Benchq

**🚨 Breaking changes**

- Renamed variables and attributes to make units consistent and explicit.
- Moved and renamed several submodules to make package organization more clear.
- ChemistryApplicationInstance has been refactored and renamed to MolecularHamiltonianGenerator.
- AutoCCZ and Litinski factories now both represented by the MagicStateFactory class to make it easier to swap them.
- Removed unused Taylorization LCU code.

**🔥 Features**

- Eliminated many warnings and updated tests to treat warnings as errors.
- Number of factories exposed as optional parameter for footprint analysis.
- Added breakdown of physical qubits into distillation vs computation for footprint analysis.
- Updated automatic resource estimator to take advantage of recent improvements to graph state compilation.

**🐛 Fixes**

- Litinski factory iterators use the physical error rate rather than architecture model type.
- Fixed bug in the number of logical qubits assumed for decoder estimates.
- Updated description of dependencies and examples in README.
- Fixed minor typing issues and added pyright as a automated check for some files.

What's Changed
* Include examples for utility-scale estimates
* Add 3 new hamiltonians given by LANL application instances
* Fix the bottleneck of truncating space with FNO
* Increasing maximum data qubit code distance
* user accessible mlflow for scf tooling
* ability to optimize ruby slippers hyperparams
* remove isolated nodes before costing
* Convex Optimization to determine phases in QSP algorithm
* Implement Preparation of |COEF_int>
* Construct time marching circuit using the USVA
* Returning DF block encoding one-norm
* Added DetailedIonTrapHardwareModel
* Banish juliapkg
* Remove Python 3.11 upper bound and bump orquestra-* packages
* Update docstring for QuantumProgram and add various type hints


**Full Changelog**: https://github.com/zapatacomputing/benchq/compare/v0.5.0...v0.6.0

Features
* Installs stim by default
* Allows costing out double factorized Hamiltonians
* Implement performance testing on each PR merge
* Implement home grown footprint analysis
* New tools for linear differential equations: Invert block encodings and compression gadget
* Report proportion of quantum volume used for routing in ResourceInfo
* Faster GSC with new Ruby Sippers Compiler

**Full Changelog**: https://github.com/zapatacomputing/benchq/compare/v0.4.0...v0.5.0

What's Changed
* test: Add tests for graph compilation resource estimation by max-radin in https://github.com/zapatacomputing/benchq/pull/13
* Changing hydrogen chain multiplicity and openfermion dependency by max-radin in https://github.com/zapatacomputing/benchq/pull/14
* Update pyLIQTR dependency by mstechly in https://github.com/zapatacomputing/benchq/pull/15
* Fix: Fix advanced example by SebastianMorawiec in https://github.com/zapatacomputing/benchq/pull/17
* Make PySCF optional by max-radin in https://github.com/zapatacomputing/benchq/pull/18
* Support AVAS in Hamiltonian generation by max-radin in https://github.com/zapatacomputing/benchq/pull/16
* Add option to pass rotations through Jabalizer. by mstechly in https://github.com/zapatacomputing/benchq/pull/20
* Feat: Remove deps on Pyquil due to conflicting deps with ray by SebastianMorawiec in https://github.com/zapatacomputing/benchq/pull/19
* Removed using deprecated methods from pyLIQTR. by mstechly in https://github.com/zapatacomputing/benchq/pull/21
* Changes to allow directly calling Jabalizer from Python by ScottPJones in https://github.com/zapatacomputing/benchq/pull/23
* feat: Implement graph sim by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/26
* Feat: Examples on how to use MS estimates on QE clusters by SebastianMorawiec in https://github.com/zapatacomputing/benchq/pull/27
* Dta2 119/Refactor estimation pipeline by dexter2206 in https://github.com/zapatacomputing/benchq/pull/25
* Create adjacency list and return with icm output by ScottPJones in https://github.com/zapatacomputing/benchq/pull/28
* feat: write graph-sim in julia by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/29
* Refactor transformers by dexter2206 in https://github.com/zapatacomputing/benchq/pull/30
* Add the feature of reducing the virtual space with frozen natural orbitals (FNOs). by mkodrycka in https://github.com/zapatacomputing/benchq/pull/22
* Replace graph compilation modules and update examples. by mstechly in https://github.com/zapatacomputing/benchq/pull/31
* Add DecoderModel class. by mstechly in https://github.com/zapatacomputing/benchq/pull/32
* Dta2 122/decoders update by mstechly in https://github.com/zapatacomputing/benchq/pull/35
* Change naming of some methods/variables in GraphResourceEstimator by dexter2206 in https://github.com/zapatacomputing/benchq/pull/36
* Dta2 98 fix how circuit gate synthesis accuracy is used by akataba in https://github.com/zapatacomputing/benchq/pull/33
* Adjustments after call with Simon by dexter2206 in https://github.com/zapatacomputing/benchq/pull/37
* Benchmarks for get_qsp_time_evolution_program by dexter2206 in https://github.com/zapatacomputing/benchq/pull/38
* Add extrapolation pipeline by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/39
* Dta 128/azure update by mstechly in https://github.com/zapatacomputing/benchq/pull/40
* Update CODEOWNERS by max-radin in https://github.com/zapatacomputing/benchq/pull/44
* Add SCF options to the ChemistryApplicationInstance class by mkodrycka in https://github.com/zapatacomputing/benchq/pull/41
* Update README.md by mstechly in https://github.com/zapatacomputing/benchq/pull/46
* Dta2 124 by mstechly in https://github.com/zapatacomputing/benchq/pull/47
* Improve performance of get qsp program by dexter2206 in https://github.com/zapatacomputing/benchq/pull/48
* Update examples by mstechly in https://github.com/zapatacomputing/benchq/pull/49
* Fix incorrectly recognizing some XPowGates as Identities by dexter2206 in https://github.com/zapatacomputing/benchq/pull/50
* Kj/fix benchmarks by dexter2206 in https://github.com/zapatacomputing/benchq/pull/56
* adding my lcu project files by ZPBQuantum in https://github.com/zapatacomputing/benchq/pull/8
* Dta2 145/example workflows by mstechly in https://github.com/zapatacomputing/benchq/pull/57
* Enforcing SCF convergence by max-radin in https://github.com/zapatacomputing/benchq/pull/45
* OpenFermion estimates without AVAS by max-radin in https://github.com/zapatacomputing/benchq/pull/59
* Loosen pyscf version constraint by max-radin in https://github.com/zapatacomputing/benchq/pull/60
* Update CODEOWNERS by mstechly in https://github.com/zapatacomputing/benchq/pull/51
* Expose rank as parameter by max-radin in https://github.com/zapatacomputing/benchq/pull/62
* DTA-2 132/Adjust expected results for commented out test cases by dexter2206 in https://github.com/zapatacomputing/benchq/pull/64
* OpenFermion estimates using ERI by max-radin in https://github.com/zapatacomputing/benchq/pull/63
* fix: extrapolation pipeline by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/61
* Added the script for generating QAOA circuits for QUBO instances by Guoming-Wang in https://github.com/zapatacomputing/benchq/pull/43
* fixup! adding my lcu project files (8) by mstechly in https://github.com/zapatacomputing/benchq/pull/58
* Fix: Fix orquestra example after recent changes by SebastianMorawiec in https://github.com/zapatacomputing/benchq/pull/65
* Removing automatic resource estimator from top level package by max-radin in https://github.com/zapatacomputing/benchq/pull/66
* Clean up ResourceInfo class by dexter2206 in https://github.com/zapatacomputing/benchq/pull/69
* fix: small data path error by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/72
* Adding openfermion resource info by max-radin in https://github.com/zapatacomputing/benchq/pull/70
* fix(architecture_model): variable names by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/68
* feat: add estimators by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/67
* Implement proportional distribution of synthesis failure tolerance by dexter2206 in https://github.com/zapatacomputing/benchq/pull/71
* fix: implement qubit remapping so it takes into account all circuits at once by dexter2206 in https://github.com/zapatacomputing/benchq/pull/75
* Implement Athena's ideas for reduced number of gate operations as well as optimize structures & performance by ScottPJones in https://github.com/zapatacomputing/benchq/pull/73
* chore: unpin sdk version by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/76
* Update benchmarks by dexter2206 in https://github.com/zapatacomputing/benchq/pull/80
* feat: small performance improvement by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/79
* feat: new decoder model by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/74
* fix(graph_estimator.py): underestimating logical cell failure rate by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/82
* chore: bump orquestra quantum version by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/84
* fix(test_graph_sim_mini): ensure tableaus do not repeat stabilizers by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/85
* Implement select_v decomposition by dexter2206 in https://github.com/zapatacomputing/benchq/pull/81
* Fix toy problem by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/83
* Implement new example workflow without pipelines by dexter2206 in https://github.com/zapatacomputing/benchq/pull/86
* Low-depth GSEE utilities by max-radin in https://github.com/zapatacomputing/benchq/pull/88
* Make BasicArchitectureModel a dataclass by dexter2206 in https://github.com/zapatacomputing/benchq/pull/87
* feat: turn DecoderModel into a dataclass by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/89
* Add reset gate by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/91
* Refactor HW models, widgets and how they are used in GraphEstimator by dexter2206 in https://github.com/zapatacomputing/benchq/pull/90
* Feat: Enable graph data reuse in workflows by SebastianMorawiec in https://github.com/zapatacomputing/benchq/pull/93
* ZQS-1334: Add COEF_k and PREP by olgOk in https://github.com/zapatacomputing/benchq/pull/94
* feat: add ability to log benchq params to mlflow by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/95
* Double-factorized QPE by max-radin in https://github.com/zapatacomputing/benchq/pull/96
* feat: add offset block encoding by AthenaCaesura in https://github.com/zapatacomputing/benchq/pull/98
* Dta2 206 enable user to input surface code cycle time by bdas4018 in https://github.com/zapatacomputing/benchq/pull/101
* fix(docs): example 5 by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/104
* docs: add new mlflow demo by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/102
* test: increase min coverage to 75 by 1ethanhansen in https://github.com/zapatacomputing/benchq/pull/99
* Feat: Workflow to release benchq to PyPi by SebastianMorawiec in https://github.com/zapatacomputing/benchq/pull/107

**Full Changelog**: https://github.com/zapatacomputing/benchq/compare/v0.3.0...v0.4.0

- Updated resource estimation techniques
- Added Orquestra example
- Updated other examples
- bugfixes

**Full Changelog**: https://github.com/zapatacomputing/benchq/commits/v0.2.0