Sequence

Added
- Added some groundwork for future topology upgrades

Changed
- made numerous bug fixes:
- BSM and optical channel components received fixes
- Some residual bugs with GUI usage have been fixed
- Error with typing in Fock quantum manager has been fixed

Removed
- Removed support for scipy version 1.11. This is currently causing some issues with qutip.

Added
- Fock state density matrix encoding
- Quantum manager to use fock state density matrix
- Add truncation attribute to quantum managers; Hilbert space dimension is truncation + 1
- Supports error channels based on kraus operators and direct operator action on state
- Hardware models to use fock state density matrix
- Absorptive quantum memory built on AFC
- Interference and direct detection for state tomography

Changed
- Moved around and updated some error checking
- Temporarily removed mpich testing for python 3.8 and 3.9 (broken)

Added
- Added some additional error checking to individual quantum states
- This includes additional error checking in the `Photon` class

Changed
- The `entangle` method for the `Photon` and `FreeQuantumState` classes has been changed to `combine_state`
- Updated chapter 1 tutorial in the documentation to match code example

Removed
- residual `json5` references in examples

Changed
- Bug fixes to the GUI and QKD tests

Added
- Added more scripts for the QCE 2022 conference

Changed
- Fixed some bugs in the GUI code for classical communication delay

Removed
- Removed `mpi4py` from install instructions on the README

Changed
- Moved all parallel execution code to the parallel directory
- Now installed as separate package `psequence`
- New setup.py file and makefile specified in parallel folder
- Minimum sequence requirement 0.5.1
- Parallel scripts are temporarily broken, will need to be rewritten for new structure

Removed
- Removed `mpi4py` and `pytest-mpi` requirements for main package