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Merge pull request #340 from UBC-DSCI/main
1st edition production
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‎.github/workflows/build_book.yml

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@@ -4,7 +4,8 @@ on:
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branches:
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- production
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paths:
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- source/**
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- 'source/**'
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- 'build_html.sh'
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jobs:
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deploy-book:
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: source/_build/html
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force_orphan: true
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cname: python.datasciencebook.ca
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force_orphan: true # this will clean up all previous PR previews / main branch preview
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‎.github/workflows/deploy_main_preview.yml

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name: Rebuild and deploy dev version of book to gh-pages branch in dev/ folder
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on:
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push:
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branches:
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- main
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paths:
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- 'source/**'
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- 'build_html.sh'
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jobs:
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deploy-main-preview:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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packages: write
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steps:
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- name: checkout
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uses: actions/checkout@v2
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with:
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ref: 'main'
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- name: Build the book
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run: |
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./build_html.sh
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# Push the book's HTML to github-pages
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- name: GitHub Pages action
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uses: peaceiris/[email protected]
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: source/_build/html
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keep_files: true
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destination_dir: dev
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# force_orphan: true # once peaceiris updates to v4, change this to true and keep_files: true for the PR / main branch deploy previews
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‎.github/workflows/deploy_pr_preview.yml

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name: "Rebuild and deploy PR version of book to gh-pages branch in pull###/ folder"
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on:
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pull_request:
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types: [opened, synchronize]
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paths:
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- 'source/**'
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- 'Dockerfile'
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branches:
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- 'main'
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jobs:
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deploy-pr-preview:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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packages: write
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pull-requests: write
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steps:
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- name: Wait for potential build environment update
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uses: fountainhead/[email protected]
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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checkName: "Rebuild docker image"
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ref: ${{ github.event.pull_request.head.sha }}
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timeoutSeconds: 60000
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- name: Checkout the repo
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uses: actions/checkout@v2
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with:
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fetch-depth: '0'
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ref: ${{ github.head_ref }}
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- name: Build the book
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run: |
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./build_html.sh
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# Push the book's HTML to github-pages
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- name: GitHub Pages action
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uses: peaceiris/[email protected]
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: source/_build/html
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keep_files: true
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destination_dir: pull${{ github.event.number }}
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# force_orphan: true # once peaceiris updates to v4, change this to true and keep_files: true for the PR / main branch deploy previews
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- name: Post URLS to PR thread
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uses: mshick/[email protected]
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with:
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message: |
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Hello! I've built a preview of your PR so that you can compare it to the current `main` branch.
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* PR deploy preview available [here](https://python.datasciencebook.ca/pull${{ github.event.number }}/index.html)
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* Current `main` deploy preview available [here](https://python.datasciencebook.ca/dev/index.html)
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* Public production build available [here](https://python.datasciencebook.ca)

‎.github/workflows/update_build_environment.yml

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name: Rebuild and publish new ubcdsci/py-intro-to-ds image on DockerHub
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on:
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push:
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branches:
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- main
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paths:
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- Dockerfile
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pull_request:
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types: [opened, synchronize]
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jobs:
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rebuild-docker:
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name: Rebuild docker image
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Checkout main
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- name: Checkout PR branch
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uses: actions/checkout@v3
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with:
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fetch-depth: '0'
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ref: 'main'
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ref: ${{ github.head_ref }}
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- name: Check if Dockerfile needs to be rebuilt
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id: check-stale
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run: |
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echo "Checking if Dockerfile was modified since last commit on this PR"
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echo "GitHub PR action type: ${{ github.event.action }}"
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if [ "${{ github.event.action }}" == "opened" ]; then
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echo "GitHub base ref: ${{ github.event.pull_request.base.sha }}"
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echo "GitHub head ref: ${{ github.event.pull_request.head.sha }}"
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BEFORE=${{ github.event.pull_request.base.sha }}
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AFTER=${{ github.event.pull_request.head.sha }}
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else
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echo "GitHub event before: ${{ github.event.before }}"
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echo "GitHub event after: ${{ github.event.after }}"
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BEFORE=${{ github.event.before }}
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AFTER=${{ github.event.after }}
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fi
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if git diff --quiet $BEFORE $AFTER Dockerfile; then
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echo "PR synchronized, but Dockerfile was not edited. Not rebuilding the image."
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echo "stale_dockerfile=false" >> "$GITHUB_OUTPUT"
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else
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echo "PR synchronized, and Dockerfile was edited, so rebuilding the image."
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echo "stale_dockerfile=true" >> "$GITHUB_OUTPUT"
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fi
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- name: Rebuild and publish image
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if: ${{ steps.check-stale.outputs.stale_dockerfile == 'true' }}
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id: rebuild
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uses: elgohr/Publish-Docker-Github-Action@v5
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with:
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dockerfile: Dockerfile
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snapshot: true
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- name: Update build_html.sh script
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if: ${{ steps.check-stale.outputs.stale_dockerfile == 'true' }}
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Action"
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git pull origin main
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git pull origin ${{ github.head_ref }}
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sed 's/ubcdsci\/py-intro-to-ds:[[:alnum:]]\+/ubcdsci\/py-intro-to-ds:${{ steps.rebuild.outputs.snapshot-tag }}/g' build_html.sh > build_html.tmp && mv build_html.tmp build_html.sh
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chmod u+x build_html.sh
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git add build_html.sh
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git commit -m "update build_html.sh script with new docker image"
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- name: Update build_pdf.sh script
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if: ${{ steps.check-stale.outputs.stale_dockerfile == 'true' }}
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Action"
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git pull origin main
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git pull origin ${{ github.head_ref }}
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sed 's/ubcdsci\/py-intro-to-ds:[[:alnum:]]\+/ubcdsci\/py-intro-to-ds:${{ steps.rebuild.outputs.snapshot-tag }}/g' build_pdf.sh > build_pdf.tmp && mv build_pdf.tmp build_pdf.sh
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chmod u+x build_pdf.sh
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git add build_pdf.sh
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git commit -m "update build_pdf.sh script with new docker image"
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- name: Push changes to build scripts
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if: ${{ steps.check-stale.outputs.stale_dockerfile == 'true' }}
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uses: ad-m/github-push-action@master
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with:
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branch: 'main'
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branch: ${{ github.head_ref }}

‎.gitignore

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*.swp
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*.swo
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source/__pycache__
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.local/
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.viminfo

‎Dockerfile

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# remove the "work/" directory added in an earlier layer...
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RUN rm -rf work
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RUN pip install docutils==0.17.1 # Need to pin docutils to an old version for now, due to https://github.com/executablebooks/jupyter-book/issues/2022
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RUN pip install referencing
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RUN pip install jupyter-book
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# Pinning pandas until altair 5.1.2 to avoid future warning https://github.com/altair-viz/altair/issues/3181
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RUN pip install numpy jinja2 pandas"<2.1" altair">=5.1.1" "vegafusion[embed]" vl-convert-python">=0.13" click ibis-framework ghp-import jupytext nodejs
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# forces scikit-learn to grab latest to avoid bug in 1.3.0 related to checking for c-contiguity breaking figures in classification 2. See https://github.com/scikit-learn/scikit-learn/pull/26772
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# TODO: remove this once scikit-learn 1.4.x or beyond releases and is incorporated into jupyter/scipy-notebook
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RUN pip install -U git+https://github.com/scikit-learn/scikit-learn.git@main
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# disable warnings that pollute build logs; seems to be related to the update to python 3.11
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# https://discourse.jupyter.org/t/debugger-warning-it-seems-that-frozen-modules-are-being-used-python-3-11-0/16544/12
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ENV PYDEVD_DISABLE_FILE_VALIDATION=1
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## Install various python packages
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# commented out for now due to various package version conflicts
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# installing via pip instead above
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#RUN mamba install --quiet --yes \
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# 'numpy' \
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# 'jinja2' \
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# 'altair_data_server' \
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# 'altair_saver' \
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# 'click' \
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# 'ibis-framework' \
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# 'ghp-import' \
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# 'jupytext' \
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# 'jupyter-book' \
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# 'nodejs' \
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# && mamba clean --all -f -y \
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# && fix-permissions "${CONDA_DIR}" \
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# && fix-permissions "/home/${NB_USER}"
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RUN mamba install --quiet --yes \
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'numpy' \
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'pandas>=2.1.3' \
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'jinja2' \
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'altair>=5.1.2' \
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'vl-convert-python>=0.14' \
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'vegafusion[embed]' \
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'click' \
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'ibis-framework' \
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'ghp-import' \
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'jupytext' \
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'jupyter-book' \
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'scikit-learn>=1.3.2' \
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'nodejs' \
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'plotly' \
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'lxml' \
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'referencing' \
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'docutils==0.17.1' \
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&& mamba clean --all -f -y \
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&& fix-permissions "${CONDA_DIR}" \
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&& fix-permissions "/home/${NB_USER}"

‎README.md

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Building the book requires Docker (instructions here: [https://docs.docker.com/get-docker/](https://docs.docker.com/get-docker/)).
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### Contributing
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Primary development in this repository happens on the `main` branch. If you want to contribute to the book,
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please branch off of `main` and make a pull request into `main`.
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The `production` branch contains the source material for the live, publicly viewable HTML book.
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### Build locally
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You can build the HTML version of the book on your own machine by running
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```
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in the root directory of this repository. The book can be viewed in a PDF reader by opening `source/_build/latex/python.pdf`.
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### Update build environment
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### Contributing
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Primary development in this repository happens on the `main` branch. If you want to contribute to the book,
37+
please branch off of `main` and make a pull request into `main`. You cannot commit directly to `main`.
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The `production` branch contains the source material corresponding to the current publicly-viewable version of the book website.
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The `gh-pages` branch serves the current book website at https://python.datasciencebook.ca.
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### Workflows
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#### Book deployment
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You can update the live, publicly viewable HTML book by making changes to the `source/` folder in the `production` branch (e.g. by merging `main` into `production`).
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GitHub will trigger a rebuild of the public HTML site, and store the built book in the root folder of the `gh-pages` branch.
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#### `main` deploy previews
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Any commit to `source/**` on the `main` branch (from a merged PR) will trigger a rebuild of the development preview site served at `https://python.datasciencebook.ca/dev`.
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The built preview book will be stored in the `dev/` folder on the `gh-pages` branch.
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#### PR deploy previews
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You can update the build environment for the book by making changes to `Dockerfile` in the root of the repository in the `main` branch.
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If you push any changes to the `Dockerfile` on the `main` branch, GitHub will trigger a rebuild of the docker image,
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push it to DockerHub, and update the `build_html.sh` script and book deploy GitHub action with the new image tag.
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Any PR to `source/` will trigger a build of a PR preview site at `https://python.datasciencebook.ca/pull###`, where `###` is the number of the pull request.
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The built preview book will be stored in the `pull###/` folder on the `gh-pages` branch.
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### Update public html
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#### Build environment updates
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49-
You can update the live, publicly viewable HTML book by making changes to the `source/` folder in the `production` branch.
50-
If you push any changes to the `source/` folder on the `production` branch, GitHub will trigger a rebuild of the public HTML site.
62+
Any PR to `Dockerfile` will trigger a rebuild of the docker image, push it to DockerHub, and update the image tags in the `build_html.sh` and `build_pdf.sh` scripts on the PR automatically.
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This new build environment will be used for the PR deploy preview mentioned above.
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‎build_html.sh

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chmod -R o+w source/
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docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20230831171718ddf538 /bin/bash -c "jupyter-book build source"
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docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20231112004031dd2207 /bin/bash -c "jupyter-book build source"

‎build_pdf.sh

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# Script to generate PDF book
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# backup original index.Rmd
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cp source/index.md index_backup.md
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# PDF book doesn't need the welcome page. I couldn't find a way to stop jupyterbook from including it.
7+
# so this script manually removes the welcome page before building the PDF. This is a bit painful, but it works...
8+
sed -n -i "/graphic/q;p" source/index.md
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echo "# Data Science: A First Introduction" >> source/index.md
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chmod -R o+w source/
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docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20230831171718ddf538 /bin/bash -c "export BOOK_BUILD_TYPE='PDF'; jupyter-book build source --builder pdflatex"
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docker run --rm -v $(pwd):/home/jovyan ubcdsci/py-intro-to-ds:20231112004031dd2207 /bin/bash -c "export BOOK_BUILD_TYPE='PDF'; jupyter-book build source --builder pdflatex"
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# restore the backed up full index.Rmd
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mv index_backup.md source/index.md

‎source/_config.yml

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# Book settings
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title: "Data Science: A First Introduction (Python Edition)"
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author: "The DSCI100 Development Team"
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author: "Tiffany Timbers, Trevor Campbell, Melissa Lee, Joel Ostblom, and Lindsey Heagy"
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copyright: "2022" # Copyright year to be placed in the footer
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logo: "" # A path to the book logo
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# Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb")
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use_multitoc_numbering: true # Continuous numbering across parts/chapters
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extra_navbar: Powered by <a href="https://jupyterbook.org">Jupyter Book</a> # Will be displayed underneath the left navbar.
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extra_footer: "" # Will be displayed underneath the footer.
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google_analytics_id: "" # A GA id that can be used to track book views.
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home_page_in_navbar: true # Whether to include your home page in the left Navigation Bar
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google_analytics_id: "G-7XBFF4RSN2" # A GA id that can be used to track book views.
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home_page_in_navbar: false # Whether to include your home page in the left Navigation Bar
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baseurl: "" # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/
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comments:
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hypothesis: false
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local_extensions: # A list of local extensions to load by sphinx specified by "name: path" items
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config: # key-value pairs to directly over-ride the Sphinx configuration
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bibtex_reference_style: author_year
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html_js_files:
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- https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
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html_context:
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default_mode: light
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‎source/_static/style.css

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margin-left: auto;
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margin-right: auto;
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}
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span.pasted-text {
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font-weight: normal;
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}

‎source/_toc.yml

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- caption: Front Matter
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chapters:
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- file: preface-text.md
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#- file: foreword.md
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- file: foreword-text.md
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- file: acknowledgements.md
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- file: authors.md
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- caption: Chapters

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