Merge branch 'main' into truncating-app-node-text

Author: ptgolden

.claude/skills/update-publications/SKILL.md

@@ -0,0 +1,154 @@
+---
+name: update-publications
+description: Updates the Monarch Initiative publications page with latest data from Google Scholar. Use this when the user asks to update publications, refresh citation metrics, or add new papers to the publications page.
+---
+
+# Update Publications Page
+
+This Skill guides you through updating the Monarch Initiative publications page with the latest publications and citation metrics from Google Scholar.
+
+## Google Scholar Profile
+
+The Monarch Initiative Google Scholar profile is:
+https://scholar.google.com/citations?hl=en&user=zmUEDj0AAAAJ&view_op=list_works&authuser=1&sortby=pubdate
+
+## Prerequisites
+
+Before starting, ensure the Python environment is set up:
+
+```bash
+uv sync --all-extras
+```
+
+This installs all dependencies including `scholarly`, `typer`, and `loguru`.
+
+## Step-by-Step Process
+
+### 1. Fetch Latest Metadata
+
+Fetch updated citation metrics from Google Scholar:
+
+```bash
+uv run python scripts/get_publications.py fetch-metadata
+```
+
+This retrieves total citations, h-index, i10-index, and citations per year, saving to `scripts/metadata.json`.
+
+### 2. Fetch Latest Publications
+
+Fetch the complete publication list (this takes several minutes):
+
+```bash
+uv run python scripts/get_publications.py fetch-publications
+```
+
+This saves raw publication data to `scripts/scholarly_output.json`.
+
+### 3. Handle Missing Links
+
+Run the update command to check for missing publication links:
+
+```bash
+uv run python scripts/get_publications.py update
+```
+
+If any publications are missing links, the script will exit with an error listing them. For each missing link:
+
+1. Search online for the publication's official URL (DOI, PubMed, publisher site, arXiv, etc.)
+2. Add to the `KNOWN_LINKS` dictionary in `scripts/get_publications.py` (around line 28)
+3. Run the update command again
+
+Example addition to KNOWN_LINKS:
+```python
+KNOWN_LINKS = {
+    "Publication Title Here": "https://doi.org/10.1234/example",
+    # ... other entries
+}
+```
+
+### 4. Review Changes
+
+Once the update succeeds, review the changes:
+
+```bash
+git diff frontend/src/data/publications.json
+```
+
+Note the key metrics:
+- Number of new publications
+- Citation count changes
+- H-index changes
+- i10-index changes
+
+### 5. Commit Changes
+
+Commit the updated files following the repository's conventions:
+
+```bash
+git add frontend/src/data/publications.json
+# Add scripts/get_publications.py if KNOWN_LINKS was updated
+git add scripts/get_publications.py
+
+git commit -m "[Month] [Year] Publications update
+
+Updated publications page with latest data from Google Scholar:
+- [X] new publications added
+- Citation count: [old] → [new]
+- H-index: [old] → [new]
+- Publications: [old] → [new]
+
+🤖 Generated with [Claude Code](https://claude.com/claude-code)
+
+Co-Authored-By: Claude <noreply@anthropic.com>"
+```
+
+### 6. Create Pull Request
+
+Push and create a PR with a detailed summary:
+
+```bash
+git push -u origin [branch-name]
+
+gh pr create --title "[Month] [Year] Publications update" --body "
+## Summary
+- Updated publications page with latest data from Google Scholar
+- Added [X] new publications
+- Updated citation metrics
+
+## Changes
+- Citation count: [old] → [new]
+- H-index: [old] → [new]
+- Total publications: [old] → [new]
+
+## New Publications
+[List new publications]
+
+🤖 Generated with [Claude Code](https://claude.com/claude-code)
+"
+```
+
+## Files Modified
+
+- `frontend/src/data/publications.json` - Main publications data
+- `scripts/metadata.json` - Citation metadata (cached, not typically committed)
+- `scripts/scholarly_output.json` - Raw publications (cached, not typically committed)
+- `scripts/get_publications.py` - Only if KNOWN_LINKS was updated
+
+## Reference Example
+
+See PR #1217 for a reference example of a publications update.
+
+## Troubleshooting
+
+**Missing Links Error**: Search for the publication online and add its URL to KNOWN_LINKS in the script.
+
+**Rate Limiting**: If Google Scholar blocks requests, wait a few minutes and retry.
+
+**Duplicate Publications**: The script automatically handles duplicates by merging metadata.
+
+## Notes
+
+- Updates are typically done monthly or quarterly
+- All publications must have valid links before the update completes
+- The script deduplicates and merges publication metadata automatically
+- Publications are organized by year in reverse chronological order

.github/workflows/build-and-deploy-images.yaml

@@ -28,7 +28,7 @@ jobs:
           echo "IMAGE_TAG=${IMAGE_TAG//v}" >> $GITHUB_OUTPUT
 
       - name: Build and Push Image
-        uses: RafikFarhad/push-to-gcr-github-action@v5-beta
+        uses: RafikFarhad/push-to-gcr-github-action@v5-rc1
         with:
           gcloud_service_key: ${{ secrets.JSON_GCLOUD_SERVICE_ACCOUNT_JSON }}
           registry: us-central1-docker.pkg.dev
@@ -51,7 +51,7 @@ jobs:
           fetch-depth: 0 # to get all tags
 
       - name: Set up Bun
-        uses: oven-sh/setup-bun@v1
+        uses: oven-sh/setup-bun@v2
 
       - name: Install packages
         run: bun install
@@ -72,7 +72,7 @@ jobs:
       # ./services/nginx/config/, copied to /etc/nginx/conf.d/ in the image
 
       - name: Build and Push Image
-        uses: RafikFarhad/push-to-gcr-github-action@v5-beta
+        uses: RafikFarhad/push-to-gcr-github-action@v5-rc1
         with:
           gcloud_service_key: ${{ secrets.JSON_GCLOUD_SERVICE_ACCOUNT_JSON }}
           registry: us-central1-docker.pkg.dev
@@ -98,8 +98,6 @@ jobs:
 
       - name: "Set up Cloud SDK"
         uses: "google-github-actions/setup-gcloud@v2"
-        with:
-          version: ">= 447.0.0"
 
       - name: "Cache SSH Key"
         uses: actions/cache@v4

.github/workflows/build-images-for-branch.yaml

@@ -0,0 +1,79 @@
+name: Build and Push to GCR for specific branches
+on:
+  push:
+    branches:
+      - issue-982-about-dropdown
+
+# This job uses RafikFarhad's GitHub action to build and
+# push a docker image to a specified GCP repository
+jobs:
+  build-and-push-to-gcr:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # to get all tags
+
+      - name: Generate Image Tag
+        id: get-tag
+        run: |
+          REV=$(git rev-list --tags --max-count=1)
+          IMAGE_TAG=$(git describe --tags $REV)
+          echo "IMAGE_TAG=${IMAGE_TAG//v}"
+          echo "IMAGE_TAG=${IMAGE_TAG//v}" >> $GITHUB_OUTPUT
+
+      - name: Build and Push Image
+        uses: RafikFarhad/push-to-gcr-github-action@v5-beta
+        with:
+          gcloud_service_key: ${{ secrets.JSON_GCLOUD_SERVICE_ACCOUNT_JSON }} # not needed if you use google-github-actions/auth
+          registry: us-central1-docker.pkg.dev
+          project_id: monarch-initiative
+          image_name: monarch-api/monarch-api
+          image_tag: ${{ github.sha }}, ${{ github.ref_name }}
+          dockerfile: ./backend/Dockerfile
+
+  build-and-push-frontend-image:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./frontend
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # to get all tags
+
+      - name: Set up Bun
+        uses: oven-sh/setup-bun@v2
+
+      - name: Install packages
+        run: bun install
+
+      - name: Build app
+        run: bun run build
+
+      - name: Generate Image Tag for Frontend Dir
+        id: get-tag
+        run: |
+          REV=$(git rev-list --tags --max-count=1 )
+          IMAGE_TAG=$(git describe --tags $REV)
+          echo "IMAGE_TAG=${IMAGE_TAG//v}"
+          echo "IMAGE_TAG=${IMAGE_TAG//v}" >> $GITHUB_OUTPUT
+
+      # the monarch-ui Dockerfile pulls from two places:
+      # ./frontend/dist/, copied to /var/www/ in the image
+      # ./services/nginx/config/, copied to /etc/nginx/conf.d/ in the image
+
+      - name: Build and Push Image
+        uses: RafikFarhad/push-to-gcr-github-action@v5-beta
+        with:
+          gcloud_service_key: ${{ secrets.JSON_GCLOUD_SERVICE_ACCOUNT_JSON }}
+          registry: us-central1-docker.pkg.dev
+          project_id: monarch-initiative
+          image_name: monarch-api/monarch-ui
+          image_tag: ${{ github.sha }}, ${{ github.ref_name }}
+          dockerfile: ./services/nginx/Dockerfile
+          context: .

.github/workflows/build-semsim-image.yaml

@@ -0,0 +1,57 @@
+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          prompt: |
+            REPO: ${{ github.repository }}
+            PR NUMBER: ${{ github.event.pull_request.number }}
+
+            Please review this pull request and provide feedback on:
+            - Code quality and best practices
+            - Potential bugs or issues
+            - Performance considerations
+            - Security concerns
+            - Test coverage
+
+            Use the repository's CLAUDE.md for guidance on style and conventions. Be constructive and helpful in your feedback.
+
+            Use `gh pr comment` with your Bash tool to leave your review as a comment on the PR.
+
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          claude_args: '--allowed-tools "Bash(gh issue view:*),Bash(gh search:*),Bash(gh issue list:*),Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr list:*)"'
+