Merge github/main into agent-ws-bridge

Author: madhavajay

examples/apol1/README.md

@@ -56,11 +56,13 @@ P003	G2/G1
 ## Classifier Details
 
 **Variants tested**:
+
 - rs73885319 (A>G) - G1 variant site 1
 - rs60910145 (T>C) - G1 variant site 2
 - rs71785313 (InDel) - G2 variant
 
 **Genotypes**:
+
 - **G0/G0** - No risk variants (healthy)
 - **G1/G0** - Heterozygous G1 (low risk)
 - **G1/G1** - Homozygous G1 (moderate risk)

lint.sh

@@ -1,27 +1,29 @@
 #!/bin/bash
-set -e
-
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 cd "$SCRIPT_DIR"
 
-# Setup venv (must be sequential)
-uv venv --quiet 2>/dev/null || true
-source .venv/bin/activate
-uv pip install -e ./python --quiet 2>/dev/null
-uv pip install pytest ruff mypy vulture --quiet 2>/dev/null
+set -e
+
+export UV_VENV_CLEAR=1
+VENV_PATH="$SCRIPT_DIR/.venv"
+export UV_PROJECT_ENVIRONMENT="$VENV_PATH"
+
+uv venv "$VENV_PATH"
+uv pip install -e ./python
+uv pip install pytest ruff mypy vulture
 
 cd "$SCRIPT_DIR/python"
 
 echo "Running ruff format..."
-ruff format .
+uv run ruff format .
 
 echo "Running ruff check with fixes..."
-ruff check . --fix
+uv run ruff check . --fix
 
 echo "Running mypy..."
-mypy src/bioscript
+uv run mypy src/bioscript
 
 echo "Running vulture to detect dead code..."
-vulture src tests --min-confidence 80
+uv run vulture src tests --min-confidence 80
 
 echo "✓ All linting checks passed!"