Pygsti

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)

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