Fix RUS reject bits and add QEC flag bits (#82)

* Added files.

* Updated the README with Read the Docs info.

* Updating docs/README since adding project to pypi.

* Small fix to README.

* Small changes to install instructions.

* Added SVG PECOS icons and ProjectQ extension.

* Included initial version of Cirq wrapper. [Not fully functional...]

* Added the shorest_logicals method to the VerifyStabilizers tool.

* Updated requirements for the simulator wrappers.

* Simplified circuit_runners and took out kwargs `param` in circuit data structures so params always given when looping over circuits.

* Changed circuit_runners method run_logic to just run. `run` now will run both LogicalCircuits and QuantumCircuit. Applying errors to both.

* Added the MS (square root of XX) gate to PySparseSim. Added simulator tests. Other minor improvements.

* Took out cirq wrapper to move it to feature branch

* Initial built initial wrapper for qcgpu

* Small improvements.

* Took out circuit_runner not longer being used. Improved `Standard.` Corrected error in ProjectQ wrapper.

* deleted old circuit runner

* Wrapped most of the gates.

* Fixed F2 definition error and made minor improvements in ProjectQ wrapper. Minor improvements to Standard and SparseSim.

* Added the MS gate (Sqrt XX).

* Removed quantum_circuit_duration to put it in a separate feature branch.

* removed two unnecessary documentation pages.

* Improved installation documentation

* More doc improvements

* Added warnings that `run_circuit` and `run_logic` are being deprecated for `run`.

* Added environment yml and described its use in the documentation.

* Updated install doc and removed unnecessary _build folder.

* First pass at updating the documentation to just have the ``run`` method.

* Updated README

* Update to docs. Corrected version number to 0.2.dev

* Small modifications to simulators.

* Fixed a test.

* Simplified circuit runners.

* Simplification to circuit runner. Added new logo. Small improvement to simulators.

* added things to gitignore

* Changed README to point to the development branch documentation.

* Added MANIFEST and setup.cfg from master branch

* Edited doc index wording.

* Edited doc index wording v2.

* Small bib fix to doc

* Simplifications for std output and error circuits.

* Improved .gitignore and manifest prune

* Small improvements to doc

* Simplified/cleaned Standard, tests, and tools.

Removed `init` method from circuit_runner `Standard`. Cleaned deprecated methods from tests and tools. Small improvement to README.

* Corrected documentation on simulators.

* Fixed other pages that included the init method of Standard.

* Simplification to Standard in circuit_runners. Moved std_output to misc.

* Removed deprecated Standard methods. Updated conda yml and requirements.

* Added a Pauli propagation simulator. Improved the ProjectQ wrapper.

* Added a possible QuantumCircuit replacement (quantum_circuit_new)

* A collection of small improvements.

* Fixed errors in Pauli prop sim and made small improvement to it.

* Added `logical_sign` method to Pauli prop sim and ProjectQ wrapper.

* Simplifying the `logical_sign` method

* Improved the docstrings and typing of quantum_circuit_new.py

* Further improvements to quantum_circuit_new

* Improvements to ProjectQ wrapper and gate_dict -> bindings in sims

* Improved wrapping of ProjectQ.

* Fix error for random circuit test.

* Updated simulators. Changed random_outcome to forced_outcome.

* added simulator class typing file

* small fix

* New circuit updates

* additional circuit update

* change type name

* accumulated updates

* Dev cleanup (#1)

* Move ruff config to its own file

* Clean up README

* Pre-commit pass on all files

* Add typos pass

* Sync gitignore with GitHub's official Python.gitignore

* Add testing instructions

* Fix docs generation and copyright

* Remove redundant gitignore

* Create python-app.yml

* Also run CI on PRs to dev branch

* Fix testing command

* Install package before running tests

* Cache dependencies for faster CI processing

* Ignore PyCharm idea folder as before

* Also run CI on dev

* Revert and exclude formatting changes to gates table

* Added more to README install section

* Setting the copyrights for The PECOS developers to original 2018

* To .gitignore, added more cython extensions, + vscode + avoiding tracking C++ extern

* Replacing Quantinuum logo with svg file

* Moved custom ignores to the top of file

* fixed README typo

* Auto-generate requirements.txt using pip-tools / pip-compile

* Updating copyright dates as suggested

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaran.ryan-anderson@quantinuum.com>

* add makefile (#2)

* Add Makefile with useful commands

* Ignore DeprecationWarning: datetime.datetime.utcfromtimestamp()

* Adding [all] options

* Removing install-all from tests and docs

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaran.ryan-anderson@quantinuum.com>

* Adding rtd yaml copied from https://docs.readthedocs.io/en/stable/config-file/v2.html

* Update documentation for modern rtd

* Until refactored, measurements need to accept **params (#13)

* Update packages, cleanup ruff.toml (#14)

* Update packages, cleanup ruff.toml

* Adding backing in ANN per directory ignore

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaran.ryan-anderson@quantinuum.com>

* Fix sim (#15)

* Fix conditional eval oversight

* Cherry-picked from c4e5ed

* Dev updates (#16)

* Fixing some documentation issues found by doctest + blackdoc

* Expanding Makefile to include additional useful options

* refactor resetting environment tracking attributes in cinterp

* unit and integration test stubs

* Adding comments to makefile + modifying .venv to replace old .venv

* Tweaked Makefile to not both with __pycache__ + added comment + removing VENV_BIN since not used right now

* Assume all tests are integration tests unless proven otherwise later

* remove print statement from cinterp

* Apply suggestions from code review

Co-authored-by: Kartik Singhal <130700862+qartik@users.noreply.github.com>

* Adding docstrings to empty test __init__.py files

* Rewriting to focus on using venv only.

* Updated Makefile given PR conversation. Hopefully improves clarity

---------

Co-authored-by: Ciaran <ciaranra@gmail.com>
Co-authored-by: Kartik Singhal <130700862+qartik@users.noreply.github.com>

* Dev update (#17)

* Removing dependencies from README + using | to separate Python versions

* Makefile refactor + help + docs now uses venv

* Testing PHIR. Fixing wasmer/wasmtime pathlib issue

* Added basic PHIR wasm tests + tests-dep to Makefile

* Adding pytest.ini

* Adding tests of PHIR and Wasm

* Move error_params and machine_params to be declased only at the object level

* Making optional dep (ProjectQ) not default.

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaran.ra@gmail.com>
Co-authored-by: Ciaran Ryan-Anderson <ciaranra@gmail.com>

* Minor fix to PHIR tests + adding pytest as metadependency (#18)

* Minor fix to PHIR tests + adding pytest as metadependency

* adding optional dep mark to test

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaranra@gmail.com>

* fix: errors found in end to end testing with pytket-phir

* reviewfix: angles only needed in QOp

* reviewfix: convert RZZ to I during phir -> pypmir conversion

* Adding very simple depolarizing error model. (#24)

* changing the dev version number from 0.5.dev1 to 0.5.0.dev1 to be more specific (#25)

* Version bump to fix pypi issue.

* Bug phir if statement (#27)

* Fixed issue with yielding instructions of blocks

* bump to 0.5.0.dev3 + avoiding [] buffer yielding

* Fixing linting because my pre-commit hook was off

* add external phir dependency + remove Python 3.8 + test both required… (#19)

* add external phir dependency + remove Python 3.8 + test both required and optional dependencies

* Updating workflow to include diff OSs. Added skipping of tests based on optional dependency OS/Python version support.

* Skip wasmer tests on for Python >= 3.11

* Skipping test if Wasmer could not be imported.

* More robust method for skipping tests of Wasmer due to unsupported systems

* Add simple test of extern phir

* Requirement update to phir 0.1.6

* Included PHIR model validation and related tests

* small bump for requirements.txt

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaranra@gmail.com>

* Added support for qparallel. (#33)

* Added support for qparallel.

* Bumping to 0.5.0.dev4

* Bug out of order seq (#35)

* Fixed buggy yielding of Sequence/QParallel blocks

* Add a test of the sequence of op buffers.

* Reworked recursive iteration through blocks to be more elegant

* Marked test using state-vec sim as optional dependency

* Added Clifford Bell qparallel test and silence tz warning

* Bumping version to 0.5.0.dev5 and updating requirements

* Fixing support of PHIR's multi-assignment (#36)

* Fixing support of PHIR's multi-assignment

* bump version to 0.5.0.dev6

* Adding coder owners file

* Fixing code owners file typo

* build: add typed marker for pecos

* Initial support for barriers (skips barriers for now). (#38)

* Initial support for barriers (skips barriers for now).

* Additional barrier testing and associated fixes

* bumping version to 0.5.0.dev7

* Update requirements

* Bumping phir req (#39)

* updating requirements to phir ~= 0.3.0

* Fixes rare test error

* Bumping version to 0.5.0.dev8 and updating requirements.txt

* Broadening wasmtime req. + simplifying [all] (#42)

* Add wasmtime support for engines/cvm/wasm (#43)

* bumping to version 0.5.0.dev9 (#44)

* Update docs (#47)

* Various small updates of docs including autogen of API docs

* Small doc tweaks + fixing FT checking file issue that was detected by generating docs automatically

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaranra@gmail.com>

* Feature more simulators (#21)

* CoinToss simulator implemented.

* Replaced the old CuStateVec simulator (C API)  with a version using the Python API.

* Updated README with installation instructions for CuStateVec.

---------

Co-authored-by: PabloAndresCQ <pablo.andres-martinez@cambridgequantum.com>
Co-authored-by: Kartik Singhal <kartik.singhal@quantinuum.com>

* Cumulative development update (#54)

* Added .sim_name to QOps. Added angle info to QOp.angle

* Added code to identify Clifford gates from more general gates

* Added conversion to Clifford support for RZ , RZZ, and R1XY

* Tweaking generic machine to clear state

* Add test of operation type before running qsims.

* Adding general Instr type and list types

* Adding slr code

* Updated linting/formatting

* Moving slr down to reduce nesting

* fix slr __version__

* Creating a slr.std folder to hold common extension to core to the DSL

* Fixing std import

* Adding in duration for MOps in PyPMIR

* Modifying qargs in mops appropriately.

* Moving the old cuquantum code to cuquantum_old for now...

* Updating actions/setup-python from v4 to v5

* Adding tests of SLR and gate name resolving + some fixes due to those

* Update .pre-commit-config.yaml

Co-authored-by: Kartik Singhal <kartik.singhal@quantinuum.com>

* Apply suggestions from code review

Co-authored-by: Kartik Singhal <kartik.singhal@quantinuum.com>

* Updating pre-commit / running ruff/black

* Updating the docs using autodoc

* Changing PHIR test to only have bits set by 1 or 0 (not bool)

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaran.ryan-anderson@quantinuum.com>
Co-authored-by: Ciarán Ryan-Anderson <70174051+qciaran@users.noreply.github.com>
Co-authored-by: Kartik Singhal <kartik.singhal@quantinuum.com>

* Bumping version number to 0.5.0.dev10

* Feat hybrid noise (#60)

* Allows noise model to generate hybrid errors (classical and quantum instructions)

* Adding internal cinterp registers for error models

* removing internally generated measurements from results

* Converts conditionals into COps

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaran.ryan-anderson@quantinuum.com>

* version bump 0.5.0.dev11

* Adding specific error messaging and enforced maximum duration to WASM calls (#62)

Preventing infinite looping of WASM calls and providing additional details to users when WASM errors occur. 

---------

Co-authored-by: Ciarán Ryan-Anderson <70174051+qciaran@users.noreply.github.com>

* 64 bit signed arithmetic support (#57)

* feat: add support for negative integers to phir

* feat: add hypothesis-enabled unit tests for BinArray2

Also, clamp only for unsigned integer types

* lint: fix typos and exclude cuquantum_old

* feat: replace BinArray with BinArray2

* fix: set BinArray2's value correctly, or it can convert to ndarray

* build: bump patch version to distinguish in testing

* feat: partition data_types into signed and unsigned

also make size optional for signed integer type

* build: update to correct phir version

Co-authored-by: Ciarán Ryan-Anderson <70174051+qciaran@users.noreply.github.com>

---------

Co-authored-by: Ciarán Ryan-Anderson <70174051+qciaran@users.noreply.github.com>

* cuStateVec bugfixes and slight refactor (#64)

* Updated argument names for new API (cuStateVec 1.6.0)

* Bumped up version requirements

* Fixing a bug in CuStateVec in the implementation of the RYY gate

* Refactor of state.vector so that it returns a numpy array for easier testing and integration

* Adding some of the changes from Dominic's PR #58

* Added more bindings requested by @dlucchetti

* Bumping version number to 0.6.0.dev3 (#65)

* Adding a numpy-based basic statevector simulator for more exhaustive testing (#55)

* Adding a basic numpy statevector simulator

* Adding more exhaustive tests against BasicSV

* Adding a reset method

* [feature] Adding support for QuEST and Qulacs statevector simulators (#68)

* Added Qulacs simulator

* Added wrapper for QuEST

* Updated readme with simulator installation instructions

* Adding tests for HybridEngine on statevector simulators

* Supporting new statevector sims on HybridEngine

* Fixed a bug in CuStateVec relating to HybridEngine

* [feature] Adding support for MPS simulation (#63)

* Adding an MPS simulator

* Adding tests for MPS

* Using non-destructive measurements

* Added a reset method to MPS

* Including MPS as a qsim backend for HybridEngine

* Adding more bindings for initialisation that are needing for the tests

* Allowing users to provide parameters for the MPS simulation from HybridEngine

* Add HybridEngine tests for MPS

* Bumping version number to 0.6.0.dev4

* [Bugfixes] Solving some issues for qemulator MPS release (#73)

* Added angles vs angle parameter handling to hybrid_engine_old

* The reset methods in simulators must return self.

* If import fails, create dummy NoneType simulator

* Updated bindings of CoinToss

* Removed filter of simulation parameters, since it is not necessary

* Using a more sensible import approach in the test file

* Debug message converted to info message.

* Bump to 0.6.0.dev5

* Feat qeclib steane (#75)

* Initial dump of qeclib code + SLR updates

* Add teleportation/application of the Tdg gate to Steane code class.

* fix register naming bug (#70)

* Add qasm regression tests

* Refactor qasm generation

* Removed some test print statements

* Use `default_rus_limit` in `Steane` class (#74)

* use default_rus_limit

* Revert "use default_rus_limit"

This reverts commit c186dd9.

* set rus_limit to None by default

* Allow passing ancillas to `Steane` class (#72)

* allow ancilla recycling in Steane class

* raise error if ancilla register is too small

* add only new variables

* Revert "add only new variables"

This reverts commit a0d8e4f.

* Fixing regression qasm issues

* lint fixes

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaranra@gmail.com>
Co-authored-by: Michael A. Perlin <mika.perlin@gmail.com>

* Typo fixed in the implementation of `p` and `tdg` in `steane_class.py` (#76)

* Typo fixed

* Another typo in definition of tdg

* Fixing regression issue due to typo fix + fixing inconsistent creg use

---------

Co-authored-by: Ciaran Ryan-Anderson <ciaran.ryan-anderson@quantinuum.com>

* fix Steane.prep_tdg_plus_state (#78)

* Fixing measurement noise causing only 0 measurement

* fix RUS reject bits and add QEC flag bits

* Automatic lint fixes

* Revert "Automatic lint fixes"

This reverts commit 8f0e928.

* More Clifford gates supported in state-vector and MPS simulators (#87)

* Added informative error if gate not supported by simulator

* Added more Clifford gates

* Test for new gates

* bump v0.6.0.dev5 to v0.6.0.dev6 + update pre-commit + fix regression version issue (#88)

* typo fix

* remove changes to pauli_states.py

* remove changes to qec_3parallel.py

* remove artifact

* consolidate measurements

* make reject optional

* set default value of log: Bit | None

* self.extend --> block.extend

* qasm file fix for regression tests

* simplify redundant code

* remove redundant error message

* recognize X/Y/Z states as +X/+Y/+Z

---------

Author: perlinm

python/pecos/qeclib/steane/preps/pauli_states.py

@@ -139,7 +139,7 @@ def __init__(
             )
 
         self.extend(
-            # Rotate to the Paulli basis of choice
+            # Rotate to the Pauli basis of choice
             LogZeroRot(q, state),
         )
 
@@ -155,9 +155,9 @@ def __init__(self, q: QReg, state: str):
                 self.extend(
                     X(q),
                 )
-            case "|0>" | "+Z":
+            case "|0>" | "+Z" | "Z":
                 pass
-            case "|+>" | "+X":
+            case "|+>" | "+X" | "X":
                 self.extend(
                     H(q),
                 )
@@ -166,7 +166,7 @@ def __init__(self, q: QReg, state: str):
                     H(q),
                     Z(q),
                 )
-            case "|+i>" | "+Y":
+            case "|+i>" | "+Y" | "Y":
                 self.extend(
                     sqrt_paulis.SXdg(q),
                 )