Merge pull request #2227 from Ericgig/qutip-5.0.0a2

Prepare v5.0.0a2

.coveragerc

@@ -3,8 +3,12 @@ source = qutip
 omit =
     # QuTiP test files
     */qutip/tests/*
+    # Tool for tests
+    */qutip/solver/sode/_noise.py
 
 [report]
 exclude_lines =
     # Skip Python wrappers which help load in C extension modules.
     __bootstrap__()
+    # Skip empty method that are never meant to be used.
+    raise NotImplementedError

.github/pull_request_template.md

@@ -5,8 +5,8 @@ Thank you for contributing to QuTiP! Please make sure you have finished the foll
 - [ ] Contributions to qutip should follow the [pep8 style](https://www.python.org/dev/peps/pep-0008/).
 You can use [pycodestyle](http://pycodestyle.pycqa.org/en/latest/index.html) to check your code automatically
 - [ ] Please add tests to cover your changes if applicable.
-- [ ] If the behavior of the code has changed or new feature has been added, please also update the documentation in the `doc` folder, and the [notebook](https://github.com/qutip/qutip-notebooks). Feel free to ask if you are not sure.
-- [ ] Include the changelog in a file named: `doc/changes/<PR number>.<type>` 'type' can be one of the following: feature, bugfix, doc, removal, misc, or deprecation (see [here](http://qutip.org/docs/latest/development/contributing.html#Changelog%20Generation) for more information).
+- [ ] If the behavior of the code has changed or new feature has been added, please also update the documentation in the `doc` folder, and the [notebook](https://github.com/qutip/qutip-tutorials). Feel free to ask if you are not sure.
+- [ ] Include the changelog in a file named: `doc/changes/<PR number>.<type>` 'type' can be one of the following: feature, bugfix, doc, removal, misc, or deprecation (see [here](http://qutip.org/docs/latest/development/contributing.html#changelog-generation) for more information).
 
 Delete this checklist after you have completed all the tasks. If you have not finished them all, you can also open a [Draft Pull Request](https://github.blog/2019-02-14-introducing-draft-pull-requests/) to let the others know this on-going work and keep this checklist in the PR description.
 

.github/workflows/tests.yml

@@ -51,6 +51,7 @@ jobs:
             numpy-requirement: ">=1.20,<1.21"
             scipy-requirement: ">=1.5,<1.6"
             condaforge: 1
+            oldcython: 1
 
           # No MKL runs.  MKL is now the default for conda installations, but
           # not necessarily for pip.
@@ -69,38 +70,24 @@ jobs:
 
           # Python 3.10 and numpy 1.22
           # Use conda-forge to provide numpy 1.22
-          # Ignore ImportWarning because pyximport registered an importer
-          # PyxImporter that does not have a find_spec method and this raises
-          # a warning on Python 3.10
-          # Ignore DeprecationWarnings raised by cvxpy importing scipy.sparse.X
-          # under SciPy 1.8.0+.
-          # Ignore DeprecationWarnings raised by versions of
-          # setuptools >= 65.0.0 during pyximport imports This can be removed
-          # once https://github.com/cython/cython/issues/4985
-          # is fixed and released.
           - case-name: Python 3.10
             os: ubuntu-latest
             python-version: "3.10"
             condaforge: 1
-            pytest-extra-options: "-W ignore::ImportWarning -W ignore::DeprecationWarning:cvxpy.interface.scipy_wrapper -W ignore:Absolute:DeprecationWarning"
+            oldcython: 1
 
           # Python 3.11 and latest numpy
           # Use conda-forge to provide Python 3.11 and latest numpy
-          # Ignore ImportWarning because pyximport registered an importer
-          # PyxImporter that does not have a find_spec method and this raises
-          # a warning on Python 3.10
-          # Ignore DeprecationWarnings raised by cvxpy importing scipy.sparse.X
-          # under SciPy 1.8.0+.
-          # Ignore DeprecationWarnings raised by versions of
-          # setuptools >= 65.0.0 during pyximport imports This can be removed
-          # once https://github.com/cython/cython/issues/4985
-          # is fixed and released.
+          # Ignore deprecation of the cgi module in Python 3.11 that is
+          # still imported by Cython.Tempita. This was addressed in
+          # https://github.com/cython/cython/pull/5128 but not backported
+          # to any currently released version.
           - case-name: Python 3.11
             os: ubuntu-latest
             python-version: "3.11"
             condaforge: 1
             conda-extra-pkgs: "suitesparse"  # for compiling cvxopt
-            pytest-extra-options: "-W ignore::ImportWarning -W ignore::DeprecationWarning:cvxpy.interface.scipy_wrapper -W ignore:Absolute:DeprecationWarning -W ignore::DeprecationWarning:Cython.Tempita"
+            pytest-extra-options: "-W ignore::DeprecationWarning:Cython.Tempita"
 
           # 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
@@ -111,7 +98,6 @@ jobs:
           - case-name: Windows Latest
             os: windows-latest
             python-version: "3.10"
-            pytest-extra-options: "-W ignore::ImportWarning -k 'not (test_correlation or test_interpolate or test_mcsolve)'"
 
     steps:
       - uses: actions/checkout@v3
@@ -131,6 +117,9 @@ jobs:
           if [[ -z "${{ matrix.nocython }}" ]]; then
             QUTIP_TARGET="$QUTIP_TARGET,runtime_compilation"
           fi
+          if [[ "${{ matrix.oldcython }}" ]]; then
+            pip install cython==0.29.36
+          fi
           export CI_QUTIP_WITH_OPENMP=${{ matrix.openmp }}
           if [[ -z "${{ matrix.nomkl }}" ]]; then
             conda install blas=*=mkl "numpy${{ matrix.numpy-requirement }}" "scipy${{ matrix.scipy-requirement }}"
@@ -220,7 +209,7 @@ jobs:
           python -m pip install towncrier
 
       - name: Verify Towncrier entry added
-        if: False # github.event_name == 'pull_request'
+        if: github.event_name == 'pull_request'
         env:
           BASE_BRANCH: ${{ github.base_ref }}
         run: |

.gitignore

@@ -29,6 +29,7 @@ rhs*.pyx
 
 qutip/cy/*.c
 *.cpp
+!qutip/core/data/src/*.cpp
 *.dat
 qutip/core/*.h
 

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+formats:
+  - pdf
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-4.10"
+
+conda:
+  environment: doc/rtd-environment.yml
+
+sphinx:
+  configuration: doc/conf.py
+  fail_on_warning: true

README.md

@@ -18,7 +18,7 @@ and [J. R. Johansson](https://github.com/jrjohansson)
 [![Build Status](https://github.com/qutip/qutip/actions/workflows/tests.yml/badge.svg?branch=master)](https://github.com/qutip/qutip/actions/workflows/tests.yml)
 [![Coverage Status](https://img.shields.io/coveralls/qutip/qutip.svg?logo=Coveralls)](https://coveralls.io/r/qutip/qutip)
 [![Maintainability](https://api.codeclimate.com/v1/badges/df502674f1dfa1f1b67a/maintainability)](https://codeclimate.com/github/qutip/qutip/maintainability)
-[![license](https://img.shields.io/badge/license-New%20BSD-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)  
+[![license](https://img.shields.io/badge/license-New%20BSD-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![PyPi Downloads](https://img.shields.io/pypi/dm/qutip?label=downloads%20%7C%20pip&logo=PyPI)](https://pypi.org/project/qutip)
 [![Conda-Forge Downloads](https://img.shields.io/conda/dn/conda-forge/qutip?label=downloads%20%7C%20conda&logo=Conda-Forge)](https://anaconda.org/conda-forge/qutip)
 
@@ -72,15 +72,31 @@ All back releases are also available for download in the [releases section of th
 For the most complete set of release notes and changelogs for historic versions, see the [changelog](https://qutip.org/docs/latest/changelog.html) section in the documentation.
 
 
+The pre-release of QuTiP 5.0 is available on PyPI and can be installed using pip:
+
+```bash
+pip install --pre qutip
+```
+
+This version breaks compatibility with QuTiP 4.7 in many small ways.
+Please see the [changelog](https://github.com/qutip/qutip/blob/master/doc/changelog.rst) for a list of changes, new features and deprecations.
+This version should be fully working. If you find any bugs, confusing documentation or missing features, please create a GitHub issue.
+
+
 Documentation
 -------------
 
+[![Documentation Status - Latest](https://readthedocs.org/projects/qutip/badge/?version=latest)](https://qutip.readthedocs.io/en/latest/?badge=latest)
+
+The documentation for the latest [stable release](https://qutip.readthedocs.io/en/latest/) and the [master](https://qutip.readthedocs.io/en/master/) branch is available for reading on Read The Docs.
+
 The documentation for official releases, in HTML and PDF formats, can be found in the [documentation section of the QuTiP website](https://qutip.org/documentation.html).
+
 The latest development documentation is available in this repository in the `doc` folder.
 
 A [selection of demonstration notebooks is available](https://qutip.org/tutorials.html), which demonstrate some of the many features of QuTiP.
-These are stored in the [qutip/qutip-notebooks repository](https://github.com/qutip/qutip-notebooks) here on GitHub.
-You can run the notebooks online using myBinder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/qutip/qutip-notebooks/master?filepath=index.ipynb)
+These are stored in the [qutip/qutip-tutorials repository](https://github.com/qutip/qutip-tutorials) here on GitHub.
+
 
 Contribute
 ----------

VERSION

@@ -1 +1 @@
-5.0.0a1
+5.0.0a2

doc/QuTiP_tree_plot/qutip-structure.py

@@ -47,7 +47,6 @@
     # States
     ("#007143", {
         "states", "continuous_variables", "qstate", "random_objects",
-        "three_level_atom",
     }),
     # QIP
     ("#36d695", {"measurement"}),