Pygsti

Added
* Wildcard support for instruments (463, 527)
* Parity benchmarking protocol (532)
* RNG seeding for BinaryRBDesign (546, 547)

Fixed
* Germ selection with ComposedOp (481)
* Basis cast in report error generator projection (455)
* Germ selection circuit line labels (507, 540)
* NumPy 2.2 deprecation fix (514)
* Various unit test fixes (519, 530)
* Plotly 0.6 API changes in reports (533)
* DataSet outcome label misordering with add_count_list (535, 536)
* Guard for fastcalc causing ImportError (540, 541)
* Per-germ global FPR simulator properly set (545)

Changed
* Simplify the TimeIndependentMDCObjectiveFunction class (515)
* Package configuration updates (530)
* Name from pyGSTi to pygsti for PEP 625 compliance
* Configuration migrated mostly from setup.py to pyproject.toml
* Python versions bumped from 3.8 - 3.11 to 3.9 - 3.12
* setuptools_scm updates more verbose version names for local/editable installs

Added
* PyTorch-backed forward simulation (390)
* Support for ECR gates in QASM translation (440, 457)
* Interleaved RB (296, 468)
* Pared-down Levenberg-Marquardt for nonlinear least-squares (500)
* Fisher information for quantum instruments (464, 503)
* Wildcard and Hessians for non-ExplicitOpModels (511)

Fixed
* Kraus operator decomposition with degenerate Choi matrix bugfix (423)
* NumPy improvements and fixes (430, 431, 451, 458, 470, 518)
* Model parameter desync bugfix (456, 482)
* FOGI parameter label accumulation bugfix (486, 488)
* Guarding `signal` to allow PyGSTi usage with Dask (489)
* Docstring escape and mismatch bugfixes (502, 504)
* CPTP deserialization sign flip bugfix (341, 509)
* LindbladErrorgen Hessian with dense representation bugfix (512)
* Test file updates (510)
* ProcessorSpec state space label bugfix (474, 521)

Changed
* Circuit primitive performance upgrades (445)
* Refactors for matrixtools.py and the Basis class (429, 442, 493)
* Layout and MDCStore creation performance upgrades (448)
* Major 2Q GST performance improvements (496, 517)

Deprecated
* We are deprecating the CVXOPT backend for CVXPY in favor of Clarabel (437). Although pyGSTi will not warn you if you continue to use the CVXOPT backend, this change will occur with no additional warning in a future release.

Removed
* Removed explicit dependency on CVXOPT for wildcard optimization (444)
* Removed deprecated QIBO interface (262, 490)
* Large "spring cleaning" of unused/commented out code (424, 452)

Added
* Deterministic Clifford compilation and native gate count statistics for `CliffordRBDesign` (314, 315, 443)


Fixed
* Truncation bugfix in `BenchmarkingDesign` objects with "paired" lists to `circuit_list` attribute (408, 443)
* Fixes and efficiency improvements for various linear algebra calls (432)
* `densitymx_slow` evotype hotfix (438, 439)

Added
* Updated Cirq parsing capabilities (411)
* Added ability for reports to use CircuitListDesigns and results without gauge optimizations (412, 415)
* Indicator that figure/title headings can be clicked for expanded details (416)


Fixed
* Several tutorial updates and fixes (282, 317, 421)
* Fixed fiducial selection with wrong qubit labels (396, 418)
* Casting operators to dense matrices to avoid type errors in `pygsti.tools.optools` (406, 414)
* LGST fitting with sparse dataset (420)


Changed
* Increased the speed of unit/integration tests in GitHub Actions (380, 403)

Added
* Warnings for JupyterLab incompatibility (328)
* Warning for modifying static DataSets (340)
* Keyword argument to change ForwardSim types at Protocol runtime (358)
* Flag to drop new `delay` instructions in QASM2 circuit output (377)
* Warning for non-TP gauge transformations on CPTPLND-parameterized objects (378)
* Code owner assignments (384)
* A new AffineShiftOp modelmember (386)

Fixed
* Several tutorial updates and fixes (247, 395)
* LGST fitting with various model parameterizations (366)
* Deprecated convolve import in scipy 1.12 (391, 392)

Changed
* Stricter enforcement of line labels when using "*" in circuits (373)
* Reimplementation of ProtectedArray (386)
* GitHub runner updates for faster runs on development branches (388)

Added
* Checkpointing for GST experiments (347)
* Binary randomized benchmarking (BiRB) protocol (348)
* Utility module for generating UML graphs of pyGSTi class inheritance structure (353)
* Support for non-standard POVMs and qudits in write_empty_protocol_data (370)
* Experimental support for updating model state spaces (375)

Fixed
* Numpy deprecation warnings (325)
* Updated deprecated code in the README (325)
* Finish migration of tests to pytest (344, 362)
* Bugfixes for instruments in pspecs (349)
* Remove mutable defaults (357)
* Reparameterize model member dicts with model (365, 367)
* Compute product of editable circuit (368)
* Error handling for single-parameter wildcard with no CVXPY (375)

Changed
* Enhances EmbeddingOpFactory to be used to create target-qubit-dependent operation factories (338)
* More efficient use of CVXPY when computing the diamond norm (345)
* Improved (germ-aware) global fiducial pair reduction (350)
* MPI-enabled Fisher information matrix calculation (350)
* Report compatibility with the `MapForwardSimulator` (350)
* Introduced new `ExperimentDevice` in `pygsti.extras.devices` as a replacement for (now legacy) device config files (359)
* Refactored and improved unit test performance (372)
* Removed Python 3.7 support and added Python 3.11 support (374)

Deprecated
* The `pygsti.algorithms.directx` module
* The `qibo` evotype (363)