Qutip

The is a patch for QuTiP 4.7.X to support scipy 1.12.

Bug Fixes
---------

- Remove use of scipy.<numpy-func> in parallel.py, incompatible with scipy==1.12 (2305 by Evan McKinney)

This is a bugfix release for QuTiP 4.7.X.

Bug Fixes
---------
- Adapt to deprecation from matplotlib 3.8 (2243, reported by Bogdan Reznychenko)
- Fix name of temp files for removal after use. (2251, reported by Qile Su)
- Avoid integer overflow in Qobj creation. (2252, reported by KianHwee-Lim)
- Ignore DeprecationWarning from pyximport (2287)
- Add partial support and tests for python 3.12. (2294)


Miscellaneous
-------------
- Rework `choi_to_kraus`, making it rely on an eigenstates solver that can choose `eigh` if the Choi matrix is Hermitian, as it is more numerically stable. (2276, by Bogdan Reznychenko)
- Rework `kraus_to_choi`, making it faster (2283, by Bogdan Reznychenko and Rafael Haenel)

This is a bugfix release for QuTiP 4.7.X.

**Bug Fixes**

- Non-oper qobj + scalar raise an error. (2208 reported by vikramkashyap)
- Fixed issue where extract_states did not preserve hermiticity.
Fixed issue where rand_herm did not set the private attribute _isherm to True. (2214 by AGaliciaMartinez)
- ssesolve average states to density matrices (2216 reported by BenjaminDAnjou)

**Miscellaneous**

- Exclude cython 3.0.0 from requirement (2204)
- Run in no cython mode with cython >=3.0.0 (2207)

This is a bugfix release for QuTiP 4.7.X. It adds support for numpy 1.25 and scipy 1.11.

**Bug Fixes**
- Fix setting of sso.m_ops in heterodyne smesolver and passing through of sc_ops to photocurrent solver. (2081 by Bogdan Reznychenko and Simon Cross)
- Update calls to SciPy eigvalsh and eigsh to pass the range of eigenvalues to return using `subset_by_index=`. (2081 by Simon Cross)
- Fixed bug where some matrices were wrongly found to be hermitian. (2082 by AGaliciaMartinez)

**Miscellaneous**
- Fixed typo in stochastic.py (2049, by eltociear)
- `ptrace` always return density matrix (2185, issue by udevd)
- `mesolve` can support mixed callable and `Qobj` for `e_ops` (2184 issue by balopat)

This is a bugfix release for QuTiP 4.7.X. In addition to the minor fixes listed below, the release adds builds for Python 3.11 and support for packaging 22.0.

Features
--------
- Improve qutip import times by setting logger names explicitly. (1980 by Pieter Eendebak)

Bug Fixes
---------
- Change floquet_master_equation_rates(...) to use an adaptive number of time steps scaled by the number of sidebands, kmax. (1961 by Christian Staufenbiel)
- Change fidelity(A, B) to use the reduced fidelity formula for pure states which is more numerically efficient and accurate. (1964 by Pierre Guilmin)
- Change `brmesolve` to raise an exception when ode integration is not successful. (1966 by Eric Giguère)
- Backport fix for IPython helper Bloch._repr_svg_ from dev.major. Previously the print_figure function returned bytes, but since ipython/ipython5452 (in 2014) it returns a Unicode string. This fix updates QuTiP's helper to match. (1970 by Asier Galicia)
- Fix correlation for case where only the collapse operators are time dependent. (1979 by Eric Giguère)
- Fix the hinton visualization method to plot the matrix instead of its transpose. (2011 by Pierre Guilmin)
- Fix the hinton visualization method to take into account all the matrix coefficients to set the squares scale, instead of only the diagonal coefficients. (2012 Pierre Guilmin)
- Fix parsing of package versions in setup.py to support packaging 22.0. (2037 by Simon Cross)
- Add back .qu suffix to objects saved with qsave and loaded with qload. The suffix was accidentally removed in QuTiP 4.7.0. (2038 by Simon Cross)
- Add a default max_step to processors. (2040 by Boxi Li)

Documentation
-------------
- Add towncrier for managing the changelog. (1927 by Trent Fridey)
- Update the version of numpy used to build documentation to 1.22.0. (1940 via dependabot)
- Clarify returned objects from bloch_redfield_tensor(). (1950 by Christian Staufenbiel)
- Update Floquet Markov solver docs. (1958 by Christian Staufenbiel)
- Update the roadmap and ideas to show completed work as of August 2022. (1967 by Simon Cross)

Miscellaneous
-------------
- Return TypeError instead of Exception for type error in sesolve argument. (1942 by Pieter Eendebak)
- Add towncrier draft build of changelog to CI tests. (1946 by Simon Cross)
- Add Python 3.11 to builds. (2041 by Simon Cross)
- Simplify version parsing by using packaging.version.Version. (2043 by Simon Cross)
- Update builds to use cibuildwheel 2.11, and to build with manylinux2014 on Python 3.8 and 3.9, since numpy and SciPy no longer support manylinux2010 on those versions of Python. (2047 by Simon Cross)

This release sees the addition of two new solvers -- `qutip.krylovsolve` based on the Krylov subspace approximation and `qutip.nonmarkov.heom` that reimplements the BoFiN HEOM solver.

Bloch sphere rendering gained support for drawing arcs and lines on the sphere, and for setting the transparency of rendered points and vectors, Hinton plots gained support for specifying a coloring style, and matrix histograms gained better default colors and more flexible styling options.

Other significant improvements include better scaling of the Floquet solver, support for passing `Path` objects when saving and loading files, support for passing callable functions as `e_ops` to `mesolve` and `sesolve`, and faster state number enumeration and Husimi Q functions.

Import bugfixes include some bugs affecting plotting with matplotlib 3.5 and fixing support for qutrits (and other non-qubit) quantum circuits.

The many other small improvements, bug fixes, documentation enhancements, and behind the scenese development changes are included in the list below.

QuTiP 4.7.X will be the last series of releases for QuTiP 4. Patch releases will continue for the 4.7.X series but the main development effort will move to QuTiP 5.

The many, many contributors who filed issues, submitted or reviewed pull requests, and improved the documentation for this release are listed next to their contributions below. Thank you to all of you.

Improvements

- **MAJOR** Added krylovsolve as a new solver based on krylov subspace approximation. ([1739](https://github.com/qutip/qutip/pull/1739) by Emiliano Fortes)
- **MAJOR** Imported BoFiN HEOM (https://github.com/tehruhn/bofin/) into QuTiP and replaced the HEOM solver with a compatibility wrapper around BoFiN bosonic solver. ([#1601](https://github.com/qutip/qutip/pull/1601), [#1726](https://github.com/qutip/qutip/pull/1726), and [#1724](https://github.com/qutip/qutip/pull/1724) by Simon Cross, Tarun Raheja and Neill Lambert)
- **MAJOR** Added support for plotting lines and arcs on the Bloch sphere. ([1690](https://github.com/qutip/qutip/pull/1690) by Gaurav Saxena, Asier Galicia and Simon Cross)
- Added transparency parameter to the add_point, add_vector and add_states methods in the Bloch and Bloch3d classes. ([1837](https://github.com/qutip/qutip/pull/1837) by Xavier Spronken)
- Support ``Path`` objects in ``qutip.fileio``. ([1813](https://github.com/qutip/qutip/pull/1813) by Adrià Labay)
- Improved the weighting in steadystate solver, so that the default weight matches the documented behaviour and the dense solver applies the weights in the same manner as the sparse solver. ([1275](https://github.com/qutip/qutip/pull/1275) and [#1802](https://github.com/qutip/qutip/pull/1802) by NS2 Group at LPS and Simon Cross)
- Added a ``color_style`` option to the ``hinton`` plotting function. ([1595](https://github.com/qutip/qutip/pull/1595) by Cassandra Granade)
- Improved the scaling of ``floquet_master_equation_rates`` and ``floquet_master_equation_tensor`` and fixed transposition and basis change errors in ``floquet_master_equation_tensor`` and ``floquet_markov_mesolve``. ([1248](https://github.com/qutip/qutip/pull/1248) by Camille Le Calonnec, Jake Lishman and Eric Giguère)
- Removed ``linspace_with`` and ``view_methods`` from ``qutip.utilities``. For the former it is far better to use ``numpy.linspace`` and for the later Python's in-built ``help`` function or other tools. ([1680](https://github.com/qutip/qutip/pull/1680) by Eric Giguère)
- Added support for passing callable functions as ``e_ops`` to ``mesolve`` and ``sesolve``. ([1655](https://github.com/qutip/qutip/pull/1655) by Marek Narożniak)
- Added the function ``steadystate_floquet``, which returns the "effective" steadystate of a periodic driven system. ([1660](https://github.com/qutip/qutip/pull/1660) by Alberto Mercurio)
- Improved mcsolve memory efficiency by not storing final states when they are not needed. ([1669](https://github.com/qutip/qutip/pull/1669) by Eric Giguère)
- Improved the default colors and styling of matrix_histogram and provided additional styling options. ([1573](https://github.com/qutip/qutip/pull/1573) and [#1628](https://github.com/qutip/qutip/pull/1628) by Mahdi Aslani)
- Sped up ``state_number_enumerate``, ``state_number_index``, ``state_index_number``, and added some error checking. ``enr_state_dictionaries`` now returns a list for ``idx2state``. ([1604](https://github.com/qutip/qutip/pull/1604) by Johannes Feist)
- Added new Husimi Q algorithms, improving the speed for density matrices, and giving a near order-of-magnitude improvement when calculating the Q function for many different states, using the new ``qutip.QFunc`` class, instead of the ``qutip.qfunc`` function. ([934](https://github.com/qutip/qutip/pull/934) and [#1583](https://github.com/qutip/qutip/pull/1583) by Daniel Weigand and Jake Lishman)
- Updated licence holders with regards to new governance model, and remove extraneous licensing information from source files. ([1579](https://github.com/qutip/qutip/pull/1579) by Jake Lishman)
- Removed the vendored copy of LaTeX's qcircuit package which is GPL licensed. We now rely on the package being installed by user. It is installed by default with TexLive. ([1580](https://github.com/qutip/qutip/pull/1580) by Jake Lishman)
- The signatures of rand_ket and rand_ket_haar were changed to allow N (the size of the random ket) to be determined automatically when dims are specified. ([1509](https://github.com/qutip/qutip/pull/1509) by Purva Thakre)

Bug Fixes

- Fix circuit index used when plotting circuits with non-reversed states. ([1847](https://github.com/qutip/qutip/pull/1847) by Christian Staufenbiel)
- Changed implementation of ``qutip.orbital`` to use ``scipy.special.spy_harm`` to remove bugs in angle interpretation. ([1844](https://github.com/qutip/qutip/pull/1844) by Christian Staufenbiel)
- Fixed ``QobjEvo.tidyup`` to use ``settings.auto_tidyup_atol`` when removing small elements in sparse matrices. ([1832](https://github.com/qutip/qutip/pull/1832) by Eric Giguère)
- Ensured that tidyup's default tolerance is read from settings at each call. ([1830](https://github.com/qutip/qutip/pull/1830) by Eric Giguère)
- Fixed ``scipy.sparse`` deprecation warnings raised by ``qutip.fast_csr_matrix``. ([1827](https://github.com/qutip/qutip/pull/1827) by Simon Cross)
- Fixed rendering of vectors on the Bloch sphere when using matplotlib 3.5 and above. ([1818](https://github.com/qutip/qutip/pull/1818) by Simon Cross)
- Fixed the displaying of ``Lattice1d`` instances and their unit cells. Previously calling them raised exceptions in simple cases. ([1819](https://github.com/qutip/qutip/pull/1819), [#1697](https://github.com/qutip/qutip/pull/1697) and [#1702](https://github.com/qutip/qutip/pull/1702) by Simon Cross and Saumya Biswas)
- Fixed the displaying of the title for ``hinton`` and ``matrix_histogram`` plots when a title is given. Previously the supplied title was not displayed. ([1707](https://github.com/qutip/qutip/pull/1707) by Vladimir Vargas-Calderón)
- Removed an incorrect check on the initial state dimensions in the ``QubitCircuit`` constructor. This allows, for example, the construction of qutrit circuits. ([1807](https://github.com/qutip/qutip/pull/1807) by Boxi Li)
- Fixed the checking of ``method`` and ``offset`` parameters in ``coherent`` and ``coherent_dm``. ([1469](https://github.com/qutip/qutip/pull/1469) and [#1741](https://github.com/qutip/qutip/pull/1741) by Joseph Fox-Rabinovitz and Simon Cross)
- Removed the Hamiltonian saved in the ``sesolve`` solver results. ([1689](https://github.com/qutip/qutip/pull/1689) by Eric Giguère)
- Fixed a bug in rand_herm with ``pos_def=True`` and ``density>0.5`` where the diagonal was incorrectly filled. ([1562](https://github.com/qutip/qutip/pull/1562) by Eric Giguère)

Documentation Improvements

- Added contributors image to the documentation. ([1828](https://github.com/qutip/qutip/pull/1828) by Leonard Assis)
- Fixed the Theory of Quantum Information bibliography link. ([1840](https://github.com/qutip/qutip/pull/1840) by Anto Luketina)
- Fixed minor grammar errors in the dynamics guide. ([1822](https://github.com/qutip/qutip/pull/1822) by Victor Omole)
- Fixed many small documentation typos. ([1569](https://github.com/qutip/qutip/pull/1569) by Ashish Panigrahi)
- Added Pulser to the list of libraries that use QuTiP. ([1570](https://github.com/qutip/qutip/pull/1570) by Ashish Panigrahi)
- Corrected typo in the states and operators guide. ([1567](https://github.com/qutip/qutip/pull/1567) by Laurent Ajdnik)
- Converted http links to https. ([1555](https://github.com/qutip/qutip/pull/1555) by Jake Lishamn)

Developer Changes

- Add GitHub actions test run on windows-latest. ([1853](https://github.com/qutip/qutip/pull/1853) and [#1855](https://github.com/qutip/qutip/pull/1855) by Simon Cross)
- Bumped the version of pillow used to build documentation from 9.0.0 to 9.0.1. ([1835](https://github.com/qutip/qutip/pull/1835) by dependabot)
- Migrated the ``qutip.superop_reps`` tests to pytest. ([1825](https://github.com/qutip/qutip/pull/1825) by Felipe Bivort Haiek)
- Migrated the ``qutip.steadystates`` tests to pytest. ([1679](https://github.com/qutip/qutip/pull/1679) by Eric Giguère)
- Changed the README.md CI badge to the GitHub Actions badge. ([1581](https://github.com/qutip/qutip/pull/1581) by Jake Lishman)
- Updated CodeClimate configuration to treat our Python source files as Python 3. ([1577](https://github.com/qutip/qutip/pull/1577) by Jake Lishman)
- Reduced cyclomatic complexity in ``qutip._mkl``. ([1576](https://github.com/qutip/qutip/pull/1576) by Jake Lishman)
- Fixed PEP8 warnings in ``qutip.control``, ``qutip.mcsolve``, ``qutip.random_objects``, and ``qutip.stochastic``. ([1575](https://github.com/qutip/qutip/pull/1575) by Jake Lishman)
- Bumped the version of urllib3 used to build documentation from 1.26.4 to 1.26.5. ([1563](https://github.com/qutip/qutip/pull/1563) by dependabot)
- Moved tests to GitHub Actions. ([1551](https://github.com/qutip/qutip/pull/1551) by Jake Lishman)
- The GitHub contributing guidelines were re-added and updated to point to the more complete guidelines in the documentation. ([1549](https://github.com/qutip/qutip/pull/1549) by Jake Lishman)
- The release documentation was reworked after the initial 4.6.1 to match the actual release process. ([1544](https://github.com/qutip/qutip/pull/1544) by Jake Lishman)