add jupyter-book CI

.github/.kodiak.toml

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+# https://kodiakhq.com/docs/recipes
+version = 1
+
+[merge]
+method = "squash"
+block_on_neutral_required_check_runs = true
+  [merge.message]
+  title = "pull_request_title"
+  body  = "pull_request_body"
+  [merge.automerge_dependencies]
+  # auto merge all PRs opened by "dependabot" that are "minor" or "patch" version upgrades. "major" version upgrades will be ignored.
+  versions = ["minor", "patch"]
+  usernames = ["dependabot"]

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: daily
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: daily

.github/workflows/ci.yml

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+name: CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  NBCONVERT_JOBS: '4'
+  LITERATE_PROC: '3'
+  ALLOWERRORS: 'false'
+  CACHE_NUM: '1'
+  JULIA_CONDAPKG_BACKEND: 'Null'
+  JULIA_CI: 'true'
+  NBCACHE: '.cache'
+
+jobs:
+  CI:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      id: setup-python
+      with:
+        python-version: '3.x'
+    - name: Cache python
+      uses: actions/cache@v4
+      if: ${{ contains(runner.name, 'GitHub Actions') }}
+      id: cache-py
+      with:
+        key: ${{ runner.os }}-pip-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
+        path: |
+          ${{ env.pythonLocation }}/lib
+          ${{ env.pythonLocation }}/bin
+    - name: Install Python dependencies
+      if: ${{ !contains(runner.name, 'GitHub Actions') || steps.cache-py.outputs.cache-hit != 'true' }}
+      run: pip install -r requirements.txt
+    - name: Cache executed notebooks
+      uses: actions/cache@v4
+      id: cache-nb
+      with:
+        path: ${{ env.NBCACHE }}
+        key: ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}-${{ hashFiles('docs/**/*.ipynb', 'docs/**/*.jl') }}
+        restore-keys: |
+          ${{ runner.os }}-nb-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}-
+    - name: Read Julia version
+      id: read_toml
+      run: echo "value=$(python -c 'import tomllib; from pathlib import Path; print(tomllib.loads(Path("Manifest.toml").read_text())["julia_version"])')" >> "$GITHUB_OUTPUT"
+    - name: Setup Julia
+      uses: julia-actions/setup-julia@v2
+      with:
+        version: ${{ steps.read_toml.outputs.value }}
+    - name: Restore Julia packages
+      uses: actions/cache/restore@v4
+      if: ${{ contains(runner.name, 'GitHub Actions') }}
+      id: cache-julia
+      with:
+        path: |
+          ~/.julia
+          !~/.julia/registries
+        key: ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-${{ hashFiles('src/**', 'Project.toml', 'Manifest.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-julia-${{ env.CACHE_NUM }}-
+    - name: Install Julia packages
+      if: ${{ !contains(runner.name, 'GitHub Actions') || steps.cache-julia.outputs.cache-hit != 'true' }}
+      env:
+        PYTHON: ${{ steps.setup-python.outputs.python-path }}
+      shell: julia --color=yes {0}
+      run: |
+        using Pkg, Dates
+        Pkg.add(["IJulia", "Literate", "PrettyTables", "JSON"])
+        Pkg.activate(".")
+        Pkg.instantiate()
+        Pkg.precompile()
+        Pkg.gc(collect_delay=Day(0))
+    - name: Save Julia packages
+      uses: actions/cache/save@v4
+      if: ${{ contains(runner.name, 'GitHub Actions') && steps.cache-julia.outputs.cache-hit != 'true' }}
+      with:
+        path: |
+          ~/.julia
+          !~/.julia/registries
+        key: ${{ steps.cache-julia.outputs.cache-primary-key }}
+    - name: Run notebooks
+      run: julia --color=yes -p ${{ env.LITERATE_PROC }} --heap-size-hint=4G run.jl
+    - name: Copy back built notebooks
+      run: cp --verbose -rf ${{ env.NBCACHE }}/docs/* docs/
+    - name: Build website
+      run: jupyter-book build docs/
+    - name: Upload pages artifact
+      if: ${{ github.ref == 'refs/heads/main' }}
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: docs/_build/html/
+
+  # Deploy pages
+  deploy:
+    needs: CI
+    if: ${{ github.ref == 'refs/heads/main' }}
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write # to deploy to Pages
+      id-token: write # to verify the deployment originates from an appropriate source
+      actions: read   # to download an artifact uploaded by `actions/upload-pages-artifact@v3`
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/clear-cache.yml

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+name: Cleanup PR caches
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    permissions:
+      actions: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH -L 100 | cut -f 1 )
+
+          ## Setting this to not fail the workflow while deleting cache keys.
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          REPO: ${{ github.repository }}
+          BRANCH: refs/pull/${{ github.event.pull_request.number }}/merge

.github/workflows/linkcheck.yml

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+name: Check markdown links
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 1 * *' # Every month
+  push:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+      - '.github/workflows/linkcheck.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  linkcheck:
+    env:
+      DIR: 'docs'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+      - name: Convert literate notebooks to ipynb files
+        shell: julia --color=yes {0}
+        working-directory: ${{ env.DIR }}
+        run: |
+          import Pkg
+          Pkg.add("Literate")
+          using Literate
+          for (root, dirs, files) in walkdir(pwd())
+            for file in files
+              if endswith(file, ".jl")
+                nb = joinpath(root, file)
+                Literate.notebook(nb, dirname(nb); mdstrings=true, execute=false)
+              end
+            end
+          end
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: '3.x'
+      - name: Cache python
+        uses: actions/cache@v4
+        if: ${{ contains(runner.name, 'GitHub Actions') }}
+        id: cache-py
+        with:
+          key: ${{ runner.os }}-pip-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('requirements.txt') }}
+          path: |
+            ${{ env.pythonLocation }}/lib
+            ${{ env.pythonLocation }}/bin
+      - name: Install Python dependencies
+        if: ${{ !contains(runner.name, 'GitHub Actions') || steps.cache-py.outputs.cache-hit != 'true' }}
+        run: pip install -r requirements.txt
+      - name: Build website
+        run: jupyter-book build ${DIR} --builder linkcheck

.github/workflows/update-manifest.yml

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+name: Auto update Julia dependencies
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * 1' # Every week
+  push:
+    branches:
+      - main
+    paths:
+      - .github/workflows/update-manifest.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  APP_ID: '189113' # https://github.com/apps/wen-wei-s-pr-bot
+
+jobs:
+  update-manifest:
+    permissions:
+      contents: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - name: Update Julia dependencies
+        env:
+          JULIA_PKG_PRECOMPILE_AUTO: '0'
+        run: julia --project=@. --color=yes -e 'import Pkg; Pkg.update()'
+      # Authenticate with a custom GitHub APP
+      # https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md#authenticating-with-github-app-generated-tokens
+      - name: Generate token for PR
+        uses: tibdex/github-app-token@v2
+        id: generate-token
+        with:
+          app_id: ${{ env.APP_ID }}
+          private_key: ${{ secrets.APP_PRIVATE_KEY }}
+      - name: Create Pull Request
+        id: cpr
+        uses: peter-evans/create-pull-request@v6
+        with:
+          title: Julia Dependency Update
+          token: ${{ steps.generate-token.outputs.token }}
+          labels: |
+            automerge