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Getting ready for 0.9.13.1.
Includes the usual README and CHANGELOG updates. Also includes a copyright banner update, and updates to the out-of-date CONTRIBUTING file.
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Diff for: ‎CHANGELOG

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# CHANGELOG
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## [0.9.13.1] - 2025-03-18
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### Added
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* Wildcard support for instruments (#463, 527)
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* Parity benchmarking protocol (#532)
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* RNG seeding for BinaryRBDesign (#546, #547)
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### Fixed
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* Germ selection with ComposedOp (#481)
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* Basis cast in report error generator projection (#455)
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* Germ selection circuit line labels (#507, #540)
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* NumPy 2.2 deprecation fix (#514)
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* Various unit test fixes (#519, #530)
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* Plotly 0.6 API changes in reports (#533)
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* DataSet outcome label misordering with add_count_list (#535, #536)
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* Guard for fastcalc causing ImportError (#540, #541)
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* Per-germ global FPR simulator properly set (#545)
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### Changed
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* Simplify the TimeIndependentMDCObjectiveFunction class (#515)
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* Package configuration updates (#530)
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* Name from pyGSTi to pygsti for PEP 625 compliance
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* Configuration migrated mostly from setup.py to pyproject.toml
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* Python versions bumped from 3.8 - 3.11 to 3.9 - 3.12
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* setuptools_scm updates more verbose version names for local/editable installs
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## [0.9.13] - 2025-01-16
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### Added

Diff for: ‎CONTRIBUTING.md

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projects like ours couldn't exist without contributors like you.
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This document contains a set of guidelines for contributing to pyGSTi
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and related packages hosted under the [pyGSTio group][pygstio]. We ask
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and related packages hosted under the SandiaLabs organization. We ask
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that contributors make an earnest effort to follow these guidelines,
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but no one's keeping score here -- just use your best judgement, and
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by all means, feel free to propose changes to these guidelines in a
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Found a bug in pyGSTi? We'd appreciate letting us know!
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* First, **see if the bug has already been reported** by searching on
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Github under [Issues][issues].
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Github under [Issues][issues]. Make sure to check for issues that
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are closed but have the *fixed-but-not-in-release* tag also - these
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mean they are fixed in our `develop` branch, so you can try that to
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see if it fixes your issue.
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* If you can't find an open issue about the problem,
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[open a new one][issues:bug]! Be sure to include a **title**, a
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#### For non-Sandians
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Unfortunately, **we can't currently accept pull requests from
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contributors outside of SNL.** We're working on setting up a
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contributor license agreement, so, someday, this may change. If you're
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interested in making contributions please let us know by email at
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[[email protected]][email] so we can make a strong case to our lawyers for
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getting this done!
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If you're interested in making contributions please let us know by email at
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[[email protected]][email] so we can get you a Contributor License Agreement
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(CLA). This needs to be signed and through our system before you can contribute.
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#### For Sandians
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* **Contact the authors** at [[email protected]][email] to
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request an invite to the [pyGSTio group][pygstio].
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* **Join the SandiaLabs organization**.
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* **Follow the guidelines** [on the project wiki][contributing].
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* **Contact the authors** at [[email protected]][email] to
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request an invite to the [repository][pygsti].
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[contributing]: https://github.com/pyGSTio/pyGSTi/wiki/Contributing
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[email]: mailto:[email protected]
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[issues:bug]: https://github.com/pyGSTio/pyGSTi/issues/new?labels=bug&template=bug_report.md
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[issues:feature]: https://github.com/pyGSTio/pyGSTi/issues/new?labels=enhancement&template=feature_request.md
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[issues:new]: https://github.com/pyGSTio/pyGSTi/issues/new
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[issues]: https://github.com/pyGSTio/pyGSTi/issues
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[pygstio]: https://github.com/pyGSTio
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[issues:bug]: https://github.com/sandialabs/pyGSTi/issues/new?labels=bug&template=bug_report.md
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[issues:feature]: https://github.com/sandialabs/pyGSTi/issues/new?labels=enhancement&template=feature_request.md
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[issues:new]: https://github.com/sandialabs/pyGSTi/issues/new
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[issues]: https://github.com/sandialabs/pyGSTi/issues
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[pygsti]: https://github.com/sandialabs/pyGSTi

Diff for: ‎NOTICE

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Python GST Implementation (PyGSTi) v. 0.9
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Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.

Diff for: ‎README.md

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********************************************************************************
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pyGSTi 0.9.13
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pyGSTi 0.9.13.1
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********************************************************************************
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[![master build](https://img.shields.io/github/actions/workflow/status/sandialabs/pyGSTi/beta-master.yml?branch=master&label=master)](https://github.com/sandialabs/pyGSTi/actions/workflows/beta-master.yml)

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================
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Python GST Implementation (PyGSTi) v. 0.9
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Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.

Diff for: ‎pygsti/__init__.py

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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/__init__.py

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LinearOperator Set Tomography Algorithms Python Package
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/compilers.py

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Clifford circuit, CNOT circuit, and stabilizer state/measurement generation compilation routines
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/contract.py

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GST contraction algorithms
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/core.py

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Core GST algorithms
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/fiducialpairreduction.py

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Functions for reducing the number of required fiducial pairs for analysis.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/fiducialselection.py

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Functions for selecting a complete set of fiducials for a GST analysis.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/gaugeopt.py

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GST gauge optimization algorithms
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/germselection.py

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Functions for selecting a complete set of germs for a GST analysis.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/grammatrix.py

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Utility functions related to Gram matrix construction.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/grasp.py

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Functions to facilitate using GRASP.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/mirroring.py

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circuit mirroring functions.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/randomcircuit.py

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Random circuit sampling functions.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/rbfit.py

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Functions for analyzing RB data
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/robust_phase_estimation.py

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Robust Phase Estimation platform agnostic portion
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"""
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# ***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/algorithms/scoring.py

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Common functions used in scoring germ and fiducial sets.
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/baseobjs/__init__.py

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A sub-package holding utility objects
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/baseobjs/_compatibility.py

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Tools for general compatibility.
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"""
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/baseobjs/advancedoptions.py

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Utilities for defining advanced low-level parameterizations for various pyGSTi operations
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/baseobjs/basis.py

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Defines the Basis object and supporting functions
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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Diff for: ‎pygsti/baseobjs/basisconstructors.py

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Functions for creating the standard sets of matrices in the standard, Pauli, Gell-Mann, and qutrit bases
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"""
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#***************************************************************************************************
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
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# in this software.
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Diff for: ‎pygsti/baseobjs/errorgenbasis.py

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Defines the ElementaryErrorgenBasis class and supporting functionality.
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"""
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# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/baseobjs/errorgenlabel.py

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Defines the ElementaryErrorgenLabel class and supporting functionality.
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"""
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/baseobjs/errorgenspace.py

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Defines the ErrorgenSpace class and supporting functionality.
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"""
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

Diff for: ‎pygsti/baseobjs/exceptions.py

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Defines GST exception classes
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"""
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# Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
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# in this software.
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# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except

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