Merge branch 'main' into issues/8301

Author: cderv

.github/workflows/actions/release-info/action.yml

@@ -27,5 +27,5 @@ inputs:
     required: true
 
 runs:
-  using: "node16"
+  using: "node20"
   main: "index.js"

.github/workflows/preview.yml

@@ -8,8 +8,9 @@ name: Deploy Preview
 
 concurrency:
   # Use github.event.pull_request.number on pull requests, so it's unique per pull request
+  # Use github.event.issue.number on issue comments, so it's unique per comment
   # Use github.ref on other branches, so it's unique per branch
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.event.issue.number || github.ref }}
+  group: ${{ github.workflow }}-${{ (github.event.pull_request && format('PR-{0}', github.event.pull_request.number)) || ( github.event.issue && format('comment-{0}', github.event.issue.number) ) || github.ref }}
   cancel-in-progress: true
 
 jobs:
@@ -23,10 +24,25 @@ jobs:
           echo "::error title=Manual action required for preview::PR from fork can't be deployed as preview to Netlify automatically. Use '/deploy-preview' command in comments to trigger the preview manually."
         shell: bash
 
+  role-of-commenter:
+    if: github.event.issue.pull_request
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if commenter is a member, owner or collaborator
+        id: commenter-check
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          commenter_role=$(gh api repos/$GITHUB_REPOSITORY/collaborators/${{ github.event.comment.user.login }}/permission --jq '.permission')
+          echo "commenter_role=$commenter_role" >> "$GITHUB_OUTPUT"
+          echo "author_association=${{ github.event.comment.author_association }}" >> "$GITHUB_OUTPUT"
+        shell: bash
+
   build-deploy-preview:
     # Deploy a preview only if 
     # - the PR is not from a fork,
     # - requested by PR comment /deploy-preview, from a repo user or github action bot (user id 41898282)
+    # FIXME: We need to change the way we filter because somehow some MEMBER in API are seen as CONTRIBUTOR in CI
     if: >
       (
         github.event_name == 'pull_request' && 
@@ -36,6 +52,7 @@ jobs:
         github.event.issue.pull_request && 
         (
           github.event.comment.user.id == '41898282' ||
+          github.event.comment.user.login == 'gordonwoodhull' ||
           github.event.comment.author_association == 'MEMBER' || 
           github.event.comment.author_association == 'OWNER' || 
           github.event.comment.author_association == 'COLLABORATOR'
@@ -102,8 +119,72 @@ jobs:
             Deploy from GHA: ${{ github.event.pull_request.title || format('manual from PR {0}', github.event.issue.number) }}
           alias: deploy-preview-${{ github.event.pull_request.number || github.event.issue.number }}
           # these all default to 'true'
-          enable-pull-request-comment: true
+          enable-pull-request-comment: false
           enable-commit-comment: false
           enable-commit-status: true
           overwrites-pull-request-comment: false
         timeout-minutes: 1
+
+      - name: Get changed files
+        id: changed-files
+        uses: tj-actions/[email protected]
+        with:
+          files: |
+            # don't consider modifications on file used for includes for now.
+            docs/**/[^_]*.qmd
+            docs/**/[^_]*.md
+            docs/extensions/listings/*.yml
+          json: true
+          escape_json: false
+      
+      - name: Create custom PR comment
+        if: github.event.pull_request || github.event.issue.pull_request
+        uses: actions/github-script@v7
+        env:
+          DEPLOY_URL: ${{ steps.netlify-deploy.outputs.deploy-url }}
+          CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const prNumber = context.payload.pull_request?.number || context.payload.issue.number;
+            const deployUrl = process.env.DEPLOY_URL;
+            const changedFiles = JSON.parse(process.env.CHANGED_FILES);
+            
+            let commentBody = `## 📝 Preview Deployment\n\n`;
+            commentBody += `🔍 Full site preview: [${deployUrl}](${deployUrl})\n\n`;
+            
+            if (changedFiles.length > 0) {
+              commentBody += `### 🔄 Modified Documents\n\n`;
+              changedFiles.forEach(file => {
+                let fileUrlPath;
+
+                // Define a mapping for special files to their corresponding URLs
+                const specialFileMapping = {
+                  'docs/extensions/listings/shortcodes-and-filters.yml': 'docs/extensions/index.html',
+                  'docs/extensions/listings/journal-articles.yml': 'docs/extensions/index.html',
+                  'docs/extensions/listings/custom-formats.yml': 'docs/extensions/index.html',
+                  'docs/extensions/listings/revealjs-formats.yml': 'docs/extensions/index.html',
+                  'docs/extensions/listings/revealjs.yml': 'docs/extensions/index.html'
+                };
+
+                // Check if the file is in the special mapping
+                if (specialFileMapping[file]) {
+                  fileUrlPath = specialFileMapping[file];
+                } else if (file.endsWith('.qmd') || file.endsWith('.md')) {
+                  // Convert path to URL (removing file extension and adding appropriate path)
+                  fileUrlPath = file.replace(/\.(qmd|md)$/, '.html');
+                }
+
+                if (fileUrlPath) {
+                  const fileUrl = `${deployUrl}/${fileUrlPath}`;
+                  commentBody += `- [${file}](${fileUrl})\n`;
+                }
+              });
+            }
+            
+            github.rest.issues.createComment({
+              issue_number: prNumber,
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              body: commentBody
+            });

.github/workflows/publish.yml

@@ -18,6 +18,10 @@ on:
 
 name: Quarto Publish
 
+concurrency:
+  group: ${{ format('{0} - {1} - {2}', github.workflow, github.ref, inputs.prerelease && 'prerelease' || 'main') }}
+  cancel-in-progress: true
+
 jobs:
   build-deploy:
     runs-on: ubuntu-latest
@@ -43,14 +47,16 @@ jobs:
       - name: Render 
         uses: quarto-dev/quarto-actions/render@v2
         env:
-          QUARTO_PROFILE: ${{ (inputs.prerelease == 'true' || (contains(fromJSON('["push", "workflow_dispatch"]'), github.event_name) && github.ref == 'refs/heads/prerelease')) && 'prerelease-docs' || '' }}
+          QUARTO_PROFILE: ${{ (inputs.prerelease || (contains(fromJSON('["push", "workflow_dispatch"]'), github.event_name) && github.ref == 'refs/heads/prerelease')) && 'prerelease-docs' || '' }}
 
       - name: Publish release website
         # Only do this step if 
         # - workflow is called for release deploy, with inputs.prerelease being false. It should not trigger if inputs.prerelease is null.
         #   and in GHA null == false is true. That is why we convert to string and compare.
         # - workflow is triggered by push event on main branch
-        if: ${{ format('{0}', inputs.prerelease) == 'false' || (contains(fromJSON('["push", "workflow_dispatch"]'), github.event_name) && github.ref == 'refs/heads/main') }}
+        # - workflow is triggered by workflow_dispatch event 
+        #   (we need to protect also from workflow_dispatch inherited from workflow_call event - where inputs.prerelease is defined)
+        if: ${{ format('{0}', inputs.prerelease) == 'false' || (!inputs.prerelease && contains(fromJSON('["push", "workflow_dispatch"]'), github.event_name) && github.ref == 'refs/heads/main') }}
         uses: quarto-dev/quarto-actions/publish@v2
         with:
           target: netlify
@@ -62,7 +68,9 @@ jobs:
         # - workflow is called for release deploy with inputs.prerelease being true. It should not trigger if inputs.prerelease is null.
         #   Though as in GHA null means false, no need to cast to string
         # - workflow is triggered by push event on main branch
-        if: ${{ inputs.prerelease || (contains(fromJSON('["push", "workflow_dispatch"]'), github.event_name) && github.ref == 'refs/heads/prerelease') }}
+        # - workflow is triggered by workflow_dispatch event 
+        #   (we need to protect also from workflow_dispatch inherited from workflow_call event - where inputs.prerelease is defined)
+        if: ${{ inputs.prerelease || (format('{0}', inputs.prerelease) != 'false' && contains(fromJSON('["push", "workflow_dispatch"]'), github.event_name) && github.ref == 'refs/heads/prerelease') }}
         id: netlify-deploy
         uses: nwtgck/actions-netlify@v3
         env:

.github/workflows/upload-algolia.rb

@@ -1,3 +1,4 @@
+gem 'algolia', '=2.3.4'
 require 'json'
 require 'algolia'
 require 'open-uri'

.github/workflows/upload-index.yml

@@ -17,7 +17,7 @@ jobs:
           ruby-version: 3.0.2
       - name: Install Algolia API Dependencies
         run: |
-          gem install algolia
+          gem install algolia -v 2.3.4
       - name: Upload Index for release website
         run: |
           pwd

.gitignore

@@ -17,3 +17,5 @@
 # Use pipenv to manage dependencies
 # so we don't want to track this file in git
 requirements.txt
+
+**/*.quarto_ipynb

.well-known/atproto-did

@@ -0,0 +1 @@
+did:plc:yvu4igag5eha3sbbbx7poz2p

DESCRIPTION

@@ -7,9 +7,12 @@ Depends:
     dygraphs,
     fs,
     ggplot2,
+    gh,
+    gt,
     htmltools,
     knitr,
     leaflet,
+    magick,
     openintro,
     palmerpenguins,
     readr,

Pipfile

@@ -26,6 +26,8 @@ shiny = "*"
 plotly = "*"
 pathlib = "*"
 nbformat = "*"
+statsmodels = "*"
+plotnine = "*"
 
 [dev-packages]