Merge branch 'qutip:master' into bosonic_fitting

.github/workflows/build.yml

@@ -57,7 +57,7 @@ jobs:
           # For the sdist we should be as conservative as possible with our
           # Python version.  This should be the lowest supported version.  This
           # means that no unsupported syntax can sneak through.
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install pip build
         run: |
@@ -107,11 +107,11 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
     env:
-      # Set up wheels matrix.  This is CPython 3.8--3.10 for all OS targets.
-      CIBW_BUILD: "cp3{8,9,10,11}-*"
+      # Set up wheels matrix.  This is CPython 3.9--3.12 for all OS targets.
+      CIBW_BUILD: "cp3{9,10,11,12}-*"
       # Numpy and SciPy do not supply wheels for i686 or win32 for
       # Python 3.10+, so we skip those:
-      CIBW_SKIP: "*-musllinux* cp3{8,9,10,11}-manylinux_i686 cp3{8,9,10,11}-win32"
+      CIBW_SKIP: "*-musllinux* cp3{10,11,12}-manylinux_i686 cp3{10,11,12}-win32"
       OVERRIDE_VERSION: ${{ github.event.inputs.override_version }}
 
     steps:
@@ -121,7 +121,7 @@ jobs:
         name: Install Python
         with:
           # This is about the build environment, not the released wheel version.
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install cibuildwheel
         run: |
@@ -165,12 +165,12 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Verify this is not a dev version
         shell: bash
         run: |
-          python -m pip install wheels/*-cp38-cp38-manylinux*.whl
+          python -m pip install wheels/*-cp39-cp39-manylinux*.whl
           python -c 'import qutip; print(qutip.__version__); assert "dev" not in qutip.__version__; assert "+" not in qutip.__version__'
 
       # We built the zipfile for convenience distributing to Windows users on
@@ -198,12 +198,12 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Verify this is not a dev version
         shell: bash
         run: |
-          python -m pip install wheels/*-cp38-cp38-manylinux*.whl
+          python -m pip install wheels/*-cp39-cp39-manylinux*.whl
           python -c 'import qutip; print(qutip.__version__); assert "dev" not in qutip.__version__; assert "+" not in qutip.__version__'
 
       # We built the zipfile for convenience distributing to Windows users on

.github/workflows/tests.yml

@@ -27,58 +27,51 @@ jobs:
         os: [ubuntu-latest]
         # Test other versions of Python in special cases to avoid exploding the
         # matrix size; make sure to test all supported versions in some form.
-        python-version: ["3.9"]
+        python-version: ["3.11"]
         case-name: [defaults]
-        numpy-requirement: [">=1.20,<1.21"]
+        numpy-requirement: [">=1.22"]
+        scipy-requirement: [">=1.8"]
         coverage-requirement: ["==6.5"]
         # Extra special cases.  In these, the new variable defined should always
         # be a truth-y value (hence 'nomkl: 1' rather than 'mkl: 0'), because
         # the lack of a variable is _always_ false-y, and the defaults lack all
         # the special cases.
         include:
-          # Mac
-          # Mac has issues with MKL since september 2022.
-          - case-name: macos
-            os: macos-latest
-            python-version: "3.10"
-            condaforge: 1
-            nomkl: 1
-
-          # Scipy 1.5
-          - case-name: old SciPy
+          # Python 3.9, Scipy 1.7, numpy 1.22
+          # On more version than suggested by SPEC 0
+          # https://scientific-python.org/specs/spec-0000/
+          # There are deprecation warnings when using cython 0.29.X
+          - case-name: Old setup
             os: ubuntu-latest
-            python-version: "3.8"
-            numpy-requirement: ">=1.20,<1.21"
-            scipy-requirement: ">=1.5,<1.6"
+            python-version: "3.9"
+            scipy-requirement: ">=1.8,<1.9"
+            numpy-requirement: ">=1.22,<1.23"
             condaforge: 1
             oldcython: 1
             pytest-extra-options: "-W ignore:dep_util:DeprecationWarning"
 
-          # No MKL runs.  MKL is now the default for conda installations, but
-          # not necessarily for pip.
-          - case-name: no MKL
-            os: ubuntu-latest
-            python-version: "3.9"
-            numpy-requirement: ">=1.20,<1.21"
-            nomkl: 1
-
-          # Builds without Cython at runtime.  This is a core feature;
-          # everything should be able to run this.
-          - case-name: no Cython
-            os: ubuntu-latest
-            python-version: "3.8"
-            nocython: 1
-
-          # Python 3.10 and numpy 1.22
-          # Use conda-forge to provide numpy 1.22
-          - case-name: Python 3.10
+          # Python 3.10, no mkl, scipy 1.9, numpy 1.23
+          # Scipy 1.9 did not support cython 3.0 yet.
+          # cython#17234
+          - case-name: no mkl
             os: ubuntu-latest
             python-version: "3.10"
+            scipy-requirement: ">=1.9,<1.10"
+            numpy-requirement: ">=1.23,<1.24"
             condaforge: 1
             oldcython: 1
+            nomkl: 1
             pytest-extra-options: "-W ignore:dep_util:DeprecationWarning"
 
-          # Python 3.11 and latest numpy
+          # Python 3.10, no cython, scipy 1.10, numpy 1.24
+          - case-name: no cython
+            os: ubuntu-latest
+            python-version: "3.10"
+            scipy-requirement: ">=1.10,<1.11"
+            numpy-requirement: ">=1.24,<1.25"
+            nocython: 1
+
+          # Python 3.11 and recent numpy
           # Use conda-forge to provide Python 3.11 and latest numpy
           # Ignore deprecation of the cgi module in Python 3.11 that is
           # still imported by Cython.Tempita. This was addressed in
@@ -88,22 +81,43 @@ jobs:
             os: ubuntu-latest
             python-version: "3.11"
             condaforge: 1
+            scipy-requirement: ">=1.11,<1.12"
+            numpy-requirement: ">=1.25,<1.26"
             conda-extra-pkgs: "suitesparse"  # for compiling cvxopt
-            pytest-extra-options: "-W ignore::DeprecationWarning:Cython.Tempita"
+
+          # Python 3.12 and latest numpy
+          # Use conda-forge to provide Python 3.11 and latest numpy
+          - case-name: Python 3.12
+            os: ubuntu-latest
+            python-version: "3.12"
+            scipy-requirement: ">=1.12,<1.13"
+            numpy-requirement: ">=1.26,<1.27"
+            condaforge: 1
+            pytest-extra-options: "-W ignore:datetime:DeprecationWarning"
+            # Install mpi4py to test mpi_pmap
+            # Should be enough to include this in one of the runs
+            includempi: 1
+
+          # Mac
+          # Mac has issues with MKL since september 2022.
+          - case-name: macos
+            os: macos-latest
+            python-version: "3.11"
+            condaforge: 1
+            nomkl: 1
 
           # Windows. Once all tests pass without special options needed, this
           # can be moved to the main os list in the test matrix. All the tests
           # that fail currently seem to do so because mcsolve uses
           # multiprocessing under the hood. Windows does not support fork()
           # well, which makes transfering objects to the child processes
           # error prone. See, e.g., https://github.com/qutip/qutip/issues/1202
-          - case-name: Windows Latest
+          - case-name: Windows
             os: windows-latest
-            python-version: "3.10"
+            python-version: "3.11"
 
     steps:
       - uses: actions/checkout@v3
-
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
@@ -115,7 +129,7 @@ jobs:
         # rather than in the GitHub Actions file directly, because bash gives us
         # a proper programming language to use.
         run: |
-          QUTIP_TARGET="tests,graphics,semidefinite,ipython"
+          QUTIP_TARGET="tests,graphics,semidefinite,ipython,extras"
           if [[ -z "${{ matrix.nocython }}" ]]; then
             QUTIP_TARGET="$QUTIP_TARGET,runtime_compilation"
           fi
@@ -135,6 +149,10 @@ jobs:
           if [[ -n "${{ matrix.conda-extra-pkgs }}" ]]; then
             conda install "${{ matrix.conda-extra-pkgs }}"
           fi
+          if [[ "${{ matrix.includempi }}" ]]; then
+            # Use openmpi because mpich causes problems. Note, environment variable names change in v5
+            conda install "openmpi<5" mpi4py
+          fi
           python -m pip install -e .[$QUTIP_TARGET]
           python -m pip install "coverage${{ matrix.coverage-requirement }}"
           python -m pip install pytest-cov coveralls pytest-fail-slow
@@ -166,6 +184,12 @@ jobs:
             # truly being executed.
             export QUTIP_NUM_PROCESSES=2
           fi
+          if [[ "${{ matrix.includempi }}" ]]; then
+            # By default, the max. number of allowed worker processes in openmpi is
+            # (number of physical cpu cores) - 1.
+            # We only have 2 physical cores, but we want to test mpi_pmap with 2 workers.
+            export OMPI_MCA_rmaps_base_oversubscribe=true
+          fi
           pytest -Werror --strict-config --strict-markers --fail-slow=300 --durations=0 --durations-min=1.0 --verbosity=1 --cov=qutip --cov-report= --color=yes ${{ matrix.pytest-extra-options }} qutip/tests
           # Above flags are:
           #  -Werror

README.md

@@ -48,7 +48,11 @@ Support
 [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org)
 
 We are proud to be affiliated with [Unitary Fund](https://unitary.fund) and [numFOCUS](https://numfocus.org).
-QuTiP development is supported by [Nori's lab](https://dml.riken.jp/) at RIKEN, by the University of Sherbrooke, and by Aberystwyth University, [among other supporting organizations](https://qutip.org/#supporting-organizations).
+
+We are grateful for [Nori's lab](https://dml.riken.jp/) at RIKEN and [Blais' lab](https://www.physique.usherbrooke.ca/blais/) at the Institut Quantique
+for providing developer positions to work on QuTiP.
+
+We also thank Google for supporting us by financing GSoC students to work on the QuTiP as well as [other supporting organizations](https://qutip.org/#supporting-organizations) that have been supporting QuTiP over the years.
 
 
 Installation

doc/QuTiP_tree_plot/qutip-structure.py

@@ -37,7 +37,7 @@
     ("#043c6b", {"settings", "configrc", "solver"}),
     # Visualisation
     ("#3f8fd2", {
-        "bloch", "bloch3d", "sphereplot", "orbital", "visualization", "wigner",
+        "bloch", "sphereplot", "orbital", "visualization", "wigner",
         "distributions", "tomography", "topology",
     }),
     # Operators

doc/apidoc/classes.rst

@@ -31,9 +31,6 @@ Bloch sphere
 .. autoclass:: qutip.bloch.Bloch
     :members:
 
-.. autoclass:: qutip.bloch3d.Bloch3d
-    :members:
-
 Distributions
 -------------
 

doc/apidoc/functions.rst

@@ -41,7 +41,7 @@ Random Operators and States
 ---------------------------
 
 .. automodule:: qutip.random_objects
-    :members: rand_dm, rand_herm, rand_ket, rand_stochastic, rand_unitary, rand_super, rand_super_bcsz
+    :members: rand_dm, rand_herm, rand_ket, rand_stochastic, rand_unitary, rand_super, rand_super_bcsz, rand_kraus_map
 
 
 Superoperators and Liouvillians
@@ -297,7 +297,7 @@ Parallelization
 ---------------
 
 .. automodule:: qutip.solver.parallel
-    :members: parallel_map, serial_map, loky_pmap
+    :members: parallel_map, serial_map, loky_pmap, mpi_pmap
 
 
 .. _functions-ipython:

doc/biblio.rst

@@ -1,5 +1,5 @@
 .. _biblo:
-    
+
 Bibliography
 ============
 
@@ -14,7 +14,7 @@ Bibliography
 
 ..  The trick with |text|_ is to get an italic link, and is described in the
     Docutils FAQ at https://docutils.sourceforge.net/FAQ.html#is-nested-inline-markup-possible.
-    
+
 .. |theory-qi| replace:: *Theory of Quantum Information*
 .. _theory-qi: https://cs.uwaterloo.ca/~watrous/TQI-notes/
 
@@ -39,10 +39,10 @@ Bibliography
 .. [WBC11]
     C. Wood, J. Biamonte, D. G. Cory, *Tensor networks and graphical calculus for
     open quantum systems*. :arxiv:`1111.6950`
-    
+
 .. [dAless08]
     D. d’Alessandro, *Introduction to Quantum Control and Dynamics*, (Chapman & Hall/CRC, 2008).
-    
+
 .. [Byrd95]
     R. H. Byrd, P. Lu, J. Nocedal, and C. Zhu, *A Limited Memory Algorithm for Bound Constrained Optimization*, SIAM J. Sci. Comput. **16**, 1190 (1995). :doi:`10.1137/0916069`
 
@@ -51,19 +51,16 @@ Bibliography
 
 .. [Lloyd14]
     S. Lloyd and S. Montangero, *Information theoretical analysis of quantum optimal control*, Phys. Rev. Lett. **113**, 010502 (2014). :doi:`10.1103/PhysRevLett.113.010502`
-    
+
 .. [Doria11]
     P. Doria, T. Calarco & S. Montangero, *Optimal Control Technique for Many-Body Quantum Dynamics*, Phys. Rev. Lett. **106**, 190501 (2011). :doi:`10.1103/PhysRevLett.106.190501`
-    
+
 .. [Caneva11]
     T. Caneva, T. Calarco, & S. Montangero, *Chopped random-basis quantum optimization*, Phys. Rev. A **84**, 022326 (2011). :doi:`10.1103/PhysRevA.84.022326`
-    
+
 .. [Rach15]
     N. Rach, M. M. Müller, T. Calarco, and S. Montangero, *Dressing the chopped-random-basis optimization: A bandwidth-limited access to the trap-free landscape*, Phys. Rev. A. **92**, 062343 (2015). :doi:`10.1103/PhysRevA.92.062343`
 
-.. [DYNAMO]
-    S. Machnes, U. Sander, S. J. Glaser, P. De Fouquieres, A. Gruslys, S. Schirmer, and T. Schulte-Herbrueggen, *Comparing, Optimising and Benchmarking Quantum Control Algorithms in a Unifying Programming Framework*, Phys. Rev. A. **84**, 022305 (2010). :arxiv:`1011.4874`
-
 .. [Wis09]
 
     Wiseman, H. M. & Milburn, G. J. *Quantum Measurement and Control*, (Cambridge University Press, 2009).
@@ -76,4 +73,4 @@ Bibliography
     B. Donvil, P. Muratore-Ginanneschi, *Quantum trajectory framework for general time-local master equations*, Nat Commun **13**, 4140 (2022). :doi:`10.1038/s41467-022-31533-8`.
 
 .. [Abd19]
-    M. Abdelhafez, D. I. Schuster, J. Koch, *Gradient-based optimal control of open quantum systems using quantumtrajectories and automatic differentiation*, Phys. Rev. A **99**, 052327 (2019). :doi:`10.1103/PhysRevA.99.052327`.
+    M. Abdelhafez, D. I. Schuster, J. Koch, *Gradient-based optimal control of open quantum systems using quantumtrajectories and automatic differentiation*, Phys. Rev. A **99**, 052327 (2019). :doi:`10.1103/PhysRevA.99.052327`.

doc/changes/1974.bugfix

@@ -0,0 +1 @@
+Add the possibility to customize point colors as in V4 and fix point plot behavior for 'l' style

doc/changes/2296.feature

@@ -0,0 +1 @@
+Added mpi_pmap, which uses the mpi4py module to run computations in parallel through the MPI interface.

doc/changes/2303.feature

@@ -0,0 +1 @@
+Only pre-compute density matricies if keep_runs_results is False

doc/changes/2306.misc

@@ -0,0 +1 @@
+Remove Bloch3D: redundant to Bloch

doc/changes/2311.misc

@@ -0,0 +1 @@
+Allow tests to run without matplotlib and ipython.

doc/changes/2313.misc

@@ -0,0 +1 @@
+Add too small step warnings in fixed dt SODE solver

doc/changes/2325.misc

@@ -0,0 +1 @@
+Add `dtype` to `Qobj` and `QobjEvo`