Merge remote-tracking branch 'template/main'

.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/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

@@ -22,9 +22,11 @@ jobs:
 
     steps:
       - name: Debug dump
+        if: runner.debug == '1'
         uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
+        if: github.event.action != 'closed'
         uses: actions/checkout@v4
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
@@ -42,25 +44,40 @@ jobs:
         id: pages
         uses: actions/configure-pages@v4
 
-      - uses: jwalton/gh-find-current-pr@master
-        if: github.event.action != 'closed'
-        id: pr
-        with:
-          state: all
-
       - name: SSH debug
         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-${{ env.pr }}"
-        env:
-          pr: ${{ steps.pr.outputs.pr }}
+          JEKYLL_ENV=production bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path || '' }}/${{ env.PREVIEWS_FOLDER }}/pr-${{ github.event.number }}"
 
       - name: Commit preview to Pages branch
+        if: github.event.action != 'closed'
         uses: rossjrw/[email protected]
         with:
           source-dir: _site
           umbrella-dir: ${{ env.PREVIEWS_FOLDER }}
+
+      - name: Checkout Pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+
+      - name: Clean up preview folders
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const { rm } = require("fs").promises;
+            const { PREVIEWS_FOLDER } = process.env;
+            const { owner, repo } = context.repo;
+            const prs = (await github.rest.pulls.list({ owner, repo, state: "closed" })).data;
+            for (const { number } of prs)
+              await rm(`${PREVIEWS_FOLDER}/pr-${number}`, { recursive: true, force: true });
+
+      - name: Commit changed files
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          branch: gh-pages
+          commit_message: "Clean up previews"

.github/workflows/build-site.yaml

@@ -21,6 +21,7 @@ jobs:
 
     steps:
       - name: Debug dump
+        if: runner.debug == '1'
         uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents

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

@@ -14,6 +14,7 @@ jobs:
 
     steps:
       - name: Debug dump
+        if: runner.debug == '1'
         uses: crazy-max/ghaction-dump-context@v2
 
       - name: Create Pages branch
@@ -34,7 +35,7 @@ jobs:
 
       # clean slate, as if starting from orphan branch
       - name: Clear Pages branch
-        run: rm -rf * .github .docker .gitignore
+        run: rm -rf ./* .github .docker .gitignore
 
       # prevent GitHub from running Jekyll a second time after build
       - name: Make .nojekyll file
@@ -70,8 +71,8 @@ jobs:
         run: |
           user="${{ github.repository_owner }}"
           description="An engaging 1-3 sentence description of your lab."
-          printf "\nUSER=${user}" >> $GITHUB_ENV
-          printf "\nDESCRIPTION=${description}" >> $GITHUB_ENV
+          printf "\nUSER=%s" "$user" >> "$GITHUB_ENV"
+          printf "\nDESCRIPTION=%s" "$description" >> "$GITHUB_ENV"
 
       - name: Personalize readme for user
         run: |
@@ -80,12 +81,12 @@ jobs:
             ![on-pull-request](../../actions/workflows/on-pull-request.yaml/badge.svg)
             ![on-schedule](../../actions/workflows/on-schedule.yaml/badge.svg)
 
-            # ${{ env.USER }}'s Website
+            # %s's Website
 
             Visit **[website url](#)** 🚀
 
             _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_
-          " > README.md
+          " "${{ env.USER }}" > README.md 
 
       - name: Personalize Jekyll config for user
         uses: actions/github-script@v7
@@ -119,4 +120,4 @@ jobs:
       - name: Commit changed files
         uses: stefanzweifel/git-auto-commit-action@v5
         with:
-          commit_message: "Setup repo"
+          commit_message: "Set up repo"

.github/workflows/update-citations.yaml

@@ -29,6 +29,7 @@ jobs:
 
     steps:
       - name: Debug dump
+        if: runner.debug == '1'
         uses: crazy-max/ghaction-dump-context@v2
 
       - name: Checkout branch contents
@@ -38,7 +39,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.head_ref }}
 
-      - name: Setup Python
+      - name: Set up Python
         if: github.event.action != 'closed'
         uses: actions/setup-python@v5
         with:

.github/workflows/update-url.yaml

@@ -20,6 +20,7 @@ jobs:
 
     steps:
       - name: Debug dump
+        if: runner.debug == '1'
         uses: crazy-max/ghaction-dump-context@v2
 
       - name: Get Pages url