cli-jaw 0.1.6 → 0.1.8

package/skills_ref/modern-python/skills/modern-python/SKILL.md

@@ -1,333 +0,0 @@
----
-name: modern-python
-description: Configures Python projects with modern tooling (uv, ruff, ty). Use when creating projects, writing standalone scripts, or migrating from pip/Poetry/mypy/black.
----
-
-# Modern Python
-
-Guide for modern Python tooling and best practices, based on [trailofbits/cookiecutter-python](https://github.com/trailofbits/cookiecutter-python).
-
-## When to Use This Skill
-
-- Creating a new Python project or package
-- Setting up `pyproject.toml` configuration
-- Configuring development tools (linting, formatting, testing)
-- Writing Python scripts with external dependencies
-- Migrating from legacy tools (when user requests it)
-
-## When NOT to Use This Skill
-
-- **User wants to keep legacy tooling**: Respect existing workflows if explicitly requested
-- **Python < 3.11 required**: These tools target modern Python
-- **Non-Python projects**: Mixed codebases where Python isn't primary
-
-## Anti-Patterns to Avoid
-
-| Avoid | Use Instead |
-|-------|-------------|
-| `[tool.ty]` python-version | `[tool.ty.environment]` python-version |
-| `uv pip install` | `uv add` and `uv sync` |
-| Editing pyproject.toml manually to add deps | `uv add <pkg>` / `uv remove <pkg>` |
-| `hatchling` build backend | `uv_build` (simpler, sufficient for most cases) |
-| Poetry | uv (faster, simpler, better ecosystem integration) |
-| requirements.txt | PEP 723 for scripts, pyproject.toml for projects |
-| mypy / pyright | ty (faster, from Astral team) |
-| `[project.optional-dependencies]` for dev tools | `[dependency-groups]` (PEP 735) |
-| Manual virtualenv activation (`source .venv/bin/activate`) | `uv run <cmd>` |
-| pre-commit | prek (faster, no Python runtime needed) |
-
-**Key principles:**
-- Always use `uv add` and `uv remove` to manage dependencies
-- Never manually activate or manage virtual environments—use `uv run` for all commands
-- Use `[dependency-groups]` for dev/test/docs dependencies, not `[project.optional-dependencies]`
-
-## Decision Tree
-
-```
-What are you doing?
-│
-├─ Single-file script with dependencies?
-│   └─ Use PEP 723 inline metadata (./references/pep723-scripts.md)
-│
-├─ New multi-file project (not distributed)?
-│   └─ Minimal uv setup (see Quick Start below)
-│
-├─ New reusable package/library?
-│   └─ Full project setup (see Full Setup below)
-│
-└─ Migrating existing project?
-    └─ See Migration Guide below
-```
-
-## Tool Overview
-
-| Tool | Purpose | Replaces |
-|------|---------|----------|
-| **uv** | Package/dependency management | pip, virtualenv, pip-tools, pipx, pyenv |
-| **ruff** | Linting AND formatting | flake8, black, isort, pyupgrade, pydocstyle |
-| **ty** | Type checking | mypy, pyright (faster alternative) |
-| **pytest** | Testing with coverage | unittest |
-| **prek** | Pre-commit hooks ([setup](./references/prek.md)) | pre-commit (faster, Rust-native) |
-
-### Security Tools
-
-| Tool | Purpose | When It Runs |
-|------|---------|--------------|
-| **shellcheck** | Shell script linting | pre-commit |
-| **detect-secrets** | Secret detection | pre-commit |
-| **actionlint** | Workflow syntax validation | pre-commit, CI |
-| **zizmor** | Workflow security audit | pre-commit, CI |
-| **pip-audit** | Dependency vulnerability scanning | CI, manual |
-| **Dependabot** | Automated dependency updates | scheduled |
-
-See [security-setup.md](./references/security-setup.md) for configuration and usage.
-
-## Quick Start: Minimal Project
-
-For simple multi-file projects not intended for distribution:
-
-```bash
-# Create project with uv
-uv init myproject
-cd myproject
-
-# Add dependencies
-uv add requests rich
-
-# Add dev dependencies
-uv add --group dev pytest ruff ty
-
-# Run code
-uv run python src/myproject/main.py
-
-# Run tools
-uv run pytest
-uv run ruff check .
-```
-
-## Full Project Setup
-If starting from scratch, ask the user if they prefer to use the Trail of Bits cookiecutter template to bootstrap a complete project with already preconfigured tooling.
-
-```bash
-uvx cookiecutter gh:trailofbits/cookiecutter-python
-```
-
-### 1. Create Project Structure
-
-```bash
-uv init --package myproject
-cd myproject
-```
-
-This creates:
-```
-myproject/
-├── pyproject.toml
-├── README.md
-├── src/
-│   └── myproject/
-│       └── __init__.py
-└── .python-version
-```
-
-### 2. Configure pyproject.toml
-
-See [pyproject.md](./references/pyproject.md) for complete configuration reference.
-
-Key sections:
-```toml
-[project]
-name = "myproject"
-version = "0.1.0"
-requires-python = ">=3.11"
-dependencies = []
-
-[dependency-groups]
-dev = [{include-group = "lint"}, {include-group = "test"}, {include-group = "audit"}]
-lint = ["ruff", "ty"]
-test = ["pytest", "pytest-cov"]
-audit = ["pip-audit"]
-
-[tool.ruff]
-line-length = 100
-target-version = "py311"
-
-[tool.ruff.lint]
-select = ["ALL"]
-ignore = ["D", "COM812", "ISC001"]
-
-[tool.pytest]
-addopts = ["--cov=myproject", "--cov-fail-under=80"]
-
-[tool.ty.terminal]
-error-on-warning = true
-
-[tool.ty.environment]
-python-version = "3.11"
-
-[tool.ty.rules]
-# Strict from day 1 for new projects
-possibly-unresolved-reference = "error"
-unused-ignore-comment = "warn"
-```
-
-### 3. Install Dependencies
-
-```bash
-# Install all dependency groups
-uv sync --all-groups
-
-# Or install specific groups
-uv sync --group dev
-```
-
-### 4. Add Makefile
-
-```makefile
-.PHONY: dev lint format test build
-
-dev:
-	uv sync --all-groups
-
-lint:
-	uv run ruff format --check && uv run ruff check && uv run ty check src/
-
-format:
-	uv run ruff format .
-
-test:
-	uv run pytest
-
-build:
-	uv build
-```
-
-## Migration Guide
-
-When a user requests migration from legacy tooling:
-
-### From requirements.txt + pip
-
-First, determine the nature of the code:
-
-**For standalone scripts**: Convert to PEP 723 inline metadata (see [pep723-scripts.md](./references/pep723-scripts.md))
-
-**For projects**:
-```bash
-# Initialize uv in existing project
-uv init --bare
-
-# Add dependencies using uv (not by editing pyproject.toml)
-uv add requests rich  # add each package
-
-# Or import from requirements.txt (review each package before adding)
-# Note: Complex version specifiers may need manual handling
-grep -v '^#' requirements.txt | grep -v '^-' | grep -v '^\s*$' | while read -r pkg; do
-    uv add "$pkg" || echo "Failed to add: $pkg"
-done
-
-uv sync
-```
-
-Then:
-1. Delete `requirements.txt`, `requirements-dev.txt`
-2. Delete virtual environment (`venv/`, `.venv/`)
-3. Add `uv.lock` to version control
-
-### From setup.py / setup.cfg
-
-1. Run `uv init --bare` to create pyproject.toml
-2. Use `uv add` to add each dependency from `install_requires`
-3. Use `uv add --group dev` for dev dependencies
-4. Copy non-dependency metadata (name, version, description, etc.) to `[project]`
-5. Delete `setup.py`, `setup.cfg`, `MANIFEST.in`
-
-### From flake8 + black + isort
-
-1. Remove flake8, black, isort via `uv remove`
-2. Delete `.flake8`, `pyproject.toml [tool.black]`, `[tool.isort]` configs
-3. Add ruff: `uv add --group dev ruff`
-4. Add ruff configuration (see [ruff-config.md](./references/ruff-config.md))
-5. Run `uv run ruff check --fix .` to apply fixes
-6. Run `uv run ruff format .` to format
-
-### From mypy / pyright
-
-1. Remove mypy/pyright via `uv remove`
-2. Delete `mypy.ini`, `pyrightconfig.json`, or `[tool.mypy]`/`[tool.pyright]` sections
-3. Add ty: `uv add --group dev ty`
-4. Run `uv run ty check src/`
-
-## Quick Reference: uv Commands
-
-| Command | Description |
-|---------|-------------|
-| `uv init` | Create new project |
-| `uv init --package` | Create distributable package |
-| `uv add <pkg>` | Add dependency |
-| `uv add --group dev <pkg>` | Add to dependency group |
-| `uv remove <pkg>` | Remove dependency |
-| `uv sync` | Install dependencies |
-| `uv sync --all-groups` | Install all dependency groups |
-| `uv run <cmd>` | Run command in venv |
-| `uv run --with <pkg> <cmd>` | Run with temporary dependency |
-| `uv build` | Build package |
-| `uv publish` | Publish to PyPI |
-
-### Ad-hoc Dependencies with `--with`
-
-Use `uv run --with` for one-off commands that need packages not in your project:
-
-```bash
-# Run Python with a temporary package
-uv run --with requests python -c "import requests; print(requests.get('https://httpbin.org/ip').json())"
-
-# Run a module with temporary deps
-uv run --with rich python -m rich.progress
-
-# Multiple packages
-uv run --with requests --with rich python script.py
-
-# Combine with project deps (adds to existing venv)
-uv run --with httpx pytest  # project deps + httpx
-```
-
-**When to use `--with` vs `uv add`:**
-- `uv add`: Package is a project dependency (goes in pyproject.toml/uv.lock)
-- `--with`: One-off usage, testing, or scripts outside a project context
-
-See [uv-commands.md](./references/uv-commands.md) for complete reference.
-
-## Quick Reference: Dependency Groups
-
-```toml
-[dependency-groups]
-dev = ["ruff", "ty"]
-test = ["pytest", "pytest-cov", "hypothesis"]
-docs = ["sphinx", "myst-parser"]
-```
-
-Install with: `uv sync --group dev --group test`
-
-## Best Practices Checklist
-
-- [ ] Use `src/` layout for packages
-- [ ] Set `requires-python = ">=3.11"`
-- [ ] Configure ruff with `select = ["ALL"]` and explicit ignores
-- [ ] Use ty for type checking
-- [ ] Enforce test coverage minimum (80%+)
-- [ ] Use dependency groups instead of extras for dev tools
-- [ ] Add `uv.lock` to version control
-- [ ] Use PEP 723 for standalone scripts
-
-## Read Next
-
-- [migration-checklist.md](./references/migration-checklist.md) - Step-by-step migration cleanup
-- [pyproject.md](./references/pyproject.md) - Complete pyproject.toml reference
-- [uv-commands.md](./references/uv-commands.md) - uv command reference
-- [ruff-config.md](./references/ruff-config.md) - Ruff linting/formatting configuration
-- [testing.md](./references/testing.md) - pytest and coverage setup
-- [pep723-scripts.md](./references/pep723-scripts.md) - PEP 723 inline script metadata
-- [prek.md](./references/prek.md) - Fast pre-commit hooks with prek
-- [security-setup.md](./references/security-setup.md) - Security hooks and dependency scanning
-- [dependabot.md](./references/dependabot.md) - Automated dependency updates

package/skills_ref/modern-python/skills/modern-python/references/dependabot.md

@@ -1,43 +0,0 @@
-# Dependabot: Automated Dependency Updates
-
-[Dependabot](https://docs.github.com/en/code-security/dependabot) automatically creates pull requests to keep your dependencies up to date. GitHub hosts it natively—no external service required.
-
-## Why Use Dependabot?
-
-- **Security**: Automatically patches known vulnerabilities
-- **Freshness**: Keeps dependencies current without manual tracking
-- **Visibility**: PRs show changelogs and compatibility notes
-
-## Configuration
-
-Copy [templates/dependabot.yml](../templates/dependabot.yml) to `.github/dependabot.yml`.
-
-The template includes:
-- Weekly update schedule for pip and GitHub Actions
-- 7-day cooldown for supply chain protection
-- Grouping to reduce PR noise
-
-## Supply Chain Protection
-
-The `cooldown.default-days: 7` setting delays updates for newly published versions. This provides time for the community to detect compromised packages before they reach your project.
-
-**Why this matters:**
-- Attackers sometimes publish malicious versions of legitimate packages
-- A 7-day delay allows time for detection and removal
-- Combined with weekly schedules, this balances security with freshness
-
-## Common Options
-
-| Option | Description |
-|--------|-------------|
-| `interval` | `daily`, `weekly`, or `monthly` |
-| `cooldown.default-days` | Days to wait before updating new releases |
-| `ignore` | Skip specific dependencies or versions |
-| `groups` | Group related updates into single PRs |
-| `reviewers` | Auto-assign reviewers to PRs |
-
-## See Also
-
-- [GitHub Dependabot docs](https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file)
-- [security-setup.md](./security-setup.md) - Security tooling overview
-- [prek.md](./prek.md) - Pre-commit hooks (complementary tool)

package/skills_ref/modern-python/skills/modern-python/references/migration-checklist.md

@@ -1,141 +0,0 @@
-# Migration Checklist
-
-Comprehensive checklist for migrating Python projects to modern tooling.
-
-## Before Migration
-
-- [ ] **Determine layout**: `src/` or flat? Configure `[tool.uv.build-backend]` if flat
-- [ ] **Decide uv.lock strategy**: app (commit) vs library (.gitignore)
-- [ ] **Backup current state**: Create a branch or tag before starting
-
-## Cleanup Old Artifacts
-
-Find and remove legacy linter comments:
-
-```bash
-# Find files with old linter pragmas
-rg "# pylint:|# noqa:|# type: ignore" --files-with-matches
-
-# Find missing __init__.py files
-uv run ruff check --select=INP001 .
-```
-
-Remove these files after migration:
-- [ ] `requirements.txt`, `requirements-dev.txt`
-- [ ] `setup.py`, `setup.cfg`, `MANIFEST.in`
-- [ ] `.flake8`, `mypy.ini`, `pyrightconfig.json`
-- [ ] `tox.ini` (if not needed)
-- [ ] `Pipfile`, `Pipfile.lock`
-- [ ] Old virtual environments (`venv/`, `.venv/`)
-
-## .gitignore Updates
-
-Add these entries:
-
-```gitignore
-# Python
-__pycache__/
-*.py[cod]
-.venv/
-
-# Tools
-.ruff_cache/
-.ty/
-
-# uv (for libraries only - apps should commit uv.lock)
-# uv.lock
-```
-
-## pyproject.toml Sections to Remove
-
-- [ ] `[tool.black]`
-- [ ] `[tool.isort]`
-- [ ] `[tool.mypy]`
-- [ ] `[tool.pyright]`
-- [ ] `[tool.pylint]`
-- [ ] `[tool.flake8]` (if present)
-
-## Post-Migration Easy Wins
-
-Run these to modernize code automatically:
-
-```bash
-# Pyupgrade modernization (typing, syntax)
-uv run ruff check --select=UP --fix .
-
-# Unnecessary variable assignments before return
-uv run ruff check --select=RET504 --fix .
-
-# Simplifications (conditionals, comprehensions)
-uv run ruff check --select=SIM --fix .
-
-# Remove commented-out code
-uv run ruff check --select=ERA --fix .
-```
-
-## CI Cleanup
-
-- [ ] Remove scheduled CI triggers (activity without progress is theater)
-- [ ] Update CI to use `uv sync` and `uv run`
-- [ ] Pin GitHub Actions to SHA hashes
-- [ ] Set up security tooling (see [security-setup.md](./security-setup.md))
-
-## Gradual ty Adoption
-
-For legacy codebases with many type errors, start lenient:
-
-```toml
-[tool.ty.terminal]
-error-on-warning = true
-
-[tool.ty.environment]
-python-version = "3.11"
-
-[tool.ty.rules]
-# Start with these ignored for legacy codebases
-possibly-missing-attribute = "ignore"
-unresolved-import = "ignore"
-invalid-argument-type = "ignore"
-not-subscriptable = "ignore"
-unresolved-attribute = "ignore"
-```
-
-Remove rules as you fix errors. Track progress:
-
-```bash
-# Count remaining issues
-uv run ty check src/ 2>&1 | grep -c "error"
-```
-
-## Supply Chain Security
-
-- [ ] Add pip-audit to dependency groups
-- [ ] Configure Dependabot with 7-day cooldown
-- [ ] Pin exact versions in production (`==` not `>=`)
-
-See [security-setup.md](./security-setup.md) for pip-audit and Dependabot configuration.
-
-## Verification
-
-After migration, verify everything works:
-
-```bash
-# Install all dependencies
-uv sync --all-groups
-
-# Run linting
-uv run ruff check .
-uv run ruff format --check .
-
-# Run type checking
-uv run ty check src/
-
-# Run tests
-uv run pytest
-
-# Security audit
-uv run pip-audit
-
-# Build package (if distributable)
-uv build
-```