nuke useless scripts

Author: soodoku

.github/workflows/ci.yml

@@ -1,30 +1,82 @@
 name: CI
+
 on:
   push:
-    branches: [ main ]
+    branches: [ main, develop ]
   pull_request:
     branches: [ main ]
+
 jobs:
-  build-and-test:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: 'release'
+    
+    - name: Install R packages
+      run: |
+        R -e "install.packages(c('plm', 'lmtest', 'sandwich', 'AER', 'jsonlite', 'forecast', 'dplyr', 'tseries', 'nortest', 'car', 'rpart', 'randomForest', 'vars', 'ggplot2', 'gridExtra', 'tidyr', 'rlang', 'urca'), repos='https://cran.rstudio.com/')"
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install click jsonschema
+        pip install -e .
+    
+    - name: Test CLI works
+      run: |
+        rmcp --version
+        rmcp list-capabilities > /dev/null
+    
+    - name: Run basic tests
+      run: |
+        python tests/test_server_basic.py
+    
+    - name: Run MCP interface tests
+      run: |
+        python tests/test_mcp_interface.py
+    
+    - name: Run realistic scenarios
+      run: |
+        python tests/realistic_scenarios.py
+
+  lint:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.10'
-      - name: Install Python dependencies
-        run: |
-          pip install --upgrade pip
-          pip install pytest
-          pip install -r requirements.txt
-      - name: Build Docker image
-        run: docker build -t mcp-r .
-      # Run unit tests inside the Docker container where R is available
-      - name: Run unit tests in container
-        run: docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace mcp-r python tests/test_mcp_interface.py
-      # End-to-end test using the container
-      - name: End-to-end test via Docker
-        run: |
-          docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace mcp-r python tests/test_direct_capabilities.py
+    - uses: actions/checkout@v4
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+    
+    - name: Install linting tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install black isort flake8 mypy click jsonschema
+        pip install -e .
+    
+    - name: Run black
+      run: black --check rmcp tests
+    
+    - name: Run isort
+      run: isort --check-only rmcp tests
+    
+    - name: Run flake8
+      run: flake8 rmcp tests
+    
+    - name: Run mypy
+      run: mypy rmcp

CLAUDE.md

@@ -55,16 +55,43 @@ The server implements comprehensive econometric and statistical tools as Python
 
 ## Development Commands
 
+### Setup with Poetry
+```bash
+# Install dependencies
+poetry install
+
+# Install with all optional groups
+poetry install --all-extras
+
+# Install development dependencies
+poetry install --with dev
+
+# Activate virtual environment
+poetry shell
+```
+
 ### CLI Commands
 ```bash
 # Check version
-rmcp version
+poetry run rmcp version
 
 # Start server (auto-detects MCP protocol vs legacy JSON)
-rmcp start
+poetry run rmcp start
 
 # Run development server
-rmcp dev [optional_dev_server_file]
+poetry run rmcp dev [optional_dev_server_file]
+```
+
+### Development Scripts (via Poetry)
+```bash
+# Format code (black + isort)
+poetry run format
+
+# Run linting and type checking
+poetry run lint
+
+# Run test suite
+poetry run test
 ```
 
 ### Testing
@@ -78,26 +105,29 @@ rmcp dev [optional_dev_server_file]
 # Run CLI tests
 ./tests/run_cli_tests.sh
 
-# Run pytest tests (if available)
-pytest
+# Run MCP interface tests
+poetry run python tests/test_mcp_interface.py
+
+# Run realistic scenarios
+poetry run python tests/realistic_scenarios.py
 ```
 
 ### Running the Server
 ```bash
-# Install in development mode
-pip install -e .
+# Install in development mode with Poetry
+poetry install
 
 # Start MCP server via CLI (supports both MCP protocol and legacy JSON)
-rmcp start
+poetry run rmcp start
 
 # Direct Python execution
-python -m rmcp
+poetry run python -m rmcp
 
 # Test with legacy JSON format
-cat tests/test_request.json | rmcp start
+cat tests/test_request.json | poetry run rmcp start
 
 # Test with MCP protocol format
-cat tests/test_mcp_protocol.json | rmcp start
+cat tests/test_mcp_protocol.json | poetry run rmcp start
 ```
 
 ### Docker Development

pyproject.toml

@@ -1,13 +1,9 @@
-[build-system]
-requires = ["setuptools>=61.0", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
+[tool.poetry]
 name = "rmcp"
 version = "0.3.4"
 description = "Comprehensive Model Context Protocol server with 33 statistical analysis tools across 8 categories"
-authors = [{name = "Gaurav Sood", email = "gsood07@gmail.com"}]
-license = {text = "MIT"}
+authors = ["Gaurav Sood <gsood07@gmail.com>"]
+license = "MIT"
 readme = "README.md"
 keywords = ["mcp", "r", "statistics", "econometrics", "model-context-protocol", "data-analysis"]
 classifiers = [
@@ -27,46 +23,43 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
     "Topic :: System :: Distributed Computing",
 ]
-requires-python = ">=3.8"
-dependencies = [
-    "click>=8.1.0",
-    "jsonschema>=4.0.0",
-]
+packages = [{include = "rmcp"}]
+
+[tool.poetry.dependencies]
+python = ">=3.8"
+click = ">=8.1.0"
+jsonschema = ">=4.0.0"
+# R integration dependencies
+subprocess32 = {version = ">=3.5.0", python = "<3.3"}
+
+[tool.poetry.group.dev.dependencies]
+pytest = ">=8.0.0"
+pytest-cov = ">=5.0.0"
+pytest-mock = ">=3.12.0"
+pytest-asyncio = ">=0.21.0"
+black = ">=23.0.0"
+isort = ">=5.12.0"
+flake8 = ">=6.0.0"
+mypy = ">=1.5.0"
+pre-commit = ">=3.0.0"
+
+[tool.poetry.group.http.dependencies]
+fastapi = ">=0.100.0"
+uvicorn = ">=0.20.0"
+sse-starlette = ">=1.6.0"
+
+[tool.poetry.scripts]
+rmcp = "rmcp.cli:cli"
 
-[project.urls]
+[tool.poetry.urls]
 Homepage = "https://github.com/gojiplus/rmcp"
 Repository = "https://github.com/gojiplus/rmcp"
 Documentation = "https://github.com/gojiplus/rmcp#readme"
 Issues = "https://github.com/gojiplus/rmcp/issues"
 
-[project.optional-dependencies]
-dev = [
-    "pytest>=8.0.0",
-    "pytest-cov>=5.0.0", 
-    "pytest-mock>=3.12.0",
-    "pytest-asyncio>=0.21.0",
-    "black>=23.0.0",
-    "isort>=5.12.0",
-    "flake8>=6.0.0",
-    "mypy>=1.5.0",
-    "pre-commit>=3.0.0",
-]
-http = [
-    "fastapi>=0.100.0",
-    "uvicorn>=0.20.0",
-    "sse-starlette>=1.6.0",
-]
-r = [
-    # R integration dependencies
-    "subprocess32>=3.5.0; python_version<'3.3'",
-]
-
-[project.scripts]
-rmcp = "rmcp.cli:cli"
-
-# Package discovery for standard layout
-[tool.setuptools.packages.find]
-where = ["."]
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
 
 # Tool configurations
 [tool.pytest.ini_options]

requirements.txt

@@ -299,7 +299,7 @@ async def _handle_initialize(self, params: Dict[str, Any]) -> Dict[str, Any]:
         logger.info(f"Initializing MCP connection with client: {client_info.get('name', 'unknown')}")
 
         return {
-            "protocolVersion": "2024-11-05",
+            "protocolVersion": "2025-06-18",
             "capabilities": {
                 "tools": {
                     "listChanged": False

rmcp/core/server.py

@@ -14,8 +14,8 @@
 import sys
 from pathlib import Path
 
-# Add src to path
-sys.path.insert(0, str(Path(__file__).parent.parent / "src"))
+# Add rmcp to path
+sys.path.insert(0, str(Path(__file__).parent.parent))
 
 from rmcp.tools.regression import linear_model, correlation_analysis, logistic_regression
 from rmcp.core.context import Context, LifespanState