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

Author: ytdHuang

.github/workflows/CI.yml

@@ -10,7 +10,7 @@ on:
       - 'ext/**'
       - 'test/runtests.jl'
       - 'test/core-test/**'
-      - 'test/ext-test/cairomakie/**'
+      - 'test/ext-test/cpu/**'
       - 'Project.toml'
   pull_request:
     branches:
@@ -21,7 +21,7 @@ on:
       - 'ext/**'
       - 'test/runtests.jl'
       - 'test/core-test/**'
-      - 'test/ext-test/cairomakie/**'
+      - 'test/ext-test/cpu/**'
       - 'Project.toml'
     types:
       - opened

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.30.0
+        uses: crate-ci/typos@v1.31.1

CHANGELOG.md

@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased](https://github.com/qutip/QuantumToolbox.jl/tree/main)
 
+- 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])
+
 ## [v0.29.1]
 Release date: 2025-03-07
 
@@ -187,3 +191,7 @@ Release date: 2024-11-13
 [#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
+[#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
+[#443]: https://github.com/qutip/QuantumToolbox.jl/issues/443

Project.toml

@@ -18,7 +18,6 @@ OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLOperators = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -56,7 +55,6 @@ OrdinaryDiffEqCore = "1"
 OrdinaryDiffEqTsit5 = "1"
 Pkg = "1"
 Random = "1"
-Reexport = "1"
 SciMLBase = "2"
 SciMLOperators = "0.3"
 SparseArrays = "1"

README.md

@@ -167,7 +167,7 @@ sol = mesolve(H_gpu, ψ0_gpu, tlist, c_ops, e_ops = e_ops)
 
 ## Performance comparison with other packages
 
-Here we provide a brief performance comparison between `QuantumToolbox.jl` and other popular quantum physics simulation packages, such as [`QuTiP`](https://github.com/qutip/qutip) (Python), [`dynamiqs`](https://github.com/dynamiqs/dynamiqs) (Python - JAX) and [`QuantumOptics.jl`](https://github.com/qojulia/QuantumOptics.jl) (Julia). We clearly show that `QuantumToolbox.jl` is the fastest package among the four. A detailed code is available [here](https://github.com/albertomercurio/QuantumToolbox.jl-Paper-Figures/blob/main/src/benchmarks.jl).
+Here we provide a brief performance comparison between `QuantumToolbox.jl` and other popular quantum physics simulation packages, such as [`QuTiP`](https://github.com/qutip/qutip) (Python), [`dynamiqs`](https://github.com/dynamiqs/dynamiqs) (Python - JAX) and [`QuantumOptics.jl`](https://github.com/qojulia/QuantumOptics.jl) (Julia). We clearly show that `QuantumToolbox.jl` is the fastest package among the four. A detailed code is available [here](https://github.com/albertomercurio/QuantumToolbox.jl-Paper-Figures/blob/main/src/benchmarks/benchmarks.jl).
 
 ![](https://raw.githubusercontent.com/albertomercurio/QuantumToolbox.jl-Paper-Figures/refs/heads/main/figures/benchmarks.svg)
 

benchmarks/runbenchmarks.jl

@@ -1,4 +1,6 @@
 using BenchmarkTools
+using LinearAlgebra
+using SparseArrays
 using QuantumToolbox
 using OrdinaryDiffEq
 using LinearSolve

docs/make.jl

@@ -10,7 +10,12 @@ using Changelog
 # Load of packages required to compile the extension documentation
 using CairoMakie
 
-DocMeta.setdocmeta!(QuantumToolbox, :DocTestSetup, :(using QuantumToolbox); recursive = true)
+doctest_setup = quote
+    using LinearAlgebra
+    using SparseArrays
+    using QuantumToolbox
+end
+DocMeta.setdocmeta!(QuantumToolbox, :DocTestSetup, doctest_setup; recursive = true)
 
 # some options for `makedocs`
 const DRAFT = false  # set `true`  to disable cell evaluation

docs/src/getting_started/type_stability.md

@@ -199,7 +199,7 @@ Which returns a tensor of size `2x2x2x2x2x2`. Let's check the `@code_warntype`:
 @code_warntype reshape_operator_data([2, 2, 2])
 ```
 
-We got a `Any` type, because the compiler doesn't know the size of the `dims` vector. We can fix this by using a `Tuple` (or `SVector`):
+We got a `Any` type, because the compiler doesn't know the size of the `dims` vector. We can fix this by using a `Tuple` (or `SVector` from [StaticArrays.jl](https://github.com/JuliaArrays/StaticArrays.jl)):
 
 ```@example type-stability
 typeof(reshape_operator_data((2, 2, 2)))
@@ -219,13 +219,15 @@ Finally, let's look at the benchmarks
 @benchmark reshape_operator_data($((2, 2, 2)))
 ```
 
-Which is an innocuous but huge difference in terms of performance. Hence, we highly recommend using `Tuple` or `SVector` when defining the dimensions of a user-defined [`QuantumObject`](@ref).
+Which is an innocuous but huge difference in terms of performance. Hence, we highly recommend using `Tuple` or `SVector` from [StaticArrays.jl](https://github.com/JuliaArrays/StaticArrays.jl) when defining the dimensions of a user-defined [`QuantumObject`](@ref).
 
 ## The use of `Val` in some `QuantumToolbox.jl` functions
 
 In some functions of `QuantumToolbox.jl`, you may find the use of the [`Val`](https://docs.julialang.org/en/v1/base/base/#Base.Val) type in the arguments. This is a trick to pass a value at compile time, and it is very useful to avoid type instabilities. Let's make a very simple example, where we want to create a Fock state ``|j\rangle`` of a given dimension `N`, and we give the possibility to create it as a sparse or dense vector. At first, we can write the function without using `Val`:
 
 ```@example type-stability
+using SparseArrays
+
 function my_fock(N::Int, j::Int = 0; sparse::Bool = false)
     if sparse
         array = sparsevec([j + 1], [1.0 + 0im], N)

docs/src/index.md

@@ -74,3 +74,25 @@ using QuantumToolbox
 QuantumToolbox.versioninfo()
 QuantumToolbox.about()
 ```
+
+# [Other Useful Packages](@id doc:Other-Useful-Packages)
+
+In order to get a better experience and take full advantage of `QuantumToolbox`, we recommend the following external packages:
+
+- Standard `Julia` Libraries: (recommended to also `using` with `QuantumToolbox.jl`)
+  - [`LinearAlgebra.jl`](https://github.com/JuliaLang/LinearAlgebra.jl)
+  - [`SparseArrays.jl`](https://github.com/JuliaSparse/SparseArrays.jl)
+- Solver `alg`orithms:
+  - [`DifferentialEquations.jl`](https://github.com/SciML/DifferentialEquations.jl) or [`OrdinaryDiffEq.jl`](https://github.com/SciML/OrdinaryDiffEq.jl)
+  - [`LinearSolve.jl`](https://github.com/SciML/LinearSolve.jl)
+- GPU support:
+  - [`CUDA.jl`](https://github.com/JuliaGPU/CUDA.jl)
+- Distributed Computing support:
+  - [`Disributed.jl`](https://github.com/JuliaLang/Distributed.jl)
+  - [`SlurmClusterManager.jl`](https://github.com/JuliaParallel/SlurmClusterManager.jl)
+- Plotting Libraries:
+  - [`Makie.jl`](https://github.com/MakieOrg/Makie.jl)
+- Packages for other advanced usage:
+  - [`StaticArrays.jl`](https://github.com/JuliaArrays/StaticArrays.jl)
+  - [`SciMLOperators.jl`](https://github.com/SciML/SciMLOperators.jl)
+  - [`DiffEqCallbacks.jl`](https://github.com/SciML/DiffEqCallbacks.jl)

docs/src/resources/api.md

@@ -1,5 +1,11 @@
 ```@meta
 CurrentModule = QuantumToolbox
+
+DocTestSetup = quote
+    using LinearAlgebra
+    using SparseArrays
+    using QuantumToolbox
+end
 ```
 
 # [API](@id doc-API)