v1.0.0 First official version

.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

@@ -1,8 +1,13 @@
-<!-- 
+STOP!!!
 
-This website is built upon Lab Website Template.
-Please read its documentation carefully before submitting your changes:
+You are about to open this pull request against THE TEMPLATE ITSELF. You probably meant to open it against your own website repo.
 
-https://github.com/greenelab/lab-website-template/wiki
+---
 
--->
+FOR THE TEMPLATE MAINTAINER(S)
+
+Checklist:
+
+- [ ] I have updated CITATION and CHANGELOG.
+- [ ] I have updated lab-website-template-docs as appropriate.
+- [ ] I have checked the testbed as appropriate.

.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
+
+jobs:
+  build-preview:
+    runs-on: ubuntu-latest
+
+    steps:
+      - 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: ${{ github.head_ref }}
+
+      - name: Install Ruby packages
+        if: github.event.action != 'closed'
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.0"
+          bundler-cache: true
+
+      - name: Get Pages url
+        if: github.event.action != 'closed'
+        id: pages
+        uses: actions/configure-pages@v2
+        with:
+          enablement: false
+
+      - name: Build preview version of site
+        if: github.event.action != 'closed'
+        run: |
+          bundle exec jekyll build --baseurl "${{ 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
+
+jobs:
+  build-site:
+    runs-on: ubuntu-latest
+
+    steps:
+      - 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: |
+          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 when called from another workflow
+  workflow_call:
+
+  # run if user manually requests it
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  first-time-setup:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Print contexts
+        uses: crazy-max/ghaction-dump-context@v1
+
+      - name: Create Pages branch
+        uses: peterjgrainger/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          branch: "gh-pages"
+
+      - name: Checkout Pages branch
+        uses: actions/checkout@v3
+        with:
+          ref: gh-pages
+
+      - name: Clear Pages branch
+        run: rm -rf * .github .gitignore
+
+      - name: Make .nojekyll file
+        run: touch .nojekyll
+
+      - name: Make placeholder homepage
+        run: echo "Placeholder homepage" > index.html
+
+      - name: Commit changes to Pages branch
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          branch: gh-pages
+          commit_message: "Clear branch"
+
+      - name: Checkout main branch
+        uses: actions/checkout@v3
+
+      - name: Remove unneeded files
+        run: |
+          rm -rf \
+            README.md \
+            CHANGELOG.md \
+            testbed.md \
+            .github/ISSUE_TEMPLATE \
+            .github/workflows/versioning.yaml \
+            .github/pull_request_template.md \
+
+      - name: Set vars for personalization
+        run: |
+          name="${{ github.repository_owner }}"
+          title="${name^}'s Website"
+          description="An engaging 1-3 sentence description of your lab."
+          echo "NAME=${name}" >> $GITHUB_ENV
+          echo "TITLE=${title}" >> $GITHUB_ENV
+          echo "DESCRIPTION=${description}" >> $GITHUB_ENV
+
+      - name: Personalize readme for user
+        run: |
+          echo "
+          # ${{ env.TITLE }}
+
+          Visit **[website url](#)** 🚀
+
+          _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
+          " > README.md
+
+      - name: Install packages
+        run: yarn add yaml
+
+      - name: Personalize Jekyll config for user
+        uses: actions/github-script@v6
+        with:
+          script: |
+            const { readFileSync, writeFileSync } = require("fs");
+            const { parse, stringify } = require("yaml");
+            const file = "_config.yaml";
+            const config = parse(readFileSync(file).toString());
+            config.title = "${{ env.TITLE }}";
+            config.description = "${{ env.DESCRIPTION }}";
+            config.email = "contact@${{ env.name }}.com";
+            config.github = "${{ env.name }}";
+            config.twitter = "${{ env.name }}";
+            config.instagram = "${{ env.name }}";
+            config.youtube = "${{ env.name }}";
+            writeFileSync(file, stringify(config));
+
+      - 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)/g;
+            const replace = `# ${{ env.TITLE }}\n\n${{ env.DESCRIPTION }}\n\n$1`;
+            contents = contents.replaceAll(find, replace);
+            writeFileSync(file, contents);
+
+      - name: Commit changed files
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: "Setup repo"

.github/workflows/on-pages.yaml

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+name: on-pages
+run-name: on pages deploy
+
+on:
+  workflow_run:
+    workflows: [pages-build-deployment]
+    types:
+      - completed
+    branches:
+      - gh-pages
+
+permissions:
+  contents: write
+
+jobs:
+  update-url:
+    # only run on user instance of template, not template itself
+    if: github.repository != 'greenelab/lab-website-template'
+    uses: ./.github/workflows/update-url.yaml
+
+  build-site:
+    needs: update-url
+    if: needs.update-url.outputs.changed == 'true'
+    uses: ./.github/workflows/build-site.yaml

.github/workflows/on-pull-request.yml

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+name: on-pull-request
+run-name: on pull request activity
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  update-citations:
+    uses: ./.github/workflows/update-citations.yaml
+
+  build-preview:
+    needs: update-citations
+    uses: ./.github/workflows/build-preview.yaml

.github/workflows/on-push.yml

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+name: on-push
+run-name: on push to main
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  update-citations:
+    # skip first run because nothing enabled or setup yet
+    if: github.run_number != 1
+    uses: ./.github/workflows/update-citations.yaml
+
+  build-site:
+    needs: update-citations
+    uses: ./.github/workflows/build-site.yaml