Update documentation with newest microimpute changes and fix deployment

.github/workflows/deploy.yml

@@ -0,0 +1,48 @@
+# This file was created automatically with `myst init --gh-pages` 🪄 💚
+# Ensure your GitHub Pages settings for this repository are set to deploy with **GitHub Actions**.
+
+name: MyST GitHub Pages Deploy
+on:
+  push:
+    # Runs on pushes targeting the default branch
+    branches: [main]
+env:
+  # `BASE_URL` determines, relative to the root of the domain, the URL that your site is served from.
+  # E.g., if your site lives at `https://mydomain.org/myproject`, set `BASE_URL=/myproject`.
+  # If, instead, your site lives at the root of the domain, at `https://mydomain.org`, set `BASE_URL=''`.
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: 'pages'
+  cancel-in-progress: false
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 18.x
+      - name: Install MyST
+        run: npm install -g mystmd
+      - name: Build HTML Assets
+        run: myst build --html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: './_build/html'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/main.yml

@@ -30,7 +30,7 @@ jobs:
           sudo Rscript -e 'install.packages("clue", repos="https://cloud.r-project.org")'
       - name: Install Python dependencies
         run: |
-          uv pip install -e ".[dev,docs,matching]" --system
+          uv pip install -e ".[dev,docs,matching,images]" --system
       - name: Run tests with coverage
         run: make test
       - name: Upload coverage to Codecov
@@ -39,20 +39,3 @@ jobs:
           file: ./coverage.xml
           fail_ci_if_error: false
           verbose: true
-      - name: Test documentation builds
-        run: make documentation
-      - name: Check documentation build
-        run: |
-          for notebook in $(find docs/_build/jupyter_execute -name "*.ipynb"); do
-            if grep -q '"output_type": "error"' "$notebook"; then
-              echo "Error found in $notebook"
-              cat "$notebook"
-              exit 1
-            fi
-          done
-      - name: Deploy documentation
-        uses: JamesIves/github-pages-deploy-action@releases/v3
-        with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages  # The branch the action should deploy to.
-          FOLDER: docs/_build/html  # The folder the action should deploy.

.github/workflows/pr.yaml → .github/workflows/pr_code_changes.yaml

@@ -57,40 +57,4 @@ jobs:
         with:
           file: ./coverage.xml
           fail_ci_if_error: false
-          verbose: true
-
-  Build:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v3
-      - name: Install uv
-        uses: astral-sh/setup-uv@v5
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.13"
-      - name: Install R and dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y r-base r-base-dev libtirpc-dev
-      - name: Install R packages
-        run: |
-          sudo Rscript -e 'install.packages("StatMatch", repos="https://cloud.r-project.org")'
-          sudo Rscript -e 'install.packages("clue", repos="https://cloud.r-project.org")'
-      - name: Install dependencies
-        run: |
-          uv pip install -e ".[dev,docs,matching]" --system
-      - name: Build package
-        run: make build
-      - name: Test documentation builds
-        run: make documentation
-      - name: Check documentation build
-        run: |
-          for notebook in $(find docs/_build/jupyter_execute -name "*.ipynb"); do
-            if grep -q '"output_type": "error"' "$notebook"; then
-              echo "Error found in $notebook"
-              cat "$notebook"
-              exit 1
-            fi
-          done
+          verbose: true

.github/workflows/pr_docs_changes.yaml

@@ -0,0 +1,52 @@
+# Workflow that runs on code changes to a pull request.
+
+name: Docs changes
+on:
+  pull_request:
+    branches:
+      - main
+
+    paths:
+      - docs/**
+      - .github/**
+  workflow_dispatch:
+
+jobs:
+  Test:
+      runs-on: ubuntu-latest
+      name: Test documentation builds
+      steps:
+          - name: Checkout repo
+            uses: actions/checkout@v4
+          - name: Install uv
+            uses: astral-sh/setup-uv@v5
+
+          - name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.13'
+
+          - name: Install R and dependencies
+            run: |
+              sudo apt-get update
+              sudo apt-get install -y r-base r-base-dev libtirpc-dev
+          - name: Install R packages
+            run: |
+              sudo Rscript -e 'install.packages("StatMatch", repos="https://cloud.r-project.org")'
+              sudo Rscript -e 'install.packages("clue", repos="https://cloud.r-project.org")'
+          - name: Install dependencies
+            run: |
+              uv pip install -e ".[dev,docs,matching,images]" --system
+          - name: Install JB
+            run: uv pip install "jupyter-book>=2.0.0a0" --system
+          - name: Test documentation builds
+            run: make documentation
+          - name: Check documentation build
+            run: |
+              for notebook in $(find docs/_build/jupyter_execute -name "*.ipynb"); do
+                if grep -q '"output_type": "error"' "$notebook"; then
+                  echo "Error found in $notebook"
+                  cat "$notebook"
+                  exit 1
+                fi
+              done

.gitignore

@@ -78,4 +78,6 @@ celerybeat.pid
 *.csv
 *.jpg
 *.html
-*.h5
+*.h5
+# MyST build outputs
+_build

Makefile

@@ -15,8 +15,9 @@ format:
 	black . -l 79
 
 documentation:
-	cd docs && jupyter-book build .
-	python docs/add_plotly_to_book.py docs/_build/html
+	cd docs && jupyter book clean . --all
+	cd docs && jupyter book build .
+	python docs/add_plotly_to_book.py docs/_build
 
 build:
 	pip install build

changelog_entry.yaml

@@ -0,0 +1,5 @@
+- bump: patch
+  changes:
+    added:
+    - Moved data loading utilities into utils and removed scf downloading functionality.
+    - Updated documentation to reflect the new structure and created a myst.yml file to deploy documentation with new jb v2.

docs/_toc.yml

@@ -1,8 +1,6 @@
 format: jb-book
 root: index
-
 parts: 
-
   - caption: Models
     chapters:
       - file: models/imputer/index