Merge branch 'main' into code-quality-Julia-1

Author: ytdHuang

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -22,7 +22,7 @@ body:
     attributes:
       label: Code Output
       description: Please paste the relevant output here (automatically formatted)
-      placeholder: "Quantum Object:   type=Operator   dims=[2]   size=(2, 2)   ishermitian=true\n2×2 Diagonal{ComplexF64, Vector{ComplexF64}}:\n 1.0+0.0im      ⋅    \n     ⋅      1.0+0.0im"
+      placeholder: "Quantum Object:   type=Operator()   dims=[2]   size=(2, 2)   ishermitian=true\n2×2 Diagonal{ComplexF64, Vector{ComplexF64}}:\n 1.0+0.0im      ⋅    \n     ⋅      1.0+0.0im"
       render: shell
   - type: textarea
     id: expected-behaviour

.github/workflows/CI.yml

@@ -67,7 +67,12 @@ jobs:
             node:
               os: 'ubuntu-latest'
               arch: 'x64'
-            group: 'CairoMakie_Ext'
+            group: 'Makie_Ext'
+          - version: '1'
+            node:
+              os: 'ubuntu-latest'
+              arch: 'x64'
+            group: 'AutoDiff_Ext'
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.31.1
+        uses: crate-ci/typos@v1.32.0

.github/workflows/documentation.yml

@@ -21,6 +21,9 @@ on:
       - synchronize
       - ready_for_review
 
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   contents: write

CHANGELOG.md

@@ -7,9 +7,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased](https://github.com/qutip/QuantumToolbox.jl/tree/main)
 
+## [v0.31.1]
+Release date: 2025-05-16
+
+- Introduce `QuantumToolbox.settings` and `auto_tidyup`. ([#460])
+
+## [v0.31.0]
+Release date: 2025-05-03
+
+- Return `sesolve` when `mesolve` allows it. ([#455])
+- Simplify structure of `QuantumObjectType`s. ([#456])
+
+## [v0.30.1]
+Release date: 2025-04-24
+
+- Support different length for `to` and `from` on GeneralDimensions. ([#448])
+- Extend the `Makie.jl` extension to all the other available backends. ([#450])
+- Fix definition of noise derivative in stochastic solvers. ([#453])
+
+## [v0.30.0]
+Release date: 2025-04-12
+
 - Make CUDA conversion more general using Adapt.jl. ([#436], [#437])
 - Make the generation of `fock` states non-mutating to support Zygote.jl. ([#438])
 - Remove Reexport.jl from the dependencies. ([#443])
+- Add support for automatic differentiation for `sesolve` and `mesolve`. ([#440])
 
 ## [v0.29.1]
 Release date: 2025-03-07
@@ -136,6 +158,10 @@ Release date: 2024-11-13
 [v0.28.0]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.28.0
 [v0.29.0]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.29.0
 [v0.29.1]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.29.1
+[v0.30.0]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.30.0
+[v0.30.1]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.30.1
+[v0.31.0]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.31.0
+[v0.31.1]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.31.1
 [#86]: https://github.com/qutip/QuantumToolbox.jl/issues/86
 [#139]: https://github.com/qutip/QuantumToolbox.jl/issues/139
 [#271]: https://github.com/qutip/QuantumToolbox.jl/issues/271
@@ -194,4 +220,11 @@ Release date: 2024-11-13
 [#436]: https://github.com/qutip/QuantumToolbox.jl/issues/436
 [#437]: https://github.com/qutip/QuantumToolbox.jl/issues/437
 [#438]: https://github.com/qutip/QuantumToolbox.jl/issues/438
+[#440]: https://github.com/qutip/QuantumToolbox.jl/issues/440
 [#443]: https://github.com/qutip/QuantumToolbox.jl/issues/443
+[#448]: https://github.com/qutip/QuantumToolbox.jl/issues/448
+[#450]: https://github.com/qutip/QuantumToolbox.jl/issues/450
+[#453]: https://github.com/qutip/QuantumToolbox.jl/issues/453
+[#455]: https://github.com/qutip/QuantumToolbox.jl/issues/455
+[#456]: https://github.com/qutip/QuantumToolbox.jl/issues/456
+[#460]: https://github.com/qutip/QuantumToolbox.jl/issues/460

CITATION.bib

@@ -0,0 +1,11 @@
+@article{QuantumToolbox-jl2025,
+    title={{QuantumToolbox.jl}: An efficient {Julia} framework for simulating open quantum systems},
+    author={Mercurio, Alberto and Huang, Yi-Te and Cai, Li-Xun and Chen, Yueh-Nan and Savona, Vincenzo and Nori, Franco},
+    journal={arXiv preprint arXiv:2504.21440},
+    year={2025},
+    publisher = {arXiv},
+    eprint={2504.21440},
+    archivePrefix={arXiv},
+    primaryClass={quant-ph},
+    doi = {10.48550/arXiv.2504.21440}
+}

Makefile

@@ -19,7 +19,6 @@ docs:
 	${JULIA} --project=docs docs/make.jl
 
 vitepress:
-	npm --prefix docs i
 	npm --prefix docs run docs:dev
 
 all: setup format changelog test docs vitepress

Project.toml

@@ -1,7 +1,7 @@
 name = "QuantumToolbox"
 uuid = "6c2fb7c5-b903-41d2-bc5e-5a7c320b9fab"
 authors = ["Alberto Mercurio", "Yi-Te Huang"]
-version = "0.29.1"
+version = "0.31.1"
 
 [deps]
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
@@ -27,19 +27,21 @@ StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 
 [weakdeps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 
 [extensions]
 QuantumToolboxCUDAExt = "CUDA"
-QuantumToolboxCairoMakieExt = "CairoMakie"
+QuantumToolboxChainRulesCoreExt = "ChainRulesCore"
 QuantumToolboxGPUArraysExt = ["GPUArrays", "KernelAbstractions"]
+QuantumToolboxMakieExt = "Makie"
 
 [compat]
 ArrayInterface = "6, 7"
 CUDA = "5"
-CairoMakie = "0.12, 0.13"
+ChainRulesCore = "1"
 DiffEqBase = "6"
 DiffEqCallbacks = "4.2.1 - 4"
 DiffEqNoiseProcess = "5"
@@ -51,12 +53,13 @@ IncompleteLU = "0.2"
 KernelAbstractions = "0.9.2"
 LinearAlgebra = "1"
 LinearSolve = "2, 3"
+Makie = "0.20, 0.21, 0.22"
 OrdinaryDiffEqCore = "1"
 OrdinaryDiffEqTsit5 = "1"
 Pkg = "1"
 Random = "1"
 SciMLBase = "2"
-SciMLOperators = "0.3"
+SciMLOperators = "0.3, 0.4"
 SparseArrays = "1"
 SpecialFunctions = "2"
 StaticArraysCore = "1"

README.md

@@ -1,6 +1,6 @@
 <!-- Logo -->
 <div align="center">
-  <img src="./docs/src/public/logo.png" alt="QuantumToolbox.jl logo" width="150">
+  <img src="./docs/src/assets/logo.png" alt="QuantumToolbox.jl logo" width="150">
 </div>
 
 # QuantumToolbox.jl
@@ -10,7 +10,7 @@
 and [Y.-T. Huang](https://github.com/ytdHuang).
 
 <!-- Table of Badges -->
-| **Release**       | [![Release][release-img]][release-url] [![License][license-img]][license-url] [![DOI][doi-img]][doi-url] [![Downloads][download-img]][download-url] |
+| **Release**       | [![Release][release-img]][release-url] [![License][license-img]][license-url] [![Cite][cite-img]][cite-url] [![Downloads][download-img]][download-url] |
 |:-----------------:|:-------------|
 | **Runtests**      | [![Runtests][runtests-img]][runtests-url] [![Coverage][codecov-img]][codecov-url] |
 | **Code Quality**  | [![Code Quality][code-quality-img]][code-quality-url] [![Aqua QA][aqua-img]][aqua-url] [![JET][jet-img]][jet-url] |
@@ -24,8 +24,8 @@ and [Y.-T. Huang](https://github.com/ytdHuang).
 [license-img]: https://img.shields.io/badge/license-New%20BSD-blue.svg
 [license-url]: https://opensource.org/licenses/BSD-3-Clause
 
-[doi-img]: https://zenodo.org/badge/DOI/10.5281/zenodo.10822816.svg
-[doi-url]: https://doi.org/10.5281/zenodo.10822816
+[cite-img]: https://img.shields.io/badge/cite-arXiv%3A2504.21440_(2023)-blue
+[cite-url]: https://doi.org/10.48550/arXiv.2504.21440
 
 [download-img]: https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Ftotal_downloads%2FQuantumToolbox&query=total_requests&label=Downloads
 [download-url]: https://juliapkgstats.com/pkg/QuantumToolbox
@@ -177,6 +177,23 @@ You are most welcome to contribute to `QuantumToolbox.jl` development by forking
 
 For more information about contribution, including technical advice, please see the [Contributing to Quantum Toolbox in Julia](https://qutip.org/QuantumToolbox.jl/stable/resources/contributing).
 
+## Cite `QuantumToolbox.jl`
+If you like `QuantumToolbox.jl`, we would appreciate it if you starred the repository in order to help us increase its visibility. Furthermore, if you find the framework useful in your research, we would be grateful if you could cite our arXiv preprint [ [arXiv:2504.21440 (2025)](https://doi.org/10.48550/arXiv.2504.21440)  ] using the following bibtex entry:
+
+```bib
+@article{QuantumToolbox-jl2025,
+    title={{QuantumToolbox.jl}: An efficient {Julia} framework for simulating open quantum systems},
+    author={Mercurio, Alberto and Huang, Yi-Te and Cai, Li-Xun and Chen, Yueh-Nan and Savona, Vincenzo and Nori, Franco},
+    journal={arXiv preprint arXiv:2504.21440},
+    year={2025},
+    publisher = {arXiv},
+    eprint={2504.21440},
+    archivePrefix={arXiv},
+    primaryClass={quant-ph},
+    doi = {10.48550/arXiv.2504.21440}
+}
+```
+
 ## Acknowledgements
 
 ### Fundings

docs/Project.toml

@@ -6,3 +6,6 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
 QuantumToolbox = "6c2fb7c5-b903-41d2-bc5e-5a7c320b9fab"
+
+[compat]
+DocumenterVitepress = "0.2"