Merge branch 'qutip:master' into bosonic_fitting

doc/changelog.rst

@@ -6,6 +6,47 @@ Change Log
 
 .. towncrier release notes start
 
+QuTiP 5.0.0b1 (2024-03-04)
+==========================
+
+Features
+--------
+
+- Create a Dimension class (#1996)
+- Add arguments of plot_wigner() and plot_wigner_fock_distribution() to specify parameters for wigner(). (#2057, by Kosuke Mizuno)
+- Restore feedback to solvers (#2210)
+- Added mpi_pmap, which uses the mpi4py module to run computations in parallel through the MPI interface. (#2296, by Paul)
+- Only pre-compute density matrices if keep_runs_results is False (#2303, by Matt Ord)
+
+
+Bug Fixes
+---------
+
+- Add the possibility to customize point colors as in V4 and fix point plot behavior for 'l' style (#1974, by Daniel Moreno Galán)
+- Disabled broken "improved sampling" for `nm_mcsolve`. (#2234, by Paul)
+- Fixed result objects storing a reference to the solver through options._feedback. (#2262, by Paul)
+- Fixed simdiag not returning orthonormal eigenvectors. (#2269, by Sola85)
+- Fix LaTeX display of Qobj state in Jupyter cell outputs (#2272, by Edward Thomas)
+- Improved behavior of `parallel_map` and `loky_pmap` in the case of timeouts, errors or keyboard interrupts (#2280, by Paul)
+- Ignore deprecation warnings from cython 0.29.X in tests. (#2288)
+- Fixed two problems with the steady_state() solver in the HEOM method. (#2333)
+
+
+Miscellaneous
+-------------
+
+- Improve fidelity doc-string (#2257)
+- Improve documentation in guide/dynamics (#2271)
+- Improve states and operator parameters documentation. (#2289)
+- Rework `kraus_to_choi` making it faster (#2284, by Bogdan Reznychenko)
+- Remove Bloch3D: redundant to Bloch (#2306)
+- Allow tests to run without matplotlib and ipython. (#2311)
+- Add too small step warnings in fixed dt SODE solver (#2313)
+- Add `dtype` to `Qobj` and `QobjEvo` (#2325)
+- Fix typos in `expect` documentation (#2331, by gabbence95)
+- Allow measurement functions to support degenerate operators. (#2342)
+
+
 QuTiP 5.0.0a2 (2023-09-06)
 ==========================
 
@@ -435,6 +476,75 @@ Feature removals
 - The ``~/.qutip/qutiprc`` config file is no longer supported. It contained settings for the OpenMP support.
 
 
+QuTiP 4.7.5 (2024-01-29)
+========================
+
+Patch release for QuTiP 4.7. It adds support for SciPy 1.12.
+
+Bug Fixes
+---------
+
+- Remove use of scipy.<numpy-func> in parallel.py, incompatible with scipy==1.12 (#2305 by Evan McKinney)
+
+
+QuTiP 4.7.4 (2024-01-15)
+========================
+
+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)
+
+
+QuTiP 4.7.3 (2023-08-22)
+========================
+
+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)
+
+
+QuTiP 4.7.2 (2023-06-28)
+========================
+
+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)
+
+
 Version 4.7.1 (December 11, 2022)
 +++++++++++++++++++++++++++++++++
 

qutip/__init__.py

@@ -50,7 +50,7 @@
 from .partial_transpose import *
 from .continuous_variables import *
 from .distributions import *
-
+from . import measurement
 
 # utilities
 from .utilities import *

qutip/animation.py

@@ -9,6 +9,7 @@
                plot_fock_distribution, plot_wigner, plot_spin_distribution,
                plot_qubism, plot_schmidt)
 from .solver import Result
+from numpy import sqrt
 
 
 def _result_state(obj):
@@ -346,9 +347,9 @@ def anim_fock_distribution(rhos, fock_numbers=None, color="green",
     return fig, ani
 
 
-def anim_wigner(rhos, xvec=None, yvec=None, method='clenshaw',
-                projection='2d', *, cmap=None, colorbar=False,
-                fig=None, ax=None):
+def anim_wigner(rhos, xvec=None, yvec=None, method='clenshaw', projection='2d',
+                g=sqrt(2), sparse=False, parfor=False, *,
+                cmap=None, colorbar=False, fig=None, ax=None):
     """
     Animation of the Wigner function for a density matrix (or ket)
     that describes an oscillator mode.
@@ -373,6 +374,18 @@ def anim_wigner(rhos, xvec=None, yvec=None, method='clenshaw',
         Specify whether the Wigner function is to be plotted as a
         contour graph ('2d') or surface plot ('3d').
 
+    g : float
+        Scaling factor for `a = 0.5 * g * (x + iy)`, default `g = sqrt(2)`.
+        See the documentation for qutip.wigner for details.
+
+    sparse : bool {False, True}
+        Flag for sparse format.
+        See the documentation for qutip.wigner for details.
+
+    parfor : bool {False, True}
+        Flag for parallel calculation.
+        See the documentation for qutip.wigner for details.
+
     cmap : a matplotlib cmap instance, optional
         The colormap.
 
@@ -395,7 +408,8 @@ def anim_wigner(rhos, xvec=None, yvec=None, method='clenshaw',
 
     rhos = _result_state(rhos)
 
-    fig, ani = plot_wigner(rhos, xvec, yvec, method, projection,
+    fig, ani = plot_wigner(rhos, xvec, yvec, method=method, g=g, sparse=sparse,
+                           parfor=parfor, projection=projection,
                            cmap=cmap, colorbar=colorbar, fig=fig, ax=ax)
 
     return fig, ani

qutip/bloch.py

@@ -310,7 +310,7 @@ def clear(self):
         self.vector_alpha = []
         self.annotations = []
         self.vector_color = []
-        self.point_color = []
+        self.point_color = None
         self._lines = []
         self._arcs = []
 

qutip/core/cy/qobjevo.pyx

@@ -613,11 +613,11 @@ cdef class QobjEvo:
 
     def __imatmul__(QobjEvo self, other):
         if isinstance(other, (Qobj, QobjEvo)):
-            if self.dims[1] != other.dims[0]:
+            if self._dims[1] != other._dims[0]:
                 raise TypeError("incompatible dimensions" +
                                 str(self.dims[1]) + ", " +
                                 str(other.dims[0]))
-            self._dims = Dimensions([self.dims[0], other.dims[1]])
+            self._dims = Dimensions([self._dims[0], other._dims[1]])
             self.shape = (self.shape[0], other.shape[1])
             if isinstance(other, Qobj):
                 other = _ConstantElement(other)

qutip/core/data/matmul.pyx

@@ -69,8 +69,10 @@ cdef int _check_shape(Data left, Data right, Data out=None) except -1 nogil:
         )
     if (
         out is not None
-        and out.shape[0] != left.shape[0]
-        and out.shape[1] != right.shape[1]
+        and (
+            out.shape[0] != left.shape[0]
+            or out.shape[1] != right.shape[1]
+        )
     ):
         raise ValueError(
             "incompatible output shape, got "

qutip/core/dimensions.py

@@ -5,6 +5,7 @@
 # Everything should be explicitly imported, not made available by default.
 
 import numpy as np
+import numbers
 from operator import getitem
 from functools import partial
 from qutip.settings import settings
@@ -16,17 +17,28 @@
 def flatten(l):
     """Flattens a list of lists to the first level.
 
-    Given a list containing a mix of scalars and lists,
-    flattens down to a list of the scalars within the original
-    list.
+    Given a list containing a mix of scalars and lists or a dimension object,
+    flattens it down to a list of the scalars within the original list.
+
+    Parameters
+    ----------
+    l : scalar, list, Space, Dimension
+        Object to flatten.
 
     Examples
     --------
 
     >>> flatten([[[0], 1], 2]) # doctest: +SKIP
     [0, 1, 2]
 
+    Notes
+    -----
+    Any scalar will be returned wrapped in a list: ``flaten(1) == [1]``.
+    A non-list iterable will not be treated as a list by flatten. For example, flatten would treat a tuple
+    as a scalar.
     """
+    if isinstance(l, (Space, Dimensions)):
+        l = l.as_list()
     if not isinstance(l, list):
         return [l]
     else:
@@ -459,12 +471,20 @@ def dims2idx(self, dims):
         """
         Transform dimensions indices to full array indices.
         """
-        return dims
+        if not isinstance(dims, list) or len(dims) != 1:
+            raise ValueError("Dimensions must be a list of one element")
+        if not (0 <= dims[0] < self.size):
+            raise IndexError("Dimensions out of range")
+        if not isinstance(dims[0], numbers.Integral):
+            raise TypeError("Dimensions must be integers")
+        return dims[0]
 
     def idx2dims(self, idx):
         """
         Transform full array indices to dimensions indices.
         """
+        if not (0 <= idx < self.size):
+            raise IndexError("Index out of range")
         return [idx]
 
     def step(self):
@@ -503,6 +523,9 @@ def replace(self, idx, new):
     def replace_superrep(self, super_rep):
         return self
 
+    def scalar_like(self):
+        return Field()
+
 
 class Field(Space):
     field_instance = None
@@ -595,7 +618,7 @@ def dims2idx(self, dims):
         pos = 0
         step = 1
         for space, dim in zip(self.spaces[::-1], dims[::-1]):
-            pos += space.dims2idx(dim) * step
+            pos += space.dims2idx([dim]) * step
             step *= space.size
         return pos
 
@@ -644,6 +667,9 @@ def replace_superrep(self, super_rep):
             *[space.replace_superrep(super_rep) for space in self.spaces]
         )
 
+    def scalar_like(self):
+        return [space.scalar_like() for space in self.spaces]
+
 
 class SuperSpace(Space):
     _stored_dims = {}
@@ -705,6 +731,9 @@ def replace(self, idx, new):
     def replace_superrep(self, super_rep):
         return SuperSpace(self.oper, rep=super_rep)
 
+    def scalar_like(self):
+        return self.oper.scalar_like()
+
 
 class MetaDims(type):
     def __call__(cls, *args, rep=None):
@@ -920,3 +949,6 @@ def replace_superrep(self, super_rep):
             self.from_.replace_superrep(super_rep),
             self.to_.replace_superrep(super_rep)
         )
+
+    def scalar_like(self):
+        return [self.to_.scalar_like(), self.from_.scalar_like()]

qutip/core/expect.py

@@ -16,7 +16,7 @@ def expect(oper, state):
     Parameters
     ----------
     oper : qobj/array-like
-        A single or a `list` or operators for expectation value.
+        A single or a `list` of operators for expectation value.
 
     state : qobj/array-like
         A single or a `list` of quantum states or density matrices.
@@ -25,8 +25,8 @@ def expect(oper, state):
     -------
     expt : float/complex/array-like
         Expectation value.  ``real`` if ``oper`` is Hermitian, ``complex``
-        otherwise. A (nested) array of expectaction values of state or operator
-        are arrays.
+        otherwise. A (nested) array of expectaction values if ``state`` or
+        ``oper`` are arrays.
 
     Examples
     --------