accepted develop conflicts

Author: juangmendoza19

Diff for: .flake8-critical

@@ -16,15 +16,18 @@
 # This list may be expanded in the future
 select=E9,F63,F7,F82
 
-exclude=
+per-file-ignores=
 	# Known issues with rb tests. Currently skipped, but technically have F821 errors
-	test/unit/extras/rb/test_analysis.py
-	test/unit/extras/rb/test_group.py
-	test/unit/extras/rb/test_sample.py
-	test/unit/extras/rb/test_theory.py
-	test/unit/tools/test_internalgates.py
-	test/test_packages/extras/test_rb.py
-	# F821 error. Should nPossible be nLocal?
-	test/test_packages/drivers/nqubitconstruction.py
-	# F821 error. Likely results existed in a deleted cell
-	scripts/profiling/gaugeopt/3Q_example.py
+	test/unit/extras/rb/test_analysis.py:F821
+	test/unit/extras/rb/test_group.py:F821
+	test/unit/extras/rb/test_sample.py:F821
+	test/unit/extras/rb/test_theory.py:F821
+	test/unit/tools/test_internalgates.py:F821
+	test/test_packages/extras/test_rb.py:F821
+	# Should nPossible be nLocal?
+	test/test_packages/drivers/nqubitconstruction.py:F821
+	# Likely results existed in a deleted cell
+	scripts/profiling/gaugeopt/3Q_example.py:F821
+	# New with flake 7.2.0, should go back to these
+	pygsti/forwardsims/termforwardsim_calc_generic.py:F824
+	pygsti/baseobjs/basisconstructors.py:F824

Diff for: .github/workflows/beta-master.yml

@@ -13,8 +13,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-13, ubuntu-latest, windows-latest] # TODO: Unpin mac version when cvxopt or Python 3.8 dropped
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: [3.9, '3.10', '3.11', '3.12']
         use-cython: ['true', 'false']
     uses: ./.github/workflows/reuseable-main.yml
     name: Run pyGSTi tests

Diff for: .github/workflows/develop.yml

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest] # No Mac
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: [3.9, '3.10', '3.11', '3.12']
         use-cython: ['true', 'false']
     uses: ./.github/workflows/reuseable-main.yml
     name: Run pyGSTi tests

Diff for: .github/workflows/feature-branches.yml

@@ -18,8 +18,8 @@ jobs:
     strategy:
       # fail-fast: true is OK here
       matrix:
-        os: [ubuntu-latest, windows-latest] # No Mac
-        python-version: [3.8, '3.11'] # Only extremal Python versions
+        os: [ubuntu-latest, windows-latest]
+        python-version: [3.9, '3.12'] # Only extremal Python versions
     uses: ./.github/workflows/reuseable-main.yml
     name: Run pyGSTi tests
     with:
@@ -28,7 +28,7 @@ jobs:
       use-cython: 'true' # Only test environment with Cython
       run-unit-tests: 'true'
       run-extra-tests: 'false' # No integration tests
-      run-notebook-tests: 'false' # No notebook tests 
+      run-notebook-tests: 'false' # No notebook tests
 
 
 

Diff for: .github/workflows/reuseable-main.yml

@@ -34,14 +34,19 @@ jobs:
     runs-on: ${{ inputs.os }}
     steps:
     - uses: actions/checkout@v4
-    - name: Set up installation environment (Linux and Windows)
-      if: ${{ inputs.os != 'macos-13' }}
+    - name: Set up installation environment (Linux)
+      if: ${{ inputs.os == 'ubuntu-latest' }}
       run: |
         ./.github/ci-scripts/before_install.sh
     - name: Set up installation environment (MacOS)
-      if: ${{ inputs.os == 'macos-13' }}
+      if: ${{ inputs.os == 'macos-latest' }}
       run: |
         ./.github/ci-scripts/before_install_macos.sh
+    - name: Set up MPI (Windows)
+      if: ${{ inputs.os == 'windows-latest' }}
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: intelmpi
     - name: Set up Python ${{ inputs.python-version }}
       uses: actions/setup-python@v5
       with:

Diff for: CHANGELOG

@@ -1,5 +1,67 @@
 # CHANGELOG
 
+## [0.9.13.1] - 2025-03-18
+
+### 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
+
+## [0.9.13] - 2025-01-16
+
+### 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)
+
 ## [0.9.12.3] - 2024-06-11
 
 ### Added

Diff for: CONTRIBUTING.md

@@ -4,7 +4,7 @@ Thanks for taking the time to contribute to pyGSTi! Open-source
 projects like ours couldn't exist without contributors like you.
 
 This document contains a set of guidelines for contributing to pyGSTi
-and related packages hosted under the [pyGSTio group][pygstio]. We ask
+and related packages hosted under the SandiaLabs organization. We ask
 that contributors make an earnest effort to follow these guidelines,
 but no one's keeping score here -- just use your best judgement, and
 by all means, feel free to propose changes to these guidelines in a
@@ -15,7 +15,10 @@ pull request.
 Found a bug in pyGSTi? We'd appreciate letting us know!
 
 * First, **see if the bug has already been reported** by searching on
-  Github under [Issues][issues].
+  Github under [Issues][issues]. Make sure to check for issues that
+  are closed but have the *fixed-but-not-in-release* tag also - these
+  mean they are fixed in our `develop` branch, so you can try that to
+  see if it fixes your issue.
 
 * If you can't find an open issue about the problem,
   [open a new one][issues:bug]! Be sure to include a **title**, a
@@ -46,24 +49,20 @@ contributors working at Sandia.
 
 #### For non-Sandians
 
-Unfortunately, **we can't currently accept pull requests from
-contributors outside of SNL.** We're working on setting up a
-contributor license agreement, so, someday, this may change.  If you're
-interested in making contributions please let us know by email at
-[[email protected]][email] so we can make a strong case to our lawyers for
-getting this done!
+If you're interested in making contributions please let us know by email at
+[[email protected]][email] so we can get you a Contributor License Agreement
+(CLA). This needs to be signed and through our system before you can contribute.
 
 #### For Sandians
 
-* **Contact the authors** at [[email protected]][email] to
-  request an invite to the [pyGSTio group][pygstio].
+* **Join the SandiaLabs organization**.
 
-* **Follow the guidelines** [on the project wiki][contributing].
+* **Contact the authors** at [[email protected]][email] to
+  request an invite to the [repository][pygsti].
 
-[contributing]: https://github.com/pyGSTio/pyGSTi/wiki/Contributing
 [email]: mailto:[email protected]
-[issues:bug]: https://github.com/pyGSTio/pyGSTi/issues/new?labels=bug&template=bug_report.md
-[issues:feature]: https://github.com/pyGSTio/pyGSTi/issues/new?labels=enhancement&template=feature_request.md
-[issues:new]: https://github.com/pyGSTio/pyGSTi/issues/new
-[issues]: https://github.com/pyGSTio/pyGSTi/issues
-[pygstio]: https://github.com/pyGSTio
+[issues:bug]: https://github.com/sandialabs/pyGSTi/issues/new?labels=bug&template=bug_report.md
+[issues:feature]: https://github.com/sandialabs/pyGSTi/issues/new?labels=enhancement&template=feature_request.md
+[issues:new]: https://github.com/sandialabs/pyGSTi/issues/new
+[issues]: https://github.com/sandialabs/pyGSTi/issues
+[pygsti]: https://github.com/sandialabs/pyGSTi

Diff for: MANIFEST.in

@@ -1,5 +1,5 @@
 include README.md CONTRIBUTING.md LICENSE
-include pyproject.toml pyproject.toml.no_cython
+include pyproject.toml
 include install_locally.py
 include requirements.txt
 include optional-requirements.txt

Diff for: NOTICE

@@ -1,4 +1,4 @@
 Python GST Implementation (PyGSTi) v. 0.9
-Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 
 Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.

Diff for: README.md

@@ -1,5 +1,5 @@
 ********************************************************************************
-  pyGSTi 0.9.12.1
+  pyGSTi 0.9.13.1
 ********************************************************************************
 
 ![master build](https://github.com/pyGSTio/pyGSTi/workflows/Build%20and%20run%20tests/badge.svg?branch=master)
@@ -37,7 +37,7 @@ In particular, there are a number of characterization protocols currently implem
 
 PyGSTi is designed with a modular structure so as to be highly customizable
 and easily integrated to new or existing python software.  It runs using
-python 3.8 or higher.  To faclilitate integration with software for running
+python 3.9 or higher.  To faclilitate integration with software for running
 cloud-QIP experiments, pyGSTi `Circuit` objects can be converted to IBM's
 **OpenQASM** and Rigetti Quantum Computing's **Quil** circuit description languages.
 

Diff for: doc/NOTICE.rst

@@ -3,6 +3,6 @@ Copyright Notice
 ================
 
 Python GST Implementation (PyGSTi) v. 0.9
-Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
+Copyright 2015, 2019, 2025 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
 
 Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.