Dev tooling setup, src/ layout migration, and notebook QA

[Palamabron]

Summary

• Migrate the project to a standard src/ layout at the repository root and enable a reproducible developer workflow with Hatch + uv and pre-commit hooks.
• Add code quality tooling (Ruff, Black, MyPy) and notebook support via nbQA.

What’s changed

• Move package to root src layout: src/alphapulse/{init.py,about.py}.
• Configure version path for Hatchling: tool.hatch.version.path -> src/alphapulse/about.py.
• Add optional-dependencies dev group (pre-commit, ruff, black, mypy, nbQA, stubs) and enable it via features=["dev"].
• Pre-commit config: Ruff (lint + format), Black, MyPy, nbQA for .ipynb; exclude .ipynb from EOF/trailing whitespace hooks.
• Update README with minimal local development setup (Hatch + uv).

Why

• Standard src/ layout prevents import path issues and aligns with modern Python packaging practices.
• Enforced formatting, linting, and typing improve code reliability and PR review speed.
• Notebook QA (nbQA + Ruff/Black/MyPy) keeps notebooks consistent with code standards.

Implementation details

• pyproject.toml:
  • [project.optional-dependencies].dev defined for tooling.
  • [tool.hatch.envs.default]: installer=uv, features=["dev"] to install editable .[dev] automatically.
  • Ruff/Black/MyPy configured for Python 3.11.
• .pre-commit-config.yaml:
  • Ruff (—fix) + ruff-format, Black, MyPy (+ types), nbQA hooks (ruff, black with —nbqa-mutate, mypy).
  • pre-commit-hooks: check-yaml, check-toml; exclude .ipynb from EOF/trailing-whitespace.

Developer setup and testing

• Create and enter environment:
  • hatch env remove default && hatch env create && hatch shell
• Verify tooling:
  • which pre-commit
  • pre-commit install
  • pre-commit run --all-files
• Project scripts (optional):
  • hatch run lint
  • hatch run format
  • hatch run types
  • hatch run all

Backward compatibility / migration notes

• All imports should continue to work with the new src/ layout (no runtime API changes).
• CI may require environment refresh to install extras via editable install (.[dev]).

Out of scope

• No production logic changes.
• No release version bump.

Checklist

• pre-commit hooks installed and pass locally
• Lint, format, types scripts pass
• README updated for local dev
• Notebooks (if any) lint/format/type check clean via nbQA

[Pheoxis]

Great :)

[Copilot]

Pull Request Overview

This PR migrates the project to a standard src/ layout and establishes a comprehensive developer tooling setup with Hatch + uv for environment management and pre-commit hooks for code quality.

• Migrates package structure to src/alphapulse/ layout with proper version configuration
• Configures development tooling including Ruff, Black, MyPy, and nbQA for notebooks
• Sets up pre-commit hooks and Hatch scripts for consistent code quality enforcement

Reviewed Changes

Copilot reviewed 7 out of 8 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/alphapulse/init.py	Package initialization file with SPDX license header
src/alphapulse/about.py	Version definition file for dynamic versioning
tests/init.py	Test package initialization with license header
pyproject.toml	Complete project configuration with dev dependencies, tooling settings, and Hatch scripts
README.md	Updated documentation with local development setup instructions
LICENSE.txt	MIT license file
.pre-commit-config.yaml	Pre-commit configuration for code quality hooks including notebook support

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