Implement Gates and Circuit

[masa10-f]

Before submitting, please check the following:

• Make sure you have tests for the new code and that test passes (run pytest)
• If applicable, add a line to the [unreleased] part of CHANGELOG.md, following keep-a-changelog.
• Format added code by ruff
• Type checking by mypy and pyright
• Make sure the checks (github actions) pass.
• Check that the docs compile without errors (run make html in ./docs/ - you may need to install dependency for sphinx docs, see docs/requirements.txt.)

Then, please fill in below:

Description of the change:

I have implemented

• gates.py which has a variety of gate classes compatible with the qiskit gate convention.
• Added Circuit module and converter to GraphState.

I have also implemented unit test for gates. A test for circuit will be implemented after implementing circuit simulator class.

Related issue:

[masato-fuk]

Remained task

• resolve sphinx build error
• check equations are properly build

[masato-fuk]

I guess Circuit.apply_macro_gate is not a smart way......

[Copilot]

Pull Request Overview

This PR implements a comprehensive quantum gate system and circuit representation for the graphix_zx library. The implementation includes both low-level unit gates (J, CZ, PhaseGadget) and high-level macro gates that decompose into unit gates, along with circuit classes to organize and execute quantum operations.

Key changes:

• Added a complete gate hierarchy with abstract base classes and concrete implementations for common quantum gates
• Implemented circuit classes to manage sequences of quantum operations
• Added conversion functionality from circuits to graph states with gflow
• Provided comprehensive unit tests to verify gate decompositions and matrix representations

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
graphix_zx/gates.py	Implements the complete gate system with unit gates (J, CZ, PhaseGadget) and macro gates that decompose to unit gates
graphix_zx/circuit.py	Provides circuit classes for organizing quantum operations and conversion to graph states
tests/test_gate.py	Unit tests verifying gate decompositions match expected matrix representations
docs/source/circuit.rst	Documentation for the new circuit and gate modules
docs/source/references.rst	Updated documentation index to include circuit module
docs/source/matrix_utility.rst	Minor documentation title correction

[EarlMilktea]

@masa10-f

Could you first resolve basic unknown types (don't have to be all, it's impossible in the first place) reported by pyright to make my review smoother?

[masa10-f]

@EarlMilktea
I have resolved pyright information warnings in 0172358

[masa10-f]

I have also added a test for circuit module in 29024b3