Initial commit

.docker/Dockerfile

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+# start with official ruby docker image as base
+FROM ruby:3.1.2
+
+# set working directory within container
+WORKDIR /usr/src/app
+
+# pull in ruby (jekyll) and python (cite process) package info
+COPY Gemfile Gemfile.lock _cite/requirements.txt ./
+
+# install ruby packages
+RUN VERSION=$(grep -A 1 'BUNDLED WITH' Gemfile.lock | tail -n 1 | xargs); \
+    gem install bundler --version ${VERSION} && \
+    bundle _${VERSION}_ install
+
+# install python
+RUN apt update && apt install -y python3 python3-pip
+
+# install python packages
+RUN python3 -m pip install --no-cache-dir --upgrade --requirement requirements.txt
+
+# install python package for listening for file changes
+RUN pip install "watchdog[watchmedo]==3.0.0"
+
+# ports used by jekyll
+EXPOSE 4000
+EXPOSE 35729
+
+# run jekyll and cite process
+COPY .docker/entrypoint.sh /var
+CMD [ "/var/entrypoint.sh" ]

.docker/entrypoint.sh

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+#! /bin/bash
+
+# print folder contents for debugging
+echo "Contents:"
+echo ""
+ls
+echo ""
+
+# run cite process
+python3 _cite/cite.py
+
+# run jekyll serve in hot-reload mode
+# rerun whenever _config.yaml changes (jekyll hot-reload doesn't work with this file)
+watchmedo auto-restart \
+    --debug-force-polling \
+    --patterns="_config.yaml" \
+    --signal SIGTERM \
+    -- bundle exec jekyll serve --open-url --force_polling --livereload --trace --host=0.0.0.0 \
+    | sed "s/LiveReload address.*//g;s/0.0.0.0/localhost/g" &
+
+# rerun cite process whenever _data files change
+watchmedo shell-command \
+    --debug-force-polling \
+    --recursive \
+    --wait \
+    --command="python3 _cite/cite.py" \
+    --patterns="_data/sources*;_data/orcid*;_data/pubmed*;_data/google-scholar*" \

.docker/run.sh

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+#! /bin/bash
+
+# name of image
+IMAGE=lab-website-renderer:latest
+
+# name of running container
+CONTAINER=lab-website-renderer
+
+# choose platform flag
+PLATFORM=""
+
+# default vars
+DOCKER_RUN="docker run"
+WORKING_DIR=$(pwd)
+
+# fix windows faux linux shells/tools
+if [[ $OSTYPE == msys* ]] || [[ $OSTYPE == cygwin* ]]; then
+    DOCKER_RUN="winpty docker run"
+    WORKING_DIR=$(cmd //c cd)
+fi
+
+# build docker image
+docker build ${PLATFORM} \
+    --tag ${IMAGE} \
+    --file ./.docker/Dockerfile . && \
+
+# run built docker image
+${DOCKER_RUN} ${PLATFORM} \
+    --name ${CONTAINER} \
+    --init \
+    --rm \
+    --interactive \
+    --tty \
+    --publish 4000:4000 \
+    --publish 35729:35729 \
+    --volume "${WORKING_DIR}:/usr/src/app" \
+    ${IMAGE} "$@"

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: true
+contact_links:
+  - name: 💬 Start a discussion
+    url: https://github.com/greenelab/lab-website-template/discussions
+    about: I need help, I have a question, or other discussion.
+  - name: 📚 Docs issue
+    url: https://github.com/greenelab/lab-website-template-docs/issues
+    about: I have a question or issue related to the template documentation.

.github/ISSUE_TEMPLATE/issue.yaml

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+name: 🐞 Create an issue
+description: I think I've discovered a bug, I want to request a feature/change, or other issue.
+
+body:
+  - type: checkboxes
+    attributes:
+      label: Checks
+      options:
+        - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first.
+          required: true
+
+  - type: input
+    id: repo
+    attributes:
+      label: Link to your website repo
+      description: "**Strongly recommended** so we can help troubleshoot your issue."
+      placeholder: ex. https://github.com/greenelab/greenelab.com
+
+  - type: input
+    id: version
+    attributes:
+      label: Version of Lab Website Template you are using
+      description: See your `CITATION.cff` file.
+      placeholder: ex. 1.0.0
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: |
+        Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in?
+      placeholder: Description
+    validations:
+      required: true

.github/pull_request_template.md

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+STOP!!!
+
+You are about to open this pull request against THE TEMPLATE ITSELF. You probably meant to open it against your own website repo.
+
+---
+
+FOR THE TEMPLATE MAINTAINER(S)
+
+New template version checklist:
+
+- [ ] I have updated CITATION and CHANGELOG as appropriate.
+- [ ] I have updated lab-website-template-docs as appropriate.
+- [ ] I have checked the testbed as appropriate.

.github/user_pull_request_template.md

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+This website is based on the Lab Website Template.
+See its documentation for working with this site:
+
+https://greene-lab.gitbook.io/lab-website-template-docs

.github/workflows/build-preview.yaml

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+name: build-preview
+run-name: build pull request preview
+
+on:
+  # run when called from another workflow
+  workflow_call:
+
+  # run if user manually requests it
+  workflow_dispatch:
+
+# variables
+env:
+  PREVIEWS_FOLDER: preview
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  build-preview:
+    runs-on: ubuntu-latest
+
+    steps:
+      # for debugging
+      - name: Print contexts
+        uses: crazy-max/ghaction-dump-context@v1
+
+      - name: Checkout branch contents
+        uses: actions/checkout@v3
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.head_ref }}
+
+      - name: Install Ruby packages
+        if: github.event.action != 'closed'
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.0"
+          bundler-cache: true
+
+      - name: Get Pages url
+        if: github.event.action != 'closed'
+        id: pages
+        uses: actions/configure-pages@v2
+        with:
+          enablement: false
+
+      - name: Build preview version of site
+        if: github.event.action != 'closed'
+        run: |
+          JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"
+
+      - name: Commit preview to Pages branch
+        uses: rossjrw/pr-preview-action@v1
+        with:
+          source-dir: _site
+          umbrella-dir: ${{ env.PREVIEWS_FOLDER }}

.github/workflows/build-site.yaml

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+name: build-site
+run-name: build live site
+
+on:
+  # run when called from another workflow
+  workflow_call:
+
+  # run if user manually requests it
+  workflow_dispatch:
+
+# variables
+env:
+  PREVIEWS_FOLDER: preview
+
+permissions:
+  contents: write
+
+jobs:
+  build-site:
+    runs-on: ubuntu-latest
+
+    steps:
+      # for debugging
+      - name: Print contexts
+        uses: crazy-max/ghaction-dump-context@v1
+
+      - name: Checkout branch contents
+        uses: actions/checkout@v3
+
+      - name: Install Ruby packages
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.0"
+          bundler-cache: true
+
+      - name: Get Pages url
+        id: pages
+        uses: actions/configure-pages@v2
+        with:
+          enablement: false
+
+      - name: Build live version of site
+        run: |
+          JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}"
+
+      - name: Commit live site to Pages branch
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: _site
+          clean-exclude: ${{ env.PREVIEWS_FOLDER }}
+          force: false

.github/workflows/first-time-setup.yaml

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+name: first-time-setup
+run-name: first time setup of repo
+
+on:
+  # run if user manually requests it
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  first-time-setup:
+    runs-on: ubuntu-latest
+
+    steps:
+      # for debugging
+      - name: Print contexts
+        uses: crazy-max/ghaction-dump-context@v1
+
+      - name: Create Pages branch
+        uses: peterjgrainger/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          branch: "gh-pages"
+
+      - name: Checkout Pages branch
+        uses: actions/checkout@v3
+        with:
+          ref: gh-pages
+
+      # clean slate, as if starting from orphan branch
+      - name: Clear Pages branch
+        run: rm -rf * .github .docker .gitignore
+
+      # prevent GitHub from running Jekyll a second time after build
+      - name: Make .nojekyll file
+        run: touch .nojekyll
+
+      - name: Make placeholder homepage
+        run: echo "Placeholder homepage" > index.html
+
+      - name: Commit changes to Pages branch
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          branch: gh-pages
+          commit_message: "Clear branch"
+
+      - name: Checkout main branch
+        uses: actions/checkout@v3
+
+      - name: Remove files user doesn't need
+        run: |
+          rm -rf \
+            CHANGELOG.md \
+            testbed.md \
+            .github/ISSUE_TEMPLATE \
+            .github/workflows/versioning.yaml \
+            .github/pull_request_template.md \
+      
+      - name: Rename files
+        run: |
+          mv .github/user_pull_request_template.md .github/pull_request_template.md
+
+      - name: Set vars for personalization
+        run: |
+          user="${{ github.repository_owner }}"
+          description="An engaging 1-3 sentence description of your lab."
+          echo "USER=${user}" >> $GITHUB_ENV
+          echo "DESCRIPTION=${description}" >> $GITHUB_ENV
+
+      - name: Personalize readme for user
+        run: |
+          echo "
+          # ${{ env.USER }}'s Website
+
+          Visit **[website url](#)** 🚀
+
+          _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+          " > README.md
+
+      - name: Personalize Jekyll config for user
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const { readFileSync, writeFileSync } = require("fs");
+            const file = "_config.yaml";
+            const contents = readFileSync(file)
+              .toString()
+              .replace(/(^title: ).*$/m, "$1${{ env.USER }}")
+              .replace(/(^subtitle: ).*$/m, "$1")
+              .replace(/(^description: ).*$/m, "$1${{ env.DESCRIPTION }}")
+              .replace(/(^  email: ).*$/m, "$1contact@${{ env.USER }}.com")
+              .replace(/(^  github: ).*$/m, "$1${{ env.USER }}")
+              .replace(/(^  twitter: ).*$/m, "$1${{ env.USER }}")
+              .replace(/(^  youtube: ).*$/m, "$1${{ env.USER }}");
+            writeFileSync(file, contents);
+
+      - name: Personalize homepage for user
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const { readFileSync, writeFileSync } = require("fs");
+            const file = "index.md";
+            let contents = readFileSync(file).toString();
+            const find = /\# Lab Website Template[\s\S]+({% include section\.html)/;
+            const replace = `# ${{ env.USER }}'s Website\n\n${{ env.DESCRIPTION }}\n\n$1`;
+            contents = contents.replace(find, replace);
+            writeFileSync(file, contents);
+
+      - name: Commit changed files
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: "Setup repo"