name} python={python} -y;
-    conda run -n {env_name} pip install -r {requirements} jupyter jupytext;
+    uv venv --python {python} {env_dir};
+    uv pip install --python {env_bin}/python -r {requirements} jupyter jupytext;
     '''
 
     print(setup_cmd)
@@ -64,7 +67,7 @@ def make_notebooks(requirements='requirements.txt',
         if src_ != dest_:
             os.system(f'cp {src_} {dest_}')
         name = os.path.split(dest_)[1]
-        build_cmd = f'''conda run -n {env_name} jupyter nbconvert --inplace --execute --ExecutePreprocessor.timeout={timeout} {dest_} '''
+        build_cmd = f'''{env_bin}/jupyter nbconvert --inplace --execute --ExecutePreprocessor.timeout={timeout} {dest_} '''
         if '02' in name:
             build_cmd += ' --allow-errors '
 
@@ -82,7 +85,7 @@ def make_notebooks(requirements='requirements.txt',
         print(tarball_cmd)
         os.system(tarball_cmd)
 
-    os.system(f'conda env remove -n {env_name}')
+    shutil.rmtree(env_dir, ignore_errors=True)
 
 if __name__ == '__main__':
 
diff --git a/docs/requirements.txt b/docs/requirements.txt
index b4f9d28..a053482 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -2,7 +2,6 @@ texext
 numpydoc
 myst_nb
 sphinx-book-theme
-rpy2
 sphinx_rtd_theme
 jupytext
 polars