From f5378266829bd06625ac6f46e861ace2f2f3f2ef Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 18:58:55 -0400
Subject: [PATCH 01/17] feat: enhance cookiecutter template with stricter
 standards
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- 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 <noreply@anthropic.com>
---
 cookiecutter.json                             |   8 +-
 .../.github/workflows/tests.yml               |   2 -
 .../.pre-commit-config.yaml                   |  45 +++++
 {{cookiecutter.project_slug}}/CLAUDE.md       | 155 ++++++++++++++++++
 {{cookiecutter.project_slug}}/Makefile        |  19 ++-
 {{cookiecutter.project_slug}}/pyproject.toml  |  65 +++-----
 {{cookiecutter.project_slug}}/ruff.toml       |  45 +++++
 7 files changed, 289 insertions(+), 50 deletions(-)
 create mode 100644 {{cookiecutter.project_slug}}/.pre-commit-config.yaml
 create mode 100644 {{cookiecutter.project_slug}}/CLAUDE.md
 create mode 100644 {{cookiecutter.project_slug}}/ruff.toml

diff --git a/cookiecutter.json b/cookiecutter.json
index 8d61f41..16b3f0e 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -23,6 +23,11 @@
         "none"
     ],
     "docstring_coverage": true,
+    "data_library": [
+        "polars",
+        "pandas",
+        "none"
+    ],
     "license": [
         "Apache 2.0",
         "AGPL v3",
@@ -32,7 +37,8 @@
         ".github/workflows/docs.yml",
         ".github/workflows/lint.yml",
         ".github/workflows/tests.yml",
-        ".github/workflows/zizmor.yml"
+        ".github/workflows/zizmor.yml",
+        "ruff.toml"
     ],
     "__prompts__": {
         "project_name": "Human-readable project name (translated into module slug and import)",
diff --git a/{{cookiecutter.project_slug}}/.github/workflows/tests.yml b/{{cookiecutter.project_slug}}/.github/workflows/tests.yml
index 18423d9..5493ee0 100644
--- a/{{cookiecutter.project_slug}}/.github/workflows/tests.yml
+++ b/{{cookiecutter.project_slug}}/.github/workflows/tests.yml
@@ -13,8 +13,6 @@ jobs:
     strategy:
       matrix:
         python:
-          - "3.9"
-          - "3.10"
           - "3.11"
           - "3.12"
     runs-on: ubuntu-latest
diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
new file mode 100644
index 0000000..0a278f4
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -0,0 +1,45 @@
+# Pre-commit hooks for code quality
+# See https://pre-commit.com for more information
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.2
+    hooks:
+      # Run the formatter
+      - id: ruff-format
+      # Run the linter
+      - id: ruff
+        args: [--fix]
+
+  - repo: local
+    hooks:
+      - id: ty
+        name: ty type check
+        entry: uv run ty check --strict
+        language: system
+        types: [python]
+        pass_filenames: false
+        require_serial: true
+
+      {%- if cookiecutter.docstring_coverage %}
+      - id: interrogate
+        name: interrogate docstring coverage
+        entry: uv run interrogate -c pyproject.toml
+        language: system
+        types: [python]
+        pass_filenames: false
+      {%- endif %}
+
+      - id: pytest
+        name: pytest
+        entry: uv run pytest -q
+        language: system
+        types: [python]
+        pass_filenames: false
+        require_serial: true
+        # Only run on commit, not on push
+        stages: [commit]
+
+# Configuration
+ci:
+  autofix_prs: true
+  autoupdate_schedule: weekly
\ No newline at end of file
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
new file mode 100644
index 0000000..f86e455
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/CLAUDE.md
@@ -0,0 +1,155 @@
+# {{ cookiecutter.project_name }} - Claude Instructions
+
+This document contains project-specific instructions for Claude when working on this codebase.
+
+## Project Overview
+
+{{ cookiecutter.project_description }}
+
+## Code Standards
+
+This project enforces strict code quality standards:
+
+### Code Complexity Limits
+- **Max 50 lines per function** - Split larger functions
+- **Cyclomatic complexity ≤ 8** - Simplify complex logic  
+- **Max 5 positional parameters** - Use keyword arguments or dataclasses
+- **Max 12 branches per function** - Extract to helper functions
+- **Max 6 return statements** - Consolidate exit points
+
+### Style Guidelines
+- **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`)
+
+## Quick Commands
+
+```bash
+# Development setup
+make dev
+
+# Run all checks
+make check  # Runs lint + tests
+
+# Code quality
+make lint   # ruff format --check + ruff check + ty check
+make fix    # Auto-fix formatting and lint issues
+make ty     # Run type checker with strict mode
+
+# Testing
+make test   # Run pytest with coverage
+
+# Development
+{% if cookiecutter.entry_point -%}
+make run ARGS="--help"  # Run the CLI
+{%- endif %}
+make doc    # Build documentation
+```
+
+## Project Structure
+
+```
+src/
+└── {{ cookiecutter.__project_import.replace('.', '/') }}/
+    ├── __init__.py
+    {%- if cookiecutter.entry_point %}
+    ├── __main__.py      # CLI entry point
+    ├── _cli.py          # CLI implementation
+    {%- endif %}
+    └── py.typed         # Type checking marker
+
+test/
+└── test_*.py            # Traditional test location
+```
+
+Tests can also live beside source files as `test_*.py` or `*_test.py`.
+
+## Key Libraries
+
+{%- if cookiecutter.data_library == "polars" %}
+- **Data processing**: Polars (preferred over pandas)
+  ```python
+  import polars as pl
+  df = pl.DataFrame({"col": [1, 2, 3]})
+  ```
+{%- elif cookiecutter.data_library == "pandas" %}
+- **Data processing**: Pandas
+  ```python
+  import pandas as pd
+  df = pd.DataFrame({"col": [1, 2, 3]})
+  ```
+{%- endif %}
+
+## Common Patterns
+
+### Error Handling
+```python
+from typing import Result  # If using result types
+
+def process_data(path: str) -> Result[Data, str]:
+    """Process data from file.
+    
+    Args:
+        path: Path to data file.
+        
+    Returns:
+        Result with Data on success, error message on failure.
+    """
+    try:
+        # Implementation
+        return Ok(data)
+    except Exception as e:
+        return Err(f"Failed to process: {e}")
+```
+
+### Logging
+```python
+import logging
+
+logger = logging.getLogger(__name__)
+```
+
+{%- if cookiecutter.entry_point %}
+
+### CLI Arguments
+Use the existing `_cli.py` structure:
+```python
+parser.add_argument(
+    "--verbose", "-v",
+    action="store_true",
+    help="Enable verbose output"
+)
+```
+{%- endif %}
+
+## Testing Guidelines
+
+- Aim for 100% test coverage (enforced by CI)
+- Use `pytest.mark.parametrize` for multiple test cases
+- Mock external dependencies
+- Test both success and error paths
+
+## CI/CD
+
+GitHub Actions run on every push/PR:
+1. **Linting**: ruff format/check + ty type checking
+2. **Tests**: pytest with coverage
+3. **Security**: zizmor workflow scanning
+{%- if cookiecutter.documentation == "pdoc" %}
+4. **Docs**: Auto-deploy to GitHub Pages
+{%- endif %}
+
+## Important Notes
+
+1. **Never commit code that violates the quality standards** - refactor instead
+2. **All public APIs need Google-style docstrings**
+3. **Type hints are mandatory** - use `ty check --strict`
+4. **Tests can live beside code** - prefer colocated tests for better maintainability
+
+## Project-Specific Instructions
+
+<!-- Add any project-specific Claude instructions here -->
+
+---
+*This file helps Claude understand project conventions. Update it as patterns emerge.*
\ No newline at end of file
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index 4f99666..d89ead1 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -44,6 +44,7 @@ all:
 
 .PHONY: dev
 dev: $(VENV)/pyvenv.cfg
+	uv run pre-commit install
 
 {%- if cookiecutter.entry_point %}
 .PHONY: run
@@ -59,20 +60,30 @@ $(VENV)/pyvenv.cfg: pyproject.toml
 lint: $(VENV)/pyvenv.cfg
 	uv run ruff format --check && \
 		uv run ruff check && \
-		uv run mypy
+		uv run ty check
 
 	{%- if cookiecutter.docstring_coverage %}
 		uv run interrogate -c pyproject.toml .
 	{%- endif %}
 
-.PHONY: reformat
-reformat:
+.PHONY: format
+format: reformat
+
+.PHONY: check
+check: lint test
+
+.PHONY: typecheck ty
+typecheck ty: $(VENV)/pyvenv.cfg
+	uv run ty check --strict
+
+.PHONY: reformat fix
+reformat fix:
 	uv run ruff format && \
 		uv run ruff check --fix
 
 .PHONY: test tests
 test tests: $(VENV)/pyvenv.cfg
-	uv run pytest --cov=$(PY_IMPORT) $(T) $(TEST_ARGS)
+	uv run pytest -q --cov=$(PY_IMPORT) $(T) $(TEST_ARGS)
 	uv run coverage report -m $(COV_ARGS)
 
 .PHONY: doc
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index b364bd1..32b9a53 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -19,8 +19,14 @@ authors = [
 classifiers = [
     "Programming Language :: Python :: 3",
 ]
-dependencies = []
-requires-python = ">=3.9"
+dependencies = [
+    {%- if cookiecutter.data_library == "polars" %}
+    "polars >= 0.20.0",
+    {%- elif cookiecutter.data_library == "pandas" %}
+    "pandas >= 2.0.0",
+    {%- endif %}
+]
+requires-python = ">=3.11"
 
 [tool.setuptools.dynamic]
 version = { attr = "{{ cookiecutter.__project_import }}.__version__" }
@@ -36,7 +42,7 @@ lint = [
     # NOTE: ruff is under active development, so we pin conservatively here
     # and let Dependabot periodically perform this update.
     "ruff ~= 0.6.2",
-    "mypy >= 1.0",
+    "ty >= 0.1.0",
     "types-html5lib",
     "types-requests",
     "types-toml",
@@ -44,7 +50,7 @@ lint = [
     "interrogate",
     {%- endif %}
 ]
-dev = ["{{ cookiecutter.project_slug }}[doc,test,lint]", "twine", "build"]
+dev = ["{{ cookiecutter.project_slug }}[doc,test,lint]", "twine", "build", "pre-commit"]
 
 {% if cookiecutter.entry_point -%}
 [project.scripts]
@@ -61,46 +67,12 @@ Source = "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.
 # don't attempt code coverage for the CLI entrypoints
 omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 
-[tool.mypy]
-mypy_path = "src"
-packages = "{{ cookiecutter.__project_import }}"
-allow_redefinition = true
-check_untyped_defs = true
-disallow_incomplete_defs = true
-disallow_untyped_defs = true
-ignore_missing_imports = true
-no_implicit_optional = true
-show_error_codes = true
-sqlite_cache = true
-strict_equality = true
-warn_no_return = true
-warn_redundant_casts = true
-warn_return_any = true
-warn_unreachable = true
-warn_unused_configs = true
-warn_unused_ignores = true
-
-[tool.ruff]
-line-length = 100
-include = ["src/**/*.py", "test/**/*.py"]
+[tool.ty]
+# Astral's experimental type checker
+search_path = ["src"]
+strict = true
 
-[tool.ruff.lint]
-select = ["ALL"]
-# D203 and D213 are incompatible with D211 and D212 respectively.
-# COM812 and ISC001 can cause conflicts when using ruff as a formatter.
-# See https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules.
-ignore = ["D203", "D213", "COM812", "ISC001"]
-
-[tool.ruff.lint.per-file-ignores]
-{% if cookiecutter.entry_point -%}
-"{{ cookiecutter.__project_src_path }}/_cli.py" = [
-    "T201", # allow `print` in cli module
-]
-{%- endif %}
-"test/**/*.py" = [
-    "D",    # no docstrings in tests
-    "S101", # asserts are expected in tests
-]
+# Ruff configuration is in ruff.toml
 
 {%- if cookiecutter.docstring_coverage %}
 [tool.interrogate]
@@ -110,3 +82,10 @@ exclude = ["env", "test", "{{ cookiecutter.__project_src_path }}/_cli.py"]
 ignore-semiprivate = true
 fail-under = 100
 {%- endif %}
+
+[tool.pytest.ini_options]
+# Support tests living beside code
+testpaths = ["src", "test"]
+python_files = ["test_*.py", "*_test.py"]
+# Show test durations
+addopts = "-q --durations=10"
diff --git a/{{cookiecutter.project_slug}}/ruff.toml b/{{cookiecutter.project_slug}}/ruff.toml
new file mode 100644
index 0000000..f08868b
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/ruff.toml
@@ -0,0 +1,45 @@
+# Ruff configuration aligned with CLAUDE.md standards
+line-length = 100
+target-version = "py311"
+
+[lint]
+select = ["ALL"]
+ignore = [
+    "D203",  # Incompatible with D211
+    "D213",  # Incompatible with D212
+    "COM812",  # Can conflict with formatter
+    "ISC001",  # Can conflict with formatter
+]
+
+[lint.mccabe]
+# Maximum cyclomatic complexity
+max-complexity = 8
+
+[lint.pydocstyle]
+# Use Google-style docstrings
+convention = "google"
+
+[lint.pylint]
+# Maximum number of branches for function or method
+max-branches = 12
+# Maximum number of return statements in function or method
+max-returns = 6
+# Maximum number of positional arguments for function or method
+max-positional-args = 5
+
+[lint.per-file-ignores]
+# CLI-specific ignores (will be removed by post-gen hook if not CLI project)
+"src/**/_cli.py" = [
+    "T201",  # Allow print in CLI module
+]
+"test/**/*.py" = [
+    "D",     # No docstrings required in tests
+    "S101",  # Allow assert in tests
+    "PLR2004",  # Allow magic values in tests
+]
+"**/conftest.py" = ["D"]  # No docstrings in pytest config
+
+[format]
+# Consistent with line-length
+line-ending = "lf"
+quote-style = "double"
\ No newline at end of file

From c975cb8d5222051e155cd9f7b5486974def73266 Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 19:13:39 -0400
Subject: [PATCH 02/17] feat: add FastAPI as preferred web framework option
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- 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 <noreply@anthropic.com>
---
 cookiecutter.json                             |  4 +++
 hooks/post_gen_project.py                     |  2 ++
 {{cookiecutter.project_slug}}/CLAUDE.md       | 22 +++++++++++++
 {{cookiecutter.project_slug}}/Makefile        |  6 ++++
 {{cookiecutter.project_slug}}/pyproject.toml  |  4 +++
 .../{{cookiecutter.__module_import}}/_app.py  | 33 +++++++++++++++++++
 6 files changed, 71 insertions(+)
 create mode 100644 {{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py

diff --git a/cookiecutter.json b/cookiecutter.json
index 16b3f0e..836a75a 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -28,6 +28,10 @@
         "pandas",
         "none"
     ],
+    "web_framework": [
+        "fastapi",
+        "none"
+    ],
     "license": [
         "Apache 2.0",
         "AGPL v3",
diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
index ff8ac06..9b27560 100644
--- a/hooks/post_gen_project.py
+++ b/hooks/post_gen_project.py
@@ -6,6 +6,8 @@
     "{% if cookiecutter.entry_point == '' %} {{ cookiecutter.__project_src_path }}/__main__.py {% endif %}",
     # We delete the docs GH workflow if the project has no documentation
     "{% if cookiecutter.documentation == 'none' %} .github/workflows/docs.yml {% endif %}",
+    # We delete _app.py if we're not generating a FastAPI app
+    "{% if cookiecutter.web_framework != 'fastapi' %} {{ cookiecutter.__project_src_path }}/_app.py {% endif %}",
 ]
 
 for path in REMOVE_PATHS:
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
index f86e455..3819bf8 100644
--- a/{{cookiecutter.project_slug}}/CLAUDE.md
+++ b/{{cookiecutter.project_slug}}/CLAUDE.md
@@ -44,6 +44,9 @@ make test   # Run pytest with coverage
 {% if cookiecutter.entry_point -%}
 make run ARGS="--help"  # Run the CLI
 {%- endif %}
+{%- if cookiecutter.web_framework == "fastapi" %}
+make serve  # Run FastAPI dev server on http://localhost:8000
+{%- endif %}
 make doc    # Build documentation
 ```
 
@@ -81,6 +84,25 @@ Tests can also live beside source files as `test_*.py` or `*_test.py`.
   ```
 {%- endif %}
 
+{%- if cookiecutter.web_framework == "fastapi" %}
+- **Web framework**: FastAPI (never use Flask)
+  ```python
+  from fastapi import FastAPI
+  
+  app = FastAPI()
+  
+  @app.get("/")
+  async def root():
+      return {"message": "Hello World"}
+  ```
+{%- endif %}
+
+## Framework Preferences
+
+- **Web**: Always use FastAPI, never Flask
+- **Data**: Prefer Polars over Pandas for new code
+- **Async**: Use native async/await, not threading
+
 ## Common Patterns
 
 ### Error Handling
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index d89ead1..31a83ac 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -52,6 +52,12 @@ run: $(VENV)/pyvenv.cfg
 	uv run {{ cookiecutter.entry_point }} $(ARGS)
 {%- endif %}
 
+{%- if cookiecutter.web_framework == "fastapi" %}
+.PHONY: serve
+serve: $(VENV)/pyvenv.cfg
+	uv run uvicorn {{ cookiecutter.__project_import }}._app:app --reload --host 0.0.0.0 --port 8000
+{%- endif %}
+
 $(VENV)/pyvenv.cfg: pyproject.toml
 	uv venv $(VENV)
 	uv pip install -e '.[$(INSTALL_EXTRA)]'
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index 32b9a53..ac6df4f 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -25,6 +25,10 @@ dependencies = [
     {%- elif cookiecutter.data_library == "pandas" %}
     "pandas >= 2.0.0",
     {%- endif %}
+    {%- if cookiecutter.web_framework == "fastapi" %}
+    "fastapi >= 0.100.0",
+    "uvicorn[standard] >= 0.23.0",
+    {%- endif %}
 ]
 requires-python = ">=3.11"
 
diff --git a/{{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py b/{{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py
new file mode 100644
index 0000000..694c193
--- /dev/null
+++ b/{{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py
@@ -0,0 +1,33 @@
+"""FastAPI application setup."""
+
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+
+from {{ cookiecutter.__project_import }} import __version__
+
+app = FastAPI(
+    title="{{ cookiecutter.project_name }}",
+    description="{{ cookiecutter.project_description }}",
+    version=__version__,
+)
+
+# Configure CORS
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=["*"],  # Configure appropriately for production
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+
+@app.get("/")
+async def root() -> dict[str, str]:
+    """Root endpoint."""
+    return {"message": "{{ cookiecutter.project_name }} API", "version": __version__}
+
+
+@app.get("/health")
+async def health() -> dict[str, str]:
+    """Health check endpoint."""
+    return {"status": "ok"}
\ No newline at end of file

From 6fa0b6a897b332fbbae6df58c95639a3b31d472b Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 19:33:34 -0400
Subject: [PATCH 03/17] fix: correct ty version and remove unsupported --strict
 flag
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- 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 <noreply@anthropic.com>
---
 {{cookiecutter.project_slug}}/.pre-commit-config.yaml | 2 +-
 {{cookiecutter.project_slug}}/CLAUDE.md               | 2 +-
 {{cookiecutter.project_slug}}/Makefile                | 4 ++--
 {{cookiecutter.project_slug}}/pyproject.toml          | 3 +--
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 0a278f4..6bffec0 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -14,7 +14,7 @@ repos:
     hooks:
       - id: ty
         name: ty type check
-        entry: uv run ty check --strict
+        entry: uv run ty check src
         language: system
         types: [python]
         pass_filenames: false
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
index 3819bf8..c46aae3 100644
--- a/{{cookiecutter.project_slug}}/CLAUDE.md
+++ b/{{cookiecutter.project_slug}}/CLAUDE.md
@@ -166,7 +166,7 @@ GitHub Actions run on every push/PR:
 
 1. **Never commit code that violates the quality standards** - refactor instead
 2. **All public APIs need Google-style docstrings**
-3. **Type hints are mandatory** - use `ty check --strict`
+3. **Type hints are mandatory** - use `ty check`
 4. **Tests can live beside code** - prefer colocated tests for better maintainability
 
 ## Project-Specific Instructions
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index 31a83ac..efc2597 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -66,7 +66,7 @@ $(VENV)/pyvenv.cfg: pyproject.toml
 lint: $(VENV)/pyvenv.cfg
 	uv run ruff format --check && \
 		uv run ruff check && \
-		uv run ty check
+		uv run ty check src
 
 	{%- if cookiecutter.docstring_coverage %}
 		uv run interrogate -c pyproject.toml .
@@ -80,7 +80,7 @@ check: lint test
 
 .PHONY: typecheck ty
 typecheck ty: $(VENV)/pyvenv.cfg
-	uv run ty check --strict
+	uv run ty check src
 
 .PHONY: reformat fix
 reformat fix:
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index ac6df4f..7d23105 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -46,7 +46,7 @@ lint = [
     # NOTE: ruff is under active development, so we pin conservatively here
     # and let Dependabot periodically perform this update.
     "ruff ~= 0.6.2",
-    "ty >= 0.1.0",
+    "ty >= 0.0.1a16",
     "types-html5lib",
     "types-requests",
     "types-toml",
@@ -74,7 +74,6 @@ omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 [tool.ty]
 # Astral's experimental type checker
 search_path = ["src"]
-strict = true
 
 # Ruff configuration is in ruff.toml
 

From 517395b4002084711855bcfd6edf90c6d8c5c19e Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 19:44:44 -0400
Subject: [PATCH 04/17] fix: apply ruff formatting to pre_gen_project.py
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Apply ruff formatting to fix CI failure.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 hooks/pre_gen_project.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/hooks/pre_gen_project.py b/hooks/pre_gen_project.py
index 8c7a3ef..80a0ff1 100644
--- a/hooks/pre_gen_project.py
+++ b/hooks/pre_gen_project.py
@@ -6,7 +6,9 @@
 namespace_import = "{{ cookiecutter.project_namespace_import }}"
 if namespace_import and not re.match(NAMESPACE_REGEX, namespace_import):
     print(f"ERROR: '{namespace_import}' is not a valid Python namespace import path!")
-    print(f"       It must follow regex '{NAMESPACE_REGEX}', i.e. 'one_two' or 'one_two.three'")
+    print(
+        f"       It must follow regex '{NAMESPACE_REGEX}', i.e. 'one_two' or 'one_two.three'"
+    )
     sys.exit(1)
 
 

From 08fb765a5ef453637c83dc17664690e3d32bf9b0 Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 19:49:56 -0400
Subject: [PATCH 05/17] refactor: remove data library option from cookiecutter
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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 <noreply@anthropic.com>
---
 cookiecutter.json                            |  5 -----
 {{cookiecutter.project_slug}}/CLAUDE.md      | 15 ---------------
 {{cookiecutter.project_slug}}/pyproject.toml |  5 -----
 3 files changed, 25 deletions(-)

diff --git a/cookiecutter.json b/cookiecutter.json
index 836a75a..bd12c5b 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -23,11 +23,6 @@
         "none"
     ],
     "docstring_coverage": true,
-    "data_library": [
-        "polars",
-        "pandas",
-        "none"
-    ],
     "web_framework": [
         "fastapi",
         "none"
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
index c46aae3..fd67013 100644
--- a/{{cookiecutter.project_slug}}/CLAUDE.md
+++ b/{{cookiecutter.project_slug}}/CLAUDE.md
@@ -70,20 +70,6 @@ Tests can also live beside source files as `test_*.py` or `*_test.py`.
 
 ## Key Libraries
 
-{%- if cookiecutter.data_library == "polars" %}
-- **Data processing**: Polars (preferred over pandas)
-  ```python
-  import polars as pl
-  df = pl.DataFrame({"col": [1, 2, 3]})
-  ```
-{%- elif cookiecutter.data_library == "pandas" %}
-- **Data processing**: Pandas
-  ```python
-  import pandas as pd
-  df = pd.DataFrame({"col": [1, 2, 3]})
-  ```
-{%- endif %}
-
 {%- if cookiecutter.web_framework == "fastapi" %}
 - **Web framework**: FastAPI (never use Flask)
   ```python
@@ -100,7 +86,6 @@ Tests can also live beside source files as `test_*.py` or `*_test.py`.
 ## Framework Preferences
 
 - **Web**: Always use FastAPI, never Flask
-- **Data**: Prefer Polars over Pandas for new code
 - **Async**: Use native async/await, not threading
 
 ## Common Patterns
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index 7d23105..c592fdb 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -20,11 +20,6 @@ classifiers = [
     "Programming Language :: Python :: 3",
 ]
 dependencies = [
-    {%- if cookiecutter.data_library == "polars" %}
-    "polars >= 0.20.0",
-    {%- elif cookiecutter.data_library == "pandas" %}
-    "pandas >= 2.0.0",
-    {%- endif %}
     {%- if cookiecutter.web_framework == "fastapi" %}
     "fastapi >= 0.100.0",
     "uvicorn[standard] >= 0.23.0",

From e80506107b5c0ae16d2d814119c917a8d9a285bc Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 20:04:32 -0400
Subject: [PATCH 06/17] refactor: simplify PR by removing FastAPI and
 consolidating config
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- 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 <noreply@anthropic.com>
---
 cookiecutter.json                             |  7 +--
 hooks/post_gen_project.py                     |  2 -
 {{cookiecutter.project_slug}}/CLAUDE.md       | 21 +-------
 {{cookiecutter.project_slug}}/Makefile        | 13 +----
 {{cookiecutter.project_slug}}/pyproject.toml  | 53 ++++++++++++++++---
 {{cookiecutter.project_slug}}/ruff.toml       | 45 ----------------
 .../{{cookiecutter.__module_import}}/_app.py  | 33 ------------
 7 files changed, 51 insertions(+), 123 deletions(-)
 delete mode 100644 {{cookiecutter.project_slug}}/ruff.toml
 delete mode 100644 {{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py

diff --git a/cookiecutter.json b/cookiecutter.json
index bd12c5b..8d61f41 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -23,10 +23,6 @@
         "none"
     ],
     "docstring_coverage": true,
-    "web_framework": [
-        "fastapi",
-        "none"
-    ],
     "license": [
         "Apache 2.0",
         "AGPL v3",
@@ -36,8 +32,7 @@
         ".github/workflows/docs.yml",
         ".github/workflows/lint.yml",
         ".github/workflows/tests.yml",
-        ".github/workflows/zizmor.yml",
-        "ruff.toml"
+        ".github/workflows/zizmor.yml"
     ],
     "__prompts__": {
         "project_name": "Human-readable project name (translated into module slug and import)",
diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
index 9b27560..ff8ac06 100644
--- a/hooks/post_gen_project.py
+++ b/hooks/post_gen_project.py
@@ -6,8 +6,6 @@
     "{% if cookiecutter.entry_point == '' %} {{ cookiecutter.__project_src_path }}/__main__.py {% endif %}",
     # We delete the docs GH workflow if the project has no documentation
     "{% if cookiecutter.documentation == 'none' %} .github/workflows/docs.yml {% endif %}",
-    # We delete _app.py if we're not generating a FastAPI app
-    "{% if cookiecutter.web_framework != 'fastapi' %} {{ cookiecutter.__project_src_path }}/_app.py {% endif %}",
 ]
 
 for path in REMOVE_PATHS:
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
index fd67013..90f4adb 100644
--- a/{{cookiecutter.project_slug}}/CLAUDE.md
+++ b/{{cookiecutter.project_slug}}/CLAUDE.md
@@ -35,7 +35,7 @@ make check  # Runs lint + tests
 # Code quality
 make lint   # ruff format --check + ruff check + ty check
 make fix    # Auto-fix formatting and lint issues
-make ty     # Run type checker with strict mode
+make ty     # Run type checker
 
 # Testing
 make test   # Run pytest with coverage
@@ -44,9 +44,6 @@ make test   # Run pytest with coverage
 {% if cookiecutter.entry_point -%}
 make run ARGS="--help"  # Run the CLI
 {%- endif %}
-{%- if cookiecutter.web_framework == "fastapi" %}
-make serve  # Run FastAPI dev server on http://localhost:8000
-{%- endif %}
 make doc    # Build documentation
 ```
 
@@ -68,24 +65,10 @@ test/
 
 Tests can also live beside source files as `test_*.py` or `*_test.py`.
 
-## Key Libraries
-
-{%- if cookiecutter.web_framework == "fastapi" %}
-- **Web framework**: FastAPI (never use Flask)
-  ```python
-  from fastapi import FastAPI
-  
-  app = FastAPI()
-  
-  @app.get("/")
-  async def root():
-      return {"message": "Hello World"}
-  ```
-{%- endif %}
-
 ## Framework Preferences
 
 - **Web**: Always use FastAPI, never Flask
+- **Data**: Prefer Polars over Pandas for new code
 - **Async**: Use native async/await, not threading
 
 ## Common Patterns
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index efc2597..7cede45 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -52,12 +52,6 @@ run: $(VENV)/pyvenv.cfg
 	uv run {{ cookiecutter.entry_point }} $(ARGS)
 {%- endif %}
 
-{%- if cookiecutter.web_framework == "fastapi" %}
-.PHONY: serve
-serve: $(VENV)/pyvenv.cfg
-	uv run uvicorn {{ cookiecutter.__project_import }}._app:app --reload --host 0.0.0.0 --port 8000
-{%- endif %}
-
 $(VENV)/pyvenv.cfg: pyproject.toml
 	uv venv $(VENV)
 	uv pip install -e '.[$(INSTALL_EXTRA)]'
@@ -72,9 +66,6 @@ lint: $(VENV)/pyvenv.cfg
 		uv run interrogate -c pyproject.toml .
 	{%- endif %}
 
-.PHONY: format
-format: reformat
-
 .PHONY: check
 check: lint test
 
@@ -82,8 +73,8 @@ check: lint test
 typecheck ty: $(VENV)/pyvenv.cfg
 	uv run ty check src
 
-.PHONY: reformat fix
-reformat fix:
+.PHONY: fix format
+fix format:
 	uv run ruff format && \
 		uv run ruff check --fix
 
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index c592fdb..f4e1ca7 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -19,12 +19,7 @@ authors = [
 classifiers = [
     "Programming Language :: Python :: 3",
 ]
-dependencies = [
-    {%- if cookiecutter.web_framework == "fastapi" %}
-    "fastapi >= 0.100.0",
-    "uvicorn[standard] >= 0.23.0",
-    {%- endif %}
-]
+dependencies = []
 requires-python = ">=3.11"
 
 [tool.setuptools.dynamic]
@@ -70,7 +65,51 @@ omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 # Astral's experimental type checker
 search_path = ["src"]
 
-# Ruff configuration is in ruff.toml
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+
+[tool.ruff.format]
+line-ending = "lf"
+quote-style = "double"
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "D203",  # Incompatible with D211
+    "D213",  # Incompatible with D212
+    "COM812",  # Can conflict with formatter
+    "ISC001",  # Can conflict with formatter
+]
+
+[tool.ruff.lint.mccabe]
+# Maximum cyclomatic complexity
+max-complexity = 8
+
+[tool.ruff.lint.pydocstyle]
+# Use Google-style docstrings
+convention = "google"
+
+[tool.ruff.lint.pylint]
+# Maximum number of branches for function or method
+max-branches = 12
+# Maximum number of return statements in function or method
+max-returns = 6
+# Maximum number of positional arguments for function or method
+max-positional-args = 5
+
+[tool.ruff.lint.per-file-ignores]
+{% if cookiecutter.entry_point -%}
+"{{ cookiecutter.__project_src_path }}/_cli.py" = [
+    "T201", # allow print in cli module
+]
+{%- endif %}
+"test/**/*.py" = [
+    "D",    # no docstrings in tests
+    "S101", # asserts are expected in tests
+    "PLR2004",  # Allow magic values in tests
+]
+"**/conftest.py" = ["D"]  # No docstrings in pytest config
 
 {%- if cookiecutter.docstring_coverage %}
 [tool.interrogate]
diff --git a/{{cookiecutter.project_slug}}/ruff.toml b/{{cookiecutter.project_slug}}/ruff.toml
deleted file mode 100644
index f08868b..0000000
--- a/{{cookiecutter.project_slug}}/ruff.toml
+++ /dev/null
@@ -1,45 +0,0 @@
-# Ruff configuration aligned with CLAUDE.md standards
-line-length = 100
-target-version = "py311"
-
-[lint]
-select = ["ALL"]
-ignore = [
-    "D203",  # Incompatible with D211
-    "D213",  # Incompatible with D212
-    "COM812",  # Can conflict with formatter
-    "ISC001",  # Can conflict with formatter
-]
-
-[lint.mccabe]
-# Maximum cyclomatic complexity
-max-complexity = 8
-
-[lint.pydocstyle]
-# Use Google-style docstrings
-convention = "google"
-
-[lint.pylint]
-# Maximum number of branches for function or method
-max-branches = 12
-# Maximum number of return statements in function or method
-max-returns = 6
-# Maximum number of positional arguments for function or method
-max-positional-args = 5
-
-[lint.per-file-ignores]
-# CLI-specific ignores (will be removed by post-gen hook if not CLI project)
-"src/**/_cli.py" = [
-    "T201",  # Allow print in CLI module
-]
-"test/**/*.py" = [
-    "D",     # No docstrings required in tests
-    "S101",  # Allow assert in tests
-    "PLR2004",  # Allow magic values in tests
-]
-"**/conftest.py" = ["D"]  # No docstrings in pytest config
-
-[format]
-# Consistent with line-length
-line-ending = "lf"
-quote-style = "double"
\ No newline at end of file
diff --git a/{{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py b/{{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py
deleted file mode 100644
index 694c193..0000000
--- a/{{cookiecutter.project_slug}}/src/{{cookiecutter.__module_import}}/_app.py
+++ /dev/null
@@ -1,33 +0,0 @@
-"""FastAPI application setup."""
-
-from fastapi import FastAPI
-from fastapi.middleware.cors import CORSMiddleware
-
-from {{ cookiecutter.__project_import }} import __version__
-
-app = FastAPI(
-    title="{{ cookiecutter.project_name }}",
-    description="{{ cookiecutter.project_description }}",
-    version=__version__,
-)
-
-# Configure CORS
-app.add_middleware(
-    CORSMiddleware,
-    allow_origins=["*"],  # Configure appropriately for production
-    allow_credentials=True,
-    allow_methods=["*"],
-    allow_headers=["*"],
-)
-
-
-@app.get("/")
-async def root() -> dict[str, str]:
-    """Root endpoint."""
-    return {"message": "{{ cookiecutter.project_name }} API", "version": __version__}
-
-
-@app.get("/health")
-async def health() -> dict[str, str]:
-    """Health check endpoint."""
-    return {"status": "ok"}
\ No newline at end of file

From 330cbb9bd27df997ee6cfc7bcd079513d5951795 Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 20:06:43 -0400
Subject: [PATCH 07/17] fix: restore 'reformat' target as alias to fix CI
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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 <noreply@anthropic.com>
---
 {{cookiecutter.project_slug}}/Makefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index 7cede45..41ca53c 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -73,8 +73,8 @@ check: lint test
 typecheck ty: $(VENV)/pyvenv.cfg
 	uv run ty check src
 
-.PHONY: fix format
-fix format:
+.PHONY: fix format reformat
+fix format reformat:
 	uv run ruff format && \
 		uv run ruff check --fix
 

From 2fbd39b7a7a01243fd870d427073c4e69ab84d5e Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 20:16:32 -0400
Subject: [PATCH 08/17] fix: correct license field syntax in pyproject.toml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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 <noreply@anthropic.com>
---
 {{cookiecutter.project_slug}}/pyproject.toml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index f4e1ca7..b7426bc 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -3,14 +3,12 @@ name = "{{ cookiecutter.project_slug }}"
 dynamic = ["version"]
 description = "{{ cookiecutter.project_description }}"
 readme = "README.md"
-license-files = ["LICENSE"]
-
 {%- if cookiecutter.license == "Apache 2.0" %}
-license = "Apache-2.0"
+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"}
 {%- endif %}
 
 authors = [

From d405f816ff37a157b6f13dfd8eb5a28e85843e50 Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 20:34:58 -0400
Subject: [PATCH 09/17] fix: correct ty configuration field name
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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 <noreply@anthropic.com>
---
 {{cookiecutter.project_slug}}/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index b7426bc..a15c466 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -61,7 +61,7 @@ omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 
 [tool.ty]
 # Astral's experimental type checker
-search_path = ["src"]
+src = ["src"]
 
 [tool.ruff]
 line-length = 100

From d4812985aede36cc858151223727184bc4d84efe Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 20:39:06 -0400
Subject: [PATCH 10/17] fix: remove ty configuration section to use defaults
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

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 <noreply@anthropic.com>
---
 {{cookiecutter.project_slug}}/pyproject.toml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index a15c466..ab6ab1b 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -59,9 +59,7 @@ Source = "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.
 # don't attempt code coverage for the CLI entrypoints
 omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 
-[tool.ty]
-# Astral's experimental type checker
-src = ["src"]
+# ty configuration - using defaults for now as ty is in early alpha
 
 [tool.ruff]
 line-length = 100

From 2902ab9d55572e93155bffcc3a06df500b4d3cb6 Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 20:53:44 -0400
Subject: [PATCH 11/17] test commit

---
 test-pyright/python-project/README.md | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 test-pyright/python-project/README.md

diff --git a/test-pyright/python-project/README.md b/test-pyright/python-project/README.md
new file mode 100644
index 0000000..bda5fad
--- /dev/null
+++ b/test-pyright/python-project/README.md
@@ -0,0 +1,27 @@
+# Python Project
+
+<!--- BADGES: START --->
+[![CI](https://github.com/trailofbits/python-project/actions/workflows/tests.yml/badge.svg)](https://github.com/trailofbits/python-project/actions/workflows/tests.yml)
+[![PyPI version](https://badge.fury.io/py/python-project.svg)](https://pypi.org/project/python-project)
+[![Packaging status](https://repology.org/badge/tiny-repos/python:python-project.svg)](https://repology.org/project/python:python-project/versions)
+<!--- BADGES: END --->
+
+
+
+## License
+```
+Copyright 2025 Trail of Bits
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+
+You may obtain a copy of the License at
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+```
+# Test

From 67244e8174ffccf11275534ca8b4340b19db5598 Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 20:56:24 -0400
Subject: [PATCH 12/17] refactor: replace ty with pyright and improve
 configurations
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- 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 <noreply@anthropic.com>
---
 .../.pre-commit-config.yaml                   | 12 ++++++------
 {{cookiecutter.project_slug}}/CLAUDE.md       | 19 +++++++++++--------
 {{cookiecutter.project_slug}}/Makefile        | 10 +++++-----
 {{cookiecutter.project_slug}}/pyproject.toml  | 11 ++++++++---
 4 files changed, 30 insertions(+), 22 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 6bffec0..01b2b4f 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -12,9 +12,9 @@ repos:
 
   - repo: local
     hooks:
-      - id: ty
-        name: ty type check
-        entry: uv run ty check src
+      - id: pyright
+        name: pyright type check
+        entry: uv run pyright
         language: system
         types: [python]
         pass_filenames: false
@@ -30,8 +30,8 @@ repos:
       {%- endif %}
 
       - id: pytest
-        name: pytest
-        entry: uv run pytest -q
+        name: pytest (fast tests only)
+        entry: uv run pytest -x --tb=short -k "not slow"
         language: system
         types: [python]
         pass_filenames: false
@@ -42,4 +42,4 @@ repos:
 # Configuration
 ci:
   autofix_prs: true
-  autoupdate_schedule: weekly
\ No newline at end of file
+  autoupdate_schedule: weekly
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
index 90f4adb..e57767c 100644
--- a/{{cookiecutter.project_slug}}/CLAUDE.md
+++ b/{{cookiecutter.project_slug}}/CLAUDE.md
@@ -33,9 +33,9 @@ make dev
 make check  # Runs lint + tests
 
 # Code quality
-make lint   # ruff format --check + ruff check + ty check
+make lint   # ruff format --check + ruff check + pyright
 make fix    # Auto-fix formatting and lint issues
-make ty     # Run type checker
+make typecheck  # Run pyright type checker
 
 # Testing
 make test   # Run pytest with coverage
@@ -65,11 +65,14 @@ test/
 
 Tests can also live beside source files as `test_*.py` or `*_test.py`.
 
-## Framework Preferences
+## General Python Guidelines
 
-- **Web**: Always use FastAPI, never Flask
-- **Data**: Prefer Polars over Pandas for new code
-- **Async**: Use native async/await, not threading
+These are general preferences for Python development:
+
+- **Web frameworks**: Prefer FastAPI over Flask for new projects
+- **Data processing**: Consider Polars for performance-critical data operations
+- **Async programming**: Use native async/await instead of threading
+- **Type checking**: Always use type hints and run pyright
 
 ## Common Patterns
 
@@ -123,7 +126,7 @@ parser.add_argument(
 ## CI/CD
 
 GitHub Actions run on every push/PR:
-1. **Linting**: ruff format/check + ty type checking
+1. **Linting**: ruff format/check + pyright type checking
 2. **Tests**: pytest with coverage
 3. **Security**: zizmor workflow scanning
 {%- if cookiecutter.documentation == "pdoc" %}
@@ -134,7 +137,7 @@ GitHub Actions run on every push/PR:
 
 1. **Never commit code that violates the quality standards** - refactor instead
 2. **All public APIs need Google-style docstrings**
-3. **Type hints are mandatory** - use `ty check`
+3. **Type hints are mandatory** - use `pyright`
 4. **Tests can live beside code** - prefer colocated tests for better maintainability
 
 ## Project-Specific Instructions
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index 41ca53c..ad0ca7b 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -60,7 +60,7 @@ $(VENV)/pyvenv.cfg: pyproject.toml
 lint: $(VENV)/pyvenv.cfg
 	uv run ruff format --check && \
 		uv run ruff check && \
-		uv run ty check src
+		uv run pyright
 
 	{%- if cookiecutter.docstring_coverage %}
 		uv run interrogate -c pyproject.toml .
@@ -69,9 +69,9 @@ lint: $(VENV)/pyvenv.cfg
 .PHONY: check
 check: lint test
 
-.PHONY: typecheck ty
-typecheck ty: $(VENV)/pyvenv.cfg
-	uv run ty check src
+.PHONY: typecheck
+typecheck: $(VENV)/pyvenv.cfg
+	uv run pyright
 
 .PHONY: fix format reformat
 fix format reformat:
@@ -80,7 +80,7 @@ fix format reformat:
 
 .PHONY: test tests
 test tests: $(VENV)/pyvenv.cfg
-	uv run pytest -q --cov=$(PY_IMPORT) $(T) $(TEST_ARGS)
+	uv run pytest --cov=$(PY_IMPORT) $(T) $(TEST_ARGS)
 	uv run coverage report -m $(COV_ARGS)
 
 .PHONY: doc
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index ab6ab1b..18a0a0a 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -34,7 +34,7 @@ lint = [
     # NOTE: ruff is under active development, so we pin conservatively here
     # and let Dependabot periodically perform this update.
     "ruff ~= 0.6.2",
-    "ty >= 0.0.1a16",
+    "pyright >= 1.1",
     "types-html5lib",
     "types-requests",
     "types-toml",
@@ -59,7 +59,12 @@ Source = "https://github.com/{{ cookiecutter.github_username }}/{{ cookiecutter.
 # don't attempt code coverage for the CLI entrypoints
 omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 
-# ty configuration - using defaults for now as ty is in early alpha
+[tool.pyright]
+# Type checking configuration
+pythonVersion = "3.11"
+typeCheckingMode = "standard"
+useLibraryCodeForTypes = true
+reportMissingTypeStubs = false
 
 [tool.ruff]
 line-length = 100
@@ -121,4 +126,4 @@ fail-under = 100
 testpaths = ["src", "test"]
 python_files = ["test_*.py", "*_test.py"]
 # Show test durations
-addopts = "-q --durations=10"
+addopts = "--durations=10"

From a249f002da262fdfc636b927f802ed444550a4bb Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 21:04:54 -0400
Subject: [PATCH 13/17] test commit

---
 {test-pyright => test-final}/python-project/README.md | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {test-pyright => test-final}/python-project/README.md (100%)

diff --git a/test-pyright/python-project/README.md b/test-final/python-project/README.md
similarity index 100%
rename from test-pyright/python-project/README.md
rename to test-final/python-project/README.md

From 0030cefbcf53d9d35d68c00cbda9625a198f81f4 Mon Sep 17 00:00:00 2001
From: Dan Guido <dan@trailofbits.com>
Date: Tue, 29 Jul 2025 21:06:01 -0400
Subject: [PATCH 14/17] fix: address all code review issues
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- 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 <noreply@anthropic.com>
---
 test-final/python-project/README.md           | 27 -------------------
 .../.pre-commit-config.yaml                   |  4 +--
 {{cookiecutter.project_slug}}/CLAUDE.md       | 19 +++++++++++++
 {{cookiecutter.project_slug}}/Makefile        |  8 ++++--
 {{cookiecutter.project_slug}}/pyproject.toml  |  3 ++-
 5 files changed, 29 insertions(+), 32 deletions(-)
 delete mode 100644 test-final/python-project/README.md

diff --git a/test-final/python-project/README.md b/test-final/python-project/README.md
deleted file mode 100644
index bda5fad..0000000
--- a/test-final/python-project/README.md
+++ /dev/null
@@ -1,27 +0,0 @@
-# Python Project
-
-<!--- BADGES: START --->
-[![CI](https://github.com/trailofbits/python-project/actions/workflows/tests.yml/badge.svg)](https://github.com/trailofbits/python-project/actions/workflows/tests.yml)
-[![PyPI version](https://badge.fury.io/py/python-project.svg)](https://pypi.org/project/python-project)
-[![Packaging status](https://repology.org/badge/tiny-repos/python:python-project.svg)](https://repology.org/project/python:python-project/versions)
-<!--- BADGES: END --->
-
-
-
-## License
-```
-Copyright 2025 Trail of Bits
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-
-You may obtain a copy of the License at
-    http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-```
-# Test
diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 01b2b4f..5980969 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -36,8 +36,8 @@ repos:
         types: [python]
         pass_filenames: false
         require_serial: true
-        # Only run on commit, not on push
-        stages: [commit]
+        # Only run on pre-commit, not on push
+        stages: [pre-commit]
 
 # Configuration
 ci:
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
index e57767c..f52d165 100644
--- a/{{cookiecutter.project_slug}}/CLAUDE.md
+++ b/{{cookiecutter.project_slug}}/CLAUDE.md
@@ -123,6 +123,25 @@ parser.add_argument(
 - Mock external dependencies
 - Test both success and error paths
 
+### Test Markers
+
+Mark slow tests to exclude them from pre-commit hooks:
+
+```python
+import pytest
+
+@pytest.mark.slow
+def test_integration_with_external_api():
+    """This test won't run during pre-commit hooks."""
+    ...
+
+def test_fast_unit_test():
+    """This test will run during pre-commit hooks."""
+    ...
+```
+
+The pre-commit hook runs `pytest -k "not slow"` to skip slow tests.
+
 ## CI/CD
 
 GitHub Actions run on every push/PR:
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index ad0ca7b..06b4586 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -73,11 +73,15 @@ check: lint test
 typecheck: $(VENV)/pyvenv.cfg
 	uv run pyright
 
-.PHONY: fix format reformat
-fix format reformat:
+.PHONY: fix
+fix:
 	uv run ruff format && \
 		uv run ruff check --fix
 
+# Alias for backwards compatibility
+.PHONY: reformat
+reformat: fix
+
 .PHONY: test tests
 test tests: $(VENV)/pyvenv.cfg
 	uv run pytest --cov=$(PY_IMPORT) $(T) $(TEST_ARGS)
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index 18a0a0a..b75c3e8 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -61,8 +61,9 @@ omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 
 [tool.pyright]
 # Type checking configuration
+include = ["src", "test"]
 pythonVersion = "3.11"
-typeCheckingMode = "standard"
+typeCheckingMode = "strict"
 useLibraryCodeForTypes = true
 reportMissingTypeStubs = false
 

From d7c9bbf6a3d690f4c202194941f088c83df3ef04 Mon Sep 17 00:00:00 2001
From: Alexis <alexis.challande@trailofbits.com>
Date: Fri, 5 Dec 2025 11:57:04 +0100
Subject: [PATCH 15/17] Fix the PR

---
 .../.github/workflows/tests.yml               |   3 +
 .../.pre-commit-config.yaml                   |  15 +-
 {{cookiecutter.project_slug}}/CLAUDE.md       | 167 ------------------
 {{cookiecutter.project_slug}}/Makefile        |   7 +-
 {{cookiecutter.project_slug}}/pyproject.toml  |  20 +--
 5 files changed, 23 insertions(+), 189 deletions(-)
 delete mode 100644 {{cookiecutter.project_slug}}/CLAUDE.md

diff --git a/{{cookiecutter.project_slug}}/.github/workflows/tests.yml b/{{cookiecutter.project_slug}}/.github/workflows/tests.yml
index f812a53..c39dec0 100644
--- a/{{cookiecutter.project_slug}}/.github/workflows/tests.yml
+++ b/{{cookiecutter.project_slug}}/.github/workflows/tests.yml
@@ -13,8 +13,11 @@ jobs:
     strategy:
       matrix:
         python:
+          - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
+          - "3.14"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 5980969..04b2646 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -2,13 +2,14 @@
 # See https://pre-commit.com for more information
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.2
+    # Ruff version.
+    rev: v0.14.8
     hooks:
-      # Run the formatter
-      - id: ruff-format
-      # Run the linter
-      - id: ruff
+      # Run the linter.
+      - id: ruff-check
         args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
 
   - repo: local
     hooks:
@@ -30,8 +31,8 @@ repos:
       {%- endif %}
 
       - id: pytest
-        name: pytest (fast tests only)
-        entry: uv run pytest -x --tb=short -k "not slow"
+        name: pytest
+        entry: uv run pytest
         language: system
         types: [python]
         pass_filenames: false
diff --git a/{{cookiecutter.project_slug}}/CLAUDE.md b/{{cookiecutter.project_slug}}/CLAUDE.md
deleted file mode 100644
index f52d165..0000000
--- a/{{cookiecutter.project_slug}}/CLAUDE.md
+++ /dev/null
@@ -1,167 +0,0 @@
-# {{ cookiecutter.project_name }} - Claude Instructions
-
-This document contains project-specific instructions for Claude when working on this codebase.
-
-## Project Overview
-
-{{ cookiecutter.project_description }}
-
-## Code Standards
-
-This project enforces strict code quality standards:
-
-### Code Complexity Limits
-- **Max 50 lines per function** - Split larger functions
-- **Cyclomatic complexity ≤ 8** - Simplify complex logic  
-- **Max 5 positional parameters** - Use keyword arguments or dataclasses
-- **Max 12 branches per function** - Extract to helper functions
-- **Max 6 return statements** - Consolidate exit points
-
-### Style Guidelines
-- **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`)
-
-## Quick Commands
-
-```bash
-# Development setup
-make dev
-
-# Run all checks
-make check  # Runs lint + tests
-
-# Code quality
-make lint   # ruff format --check + ruff check + pyright
-make fix    # Auto-fix formatting and lint issues
-make typecheck  # Run pyright type checker
-
-# Testing
-make test   # Run pytest with coverage
-
-# Development
-{% if cookiecutter.entry_point -%}
-make run ARGS="--help"  # Run the CLI
-{%- endif %}
-make doc    # Build documentation
-```
-
-## Project Structure
-
-```
-src/
-└── {{ cookiecutter.__project_import.replace('.', '/') }}/
-    ├── __init__.py
-    {%- if cookiecutter.entry_point %}
-    ├── __main__.py      # CLI entry point
-    ├── _cli.py          # CLI implementation
-    {%- endif %}
-    └── py.typed         # Type checking marker
-
-test/
-└── test_*.py            # Traditional test location
-```
-
-Tests can also live beside source files as `test_*.py` or `*_test.py`.
-
-## General Python Guidelines
-
-These are general preferences for Python development:
-
-- **Web frameworks**: Prefer FastAPI over Flask for new projects
-- **Data processing**: Consider Polars for performance-critical data operations
-- **Async programming**: Use native async/await instead of threading
-- **Type checking**: Always use type hints and run pyright
-
-## Common Patterns
-
-### Error Handling
-```python
-from typing import Result  # If using result types
-
-def process_data(path: str) -> Result[Data, str]:
-    """Process data from file.
-    
-    Args:
-        path: Path to data file.
-        
-    Returns:
-        Result with Data on success, error message on failure.
-    """
-    try:
-        # Implementation
-        return Ok(data)
-    except Exception as e:
-        return Err(f"Failed to process: {e}")
-```
-
-### Logging
-```python
-import logging
-
-logger = logging.getLogger(__name__)
-```
-
-{%- if cookiecutter.entry_point %}
-
-### CLI Arguments
-Use the existing `_cli.py` structure:
-```python
-parser.add_argument(
-    "--verbose", "-v",
-    action="store_true",
-    help="Enable verbose output"
-)
-```
-{%- endif %}
-
-## Testing Guidelines
-
-- Aim for 100% test coverage (enforced by CI)
-- Use `pytest.mark.parametrize` for multiple test cases
-- Mock external dependencies
-- Test both success and error paths
-
-### Test Markers
-
-Mark slow tests to exclude them from pre-commit hooks:
-
-```python
-import pytest
-
-@pytest.mark.slow
-def test_integration_with_external_api():
-    """This test won't run during pre-commit hooks."""
-    ...
-
-def test_fast_unit_test():
-    """This test will run during pre-commit hooks."""
-    ...
-```
-
-The pre-commit hook runs `pytest -k "not slow"` to skip slow tests.
-
-## CI/CD
-
-GitHub Actions run on every push/PR:
-1. **Linting**: ruff format/check + pyright type checking
-2. **Tests**: pytest with coverage
-3. **Security**: zizmor workflow scanning
-{%- if cookiecutter.documentation == "pdoc" %}
-4. **Docs**: Auto-deploy to GitHub Pages
-{%- endif %}
-
-## Important Notes
-
-1. **Never commit code that violates the quality standards** - refactor instead
-2. **All public APIs need Google-style docstrings**
-3. **Type hints are mandatory** - use `pyright`
-4. **Tests can live beside code** - prefer colocated tests for better maintainability
-
-## Project-Specific Instructions
-
-<!-- Add any project-specific Claude instructions here -->
-
----
-*This file helps Claude understand project conventions. Update it as patterns emerge.*
\ No newline at end of file
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index 06b4586..44fc66e 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -60,11 +60,8 @@ $(VENV)/pyvenv.cfg: pyproject.toml
 lint: $(VENV)/pyvenv.cfg
 	uv run ruff format --check && \
 		uv run ruff check && \
-		uv run pyright
-
-	{%- if cookiecutter.docstring_coverage %}
-		uv run interrogate -c pyproject.toml .
-	{%- endif %}
+		uv run pyright{% if cookiecutter.docstring_coverage %} && \
+		uv run interrogate -c pyproject.toml .{% endif %}
 
 .PHONY: check
 check: lint test
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index b75c3e8..e8cc6bb 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -3,12 +3,13 @@ name = "{{ cookiecutter.project_slug }}"
 dynamic = ["version"]
 description = "{{ cookiecutter.project_description }}"
 readme = "README.md"
+license-files = ["LICENSE"]
 {%- if cookiecutter.license == "Apache 2.0" %}
-license = {text = "Apache-2.0"}
+license = "Apache-2.0"
 {%- elif cookiecutter.license == "AGPL v3" %}
-license = {text = "AGPL-3.0-or-later"}
+license = "AGPL-3.0-or-later"
 {%- elif cookiecutter.license == "Proprietary" %}
-license = {file = "LICENSE"}
+license = "LicenseRef-Proprietary-License"
 {%- endif %}
 
 authors = [
@@ -18,7 +19,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
 ]
 dependencies = []
-requires-python = ">=3.11"
+requires-python = ">=3.10"
 
 [tool.setuptools.dynamic]
 version = { attr = "{{ cookiecutter.__project_import }}.__version__" }
@@ -33,7 +34,7 @@ test = ["pytest", "pytest-cov", "pretend", "coverage[toml]"]
 lint = [
     # NOTE: ruff is under active development, so we pin conservatively here
     # and let Dependabot periodically perform this update.
-    "ruff ~= 0.6.2",
+    "ruff ~= 0.14.8",
     "pyright >= 1.1",
     "types-html5lib",
     "types-requests",
@@ -62,14 +63,14 @@ omit = ["{{ cookiecutter.__project_src_path }}/_cli.py"]
 [tool.pyright]
 # Type checking configuration
 include = ["src", "test"]
-pythonVersion = "3.11"
+pythonVersion = "3.10"
 typeCheckingMode = "strict"
 useLibraryCodeForTypes = true
 reportMissingTypeStubs = false
 
 [tool.ruff]
 line-length = 100
-target-version = "py311"
+target-version = "py310"
 
 [tool.ruff.format]
 line-ending = "lf"
@@ -123,8 +124,7 @@ fail-under = 100
 {%- endif %}
 
 [tool.pytest.ini_options]
-# Support tests living beside code
-testpaths = ["src", "test"]
-python_files = ["test_*.py", "*_test.py"]
+testpaths = ["test"]
+python_files = ["test_*.py"]
 # Show test durations
 addopts = "--durations=10"

From 08e45c62d10ddfa266e4729dff74f74a09224e0b Mon Sep 17 00:00:00 2001
From: Alexis <alexis.challande@trailofbits.com>
Date: Mon, 8 Dec 2025 15:14:07 +0100
Subject: [PATCH 16/17] Update Makefile

---
 {{cookiecutter.project_slug}}/Makefile | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index 44fc66e..be0bd66 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -63,22 +63,11 @@ lint: $(VENV)/pyvenv.cfg
 		uv run pyright{% if cookiecutter.docstring_coverage %} && \
 		uv run interrogate -c pyproject.toml .{% endif %}
 
-.PHONY: check
-check: lint test
-
-.PHONY: typecheck
-typecheck: $(VENV)/pyvenv.cfg
-	uv run pyright
-
-.PHONY: fix
-fix:
+.PHONY: reformat
+reformat:
 	uv run ruff format && \
 		uv run ruff check --fix
 
-# Alias for backwards compatibility
-.PHONY: reformat
-reformat: fix
-
 .PHONY: test tests
 test tests: $(VENV)/pyvenv.cfg
 	uv run pytest --cov=$(PY_IMPORT) $(T) $(TEST_ARGS)

From 3726689f3824d403f1581391fe86c84a077a55d0 Mon Sep 17 00:00:00 2001
From: Alexis <alexis.challande@trailofbits.com>
Date: Tue, 9 Dec 2025 11:03:11 +0100
Subject: [PATCH 17/17] Update the pre-commit

---
 .../.pre-commit-config.yaml                   | 34 ++++++-------------
 {{cookiecutter.project_slug}}/Makefile        |  5 +++
 {{cookiecutter.project_slug}}/pyproject.toml  |  8 ++---
 3 files changed, 18 insertions(+), 29 deletions(-)

diff --git a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
index 04b2646..67afd28 100644
--- a/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
+++ b/{{cookiecutter.project_slug}}/.pre-commit-config.yaml
@@ -1,46 +1,32 @@
 # Pre-commit hooks for code quality
 # See https://pre-commit.com for more information
 repos:
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    # Ruff version.
-    rev: v0.14.8
-    hooks:
-      # Run the linter.
-      - id: ruff-check
-        args: [--fix]
-      # Run the formatter.
-      - id: ruff-format
-
   - repo: local
     hooks:
-      - id: pyright
-        name: pyright type check
-        entry: uv run pyright
+      - id: format
+        name: format code
+        entry: make format
         language: system
         types: [python]
         pass_filenames: false
-        require_serial: true
 
-      {%- if cookiecutter.docstring_coverage %}
-      - id: interrogate
-        name: interrogate docstring coverage
-        entry: uv run interrogate -c pyproject.toml
+      - id: lint
+        name: lint code
+        entry: make lint
         language: system
         types: [python]
         pass_filenames: false
-      {%- endif %}
+        require_serial: true
 
-      - id: pytest
-        name: pytest
-        entry: uv run pytest
+      - id: test
+        name: run tests
+        entry: make test
         language: system
         types: [python]
         pass_filenames: false
         require_serial: true
-        # Only run on pre-commit, not on push
         stages: [pre-commit]
 
 # Configuration
 ci:
   autofix_prs: true
-  autoupdate_schedule: weekly
diff --git a/{{cookiecutter.project_slug}}/Makefile b/{{cookiecutter.project_slug}}/Makefile
index e029b32..6988f95 100644
--- a/{{cookiecutter.project_slug}}/Makefile
+++ b/{{cookiecutter.project_slug}}/Makefile
@@ -21,6 +21,11 @@ endif
 all:
 	@echo "Run my targets individually!"
 
+.PHONY: dev
+dev:
+	uv sync --group dev
+	uv run pre-commit install
+
 {%- if cookiecutter.entry_point %}
 .PHONY: run
 run:
diff --git a/{{cookiecutter.project_slug}}/pyproject.toml b/{{cookiecutter.project_slug}}/pyproject.toml
index 288d148..6bda506 100644
--- a/{{cookiecutter.project_slug}}/pyproject.toml
+++ b/{{cookiecutter.project_slug}}/pyproject.toml
@@ -36,10 +36,7 @@ lint = [
     # NOTE: ruff is under active development, so we pin conservatively here
     # and let Dependabot periodically perform this update.
     "ruff ~= 0.14.0",
-    "pyright ~= 1.1.407",
-    "types-html5lib",
-    "types-requests",
-    "types-toml",
+    "pyright",
     {%- if cookiecutter.docstring_coverage %}
     "interrogate",
     {%- endif %}
@@ -48,6 +45,7 @@ dev = [
     {include-group = "doc"},
     {include-group = "test"},
     {include-group = "lint"},
+    "pre-commit",
 ]
 
 {% if cookiecutter.entry_point -%}
@@ -72,7 +70,7 @@ typeCheckingMode = "strict"
 reportUnusedImport = "warning"
 reportUnusedVariable = "warning"
 reportGeneralTypeIssues = "error"
-reportMissingTypeStubs = false
+reportMissingTypeStubs = true
 
 [tool.ruff]
 line-length = 100