Pygsti

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)

Fixed

- Fixed FAQ hyperlinks (304)
- Removed deprecated functions for NumPy 1.25+ (335)
- Fixed pickling of TPPOVM objects (336)
- Updated the ReadTheDocs builds (331)
- Fixed dataset pickling (326)
- Removed deprecated functions for notebook 7+ (337)

Changed

- Slight performance improvements for GST fitting (305)

Fixed

- Guarded an optional markupsafe import for report generation

Added

- WeakForwardSimulator class and Kraus operator representation to facilitate weak simulation via "unraveling" (255)
- Experimental forward simulator interface with the qibo<=0.1.7 package (257)
- Support for single-parameter wildcard models and serialization of wildcard models (267)
- MongoDB serialization support (276, 284)
- Modelpacks for Molmer-Sorenson gates (281)
- Utility functions for mapping qubit labels and padding ExperimentDesigns (283, 290)
- CI integration for example and tutorial Jupyter notebooks

Fixed

- Various fixes to enable forward simulation with CHP for many qubits (241)
- Various fixes in report generation (242)
- Various circuit mirroring fixes (243)
- Various RNG seeding fixes (246, 254)
- Various fixes for fiducial selection, germ selection, and fiducial pair reduction (261, 292)
- Improved performance of entanglement fidelity calculations (263)
- Various linear algebra routine exception handling fixes (268)
- Various wildcard model fixes (279, 294)
- Various NumPy deprecations and fixes for Windows (285, 287, 288)

Changed

- Updates to first-order gauge-invariant (FOGI) model parameterizations (258)
- Moved to jinja2>=3.0 (259)
- Significant performance enhancements for fiducial selection, germ selection, and fiducial pair reduction (270, 274, 280)
- Python 3.6 support dropped and 3.10 support added
- Testing framework moved from nose to pytest

Deprecated

- Serialization functions with prefix 'load_' are deprecated for 'read_' versions for consistency

Removed

- CHPForwardSimulator has been removed in favor of WeakForwardSimulator with 'chp' evotype
- install_locally.py script has been removed