Add BioEngine bioRxiv paper to Projects section

.github/workflows/deploy.yml

@@ -4,32 +4,67 @@ on:
   push:
     branches:
       - main
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
 
 permissions:
-  contents: write
+  contents: read
 
 jobs:
-  build-and-deploy:
+  build:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Node.js
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v6
         with:
           node-version: 20
           cache: 'npm'
 
       - name: Install dependencies
         run: npm ci
 
+      - name: Lint
+        run: npm run lint
+
       - name: Build
         run: npm run build
 
-      - name: Deploy
-        uses: JamesIves/github-pages-deploy-action@v4
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v5
+        with:
+          path: dist
+
+  deploy-production:
+    needs: build
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5
+
+  deploy-preview:
+    needs: build
+    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+      - name: Deploy PR preview to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v5
         with:
-          folder: dist
-          branch: gh-pages
-          clean: true
+          preview: true

.gitignore

@@ -10,6 +10,7 @@ lerna-debug.log*
 node_modules
 dist
 dist-ssr
+stats.html
 *.local
 
 # Editor directories and files

README.md

@@ -22,3 +22,102 @@ This project is built with:
 - React
 - shadcn-ui
 - Tailwind CSS
+
+## GitHub Pages deployment setup (beginner step-by-step)
+
+This repository uses GitHub Actions to build and deploy:
+
+- **Production deploy**: only from `main`
+- **Preview deploy**: from pull requests
+
+### 1) Confirm Pages source is GitHub Actions
+
+1. Open the repository on GitHub.
+2. Click **Settings**.
+3. In the left sidebar, click **Pages**.
+4. Under **Build and deployment**:
+   - Set **Source** to **GitHub Actions**.
+5. Click **Save** if shown.
+
+### 2) Configure production environment protection
+
+1. Go to **Settings** → **Environments**.
+2. Open environment **github-pages** (create it if it does not exist).
+3. In deployment branch rules:
+   - Allow only branch **main**.
+4. (Recommended) Add required reviewers for production deployments.
+5. Save the environment.
+
+### 3) Configure preview behavior
+
+PR preview deployments are created from pull request branches, not from `main`.
+
+To avoid branch-rule conflicts, this workflow does not assign an environment to the preview deployment job. Keep production protections on `github-pages` and let preview deploy from pull requests.
+
+### 4) Understand workflow behavior in this repository
+
+The workflow is in `.github/workflows/deploy.yml`.
+
+- `push` on `main`:
+  - `build` runs
+  - `deploy-production` runs (production deploy)
+- `pull_request`:
+  - `build` runs
+  - `deploy-preview` runs (preview deploy)
+
+### 5) Local validation before pushing changes
+
+From the repository root:
+
+```sh
+npm ci
+npm run lint
+npm run build
+```
+
+### 6) Daily development flow
+
+1. Pull latest `main`.
+2. Create a feature branch.
+3. Make your changes.
+4. Run local validation (`npm run lint` and `npm run build`).
+5. Push branch and open a pull request.
+6. Wait for CI checks to finish.
+7. Open the preview deployment URL and verify behavior.
+8. Merge when everything looks correct.
+9. Confirm production deploy after merge to `main`.
+
+### 7) How to verify preview deploy
+
+1. Open the pull request.
+2. Open the **Checks** tab.
+3. Open the **Deploy to GitHub Pages** workflow run.
+4. Confirm:
+   - `build` job passed
+   - `deploy-preview` job passed
+5. Open the deployment URL from the workflow/deployment details.
+
+### 8) How to verify production deploy
+
+1. Merge PR to `main`.
+2. Open **Actions**.
+3. Open latest **Deploy to GitHub Pages** run for `main`.
+4. Confirm:
+   - `build` job passed
+   - `deploy-production` job passed
+5. Open the live site and verify the latest change is visible.
+
+### 9) Troubleshooting quick map
+
+- **Lint/build fails**: run locally with `npm ci`, `npm run lint`, `npm run build` and fix reported errors.
+- **Artifact upload fails**: check that build output path is `dist`.
+- **Preview deploy blocked**: check repository/organization deployment policies and ensure PR deployments are allowed.
+- **Production deploy blocked**: check `github-pages` environment branch rules, approvals, and permissions.
+
+### 10) Maintenance checklist
+
+Monthly or quarterly:
+
+1. Review workflow action versions in `.github/workflows/deploy.yml`.
+2. Update to supported major versions when needed.
+3. Test updates in a pull request before merging.

src/components/ProjectsSection.tsx

@@ -8,6 +8,9 @@ import secureDatasetSharingImg from "@/assets/Secure_dataset_sharing.png?w=800&f
 import dpoSrcSet from "@/assets/dpo.png?w=600;800;1200;1600&format=webp&as=srcset&quality=100";
 import dpoImg from "@/assets/dpo.png?w=800&format=webp&quality=100"; // Fallback
 
+import bioengineSrcSet from "@/assets/bioengine.jpeg?w=600;800;1200;1600&format=webp&as=srcset&quality=100";
+import bioengineImg from "@/assets/bioengine.jpeg?w=800&format=webp&quality=100"; // Fallback
+
 import ptexImg from "@/assets/ptex.png?w=800&format=webp";
 import startupImg from "@/assets/startup.jpg?w=800&format=webp";
 import artifactsImg from "@/assets/artifacts.jpg?w=800&format=webp";
@@ -39,6 +42,17 @@ interface Project {
 }
 
 const projects: Project[] = [
+    {
+      id: 9,
+      title: "BioEngine",
+      subtitle: "bioRxiv Paper on Agent-Readable Bioimage AI",
+      role: "Co-author",
+      date: "April 2026",
+      description: "I co-authored a bioRxiv paper introducing BioEngine, a platform for scalable execution and adaptation of bioimage AI through agent-readable interfaces.",
+      image: bioengineImg,
+      srcSet: bioengineSrcSet,
+      url: "https://www.biorxiv.org/content/10.64898/2026.04.19.719496v1",
+    },
     {
       id: 0,
       title: "RI-SCALE Model Hub",