refactor: introduce typed simulation state and improve type safety

[Boussetta]

Closes #4

Summary

Improve type safety and maintainability across the simulation and GUI layers.

Changes

• Normalize signal time vectors as typed NumPy arrays.
• Add explicit typing for FFT reconstruction buffers.
• Correct Matplotlib callback annotations.
• Align mypy configuration with current NumPy and Python toolchains.
• Update README instructions for virtual environments, testing, and application startup.

Validation

• pytest -q: 19 passed
• ruff check src tests: passed
• mypy src/aliasing_atlas --ignore-missing-imports: passed
• Notebook JSON validation: passed
• Package wheel build: passed
• git diff --check: passed

Notes

This PR contains four focused commits:

• Documentation workflow updates
• Mypy configuration
• Matplotlib callback typing
• FFT buffer annotation

[Copilot]

🟡 Changes recommended

The mypy configuration changes are inconsistent with the declared supported Python version range, and the README updates introduce platform-specific commands without Windows equivalents despite claiming Windows support.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR refactors and tightens typing across the DSP and UI layers, while updating developer-facing workflows (type-checking configuration and README instructions) to better support maintenance and static analysis.

Changes:

• Adds explicit typing for FFT reconstruction buffers in DSP utilities.
• Adjusts Matplotlib callback type annotations to match widget callback signatures.
• Updates mypy configuration and expands README guidance for virtual environments, testing, and running the app.

File summaries

File	Description
src/aliasing_atlas/dsp.py	Adds an explicit ndarray annotation for the zero-padding FFT reconstruction buffer.
src/aliasing_atlas/app.py	Updates callback parameter types for Matplotlib widget callbacks and guards against None labels.
README.md	Revises setup/run/test instructions to use a local virtual environment and module entrypoint.
pyproject.toml	Updates mypy settings intended to align type-checking with the current toolchain.

Review details

Suppressed comments (2)

pyproject.toml:79

• Setting follow_imports = "skip" significantly reduces mypy’s ability to type-check dependencies (including internal modules when checking entry points), which runs counter to the PR’s type-safety goal; ignore_missing_imports already handles missing third-party stubs.

ignore_missing_imports = true
no_site_packages = true
follow_imports = "skip"
check_untyped_defs = true

README.md:130

• The activation command is POSIX-specific; add Windows activation commands to match the project’s stated Windows support.

source .venv/bin/activate

• Files reviewed: 4/4 changed files
• Comments generated: 3
• Review effort level: Lite

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[Copilot]

Implemented in commit 634fb73 by adding explicit Windows PowerShell equivalents for the .venv/bin/python and activation commands in the installation section of README.md.