Merge branch 'dev.major' into feature/intidx-64-compilation-option

.codeclimate.yml

@@ -1,4 +1,8 @@
 version: "2"
+exclude_patterns:
+- "doc/"
+- "dist/"
+- "**/tests/"
 checks:
   argument-count:
     config:
@@ -34,3 +38,9 @@ plugins:
     enabled: true
   pep8:
     enabled: true
+  duplication:
+    enabled: true
+    config:
+      languages:
+        python:
+          python_version: 3

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -0,0 +1,53 @@
+name: 🐛 Bug Report
+description: Spotted a bug? Report it to us!
+labels: ["bug"]
+body:
+  - type: textarea
+    id: bug-description
+    attributes:
+      label: Bug Description
+      description: Tell us what went wrong (including what triggered the bug)
+      placeholder: "A clear and concise description of what the bug is, and the steps to reproduce it"
+    validations:
+      required: true
+  - type: textarea
+    id: code-to-reproduce
+    attributes:
+      label: Code to Reproduce the Bug
+      description: Please provide a minimal working example. Paste your code directly (It will be automatically formatted, so there's no need for backticks)
+      placeholder: "from qutip import identity\nprint(identity(2))"
+      render: shell
+  - type: textarea
+    id: bug-output
+    attributes:
+      label: Code Output
+      description: Please paste the relevant output here (automatically formatted)
+      placeholder: "Quantum object: dims = [[2], [2]], shape = (2, 2), type = oper, isherm = True\nQobj data =\n[[1. 0.]\n[0. 1.]]"
+      render: shell
+  - type: textarea
+    id: expected-behaviour
+    attributes:
+      label: Expected Behaviour
+      description: What should have happened instead?
+      placeholder: "A clear and concise description of what you expected to happen"
+    validations:
+      required: true
+  - type: textarea
+    id: your-environment
+    attributes:
+      label: Your Environment
+      description: Please use `qutip.about()` to get the information about your environment and paste it here (automatically formatted)
+      placeholder: "QuTiP Version:      ***\nNumpy Version:      ***\nScipy Version:      ***\nCython Version:     ***\nMatplotlib Version: ***\nPython Version:     ***\nNumber of CPUs:     ***\nBLAS Info:          ***\nOPENMP Installed:   ***\nINTEL MKL Ext:      ***\nPlatform Info:      ***"
+      render: shell
+    validations:
+      required: true
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: Add anything else you want to tell us. You can include images, plots, etc.
+      placeholder: "Additional information, images, graphs, plots, etc."
+  - type: markdown
+    id: thank-you
+    attributes:
+      value: Thanks for taking the time to fill out this bug report!

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -0,0 +1,36 @@
+name: 🚀 Feature Request
+description: Suggest an idea for this project!
+labels: ["ENH"]
+body:
+  - type: textarea
+    id: problem-description
+    attributes:
+      label: Problem Description
+      description: Give us a clear and concise description of what the problem is!
+      placeholder: "Example - It would be better if [...]"
+    validations:
+      required: true
+  - type: textarea
+    id: proposed-solution
+    attributes:
+      label: Proposed Solution
+      description: Give us a description of your proposed solution
+      placeholder: "A clear and concise description of what you want to happen"
+    validations:
+      required: true
+  - type: textarea
+    id: alternate-solutions
+    attributes:
+      label: Alternate Solutions
+      description: Are there other ways of implementing this feature?
+      placeholder: "A clear and concise description of any alternative solutions or features you've considered"
+  - type: textarea
+    id: additional-context
+    attributes:
+      label: Additional Context
+      description: You can tell us more about your idea, add code snippets or images, etc.
+      placeholder: "Give us more context or screenshots about the feature request here"
+  - type: markdown
+    id: thank-you
+    attributes:
+      value: Thanks for taking the time to fill out this feature request!

.github/ISSUE_TEMPLATE/others.yaml

@@ -0,0 +1,15 @@
+name: 🤔 Others
+description: Tell us about issues that aren't exactly bugs or features
+body:
+  - type: textarea
+    id: issue-description
+    attributes:
+      label: Describe the Issue!
+      description: Tell us about your issue. You can include screenshots, code snippets, etc.
+      placeholder: "Please describe the issue here"
+    validations:
+      required: true
+  - type: markdown
+    id: thank-you
+    attributes:
+      value: Thanks for taking the time to fill out this issue!

.github/pull_request_template.md

@@ -1,11 +1,11 @@
 **Checklist**
 Thank you for contributing to QuTiP! Please make sure you have finished the following tasks before opening the PR.
 
-- [ ] Please read [Contributing to QuTiP Development](https://github.com/qutip/qutip-doc/blob/master/CONTRIBUTING.md)
+- [ ] Please read [Contributing to QuTiP Development](http://qutip.org/docs/latest/development/contributing.html)
 - [ ] 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](https://github.com/qutip/qutip-doc) and the [notebook](https://github.com/qutip/qutip-notebooks). Feel free to ask if you are not sure.
+- [ ] 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.
 
 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/build.yml

@@ -104,8 +104,11 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
     env:
-      # Set up wheels matrix.  This is CPython 3.6--3.9 for all OS targets.
-      CIBW_BUILD: "cp3[6-9]-*"
+      # Set up wheels matrix.  This is CPython 3.6--3.10 for all OS targets.
+      CIBW_BUILD: "cp3{6,7,8,9,10}-*"
+      # Numpy and SciPy do not supply wheels for i686 for Python 3.10, so we
+      # skip those too:
+      CIBW_SKIP: "*-musllinux* cp310-manylinux_i686 cp310-win32"
       OVERRIDE_VERSION: ${{ github.event.inputs.override_version }}
 
     steps:
@@ -120,8 +123,8 @@ jobs:
       - name: Install cibuildwheel
         run: |
           # cibuildwheel does the heavy lifting for us. Originally tested on
-          # 1.8.0, but should be fine at least up to any major new release.
-          python -m pip install 'cibuildwheel<2.0'
+          # 2.3.0, but should be fine at least up to any minor new release.
+          python -m pip install 'cibuildwheel==2.3.*'
 
       - name: Build wheels
         shell: bash
@@ -164,7 +167,7 @@ jobs:
       - name: Verify this is not a dev version
         shell: bash
         run: |
-          python -m pip install wheels/*-cp37-cp37m-manylinux2010_x86_64.whl
+          python -m pip install wheels/*-cp37-cp37m-*.manylinux2010_x86_64.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/build_documentation.yml

@@ -0,0 +1,47 @@
+name: Build HTML documentation
+
+on:
+  [push, pull_request]
+
+jobs:
+  build:
+    name: Build documentation
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Install documentation dependencies
+        run: |
+          python -mpip install -r doc/requirements.txt
+
+      - name: Install QuTiP from GitHub
+        run: |
+          # Build without build isolation so that we use the build
+          # dependencies already installed from doc/requirements.txt.
+          python -m pip install -e .[full] --no-build-isolation
+          # Install in editable mode so it doesn't matter if we import from
+          # inside the installation directory, otherwise we can get some errors
+          # because we're importing from the wrong location.
+          python -c 'import qutip; qutip.about()'
+
+      - name: Build documentation
+        working-directory: doc
+        run: |
+          make html SPHINXOPTS="--keep-going -T"
+          # Above flags are:
+          #   -W : turn warnings into errors
+          #   --keep-going : do not stop after the first error
+          #   -T : display a full traceback if a Python exception occurs
+
+      - name: Upload built files
+        uses: actions/upload-artifact@v2
+        with:
+          name: qutip_html_docs
+          path: doc/_build/html/*
+          if-no-files-found: error

.github/workflows/tests.yml

@@ -69,11 +69,23 @@ jobs:
           # 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+.
           - case-name: Python 3.10
             os: ubuntu-latest
             python-version: "3.10"
             condaforge: 1
-            pytest-extra-options: "-W ignore::ImportWarning"
+            pytest-extra-options: "-W ignore::ImportWarning -W ignore::DeprecationWarning:cvxpy.interface.scipy_wrapper"
+
+          # 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
+            os: windows-latest
+            pytest-extra-options: "-k 'not (test_correlation or test_interpolate or test_mcsolve)'"
 
     steps:
       - uses: actions/checkout@v2
@@ -108,12 +120,13 @@ jobs:
           fi
           python -m pip install -e .[$QUTIP_TARGET]
           python -m pip install coverage==6.2
-          python -m pip install pytest-cov coveralls
+          python -m pip install pytest-cov coveralls pytest-fail-slow
 
       - name: Package information
         run: |
           conda list
           python -c "import qutip; qutip.about()"
+          python -c "import qutip; print(qutip.settings.install)"
 
       - name: Environment information
         run: |
@@ -136,13 +149,17 @@ jobs:
             # truly being executed.
             export QUTIP_NUM_PROCESSES=2
           fi
-          pytest --strict-config --strict-markers --durations=0 --durations-min=1.0 --verbosity=1 --cov=qutip --cov-report= --color=yes ${{ matrix.pytest-extra-options }} qutip/tests
+          pytest --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
+          #     treat warnings as errors
           #  --strict-config
           #     error out if the configuration file is not parseable
           #  --strict-markers
           #     error out if a marker is used but not defined in the
           #     configuration file
+          #  --timeout=300
+          #     error any individual test that goes longer than the given time
           #  --durations=0 --durations-min=1.0
           #     at the end, show a list of all the tests that took longer than a
           #     second to run

.gitignore

@@ -4,6 +4,7 @@
 .DS_Store
 .f2py_f2cmap
 .idea/
+.vscode/
 
 # Packages
 *.egg
@@ -41,3 +42,4 @@ qutip/solver/ode/*.c
 benchmark/benchmark_data.js
 *-tasks.txt
 *compiled_coeff*
+result_images/