[codex] patch Vite security advisory

.env.vercel

@@ -0,0 +1,4 @@
+CATPRED_DEFAULT_BACKEND=modal
+CATPRED_MODAL_ENDPOINT=https://kaalabhairava2026--catpred-modal-api-predict.modal.run
+CATPRED_MODAL_TOKEN=
+CATPRED_MODAL_FALLBACK_TO_LOCAL=0

.github/workflows/ci.yml

@@ -0,0 +1,42 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install minimal runtime dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Compile Python sources
+        run: |
+          git ls-files '*.py' | xargs -r python -m py_compile
+
+      - name: Smoke test API entrypoints
+        run: |
+          python - <<'PY'
+          from catpred.web.app import create_app
+          from api.index import app as vercel_app
+
+          api_app = create_app()
+          assert api_app.title == "CatPred API"
+          assert vercel_app is not None
+          print("API smoke checks passed.")
+          PY

.github/workflows/deploy-modal.yml

@@ -0,0 +1,49 @@
+name: Deploy Modal
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths:
+      - ".github/workflows/deploy-modal.yml"
+      - "modal_app.py"
+      - "predict.py"
+      - "scripts/create_pdbrecords.py"
+      - "catpred/**"
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    concurrency:
+      group: modal-production-deploy
+      cancel-in-progress: true
+    env:
+      MODAL_TOKEN_ID: ${{ secrets.MODAL_TOKEN_ID }}
+      MODAL_TOKEN_SECRET: ${{ secrets.MODAL_TOKEN_SECRET }}
+    steps:
+      - name: Skip when Modal credentials are not configured
+        if: ${{ env.MODAL_TOKEN_ID == '' || env.MODAL_TOKEN_SECRET == '' }}
+        run: echo "Skipping Modal deploy because MODAL_TOKEN_ID / MODAL_TOKEN_SECRET are not configured."
+
+      - name: Checkout
+        if: ${{ env.MODAL_TOKEN_ID != '' && env.MODAL_TOKEN_SECRET != '' }}
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        if: ${{ env.MODAL_TOKEN_ID != '' && env.MODAL_TOKEN_SECRET != '' }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install Modal CLI
+        if: ${{ env.MODAL_TOKEN_ID != '' && env.MODAL_TOKEN_SECRET != '' }}
+        run: |
+          python -m pip install --upgrade pip
+          pip install "modal>=0.73"
+
+      - name: Deploy modal_app.py
+        if: ${{ env.MODAL_TOKEN_ID != '' && env.MODAL_TOKEN_SECRET != '' }}
+        run: modal deploy modal_app.py

.gitignore

@@ -32,3 +32,16 @@ catpred/data/__pycache__/esm_utils.cpython-312.pyc
 catpred/data/__pycache__/data.cpython-312.pyc
 catpred/data/__pycache__/cache_utils.cpython-312.pyc
 catpred/data/__pycache__/__init__.cpython-312.pyc
+
+# Generic Python/OS artifacts
+__pycache__/
+*.pyo
+*.pyd
+.DS_Store
+*.egg-info/
+.venv/
+.ipynb_checkpoints/
+
+# Local validation artifacts
+.e2e-assets/
+.e2e-tests/

.vercelignore

@@ -0,0 +1,8 @@
+.venv/
+.e2e-assets/
+.e2e-tests/
+results/
+output/
+checkpoints/
+external/
+*.ipynb