Sequence

Added
New Component Modules from this paper: https://arxiv.org/pdf/2411.11377.
- `Transducer`
- `Transmon`
- `FockDetector`
- `FockBeamSplitter2`
- The unit tests in the folder `tests`
- Examples in the folder `example/quantum_transduction`. NOTE: Still work in progress.

Changed
- Reorganized the `absorptive_memory` related files
- Update the `requirements.txt`
- Update `constants` module
- Update comments here and there

Added
- Add support for Python 3.13
- Add support for the latest Numpy (2.2), SciPy (1.14), and QuTiP (5.0)

Changed
- Updated the demos of the tutorial for easy of understanding.
- Updated some comments, typing, arguments, and some other minor changes.
- Changelog updates:
- Reversed the changelog, now the latest version update is at the top of the changelog, instead of previously at the bottom.
- Added the timestamp for the version updates.

Removed
- Removed support for Python 3.9

Added
- Add new class BellDiagonalState for Bell Diagonal State.
- Add new Quantum Manager for Bell Diagonal State, i.e., QuantumManagerBellDiagonal.
- Add new class SingleHeralded BSM to support single heralded entanglement generation.
- Add support for time-dependent decoherence for the Bell Diagonal State in Memory class.

Changed
- Remove existing handlers in logging before setting the new handler

Changed
- Use `Read the Docs` for documentation. Update documentation. Old documentation website becomes obsolete.
- Update comments and README.md

Fixed
- Fix a bug in reservation protocol and routing protocol that may lead to route for src->dst being different than dst->src when the network has same length edges.

Added
- We have an Icon for SeQUeNCe!
- `pip install sequence` is now available!
- `src` folder is renamed to `sequence`
- Add `sequence/constants.py` to organize the common constants
- Add support for Python 3.12
- Add `pyproject.toml`

Changed
- Various refactoring, include but not limited to updating variable/method names, moving/deleting code, adding/rewriting comments, and making the code more succinct, etc.
- In README.md, installation with option `--editable` is encouraged.
- `logging` looks better
- In `class Reservation`, added attribute `entanglement_number` and `id`
- Update `ResourceReservationProtocol.load_rules()`
- Move `utils/json_config_generators/generator_utils.py` to `sequence/utils/config_generator.py`

Removed
- Removed support for Python 3.8
- Removed `setup.py`
- Removed `MANIFEST.in`

Added
- Moved around and added a few files in the `examples` folder
- These are primarily for the IEEE QCE 2023 conference

Changed
- Modified the topology output of the GUI to be compatible with new topology upgrades
- Several bug fixes in the GUI