Add more MCP tools and expand testing

.github/workflows/ci.yml

@@ -0,0 +1,54 @@
+name: Test and Install Package
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        version: "latest"
+
+    - name: Install dependencies
+      run: uv sync --group dev
+
+    - name: Build and test
+      run: make all
+
+    - name: Upload coverage reports
+      uses: codecov/codecov-action@v4
+      if: matrix.python-version == '3.13'
+      with:
+        file: ./htmlcov/index.html
+        fail_ci_if_error: false
+
+    - name: Archive test artifacts
+      uses: actions/upload-artifact@v4
+      if: always()
+      with:
+        name: test-artifacts-${{ matrix.python-version }}
+        path: |
+          claude-mcp-test.log
+          htmlcov/
+          dist/
+        retention-days: 7

.github/workflows/publish.yml.disabled

@@ -0,0 +1,108 @@
+name: Build and Publish to PyPI
+
+on:
+  push:
+    tags:
+      - 'v*'  # Trigger on version tags (v1.0.0, v0.8.1, etc.)
+  workflow_dispatch:  # Allow manual triggering
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
+
+      - name: Install dependencies
+        run: uv sync --group dev
+
+      - name: Run comprehensive tests
+        run: make all
+
+  build-and-publish:
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+        with:
+          version: "latest"
+
+      - name: Install dependencies
+        run: uv sync --group dev
+
+      - name: Build package
+        run: make build
+
+      - name: Check package
+        run: |
+          uv tool install twine
+          uv tool run twine check dist/*
+
+      - name: Verify version matches tag
+        run: |
+          TAG_VERSION=${GITHUB_REF#refs/tags/v}
+          PACKAGE_VERSION=$(uv run python -c "from src.bertron_mcp.main import __version__; print(__version__)")
+          echo "Tag version: $TAG_VERSION"
+          echo "Package version: $PACKAGE_VERSION"
+          if [ "$TAG_VERSION" != "$PACKAGE_VERSION" ]; then
+            echo "Version mismatch! Tag: $TAG_VERSION, Package: $PACKAGE_VERSION"
+            exit 1
+          fi
+
+      - name: Publish to PyPI (using token-based auth)
+        if: "!contains(github.ref, 'test') && !contains(github.ref, 'dryrun')"
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verify-metadata: true
+          verbose: true
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+      - name: Publish to TestPyPI (using token-based auth)
+        if: "contains(github.ref, 'test') && !contains(github.ref, 'dryrun')"
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          verify-metadata: true
+          verbose: true
+          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+
+      - name: Dry run (build only)
+        if: "contains(github.ref, 'dryrun')"
+        run: |
+          echo "Dry run mode - would publish these files:"
+          ls -la dist/
+          echo "Package contents:"
+          uv tool run twine check dist/* --verbose
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: build-artifacts-${{ github.ref_name }}
+          path: dist/

Makefile

@@ -1,8 +1,16 @@
-.PHONY: test-coverage clean install dev format lint all server build upload-test upload release deptry mypy test-mcp test-mcp-extended test-integration test-version test-mcp-protocol test-claude-mcp
+.PHONY: test-coverage clean install dev format lint all server build upload-test upload release deptry mypy test-mcp test-mcp-extended test-mcp-tools test-mcp-constraints test-mcp-errors test-integration test-version test-mcp-protocol test-claude-mcp test-uvx test-uvx-mcp
 
 # Default target
 all: clean install dev test-coverage format lint mypy deptry build test-mcp test-mcp-extended test-integration test-version
 
+# CI-safe target (no external dependencies)
+ci: clean install dev test-coverage format lint mypy build test-version
+	@echo "✅ CI pipeline completed successfully!"
+
+# CI with network tests (for environments with reliable network)
+ci-network: ci test-mcp test-mcp-extended test-integration
+	@echo "✅ CI pipeline with network tests completed!"
+
 # Install everything for development
 dev:
 	uv sync --group dev
@@ -61,6 +69,10 @@ upload:
 # Complete release workflow
 release: clean install test-coverage build
 
+# Comprehensive MCP testing
+test-mcp-comprehensive: test-mcp test-mcp-extended test-mcp-tools test-mcp-constraints test-mcp-errors
+	@echo "✅ All MCP JSON-RPC tests completed successfully!"
+
 # Integration Testing
 test-integration:
 	@echo "🌤️ Testing BERtron MCP integration..."
@@ -112,3 +124,53 @@ test-claude-mcp:
 		2>&1 | tee claude-mcp-test.log
 
 
+# Test uvx installation from GitHub
+test-uvx:
+	@echo "📦 Testing uvx installation from GitHub..."
+	uvx --from git+https://github.com/ber-data/bertron-mcp.git bertron-mcp --version
+
+# Test uvx MCP server
+test-uvx-mcp:
+	@echo "🔧 Testing uvx MCP server functionality..."
+	@(echo '{"jsonrpc": "2.0", "method": "initialize", "params": {"protocolVersion": "2025-03-26", "capabilities": {"tools": {}}, "clientInfo": {"name": "test-client", "version": "1.0.0"}}, "id": 1}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "notifications/initialized", "params": {}}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "tools/list", "id": 2}') | \
+	timeout 10 uvx --from git+https://github.com/ber-data/bertron-mcp.git bertron-mcp
+
+# Test multiple MCP tools via JSON-RPC
+test-mcp-tools:
+	@echo "🛠️ Testing multiple MCP tools via JSON-RPC..."
+	@(echo '{"jsonrpc": "2.0", "method": "initialize", "params": {"protocolVersion": "2025-03-26", "capabilities": {"tools": {}}, "clientInfo": {"name": "test-client", "version": "1.0.0"}}, "id": 1}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "notifications/initialized", "params": {}}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "tools/call", "params": {"name": "health_check", "arguments": {}}, "id": 2}'; \
+	 sleep 0.5; \
+	 echo '{"jsonrpc": "2.0", "method": "tools/call", "params": {"name": "search_by_source", "arguments": {"source": "NMDC", "limit": 5}}, "id": 3}'; \
+	 sleep 0.5; \
+	 echo '{"jsonrpc": "2.0", "method": "tools/call", "params": {"name": "search_by_type", "arguments": {"entity_type": "sample", "limit": 3}}, "id": 4}') | \
+	timeout 15 uv run python src/bertron_mcp/main.py
+
+# Test constraint enforcement via JSON-RPC
+test-mcp-constraints:
+	@echo "🚧 Testing constraint enforcement via JSON-RPC..."
+	@(echo '{"jsonrpc": "2.0", "method": "initialize", "params": {"protocolVersion": "2025-03-26", "capabilities": {"tools": {}}, "clientInfo": {"name": "test-client", "version": "1.0.0"}}, "id": 1}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "notifications/initialized", "params": {}}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "tools/call", "params": {"name": "search_by_source", "arguments": {"source": "NMDC", "limit": 5000}}, "id": 2}') | \
+	timeout 10 uv run python src/bertron_mcp/main.py
+
+# Test error handling via JSON-RPC
+test-mcp-errors:
+	@echo "❌ Testing error handling via JSON-RPC..."
+	@(echo '{"jsonrpc": "2.0", "method": "initialize", "params": {"protocolVersion": "2025-03-26", "capabilities": {"tools": {}}, "clientInfo": {"name": "test-client", "version": "1.0.0"}}, "id": 1}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "notifications/initialized", "params": {}}'; \
+	 sleep 0.1; \
+	 echo '{"jsonrpc": "2.0", "method": "tools/call", "params": {"name": "nonexistent_tool", "arguments": {}}, "id": 2}'; \
+	 sleep 0.5; \
+	 echo '{"jsonrpc": "2.0", "method": "tools/call", "params": {"name": "geosearch", "arguments": {"latitude": 91.0, "longitude": 0.0}}, "id": 3}') | \
+	timeout 10 uv run python src/bertron_mcp/main.py