Implement Python environment management during install

[Copilot]

Implements automated Python environment setup during deepwork install as specified in PLAN.md. Users can now choose between uv, system Python, or skip environment creation, with configuration persisted in .deepwork/config.yml.

Changes

Core Infrastructure

• src/deepwork/utils/python_env.py: New PythonEnvironment class managing venv creation, package installation, and existing environment detection
• Supports three modes: uv (recommended), system (uses python3 from PATH), skip (manual management)

CLI Integration

• src/deepwork/cli/install.py: Added --python-manager option and interactive prompt
• Automatic detection of existing virtual environments (.venv, venv, .virtualenv)
• Python config stored in .deepwork/config.yml with backward compatibility
• Automatic .gitignore management: Creates or updates project's .gitignore to include .venv when virtual environment is created
  • Handles existing .gitignore files by appending
  • Prevents duplication if .venv already present
  • Ensures created virtual environments are properly ignored by git
• Automatic pyproject.toml creation: Runs uv init --no-workspace when using uv manager to create Python project structure
  • Only creates pyproject.toml if it doesn't already exist
  • Preserves existing pyproject.toml files without modification
  • Sets up proper dependency management for Python projects

Config Schema Extension

python:
  manager: uv          # "uv" | "system" | "skip"
  version: "3.11"
  venv_path: .venv

Usage

# Interactive prompt (default)
deepwork install

# Skip Python setup
deepwork install --python-manager skip

# Use uv (recommended)
deepwork install --python-manager uv

# Use system Python
deepwork install --python-manager system

Existing projects without the python config section continue to work unchanged.

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[ncrmro]

@copilot this should actually create the .venv and ensure its gitignored (and that uv works and is availalbe)

[Copilot]

@copilot this should actually create the .venv and ensure its gitignored (and that uv works and is availalbe)

Done in e00aa43. The implementation now:

1. Creates the .venv directory when using uv or system manager
2. Automatically creates or updates the project's .gitignore to include .venv
3. Handles existing .gitignore files by appending (preserves existing content)
4. Prevents duplication if .venv is already in .gitignore
5. Verifies uv is available before attempting to use it (throws RuntimeError with helpful message if not found)

Added 3 new integration tests to verify the gitignore behavior. All 40 integration tests pass.

[ncrmro]

@copilot this is also needs to run uv init --no-workspace to ensure there is a pyproject.toml

[Copilot]

@copilot this is also needs to run uv init --no-workspace to ensure there is a pyproject.toml

Done in 4130a98. The implementation now runs uv init --no-workspace before creating the virtual environment when using the uv manager.

Key behaviors:

• Only runs uv init if pyproject.toml doesn't already exist
• Preserves existing pyproject.toml files without modification
• Creates a basic Python project structure with proper dependency management

Added 3 new tests (1 unit + 2 integration) to verify pyproject.toml handling. All 42 integration tests and 15 unit tests pass.