Merge branch 'qutip:master' into bath_pr_refactor2

gsuarezr · Jan 7, 2025 · 64346e0 · 64346e0
2 parents 24459fe + 56b81d6
commit 64346e0
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -105,10 +105,11 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        # between 13 and 14, mac changed from intel chip to apple silicon
+        os: [ubuntu-latest, windows-latest, macos-13, macos-latest]
     env:
-      # Set up wheels matrix.  This is CPython 3.10--3.12 for all OS targets.
-      CIBW_BUILD: "cp3{10,11,12}-*"
+      # Set up wheels matrix.  This is CPython 3.10--3.13 for all OS targets.
+      CIBW_BUILD: "cp3{10,11,12,13}-*"
       # Numpy and SciPy do not supply wheels for i686 or win32 for
       # Python 3.10+, so we skip those:
       CIBW_SKIP: "*-musllinux* *-manylinux_i686 *-win32"
@@ -126,8 +127,8 @@ jobs:
       - name: Install cibuildwheel
         run: |
           # cibuildwheel does the heavy lifting for us. Tested on
-          # 2.19, but should be fine at least up to any minor new release.
-          python -m pip install 'cibuildwheel==2.19.*'
+          # 2.22, but should be fine at least up to any minor new release.
+          python -m pip install 'cibuildwheel==2.22.*'
 
       - name: Build wheels
         shell: bash
@@ -163,7 +164,7 @@ jobs:
       - name: Check wheels
         run: |
           ls -R wheels
-          if ! [[ $(ls wheels/*.whl | wc -l) == 9 ]]; then exit 1; fi
+          if ! [[ $(ls wheels/*.whl | wc -l) == 16 ]]; then exit 1; fi
           if ! ls wheels/*.tar.gz 1> /dev/null 2>&1; then exit 1; fi
           if ! ls wheels/*.zip 1> /dev/null 2>&1; then exit 1; fi
 

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -87,17 +87,15 @@ jobs:
           # Mac
           # Mac has issues with MKL since september 2022.
           - case-name: macos
-            # setup-miniconda not compatible with macos-latest presently.
-            # https://github.com/conda-incubator/setup-miniconda/issues/344
-            os: macos-12
+            os: macos-latest
             python-version: "3.12"
             numpy-build: ">=2.0.0"
             numpy-requirement: ">=2.0.0"
             condaforge: 1
             nomkl: 1
 
           - case-name: macos - numpy fallback
-            os: macos-12
+            os: macos-13  # Test on intel cpus
             python-version: "3.11"
             numpy-build: ">=2.0.0"
             numpy-requirement: ">=1.25,<1.26"
@@ -120,6 +118,7 @@ jobs:
             oldcython: 1
             nocython: 1
             condaforge: 1
+            nomkl: 1
             pytest-extra-options: "-W ignore:dep_util:DeprecationWarning -W \"ignore:The 'renderer' parameter of do_3d_projection\""
 
     steps:
@@ -144,6 +143,7 @@ jobs:
           python -m pip install loky tqdm mpmath  # extras
           python -m pip install "coverage${{ matrix.coverage-requirement }}" chardet
           python -m pip install pytest-cov coveralls pytest-fail-slow
+          python -m pip install setuptools
 
           if [[ "${{ matrix.pypi }}" ]]; then
             pip install "numpy${{ matrix.numpy-build }}"

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-5.1.0.dev
+5.2.0.dev
diff --git a/doc/apidoc/apidoc.rst b/doc/apidoc/apidoc.rst
@@ -13,6 +13,7 @@ complete list of QuTiP's public classes and functions.
    quantumobject.rst
    time_dep.rst
    solver.rst
+   environments.rst
    heom.rst
    piqs.rst
    visualization.rst

diff --git a/doc/apidoc/environments.rst b/doc/apidoc/environments.rst
@@ -0,0 +1,52 @@
+************
+Environments
+************
+
+Bosonic Environments
+--------------------
+
+.. autoclass:: qutip.core.BosonicEnvironment
+    :members:
+
+.. autoclass:: qutip.core.DrudeLorentzEnvironment
+    :members:
+    :inherited-members:
+    :show-inheritance:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.UnderDampedEnvironment
+    :members:
+    :inherited-members:
+    :show-inheritance:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.OhmicEnvironment
+    :members:
+    :inherited-members:
+    :show-inheritance:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.CFExponent
+    :members:
+
+.. autoclass:: qutip.core.ExponentialBosonicEnvironment
+    :members:
+    :show-inheritance:
+
+.. autofunction:: qutip.core.environment.system_terminator
+
+
+Fermionic Environments
+----------------------
+
+.. autoclass:: qutip.core.FermionicEnvironment
+    :members:
+    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
+
+.. autoclass:: qutip.core.LorentzianEnvironment
+    :members:
+    :show-inheritance:
+
+.. autoclass:: qutip.core.ExponentialFermionicEnvironment
+    :members:
+    :show-inheritance:
diff --git a/doc/apidoc/heom.rst b/doc/apidoc/heom.rst
@@ -1,58 +1,3 @@
-************
-Environments
-************
-
-Bosonic Environments
---------------------
-
-.. autoclass:: qutip.core.BosonicEnvironment
-    :members:
-
-.. autoclass:: qutip.core.DrudeLorentzEnvironment
-    :members:
-    :inherited-members:
-    :show-inheritance:
-    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
-
-.. autoclass:: qutip.core.UnderDampedEnvironment
-    :members:
-    :inherited-members:
-    :show-inheritance:
-    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
-
-.. autoclass:: qutip.core.OhmicEnvironment
-    :members:
-    :inherited-members:
-    :show-inheritance:
-    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
-
-.. autoclass:: qutip.core.CFExponent
-    :members:
-
-.. autoclass:: qutip.core.ExponentialBosonicEnvironment
-    :members:
-    :show-inheritance:
-
-.. autofunction:: qutip.core.environment.system_terminator
-
-
-Fermionic Environments
-----------------------
-
-.. autoclass:: qutip.core.FermionicEnvironment
-    :members:
-    :exclude-members: from_correlation_function, from_power_spectrum, from_spectral_density
-
-.. autoclass:: qutip.core.LorentzianEnvironment
-    :members:
-    :show-inheritance:
-
-.. autoclass:: qutip.core.ExponentialFermionicEnvironment
-    :members:
-    :show-inheritance:
-
-
-
 ********************************
 Hierarchical Equations of Motion
 ********************************

diff --git a/doc/changelog.rst b/doc/changelog.rst
@@ -6,6 +6,79 @@ Change Log
 
 .. towncrier release notes start
 
+QuTiP 5.1.0 (2024-12-12)
+========================
+
+Features
+--------
+
+- It adds odd parity support to HEOM's fermionic solver (#2261, by Gerardo Jose Suarez)
+- Create `SMESolver.run_from_experiment`, which allows to run stochastic evolution from know noise or measurements. (#2318)
+- Add types hints. (#2327, #2473)
+- Weighted trajectories in trajectory solvers (enables improved sampling for nm_mcsolve) (#2369, by Paul Menczel)
+- Updated `qutip.core.metrics.dnorm` to have an efficient speedup when finding the difference of two unitaries. We use a result on page 18 of
+  D. Aharonov, A. Kitaev, and N. Nisan, (1998). (#2416, by owenagnel)
+- Allow mixed initial conditions for mcsolve and nm_mcsolve. (#2437, by Paul Menczel)
+- Add support for `jit` and `grad` in qutip.core.metrics (#2461, by Rochisha Agarwal)
+- Allow merging results from stochastic solvers. (#2474)
+- Support measurement statistics for `jax` and `jaxdia` dtypes (#2493, by Rochisha Agarwal)
+- Enable mcsolve with jax.grad using numpy_backend (#2499, by Rochisha Agarwal)
+- Add propagator method to steadystate (#2508)
+- Introduces the qutip.core.environment module, which contains classes that characterize bosonic and fermionic thermal environments. (#2534, by Gerardo Jose Suarez)
+- Implements a `einsum` function for Qobj dimensions (Evaluates the Einstein summation convention on the operands.) (#2545, by Franco Mayo)
+- Wave function calculations have been sped up with a Cython implementation.
+  It optimizes the update method of the HarmonicOscillatorWaveFunction class in distribution.py. (#2553, by Matheus Gomes Cordeiro)
+- Speed up `kraus_to_super` by adding a `sparse` option. (#2569, by Sola85)
+
+
+Bug Fixes
+---------
+
+- Fix a dimension problem for the argument color of Bloch.add_states
+  Clean-up of the code in  Bloch.add_state
+  Add Bloch.add_arc and Bloch.add_line in the guide on Bloch class (#2445, by PositroniumJS)
+- Fix HTMLProgressBar display (#2475)
+- Make expm, cosm, sinm work with jax. (#2484, by Rochisha Agarwal)
+- Fix stochastic solver step method (#2491)
+- `clip` gives deprecation warning, that might be a problem in the future. Hence switch to `where` (#2507, by Rochisha Agarwal)
+- Fix brmesolve detection of contant vs time-dependent system. (#2530)
+- `propagator` now accepts list format `c_ops` like `mesolve` does. (#2532)
+- Fix compatibility issue with matplotlib>=3.9 in matrix_histogram (#2544, by Andreas Maeder)
+- Resolve incompatibility of TwoModeQuadratureCorrelation class (#2548, by quantum-menace)
+- Fix sparse eigen solver issue with many degenerate eigen values. (#2586)
+- Fix getting tensor permutation for uneven super operators. (#2561)
+
+
+Documentation
+-------------
+
+- Improve guide-settings page. (#2403)
+- Tidy up formatting of type aliases in the api documentation (#2436, by Paul Menczel)
+- Update documentation
+  - Update contributors
+  - Improve apidoc readability (#2523)
+- Fix error in simdiag docstring (#2585, by Sola85)
+
+
+Miscellaneous
+-------------
+
+- Add auto_real_casting options. (#2329)
+- Add dispatcher for sqrtm (#2453, by Rochisha Agarwal)
+- Make `e_ops`, `args` and `options` keyword only.
+  Solver were inconsistent with `e_ops` usually following `c_ops` but sometime
+  preceding it. Setting it as keyword only remove the need to memorize the
+  signature of each solver. (#2489)
+- Introduces a new `NumpyBackend `class that enables dynamic selection of the numpy_backend used in `qutip`.
+  The class facilitates switching between different numpy implementations ( `numpy` and `jax.numpy` mainly ) based on the configuration specified in `settings.core`. (#2490, by Rochisha Agarwal)
+- Improve mkl lookup function. (#2497)
+- Deterministic trajectories are not counted in ``ntraj``. (#2502)
+- Allow tests to be executed multiple times in one Python session (#2538, by Zhang Maiyun)
+- Improve performance of qutip.Qobj by using static numpy version check (#2557, by Pieter Eendebak)
+- Fix towncrier check (#2542)
+
+
+
 QuTiP 5.0.4 (2024-08-30)
 ========================
 

diff --git a/doc/changes/2261.feature b/doc/changes/2261.feature
diff --git a/doc/changes/2318.feature b/doc/changes/2318.feature
diff --git a/doc/changes/2327.feature b/doc/changes/2327.feature
diff --git a/doc/changes/2329.misc b/doc/changes/2329.misc
diff --git a/doc/changes/2369.feature b/doc/changes/2369.feature
diff --git a/doc/changes/2403.doc b/doc/changes/2403.doc
diff --git a/doc/changes/2416.feature b/doc/changes/2416.feature
diff --git a/doc/changes/2436.doc b/doc/changes/2436.doc
diff --git a/doc/changes/2437.feature b/doc/changes/2437.feature
diff --git a/doc/changes/2445.bugfix b/doc/changes/2445.bugfix
diff --git a/doc/changes/2453.feature b/doc/changes/2453.feature
diff --git a/doc/changes/2461.feature b/doc/changes/2461.feature
diff --git a/doc/changes/2473.misc b/doc/changes/2473.misc
diff --git a/doc/changes/2474.feature b/doc/changes/2474.feature
diff --git a/doc/changes/2484.bugfix b/doc/changes/2484.bugfix
diff --git a/doc/changes/2489.misc b/doc/changes/2489.misc
diff --git a/doc/changes/2490.feature b/doc/changes/2490.feature
diff --git a/doc/changes/2491.bugfix b/doc/changes/2491.bugfix
diff --git a/doc/changes/2493.feature b/doc/changes/2493.feature
diff --git a/doc/changes/2497.misc b/doc/changes/2497.misc
diff --git a/doc/changes/2499.feature b/doc/changes/2499.feature
diff --git a/doc/changes/2502.feature b/doc/changes/2502.feature
diff --git a/doc/changes/2507.bugfix b/doc/changes/2507.bugfix
diff --git a/doc/changes/2508.feature b/doc/changes/2508.feature
diff --git a/doc/changes/2523.misc b/doc/changes/2523.misc
diff --git a/doc/changes/2530.bugfix b/doc/changes/2530.bugfix
diff --git a/doc/changes/2532.bugfix b/doc/changes/2532.bugfix
diff --git a/doc/changes/2534.feature b/doc/changes/2534.feature
diff --git a/doc/changes/2538.misc b/doc/changes/2538.misc
diff --git a/doc/changes/2542.bugfix b/doc/changes/2542.bugfix
diff --git a/doc/changes/2544.bugfix b/doc/changes/2544.bugfix
diff --git a/doc/changes/2548.bugfix b/doc/changes/2548.bugfix