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qutip · Feb 3, 2024 · d2e17be · d2e17be
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diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -10,4 +10,4 @@ jobs:
       - uses: psf/black@stable
         with:
           options: "--check --diff"
-          src: "./src"
+          src: "./src"
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -10,7 +10,6 @@ on:
         description: "Override version number (optional):"
         default: ""
 
-
 jobs:
   # The deploy_test job is part of the test of whether we should deploy to PyPI.
   # The job will succeed if either the confirmation reference is empty or if the
@@ -37,7 +36,6 @@ jobs:
             echo "Full build and deploy.  Wheels and source will be uploaded to PyPI."
           fi
 
-
   build_sdist:
     name: Build sdist on Ubuntu
     needs: deploy_test
@@ -54,7 +52,7 @@ 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: '3.10'
+          python-version: "3.10"
 
       - name: Install pip build
         run: |
@@ -74,7 +72,6 @@ jobs:
           path: dist/*.tar.gz
           if-no-files-found: error
 
-
   build_wheels:
     name: Build wheels
     needs: deploy_test
@@ -89,7 +86,7 @@ jobs:
         name: Install Python
         with:
           # This is about the build environment, not the released wheel version.
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Install pip build
         run: |
@@ -111,7 +108,6 @@ jobs:
           path: ./wheelhouse/*.whl
           if-no-files-found: error
 
-
   deploy:
     name: "Deploy to PyPI if desired"
     # The confirmation is tested explicitly in `deploy_test`, so we know it is
@@ -129,7 +125,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.10'
+          python-version: "3.10"
 
       - name: Verify this is not a dev version
         shell: bash

diff --git a/.github/workflows/build_documentation.yml b/.github/workflows/build_documentation.yml
@@ -1,7 +1,6 @@
 name: Build HTML documentation
 
-on:
-  [push, pull_request]
+on: [push, pull_request]
 
 jobs:
   build:
@@ -14,8 +13,8 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.8'
-          
+          python-version: "3.8"
+
       - name: Install Pandoc
         run: |
           sudo apt update

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -2,7 +2,7 @@ name: Tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
 
 jobs:
@@ -14,77 +14,76 @@ jobs:
         include:
           - case-name: ubuntu-python3.10
             os: ubuntu-latest
-            qutip-version: '@master'
-            python-version: '3.10'
+            qutip-version: "@master"
+            python-version: "3.10"
           - case-name: macOs-python3.10
             os: macOS-latest
-            qutip-version: '@master'
-            python-version: '3.10'
+            qutip-version: "@master"
+            python-version: "3.10"
           - case-name: windows-python3.10
             os: windows-latest
-            qutip-version: '@master'
-            python-version: '3.10'
+            qutip-version: "@master"
+            python-version: "3.10"
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Install QuTiP from GitHub
-      if: ${{ matrix.qutip-version == '@master'}}
-      run: |
-        python -m pip install 'git+https://github.com/qutip/qutip.git${{ matrix.qutip-version }}'
-
-    - name: Install qutip-qtrl from GitHub
-      if: ${{ matrix.qutip-version == '@master'}}
-      run: |
-        python -m pip install 'git+https://github.com/qutip/qutip-qtrl.git'
+      - name: Install QuTiP from GitHub
+        if: ${{ matrix.qutip-version == '@master'}}
+        run: |
+          python -m pip install 'git+https://github.com/qutip/qutip.git${{ matrix.qutip-version }}'
 
-    - name: Install qutip-jax from GitHub
-      if: ${{ matrix.qutip-version == '@master'}}
-      run: |
-        python -m pip install 'git+https://github.com/qutip/qutip-jax.git'
+      - name: Install qutip-qtrl from GitHub
+        if: ${{ matrix.qutip-version == '@master'}}
+        run: |
+          python -m pip install 'git+https://github.com/qutip/qutip-qtrl.git'
 
+      - name: Install qutip-jax from GitHub
+        if: ${{ matrix.qutip-version == '@master'}}
+        run: |
+          python -m pip install 'git+https://github.com/qutip/qutip-jax.git'
 
-    - name: Install qutip-qoc
-      # Installing in-place so that coveralls can locate the source code.
-      run: |
-        pip install -e .[full]
-    - name: Test with pytest and generate coverage report
-      run: |
-        pip install pytest-cov coveralls
-        pytest tests --strict-markers --cov=qutip_qoc --cov-report= --color=yes
-    - name: Upload to Coveralls
-      env:
-        GITHUB_TOKEN: ${{ secrets.github_token }}
-        COVERALLS_PARALLEL: true
-      run: coveralls --service=github
+      - name: Install qutip-qoc
+        # Installing in-place so that coveralls can locate the source code.
+        run: |
+          pip install -e .[full]
+      - name: Test with pytest and generate coverage report
+        run: |
+          pip install pytest-cov coveralls
+          pytest tests --strict-markers --cov=qutip_qoc --cov-report= --color=yes
+      - name: Upload to Coveralls
+        env:
+          GITHUB_TOKEN: ${{ secrets.github_token }}
+          COVERALLS_PARALLEL: true
+        run: coveralls --service=github
 
   doctest:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.10
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -mpip install -r doc/requirements.txt
-        pip install .
-    - name: Test code snippets in the documentation
-      run: |
-        cd doc
-        make doctest
-    - name: Test code examples for the pulse paper
-      run: |
-        python -m pip install joblib pytest pytest-custom_exit_code
-        cd doc/pulse-paper
-        pytest *.py --suppress-no-test-exit-code
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.10
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -mpip install -r doc/requirements.txt
+          pip install .
+      - name: Test code snippets in the documentation
+        run: |
+          cd doc
+          make doctest
+      - name: Test code examples for the pulse paper
+        run: |
+          python -m pip install joblib pytest pytest-custom_exit_code
+          cd doc/pulse-paper
+          pytest *.py --suppress-no-test-exit-code
 
   finalise:
     name: Finalise coverage reporting

diff --git a/.gitignore b/.gitignore
@@ -131,4 +131,4 @@ dmypy.json
 .pyre/
 
 # Visual Studio Code
-.vscode/
+.vscode/
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -6,12 +6,12 @@ We are committed to making participation in this project a harassment-free exper
 
 Examples of unacceptable behavior by participants include:
 
-* The use of sexualized language or imagery
-* Personal attacks
-* Trolling or insulting/derogatory comments
-* Public or private harassment
-* Publishing other's private information, such as physical or electronic addresses, without explicit permission
-* Other unethical or unprofessional conduct
+- The use of sexualized language or imagery
+- Personal attacks
+- Trolling or insulting/derogatory comments
+- Public or private harassment
+- Publishing other's private information, such as physical or electronic addresses, without explicit permission
+- Other unethical or unprofessional conduct
 
 Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. By adopting this Code of Conduct, project maintainers commit themselves to fairly and consistently applying these principles to every aspect of managing this project. Project maintainers who do not follow or enforce the Code of Conduct may be permanently removed from the project team.
 

diff --git a/README.md b/README.md
@@ -1,43 +1,46 @@
 # QuTiP - Quantum Optimal Control
 
-The qutip-qoc package builds up on the ``qutip-qtrl`` [package](https://github.com/qutip/qutip-qtrl).
+The qutip-qoc package builds up on the `qutip-qtrl` [package](https://github.com/qutip/qutip-qtrl).
 
 It enhances it by providing two additional algorithms to optimize analytically defined control functions.
 The first one is an extension of Gradient Optimization of Analytic conTrols [(GOAT)](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.150401).
-The second leverages QuTiPs version 5 new diffrax abilities to directly calculate gradients of JAX defined contol functinos using automatic differentiation. 
+The second leverages QuTiPs version 5 new diffrax abilities to directly calculate gradients of JAX defined contol functinos using automatic differentiation.
 
 The procedure consists of a two-layer approach to find global optimal values for parameterized analytical control functions.
-The global optimization layer provides ``scipy.optimize.dual_annealing`` and ``scipy.optimize.basinhopping``, while the local minimization layer supports all 
-gradient driven ``scipy.optimize.minimize`` methods.
+The global optimization layer provides `scipy.optimize.dual_annealing` and `scipy.optimize.basinhopping`, while the local minimization layer supports all
+gradient driven `scipy.optimize.minimize` methods.
 
 The package also aims for a more general way of defining control problems with QuTiP and makes switching between the four control algorithms very easy.
 
 As with qutip-qtrl, the qutip-qoc package aims at providing advanced tools for the optimal control of quantum devices.
 Compared to other libraries for quantum optimal control, qutip-qoc puts additional emphasis on the physics layer and the interaction with the QuTiP package.
-Along with the extended GOAT and JOAT algorithms the package offers support for both the CRAB and GRAPE methods defined in ``qutip-qtrl``.
+Along with the extended GOAT and JOAT algorithms the package offers support for both the CRAB and GRAPE methods defined in `qutip-qtrl`.
 
 If you would like to know the future development plan and ideas, have a look at the [qutip documentation for ideas](https://qutip.org/docs/latest/development/ideas.html).
 
-Quick start
------------
+## Quick start
+
 To install the package, use
+
 ```
 pip install qutip-qoc
 ```
 
-Documentation and tutorials
----------------------------
+## Documentation and tutorials
+
 The documentation of `qutip-qoc` updated to the latest development version is hosted at [qutip-qoc.readthedocs.io/](https://qutip-qoc.readthedocs.io/en/stable/).
-Tutorials related to using quantum optimal control in `qutip-qoc` can be found [*here*](https://qutip.org/qutip-tutorials/#optimal-control).
+Tutorials related to using quantum optimal control in `qutip-qoc` can be found [_here_](https://qutip.org/qutip-tutorials/#optimal-control).
+
+## Installation from source
 
-Installation from source
-------------------------
 If you want to edit the source code, please download the source code and run the following command under the root `qutip-qoc` folder,
+
 ```
 pip install --upgrade pip
 pip install -e .
 ```
-which makes sure that you are up to date with the latest `pip` version. Contribution guidelines are available [*here*](https://qutip-qoc.readthedocs.io/en/latest/contribution-code.html).
+
+which makes sure that you are up to date with the latest `pip` version. Contribution guidelines are available [_here_](https://qutip-qoc.readthedocs.io/en/latest/contribution-code.html).
 
 To build and test the documentation, additional packages need to be installed:
 
@@ -46,28 +49,33 @@ pip install pytest matplotlib sphinx sphinxcontrib-bibtex numpydoc sphinx_rtd_th
 ```
 
 Under the `doc` directory, use
+
 ```
 make html
 ```
+
 to build the documentation, or
+
 ```
 make doctest
 ```
+
 to test the code in the documentation.
 
-Testing
--------
+## Testing
+
 To test the installation, choose the correct branch that matches with the version, e.g., `qutip-qoc-0.2.X` for version 0.2. Then download the source code and run from the `qutip-qoc` directory.
+
 ```
 pytest tests
 ```
 
-Citing `qutip-qoc`
--------------------
+## Citing `qutip-qoc`
+
 If you use `qutip-qoc` in your research, please cite the original QuTiP papers that are available [here](https://dml.riken.jp/?s=QuTiP).
 
-Support
--------
+## Support
+
 This package is supported and maintained by the same developers group as QuTiP.
 
 [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org)
@@ -77,8 +85,8 @@ QuTiP development is supported by [Nori's lab](http://dml.riken.jp/)
 at RIKEN, by the University of Sherbrooke, by Chalmers University of Technology, by Macquarie University and by Aberystwyth University,
 [among other supporting organizations](http://qutip.org/#supporting-organizations).
 
-License
--------
+## License
+
 [![license](https://img.shields.io/badge/license-New%20BSD-blue.svg)](http://en.wikipedia.org/wiki/BSD_licenses#3-clause_license_.28.22Revised_BSD_License.22.2C_.22New_BSD_License.22.2C_or_.22Modified_BSD_License.22.29)
 
 You are free to use this software, with or without modification, provided that the conditions listed in the LICENSE.txt file are satisfied.
diff --git a/doc/apidoc.rst b/doc/apidoc.rst
@@ -41,4 +41,4 @@ Internal interfaces to the optimal control features.
 
    qutip_qoc.analytical_control
    qutip_qoc.goat
-   qutip_qoc.joat
+   qutip_qoc.joat