Merge remote-tracking branch 'template/main' into main

.docker/entrypoint.sh

@@ -1,10 +1,8 @@
 #! /bin/bash
 
 # print folder contents for debugging
-echo "Contents:"
-echo ""
+printf "\n\nContents:\n\n"
 ls
-echo ""
 
 # run cite process
 python3 _cite/cite.py

.github/DISCUSSION_TEMPLATE/general.yaml

@@ -0,0 +1,35 @@
+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: "In almost all cases, **we cannot help you if you don't provide this**."
+      placeholder: ex. https://github.com/greenelab/greenelab.com
+    validations:
+      required: true
+
+  - 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
+    validations:
+      required: true
+
+  - 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/DISCUSSION_TEMPLATE/q-a.yaml

@@ -0,0 +1,35 @@
+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: "In almost all cases, **we cannot help you if you don't provide this**."
+      placeholder: ex. https://github.com/greenelab/greenelab.com
+    validations:
+      required: true
+
+  - 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
+    validations:
+      required: true
+
+  - 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/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+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

@@ -0,0 +1,38 @@
+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: "In almost all cases, **we cannot help you if you don't provide this**."
+      placeholder: ex. https://github.com/greenelab/greenelab.com
+    validations:
+      required: true
+
+  - 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
+    validations:
+      required: true
+
+  - 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

@@ -1,4 +1,13 @@
-This website is based on the Lab Website Template.
-See its documentation for working with this site:
+STOP!!!
 
-https://greene-lab.gitbook.io/lab-website-template-docs
+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

@@ -0,0 +1,4 @@
+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

@@ -22,36 +22,37 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         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
+        uses: ruby/setup-ruby@v1.172.0
         with:
-          ruby-version: "3.0"
+          ruby-version: "3.1"
           bundler-cache: true
 
       - name: Get Pages url
         if: github.event.action != 'closed'
         id: pages
-        uses: actions/configure-pages@v2
-        with:
-          enablement: false
+        uses: actions/configure-pages@v4
+
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
 
       - 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
+        uses: rossjrw/pr-preview-action@v1.4.7
         with:
           source-dir: _site
           umbrella-dir: ${{ env.PREVIEWS_FOLDER }}

.github/workflows/build-site.yaml

@@ -21,30 +21,35 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Ruby packages
-        uses: ruby/setup-ruby@v1
+        uses: ruby/setup-ruby@v1.172.0
         with:
-          ruby-version: "3.0"
+          ruby-version: "3.1"
           bundler-cache: true
 
       - name: Get Pages url
         id: pages
-        uses: actions/configure-pages@v2
-        with:
-          enablement: false
+        uses: actions/configure-pages@v4
+
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
+      - name: Set root url
+        run: |
+          printf "\n\nurl: ${{ steps.pages.outputs.origin }}" >> _config.yaml
 
       - 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
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           folder: _site
           clean-exclude: ${{ env.PREVIEWS_FOLDER }}

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

@@ -14,21 +14,24 @@ jobs:
 
     steps:
       # for debugging
-      - name: Print contexts
-        uses: crazy-max/ghaction-dump-context@v1
+      - uses: crazy-max/ghaction-dump-context@v2
 
       - name: Create Pages branch
-        uses: peterjgrainger/action-create-branch@v2.4.0
+        uses: peterjgrainger/action-create-branch@v3.0.0
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           branch: "gh-pages"
 
       - name: Checkout Pages branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
 
+      # for debugging
+      - if: runner.debug == '1'
+        uses: mxschmitt/action-tmate@v3
+
       # clean slate, as if starting from orphan branch
       - name: Clear Pages branch
         run: rm -rf * .github .docker .gitignore
@@ -38,40 +41,41 @@ jobs:
         run: touch .nojekyll
 
       - name: Make placeholder homepage
-        run: echo "Placeholder homepage" > index.html
+        run: printf "Placeholder homepage" > index.html
 
       - name: Commit changes to Pages branch
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           branch: gh-pages
           commit_message: "Clear branch"
 
       - name: Checkout main branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Remove files user doesn't need
         run: |
           rm -rf \
             CHANGELOG.md \
             testbed.md \
             .github/ISSUE_TEMPLATE \
+            .github/DISCUSSION_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
+          mv -f .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}" >> $GITHUB_ENV
+          printf "USER=${user}" >> $GITHUB_ENV
+          printf "DESCRIPTION=${description}" >> $GITHUB_ENV
 
       - name: Personalize readme for user
         run: |
-          echo "
+          printf "
           # ${{ env.USER }}'s Website
 
           Visit **[website url](#)** 🚀
@@ -80,7 +84,7 @@ jobs:
           " > README.md
 
       - name: Personalize Jekyll config for user
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -97,7 +101,7 @@ jobs:
             writeFileSync(file, contents);
 
       - name: Personalize homepage for user
-        uses: actions/github-script@v6
+        uses: actions/github-script@v7
         with:
           script: |
             const { readFileSync, writeFileSync } = require("fs");
@@ -109,6 +113,6 @@ jobs:
             writeFileSync(file, contents);
 
       - name: Commit changed files
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@v5
         with:
           commit_message: "Setup repo"