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‎.github/workflows/render-and-publish-incremental.yml‎

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on:
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push:
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branches:
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- main
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workflow_dispatch:
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inputs:
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publish:
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description: "Deploy to Pages (manual runs only)"
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type: boolean
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default: false
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name: Incremental Render and Publish
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permissions:
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contents: read
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env:
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SITE_CACHE_REPO: ${{ secrets.SITE_CACHE_REPO }}
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SITE_CACHE_TOKEN: ${{ secrets.SITE_CACHE_TOKEN }}
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0 # need history to get mtimes
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- name: Normalize source repo file mtimes to last commit
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run: |
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set -euo pipefail
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git ls-files -z | xargs -0 -I{} sh -c 'ts=$(git log -1 --format=%ct -- "{}" || true); if [ -n "$ts" ]; then touch -d "@$ts" "{}"; fi'
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- name: Restore `site` from cache repo without overwriting source controlled files
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run: |
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set -euo pipefail
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git clone "https://x-access-token:${SITE_CACHE_TOKEN}@github.com/${SITE_CACHE_REPO}.git" /tmp/site-cache
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cd /tmp/site-cache
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git ls-files -z -- site/ | xargs -0 -I{} sh -c 'ts=$(git log -1 --format=%ct -- "{}" || true); if [ -n "$ts" ]; then touch -d "@$ts" "{}"; fi'
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cd -
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rsync -a --ignore-existing /tmp/site-cache/site/ site/ || true
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echo "Contents of site/ after restore:"
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ls -lah site/ | head -50
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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pip install plotly kaleido
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- name: Set up Java
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uses: actions/setup-java@v4
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with:
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distribution: 'temurin'
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java-version: '21'
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- name: Set up Clojure
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uses: DeLaGuardo/setup-clojure@main
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with:
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cli: 'latest'
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- name: Cache clojure dependencies
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uses: actions/cache@v3
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with:
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path: |
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~/.m2/repository
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~/.gitlibs
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~/.deps.clj
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key: cljdeps-${{ runner.os }}
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- name: Detect changed Clojure sources
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id: changed_clj
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run: |
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set -euo pipefail
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changed=""
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if [ -f /tmp/site-cache/SOURCE_COMMIT ]; then
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source_commit=$(cat /tmp/site-cache/SOURCE_COMMIT)
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echo "Using source commit recorded in cache: $source_commit"
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changed=$(git diff --name-only --diff-filter=ACMR "$source_commit" HEAD -- 'src/**/*.clj' | tr '\n' ' ')
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fi
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if [ -z "$changed" ]; then
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echo "No changed Clojure sources detected"
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exit 0
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fi
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echo "Changed Clojure source files:" $changed
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echo "files=$changed" >> "$GITHUB_OUTPUT"
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- name: Build notebooks
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run: clojure -M:clay -A:markdown ${{ steps.changed_clj.outputs.files }}
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- name: Set up Quarto
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uses: quarto-dev/quarto-actions/setup@v2
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with:
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tinytex: true
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- name: Render Quarto
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uses: quarto-dev/quarto-actions/render@v2
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with:
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path: site
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- name: Upload artifact for Pages
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uses: actions/upload-pages-artifact@v3
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with:
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path: site/_site
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- name: Push site to cache repo
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run: |
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set -euo pipefail
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source_commit=$(git rev-parse HEAD)
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rm -rf /tmp/site-cache/site
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cp -r site /tmp/site-cache/
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echo "$source_commit" > /tmp/site-cache/SOURCE_COMMIT
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cd /tmp/site-cache
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git config user.email "github-actions@github.com"
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git config user.name "GitHub Actions"
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git add -A
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if ! git diff --cached --quiet; then
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git commit -m "Cache update from build ${source_commit}"
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git checkout -b temp
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git push --force origin main
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else
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echo "No changes to cache."
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fi
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deploy:
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needs: build
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if: (github.event_name == 'workflow_dispatch' && github.event.inputs.publish == 'true' && github.ref == 'refs/heads/main')
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permissions:
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pages: write
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id-token: write
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.gitignore‎

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/temp
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/site/*/
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/site
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.clj-kondo/
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.quarto/
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_site/

‎README.md‎

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@@ -181,6 +181,8 @@ If you `git add -f site/my-ns/my-post.qmd`,
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it will prevent the source `src/my-ns/my-post.clj` file from executing in the publish process.
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Only you will run the code locally (where you have secrets and large files available).
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If your notebook displays locally stored images, you will also need to commit these. Quarto puts them under `site/my-ns/my-post_files`.
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See [Some notebooks should only be run locally](https://clojurecivitas.github.io/scicloj/clay/skip_if_unchanged_example.html) for more detail.
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### Styling and other features
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## Deployment
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See [.github/workflows/render-and-publish.yml](.github/workflows/render-and-publish.yml)
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The site is built and deployed using GitHub Actions with two workflows:
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- **Full Build and Publish**: Triggered on pushes to `main`.
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Rebuilds all notebooks with Clay, renders the entire site with Quarto, and deploys to GitHub Pages.
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See [.github/workflows/render-and-publish.yml](.github/workflows/render-and-publish.yml).
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- **Incremental Build**: Triggered on pushes to `main`.
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Uses a separate cache repository to enable partial rebuilds.
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Restores the cached site (containing rendered HTML and generated files) without overwriting source-controlled files in `site/`.
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Sets file mtimes of source and cache files based on the last commit so that Quarto will know if the cached file is newer than the source.
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Compares the current source commit to the last build source commit (stored in the cache) to detect changes in Clojure sources.
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Rebuilds affected notebooks with Clay (rebuilds all if no changes detected).
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Renders the site incrementally with Quarto.
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Replaces the cache with the new site, and writes the source commit in a file in the cache.
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See [.github/workflows/render-and-publish-incremental.yml](.github/workflows/render-and-publish-incremental.yml).
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## License
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‎deps.edn‎

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io.github.clojure/core.async.flow-monitor {:git/tag "v0.1.2"
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:git/url "https://github.com/clojure/core.async.flow-monitor"
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:git/sha "6248a5d"}
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criterium/criterium {:mvn/version "0.4.6"}
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metosin/malli {:mvn/version "0.19.1"}
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clj-fuzzy/clj-fuzzy {:mvn/version "0.4.1"}
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clj-thamil/clj-thamil {:mvn/version "0.2.0"}
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org.scicloj/clay {:mvn/version "2.0.2"}
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org.scicloj/clay {:mvn/version "2.0.5"}
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org.scicloj/kindly {:mvn/version "4-beta21"}
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thi.ng/geom {:mvn/version "1.0.1"}
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org.eclipse.elk/org.eclipse.elk.core {:mvn/version "0.10.0"}
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camel-snake-kebab/camel-snake-kebab {:mvn/version "0.4.3"}
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io.github.alza-bitz/snowpark-clj {:git/url "https://github.com/alza-bitz/snowpark-clj.git"
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:git/sha "7856d9ca2080b188f9feec115ca709d3f54877b0"}
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org.lwjgl/lwjgl {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl$natives-linux {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-opengl {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-opengl$natives-linux {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-opengl$natives-windows {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-opengl$natives-macos {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-glfw {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-glfw$natives-linux {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-glfw$natives-windows {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-glfw$natives-macos {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-stb {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-stb$natives-linux {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-stb$natives-windows {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl-stb$natives-macos {:mvn/version "3.3.6"}
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org.lwjgl/lwjgl {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl$natives-linux {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-opengl {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-opengl$natives-linux {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-opengl$natives-windows {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-opengl$natives-macos {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-glfw {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-glfw$natives-linux {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-glfw$natives-windows {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-glfw$natives-macos {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-stb {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-stb$natives-linux {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-stb$natives-windows {:mvn/version "3.4.0"}
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org.lwjgl/lwjgl-stb$natives-macos {:mvn/version "3.4.0"}
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comb/comb {:mvn/version "1.0.0"}
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midje/midje {:mvn/version "1.10.10"}
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dev.data-star.clojure/sdk {:mvn/version "1.0.0-RC4"}
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dev.data-star.clojure/http-kit {:mvn/version "1.0.0-RC4"}
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dev.data-star.clojure/brotli {:mvn/version "1.0.0-RC4"}
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dev.data-star.clojure/malli-schemas {:mvn/version "1.0.0-RC4"}
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dev.data-star.clojure/http-kit-malli-schemas {:mvn/version "1.0.0-RC4"}
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dev.data-star.clojure/ring-malli-schemas {:mvn/version "1.0.0-RC4"}
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;; libraries for GIS work
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org.apache.sis.storage/sis-geotiff {:mvn/version "1.5"}
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org.apache.sis.core/sis-referencing {:mvn/version "1.5"}
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org.geotools/gt-geotiff {:mvn/version "31.2"}
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org.geotools/gt-main {:mvn/version "31.2"}
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org.geotools/gt-epsg-hsql {:mvn/version "31.2"}
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org.geotools/gt-geojson {:mvn/version "31.2"}
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clj-http/clj-http {:mvn/version "3.13.1"}
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generateme/fastmath {:mvn/version "3.0.0-alpha4"}
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org.soulspace/qclojure {:mvn/version "0.22.0"}
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org.babashka/http-client {:mvn/version "0.4.22"}
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com.github.danielsz/bioscoop {:mvn/version "1.0.5"}
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io.github.babashka/sci.nrepl {:mvn/version "0.0.2"}
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com.github.danielsz/bioscoop {:mvn/version "1.0.5"
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:exclusions [ch.qos.logback/logback-classic]}
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yamlscript/core {:git/url "https://github.com/yaml/yamlscript"
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:git/sha "ed7adfbf90a39f379d5a7193bb2e4bdd7f0eecf8"
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:deps/root "core"}
55-
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com.hyperphor/multitool {:mvn/version "0.2.3"}
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datascript/datascript {:mvn/version "1.7.8"}}
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58-
}
78+
:mvn/repos {"osgeo" {:url "https://repo.osgeo.org/repository/release/"}}
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:aliases
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{;; Build the site with `clojure -M:clay -A:markdown`

‎site/_quarto.yml‎

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- "*.cljs"
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- "*.svg"
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- "*.png"
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- "*.tif"
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website:
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title: "Clojure Civitas"
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favicon: "favicon.ico"
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site-url: "https://clojurecivitas.github.io"
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image: "/images/civitas-icon.svg"
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draft-mode: unlinked
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draft-mode: visible
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open-graph: true
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navbar:
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logo: "/images/civitas-icon.svg"
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logo-alt: "Clojure Civitas Logo"
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right:
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- about.qmd
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- posts.qmd
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- drafts.qmd
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- civitas/authors.qmd
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- civitas/explorer.qmd
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- icon: github
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href: "https://github.com/ClojureCivitas/clojurecivitas.github.io"
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- icon: rss
2628
href: posts.xml
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sidebar:
30+
- id: emmy-fdg
31+
title: "Functional Differential Geometry in Emmy"
32+
logo: "https://raw.githubusercontent.com/mentat-collective/emmy/main/doc/img/logo.png"
33+
contents:
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- href: mentat_collective/emmy/fdg_prologue.qmd
35+
text: "Prologue"
36+
- section: "Chapters"
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contents:
38+
- href: mentat_collective/emmy/fdg_ch01.qmd
39+
text: "FDG Chapter 1"
40+
- href: mentat_collective/emmy/sicm_original_ch01.qmd
41+
text: "SICM Chapter 1"
42+
- href: mentat_collective/emmy/fdg_ch02.qmd
43+
text: "FDG Chapter 2"
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- href: mentat_collective/emmy/fdg_ch03.qmd
45+
text: "FDG Chapter 3"
46+
- href: mentat_collective/emmy/fdg_ch01_ys.qmd
47+
text: "FDG Ch01 Infix"
48+
- href: mentat_collective/emmy/sicm_ch01.qmd
49+
text: "SICM Ch01 Graphics"
50+
- href: mentat_collective/emmy/debroglie.qmd
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text: "deBroglie Waves"
52+
- href: mentat_collective/emmy/silcm_ch01.qmd
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text: "Lorentz Covariant"
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format:
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html:
@@ -32,6 +59,7 @@ format:
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dark: [ darkly, brand, styles.scss, styles-dark.scss ]
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respect-user-color-scheme: true
3461
lightbox: true
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include-after-body: zulip_script.html
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include-in-header:
3664
- text: |
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<script data-goatcounter="https://clojurecivitas.goatcounter.com/count" async src="//gc.zgo.at/count.js"></script>

‎site/db.edn‎

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{:id :kloimhardt
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:name "Markus Agwin Kloimwieder"
121121
:url "https://github.com/kloimhardt"
122+
:image "https://github.com/kloimhardt.png"
122123
:affiliation [:scicloj]}
123124
{:id :edwardaw
124125
:name "Edward Widjaja"
@@ -135,17 +136,22 @@
135136
:links [{:icon "github" :href "https://github.com/tombarys"}]}
136137
{:id :mattb
137138
:name "Matthias Buehlmaier"
139+
:url "https://github.com/buehlmaier"
140+
:image "https://github.com/buehlmaier.png"
138141
:affiliation [:cim]}
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{:id :tanvi
140143
:name "Tanvi Nagar"
141144
:email "tanvi@connect.hku.hk"
142145
:affiliation [:cim]}
143146
{:id :luke-zeitlin
144147
:name "Luke Zeitlin"
148+
:url "https://github.com/larzeitlin"
149+
:image "https://github.com/larzeitlin.png"
145150
:affiliation []}
146151
{:id :ludgersolbach
147152
:name "Ludger Solbach"
148153
:url "https://github.com/lsolbach"
154+
:image "https://github.com/lsolbach.png"
149155
:links [{:icon "github" :href "https://github.com/lsolbach"}]
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:affiliation []}
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{:id :bsless
@@ -170,7 +176,22 @@
170176
:image "https://avatars.githubusercontent.com/burinc"
171177
:links [{:icon "github" :href "https://github.com/burinc"}]
172178
:affiliation []}
173-
,]
179+
{:id :proffitt
180+
:name "William Proffitt"
181+
:url "https://github.com/doogiecode"
182+
:image "https://avatars.githubusercontent.com/doogiecode"}
183+
{:id :jclaggett
184+
:name "Jonathan Claggett"
185+
:image "https://avatars.githubusercontent.com/u/100909?v=4"
186+
:url "https://github.com/jclaggett"
187+
:links [{:icon "github" :href "https://github.com/jclaggett"}]}
188+
{:id :rafd
189+
:name "Rafal Dittwald"
190+
:image "https://avatars.githubusercontent.com/u/89664?v=4"
191+
:affiliation [:clojurecamp]
192+
:url "https://github.com/rafd"
193+
:links [{:icon "github" :href "https://github.com/rafd"}]}
194+
]
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:affiliation
176197
[{:id :clojure.core

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