refactor: consolidate dependencies into pyproject.toml

.github/workflows/automation.yml

@@ -28,9 +28,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -e .
-        pip install pytest pytest-cov pytest-mock pytest-asyncio pytest-timeout
+        pip install -e ".[dev]"
 
     - name: Run tests
       env:
@@ -97,5 +95,5 @@ jobs:
 
     - name: Check dependencies with safety
       run: |
-        pip install -r requirements.txt
+        pip install -e ".[dev]"
         safety check --full-report || echo "::warning::Vulnerable dependencies found."

.github/workflows/ci.yml

@@ -60,18 +60,15 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('requirements*.txt') }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-${{ matrix.python-version }}-
             ${{ runner.os }}-pip-
 
       - name: Install dependencies
         run: |
           python -m pip install -U pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-          pip install -e .
-          pip install pytest pytest-cov pytest-timeout pytest-asyncio pytest-mock
+          pip install -e ".[dev]"
 
       - name: Run tests with coverage
         env:

AGENTS.md

@@ -37,8 +37,7 @@ cortex install nginx --dry-run
 ```bash
 python3 -m venv venv
 source venv/bin/activate
-pip install -e .
-pip install -r requirements-dev.txt
+pip install -e ".[dev]"
 pytest tests/ -v
 ```
 

CONTRIBUTING.md

@@ -123,24 +123,19 @@ git remote add upstream https://github.com/cortexlinux/cortex.git
 python3 -m venv venv
 source venv/bin/activate  # On Windows: venv\Scripts\activate
 
-# Install dependencies
-pip install -r requirements.txt
-pip install -r requirements-dev.txt
-
-# Install in development mode
-pip install -e .
+# Install in development mode (includes all dependencies)
+pip install -e ".[dev]"
 
 # Run tests to verify setup
 pytest tests/ -v
 ```
 
-### Requirements Files
-
-If `requirements-dev.txt` doesn't exist, install these manually:
+### Dependencies
 
-```bash
-pip install pytest pytest-cov pytest-mock black pylint mypy bandit
-```
+All dependencies are defined in `pyproject.toml`. To install:
+- **Core dependencies**: `pip install -e .`
+- **With dev tools**: `pip install -e ".[dev]"`
+- **All extras**: `pip install -e ".[all]"`
 
 ### IDE Setup
 

Makefile

@@ -18,8 +18,7 @@ help:
 
 dev:
 	$(PYTHON) -m pip install -U pip
-	$(PYTHON) -m pip install -e .
-	$(PYTHON) -m pip install -r requirements-dev.txt
+	$(PYTHON) -m pip install -e ".[dev]"
 	@echo "✅ Dev environment ready"
 
 test:

README.md

@@ -94,8 +94,12 @@ python3 -m venv venv
 source venv/bin/activate
 
 # 3. Install Cortex
+# Using pyproject.toml (recommended)
 pip install -e .
 
+# Or install with dev dependencies
+pip install -e ".[dev]"
+
 # 4. Configure AI Provider (choose one):
 
 ## Option A: Ollama (FREE - Local LLM, no API key needed)

docs/guides/Developer-Guide.md

@@ -11,8 +11,7 @@ python3 -m venv venv
 source venv/bin/activate
 
 # Install dev dependencies
-pip install -r requirements.txt
-pip install -r requirements-dev.txt
+pip install -e ".[dev]"
 
 # Run tests
 pytest tests/

docs/guides/Getting-Started.md

@@ -12,8 +12,8 @@
 git clone https://github.com/cortexlinux/cortex.git
 cd cortex
 
-# Install dependencies
-pip install -r requirements.txt
+# Install Cortex
+pip install -e .
 
 # Configure API key
 export ANTHROPIC_API_KEY="your-key-here"

pyproject.toml

@@ -42,23 +42,36 @@ classifiers = [
 ]
 requires-python = ">=3.10"
 dependencies = [
+    # LLM Provider APIs
     "anthropic>=0.18.0",
     "openai>=1.0.0",
-    "rich>=13.0.0",
+    # HTTP requests (for GitHub API, network operations)
+    "requests>=2.32.4",
+    # Configuration file parsing
     "pyyaml>=6.0.0",
+    # Environment variable loading from .env files
     "python-dotenv>=1.0.0",
+    # Encryption for environment variable secrets
+    "cryptography>=42.0.0",
+    # Terminal UI and formatting
+    "rich>=13.0.0",
+    # Type hints for older Python versions
+    "typing-extensions>=4.0.0",
 ]
 
 [project.optional-dependencies]
 dev = [
     "pytest>=7.0.0",
     "pytest-cov>=4.0.0",
-    "pytest-timeout>=2.0.0",
-    "black>=23.0.0",
-    "ruff>=0.1.0",
+    "pytest-asyncio>=0.23.0",
+    "pytest-mock>=3.12.0",
+    "pytest-timeout>=2.3.0",
+    "black>=24.0.0",
+    "ruff>=0.8.0",
     "mypy>=1.0.0",
     "pre-commit>=3.0.0",
     "isort>=5.0.0",
+    "build>=0.10.0",
 ]
 security = [
     "bandit>=1.7.0",

tests/integration/test_end_to_end.py

@@ -17,8 +17,8 @@
     "PYTHONPATH": "/workspace",
     "PYTHONDONTWRITEBYTECODE": "1",
 }
-PIP_BOOTSTRAP = "python -m pip install --quiet --upgrade pip setuptools && python -m pip install --quiet --no-cache-dir -r /workspace/requirements.txt"
-PIP_BOOTSTRAP_DEV = "python -m pip install --quiet --upgrade pip setuptools && python -m pip install --quiet --no-cache-dir -r /workspace/requirements.txt -r /workspace/requirements-dev.txt"
+PIP_BOOTSTRAP = "python -m pip install --quiet --upgrade pip setuptools build && python -m pip install --quiet --no-cache-dir -e /workspace"
+PIP_BOOTSTRAP_DEV = "python -m pip install --quiet --upgrade pip setuptools build && python -m pip install --quiet --no-cache-dir -e /workspace[dev]"
 
 
 @unittest.skipUnless(docker_available(), "Docker is required for integration tests")