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

Author: ytdHuang

.buildkite/CUDA_Ext.yml

@@ -22,12 +22,3 @@ steps:
       GROUP: "CUDA_Ext"
       SECRET_CODECOV_TOKEN: "ZfhQu/IcRLqNyZ//ZNs5sjBPaV76IHfU5gui52Qn+Rp8tOurukqgScuyDt+3HQ4R0hJYBw1/Nqg6jmBsvWSc9NEUx8kGsUJFHfN3no0+b+PFxA8oJkWc9EpyIsjht5ZIjlsFWR3f0DpPqMEle/QyWOPcal63CChXR8oAoR+Fz1Bh8GkokLlnC8F9Ugp9xBlu401GCbyZhvLTZnNIgK5yy9q8HBJnBg1cPOhI81J6JvYpEmcIofEzFV/qkfpTUPclu43WNoFX2DZPzbxilf3fsAd5/+nRkRfkNML8KiN4mnmjHxPPbuY8F5zC/PS5ybXtDpfvaMQc01WApXCkZk0ZAQ==;U2FsdGVkX1+eDT7dqCME5+Ox5i8GvWRTQbwiP/VYjapThDbxXFDeSSIC6Opmon+M8go22Bun3bat6Fzie65ang=="
     timeout_in_minutes: 60
-    if: | 
-        // Don't run Buildkite if the commit message includes the text [skip ci], [ci skip], or [no ci]
-        // Don't run Buildkite for PR draft
-        // Only run Buildkite when new commits and PR are made to main branch
-        build.message !~ /\[skip ci\]/ &&
-        build.message !~ /\[ci skip\]/ &&
-        build.message !~ /\[no ci\]/   &&
-        !build.pull_request.draft      &&
-        (build.branch =~ /main/ || build.pull_request.base_branch =~ /main/)

.buildkite/pipeline.yml

@@ -1,6 +1,17 @@
 # see: https://github.com/staticfloat/forerunner-buildkite-plugin
 steps:
   - label: ":runner: Dynamically launch pipelines"
+    if: | 
+        // Don't run Buildkite if the commit message includes the text [skip ci], [ci skip], or [no ci]
+        // Don't run Buildkite for PR draft
+        // Only run Buildkite when new commits and PR are made to main branch
+        build.message !~ /\[skip ci\]/ &&
+        build.message !~ /\[ci skip\]/ &&
+        build.message !~ /\[no ci\]/   &&
+        !build.pull_request.draft      &&
+        (build.branch =~ /main/ || build.pull_request.base_branch =~ /main/)
+    agents:
+      queue: "juliagpu"
     plugins:
       - staticfloat/forerunner: # CUDA.jl tests
           watch:
@@ -12,5 +23,3 @@ steps:
             - "test/ext-test/gpu/**"
             - "Project.toml"
           target: ".buildkite/CUDA_Ext.yml"
-    agents:
-      queue: "juliagpu"

.github/dependabot.yml

@@ -4,4 +4,8 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "weekly"
+    labels:
+      - "dependencies"
+      - "Skip ChangeLog"
+      

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.29.7
+        uses: crate-ci/typos@v1.30.0

CHANGELOG.md

@@ -7,9 +7,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased](https://github.com/qutip/QuantumToolbox.jl/tree/main)
 
+## [v0.29.1]
+Release date: 2025-03-07
+
+- Minor changes for GPU matrices element type and word size handling. ([#430])
+
+## [v0.29.0]
+Release date: 2025-03-07
+
+- Add support for `OperatorKet` state input for `mesolve` and `smesolve`. ([#423])
+- Introduce `plot_fock_distribution` to plot the population of a state (ket, bra, or density matrix) in its basis (assumed to be Fock basis). ([#428])
+
+## [v0.28.0]
+Release date: 2025-02-22
+
 - Support for single `AbstractQuantumObject` in `sc_ops` for faster specific method in `ssesolve` and `smesolve`. ([#408])
 - Change save callbacks from `PresetTimeCallback` to `FunctionCallingCallback`. ([#410])
 - Align `eigenstates` and `eigenenergies` to QuTiP. ([#411])
+- Introduce `vector_to_operator` and `operator_to_vector`. ([#413])
+- Introduce some entropy related functions. ([#414], [#416])
+  - `entropy_linear`
+  - `entropy_mutual`
+  - `entropy_conditional`
+  - `entropy_relative`
+- Fix `entanglement` and introduce `concurrence`. ([#414], [#418], [#419])
+- Introduce some metric functions. ([#414], [#420])
+  - `hilbert_dist`
+  - `hellinger_dist`
+  - `bures_dist`
+  - `bures_angle`
+- Align `steadystate` ODE solver to other methods and improve GPU support. ([#421])
 
 ## [v0.27.0]
 Release date: 2025-02-14
@@ -102,6 +129,9 @@ Release date: 2024-11-13
 [v0.25.2]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.25.2
 [v0.26.0]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.26.0
 [v0.27.0]: https://github.com/qutip/QuantumToolbox.jl/releases/tag/v0.27.0
+[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
 [#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
@@ -147,3 +177,13 @@ Release date: 2024-11-13
 [#408]: https://github.com/qutip/QuantumToolbox.jl/issues/408
 [#410]: https://github.com/qutip/QuantumToolbox.jl/issues/410
 [#411]: https://github.com/qutip/QuantumToolbox.jl/issues/411
+[#413]: https://github.com/qutip/QuantumToolbox.jl/issues/413
+[#414]: https://github.com/qutip/QuantumToolbox.jl/issues/414
+[#416]: https://github.com/qutip/QuantumToolbox.jl/issues/416
+[#418]: https://github.com/qutip/QuantumToolbox.jl/issues/418
+[#419]: https://github.com/qutip/QuantumToolbox.jl/issues/419
+[#420]: https://github.com/qutip/QuantumToolbox.jl/issues/420
+[#421]: https://github.com/qutip/QuantumToolbox.jl/issues/421
+[#423]: https://github.com/qutip/QuantumToolbox.jl/issues/423
+[#428]: https://github.com/qutip/QuantumToolbox.jl/issues/428
+[#430]: https://github.com/qutip/QuantumToolbox.jl/issues/430

Project.toml

@@ -1,7 +1,7 @@
 name = "QuantumToolbox"
 uuid = "6c2fb7c5-b903-41d2-bc5e-5a7c320b9fab"
 authors = ["Alberto Mercurio", "Yi-Te Huang"]
-version = "0.27.0"
+version = "0.29.1"
 
 [deps]
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"

docs/src/resources/api.md

@@ -176,6 +176,8 @@ unit
 tensor
 ⊗
 qeye
+vector_to_operator
+operator_to_vector
 sqrtm
 logm
 expm
@@ -248,13 +250,23 @@ ExponentialSeries
 PseudoInverse
 ```
 
-## [Metrics](@id doc-API:Metrics)
+## [Entropy and Metrics](@id doc-API:Entropy-and-Metrics)
 
 ```@docs
 entropy_vn
+entropy_relative
+entropy_linear
+entropy_mutual
+entropy_conditional
 entanglement
-tracedist
+concurrence
+negativity
 fidelity
+tracedist
+hilbert_dist
+hellinger_dist
+bures_dist
+bures_angle
 ```
 
 ## [Spin Lattice](@id doc-API:Spin-Lattice)
@@ -276,7 +288,6 @@ BlockDiagonalForm
 
 ```@docs
 wigner
-negativity
 ```
 
 ## [Linear Maps](@id doc-API:Linear-Maps)
@@ -302,4 +313,5 @@ meshgrid
 
 ```@docs
 plot_wigner
+plot_fock_distribution
 ```

docs/src/resources/bibliography.bib

@@ -81,3 +81,26 @@ @book{Wiseman2009Quantum
   year={2009},
   month=nov
 } 
+
+@article{Vedral-Plenio1998,
+  title = {Entanglement measures and purification procedures},
+  author = {Vedral, V. and Plenio, M. B.},
+  journal = {Phys. Rev. A},
+  volume = {57},
+  issue = {3},
+  pages = {1619--1633},
+  numpages = {0},
+  year = {1998},
+  month = {Mar},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevA.57.1619},
+  url = {https://link.aps.org/doi/10.1103/PhysRevA.57.1619}
+}
+
+@article{Spehner2017,
+      title={Geometric measures of quantum correlations with Bures and Hellinger distances}, 
+      author={D. Spehner and F. Illuminati and M. Orszag and W. Roga},
+      year={2017},
+      journal={arXiv:1611.03449},
+      url={https://arxiv.org/abs/1611.03449}, 
+}

docs/src/users_guide/extensions/cairomakie.md

@@ -18,4 +18,5 @@ The supported plotting functions are listed as follows:
 
 | **Plotting Function** | **Description** |
 |:----------------------|:----------------|
-| [`plot_wigner`](@ref) | [Wigner quasipropability distribution](https://en.wikipedia.org/wiki/Wigner_quasiprobability_distribution) |
+| [`plot_wigner`](@ref) | [Wigner quasipropability distribution](https://en.wikipedia.org/wiki/Wigner_quasiprobability_distribution) |
+| [`plot_fock_distribution`](@ref) | [Fock state](https://en.wikipedia.org/wiki/Fock_state) distribution |

docs/src/users_guide/states_and_operators.md

@@ -161,7 +161,7 @@ coherent_dm(5, 1.25)
 thermal_dm(5, 1.25)
 ```
 
-`QuantumToolbox` also provides a set of distance metrics for determining how close two density matrix distributions are to each other. Included are the [`fidelity`](@ref), and trace distance ([`tracedist`](@ref)).
+`QuantumToolbox` also provides a set of distance metrics for determining how close two density matrix distributions are to each other. For example, [`fidelity`](@ref), and trace distance ([`tracedist`](@ref)) are included. For more metric functions, see section [Entropy and Metrics](@ref doc-API:Entropy-and-Metrics) in the API page.
 
 ```@example states_and_operators
 x = coherent_dm(5, 1.25)
@@ -314,7 +314,7 @@ Therefore, a given density matrix ``\hat{\rho}`` can then be vectorized, denoted
 |\hat{\rho}\rangle\rangle = \textrm{vec}(\hat{\rho}).
 ```
 
-`QuantumToolbox` uses the column-stacking convention for the isomorphism between ``\mathcal{L}(\mathcal{H})`` and ``\mathcal{H}\otimes\mathcal{H}``. This isomorphism is implemented by the functions [`mat2vec`](@ref) and [`vec2mat`](@ref):
+`QuantumToolbox` uses the column-stacking convention for the isomorphism between ``\mathcal{L}(\mathcal{H})`` and ``\mathcal{H}\otimes\mathcal{H}``. This isomorphism is implemented by the functions [`mat2vec`](@ref) (or [`operator_to_vector`](@ref)) and [`vec2mat`](@ref) (or [`vector_to_operator`](@ref)):
 
 ```@example states_and_operators
 rho = Qobj([1 2; 3 4])