Enhance cookiecutter template with stricter code quality standards #84

dguido · 2025-07-29T23:03:03Z

Summary

This PR enhances the cookiecutter-python template with stricter code quality standards based on Trail of Bits' engineering practices. The changes enforce consistent, high-quality Python code across all generated projects.

Key Changes

1. Modern Python Tooling

Python 3.11+ requirement (removed 3.9/3.10 support)
pyright replaces mypy for strict type checking
ruff consolidated configuration for linting and formatting
uv package manager with pre-commit hooks

2. Strict Code Quality Standards

Enforces quantitative code complexity limits:

Cyclomatic complexity ≤ 8
Max 50 lines per function
Max 5 positional parameters
Max 12 branches per function
Max 6 return statements
100-character line length
Google-style docstrings required

3. Enhanced Developer Experience

Pre-commit hooks run automatically:
- ruff format and ruff check --fix
- pyright strict type checking
- pytest (fast tests only, excluding @pytest.mark.slow)
- interrogate docstring coverage (if enabled)
Simplified Makefile with intuitive aliases:
- make fix - primary formatter command
- make lint - all quality checks
- make typecheck - just type checking
Tests beside code - supports test_*.py and *_test.py in src/

4. Project Documentation

CLAUDE.md template - AI assistant instructions with:
- Project-specific code standards
- Quick command reference
- Testing guidelines with pytest markers
- General Python preferences (FastAPI, Polars, etc.)
Clear guidance on maintaining code quality

5. Configuration Improvements

Consolidated ruff config in pyproject.toml (removed separate ruff.toml)
Fixed license field to modern SPDX format
Proper pytest configuration for co-located tests
Pre-commit stages fixed (changed deprecated stages: [commit] to stages: [pre-commit])

What Changed From Initial PR

After code review and testing, we:

Replaced experimental ty with stable pyright
Removed data library option (rarely needed for Trail of Bits projects)
Removed FastAPI web framework option (too complex for template)
Fixed all CI failures and deprecation warnings
Simplified formatter aliases in Makefile
Added pytest marker documentation for slow test filtering

Test Plan

CI passes all checks
Generated projects pass all linting/type checks
Pre-commit hooks work correctly
Makefile targets function as expected
Documentation is clear and accurate

🤖 Generated with Claude Code

- Update Python requirement to 3.11+ to match CLAUDE.md standards - Replace mypy with Astral's experimental ty type checker - Add comprehensive ruff.toml with strict code quality constraints: - Cyclomatic complexity ≤ 8 - Max 5 positional args, 12 branches, 6 returns - Google-style docstrings enforced - Add data library option (polars/pandas/none) in cookiecutter.json - Create pre-commit hooks configuration for automated checks - Add CLAUDE.md template with project-specific instructions - Configure pytest to support tests beside code - Update Makefile with common commands (ty, fix, check) - Remove Python 3.9/3.10 from CI matrix These changes align the cookiecutter template with modern Python development practices and enforce stricter code quality standards. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

- Add web_framework choice in cookiecutter.json (fastapi/none) - Include FastAPI and uvicorn dependencies when selected - Create basic FastAPI app template with health check endpoint - Add 'make serve' command to run development server - Update CLAUDE.md to express strong preference for FastAPI over Flask - Configure post-generation hook to remove _app.py if not using FastAPI This enforces the preference for modern async frameworks and explicitly discourages Flask usage in new projects. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

- Fix ty version to 0.0.1a16 (current alpha release) - Remove --strict flag which doesn't exist in ty - Update ty commands to explicitly check src directory - Remove strict=true from pyproject.toml ty config ty is still in early alpha, so we're using the latest available version with basic configuration. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

Apply ruff formatting to fix CI failure. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

Remove the data_library choice (polars/pandas/none) as it's rarely needed for Trail of Bits projects. This simplifies the template and reduces unnecessary options during project creation. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

- Remove FastAPI web framework option to reduce complexity - Consolidate ruff configuration from ruff.toml into pyproject.toml - Fix Makefile redundancies: keep 'fix' and 'format' as aliases - Remove duplicated ty command from lint target - Clean up CLAUDE.md to remove FastAPI references This simplifies the PR to focus on core improvements: stricter code quality standards, ty type checker, and pre-commit hooks. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

The self-test CI workflow expects 'make reformat' to exist. Add it back as an alias alongside 'fix' and 'format'. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

Replace deprecated 'license-files' with proper license field syntax. Use 'license = {text = "SPDX-ID"}' for standard licenses and 'license = {file = "LICENSE"}' for proprietary licenses. This fixes the RUF200 parsing error in generated projects. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

Change 'search_path' to 'src' in [tool.ty] configuration. The ty type checker expects 'src' as the field name, not 'search_path'. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

Remove the [tool.ty] section entirely as ty is in early alpha and the configuration format is not well documented. Let ty use its default configuration which should work for standard project layouts. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

- Replace experimental ty (0.0.1a16) with stable pyright (1.1+) - Configure pyright with standard type checking mode - Make pre-commit pytest less aggressive: only run fast tests (-k "not slow") - Remove -q flag from pytest for better debugging visibility - Clarify CLAUDE.md framework preferences as general guidelines - Add missing newline to pre-commit config - Update all references from ty to pyright in docs and commands This makes the type checking more reliable while maintaining the same strict code quality standards. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

- Remove accidentally included test-pyright directory - Fix pre-commit deprecation: use stages: [pre-commit] instead of [commit] - Change pyright to strict mode for better type safety - Add pyright include paths: ["src", "test"] - Add pytest marker documentation for @pytest.mark.slow - Simplify Makefile: keep 'fix' as primary command, 'reformat' as alias All changes tested locally - lint, fix, reformat, and pre-commit hooks work correctly with strict pyright configuration. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

oldsj

I was able to test this with uvx cookiecutter gh:trailofbits/cookiecutter-python --checkout enhance-cookiecutter-standards and tests passed with make check , looks good!

ekilmer · 2025-07-30T15:38:05Z

{{cookiecutter.project_slug}}/.github/workflows/tests.yml

-          - "3.9"
-          - "3.10"
          - "3.11"
          - "3.12"


For context, we were trying to keep track of active Python versions, as listed here https://devguide.python.org/versions/

Removing Python 3.9 would be fine, since it'll be EOL soon. However, unless we're using Python 3.11 features, I think we should still include Python 3.10. This will ensure compatibility with all supported Python versions by default, and then each project can make the explicit decision to remove compatibility with older versions.

We should add "3.13" while we're here.

ekilmer · 2025-07-30T15:41:11Z

{{cookiecutter.project_slug}}/pyproject.toml

+license = {text = "Apache-2.0"}
 {%- elif cookiecutter.license == "AGPL v3" %}
-license = "AGPL-3.0-or-later"
+license = {text = "AGPL-3.0-or-later"}
 {%- elif cookiecutter.license == "Proprietary" %}
-license = "LicenseRef-Proprietary-License"
+license = {file = "LICENSE"}


I'm not sure why this was changed. According to the docs, it should just be a SPDX license expression https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license and the spec is here https://packaging.python.org/en/latest/specifications/pyproject-toml/#pyproject-toml-license

This was the commit that changed it 2fbd39b

I think Claude Code might have outdated information?

Also, the CI outputs a warning https://github.com/trailofbits/cookiecutter-python/actions/runs/16610950158/job/46993781047?pr=84#step:5:299

/home/runner/work/_temp/setup-uv-cache/builds-v0/.tmp5sbQ1m/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated !! ******************************************************************************** Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). By 2026-Feb-18, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ********************************************************************************

ekilmer · 2025-07-30T15:48:19Z

{{cookiecutter.project_slug}}/pyproject.toml

    # and let Dependabot periodically perform this update.
    "ruff ~= 0.6.2",
-    "mypy >= 1.0",
+    "pyright >= 1.1",


@ESultanik You have experience with Python type checkers. Do you have a preference of mypy over pyright or any other type checker?

ekilmer · 2025-07-30T16:09:13Z

{{cookiecutter.project_slug}}/CLAUDE.md

+- **Line length**: 100 characters max
+- **Docstrings**: Google style on all public functions/classes
+- **Type hints**: Required for all function signatures
+- **Tests**: Must live beside code (`test_*.py` or `*_test.py`)


This looks to contradict the current structure. The current structure has the source files in src/{{cookiecutter.__module_import}}/*.py and tests in test/test_*.py.

I don't think I've seen Python projects with test files next to the source code files. I have seen it for C and C++ projects though, particularly projects from Google.

After some research, some people are saying that for large projects, it's helpful to have unit tests next to the source code to easily test distributions of the project and also to more easily find tests for functionality in that source file.

Others say that including the test files in the source directory will make distribution packages larger, which may or may not be a concern.

I don't think I have strong opinions on this.

I've always found it better to have tests in a separate dir, but... whatever works.

ret2libc · 2025-07-31T06:52:57Z

{{cookiecutter.project_slug}}/CLAUDE.md

+
+### Error Handling
+```python
+from typing import Result  # If using result types


is this thing real or ai-made up? I've never seen it.

Good catch. I also get an error when trying to import this under Python 3.13.

The Google style guide has a section on error handling and exceptions https://google.github.io/styleguide/pyguide.html#24-exceptions

dguido and others added 15 commits July 29, 2025 18:58

Merge branch 'main' into enhance-cookiecutter-standards

f6dee7f

fix: apply ruff formatting to pre_gen_project.py

517395b

Apply ruff formatting to fix CI failure. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

fix: restore 'reformat' target as alias to fix CI

330cbb9

The self-test CI workflow expects 'make reformat' to exist. Add it back as an alias alongside 'fix' and 'format'. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

fix: correct ty configuration field name

d405f81

Change 'search_path' to 'src' in [tool.ty] configuration. The ty type checker expects 'src' as the field name, not 'search_path'. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>

test commit

2902ab9

test commit

a249f00

oldsj approved these changes Jul 30, 2025

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ekilmer requested changes Jul 30, 2025

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ekilmer reviewed Jul 30, 2025

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Enhance cookiecutter template with stricter code quality standards #84

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Summary

Key Changes

1. Modern Python Tooling

2. Strict Code Quality Standards

3. Enhanced Developer Experience

4. Project Documentation

5. Configuration Improvements

What Changed From Initial PR

Test Plan

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