update footer and fix toc

ytdHuang · ytdHuang · commit 34d296c7891c · 2024-11-11T17:29:41.000+09:00
diff --git a/docs/src/.vitepress/config.mts b/docs/src/.vitepress/config.mts
@@ -28,6 +28,11 @@ export default defineConfig({
 
     markdown: {
         math: true,
+
+        // options for @mdit-vue/plugin-toc
+        // https://github.com/mdit-vue/mdit-vue/tree/main/packages/plugin-toc#options
+        toc: { level: [1, 2] },
+
         config(md) {
             md.use(tabsMarkdownPlugin),
                 md.use(mathjax3),
@@ -54,8 +59,8 @@ export default defineConfig({
             { icon: 'github', link: 'REPLACE_ME_DOCUMENTER_VITEPRESS' }
         ],
         footer: {
-            message: 'Made with <a href="https://luxdl.github.io/DocumenterVitepress.jl/dev/" target="_blank"><strong>DocumenterVitepress.jl</strong></a><br>',
-            copyright: `© Copyright ${new Date().getUTCFullYear()}.`
+            message: 'Made with <a href="https://documenter.juliadocs.org/stable/" target="_blank"><strong>Documenter.jl</strong></a>, <a href="https://vitepress.dev" target="_blank"><strong>VitePress</strong></a> and <a href="https://luxdl.github.io/DocumenterVitepress.jl/stable" target="_blank"><strong>DocumenterVitepress.jl</strong></a><br>Released under the BSD 3-Clause License. Powered by the <a href="https://www.julialang.org" target="_blank">Julia Programming Language</a>.<br>',
+            copyright: `© Copyright ${new Date().getUTCFullYear()} <a href="https://qutip.org/" target="_blank"><strong>QuTiP.org</strong></a>.`
         }
     }
 })
diff --git a/docs/src/resources/api.md b/docs/src/resources/api.md
@@ -4,13 +4,9 @@ CurrentModule = QuantumToolbox
 
 # [API](@id doc-API)
 
-<!-- Disable this first (until we find a way to fix it)
 **Table of contents**
 
-```@contents
-Pages = ["api.md"]
-```
--->
+[[toc]]
 
 ## [Quantum object (Qobj) and type](@id doc-API:Quantum-object-and-type)
 
diff --git a/docs/src/users_guide/time_evolution/intro.md b/docs/src/users_guide/time_evolution/intro.md
@@ -1,21 +1,24 @@
 # [Time Evolution and Quantum System Dynamics](@id doc:Time-Evolution-and-Quantum-System-Dynamics)
 
-<!-- Disable this first (until we find a way to fix it)
 **Table of contents**
 
-```@contents
-Pages = [
-    "intro.md",
-    "solution.md",
-    "sesolve.md",
-    "mesolve.md",
-    "mcsolve.md",
-    "stochastic.md",
-    "time_dependent.md",
-]
-Depth = 1:2
-```
--->
+- [Introduction](@ref doc-TE:Introduction)
+- [Time Evolution Solutions](@ref doc-TE:Time-Evolution-Solutions)
+    - [Solution](@ref doc-TE:Solution)
+    - [Multiple trajectories solution](@ref doc-TE:Multiple-trajectories-solution)
+    - [Accessing data in solutions](@ref doc-TE:Accessing-data-in-solutions)
+- [Schrödinger Equation Solver](@ref doc-TE:Schrödinger-Equation-Solver)
+    - [Unitary evolution](@ref doc-TE:Unitary-evolution)
+    - [Example: Spin dynamics](@ref doc-TE:Example:Spin-dynamics)
+- [Lindblad Master Equation Solver](@ref doc-TE:Lindblad-Master-Equation-Solver)
+    - [Von Neumann equation](@ref doc-TE:Von-Neumann-equation)
+    - [The Lindblad master equation](@ref doc-TE:The-Lindblad-master-equation)
+    - [Example: Dissipative Spin dynamics](@ref doc-TE:Example:Dissipative-Spin-dynamics)
+    - [Example: Harmonic oscillator in thermal bath](@ref doc-TE:Example:Harmonic-oscillator-in-thermal-bath)
+    - [Example: Two-level atom coupled to dissipative single-mode cavity](@ref doc-TE:Example:Two-level-atom-coupled-to-dissipative-single-mode-cavity)
+- [Monte-Carlo Solver](@ref doc-TE:Monte-Carlo-Solver)
+- [Stochastic Solver](@ref doc-TE:Stochastic-Solver)
+- [Solving Problems with Time-dependent Hamiltonians](@ref doc-TE:Solving-Problems-with-Time-dependent-Hamiltonians)
 
 # [Introduction](@id doc-TE:Introduction)
 
diff --git a/docs/src/users_guide/time_evolution/mesolve.md b/docs/src/users_guide/time_evolution/mesolve.md
@@ -4,7 +4,7 @@
 using QuantumToolbox
 ```
 
-## Von Neumann equation
+## [Von Neumann equation](@id doc-TE:Von-Neumann-equation)
 
 While the evolution of the state vector in a closed quantum system is deterministic (as we discussed in the previous section: [Schrödinger Equation Solver](@ref doc-TE:Schrödinger-Equation-Solver)), open quantum systems are stochastic in nature. The effect of an environment on the system of interest is to induce stochastic transitions between energy levels, and to introduce uncertainty in the phase difference between states of the system. The state of an open quantum system is therefore described in terms of ensemble averaged states using the density matrix formalism. A density matrix ``\hat{\rho}`` describes a probability distribution of quantum states ``|\psi_n\rangle`` in a matrix representation, namely
 
@@ -62,7 +62,7 @@ sol.expect
 sol.states
 ```
 
-## The Lindblad master equation
+## [The Lindblad master equation](@id doc-TE:The-Lindblad-master-equation)
 
 The standard approach for deriving the equations of motion for a system interacting with its environment is to expand the scope of the system to include the environment. The combined quantum system is then closed, and its evolution is governed by the von Neumann equation given in Eq. \eqref{von-Neumann-Eq}
 
@@ -108,7 +108,7 @@ Furthermore, `QuantumToolbox` solves the master equation in the [`SuperOperator`
 - [`liouvillian`](@ref)
 - [`lindblad_dissipator`](@ref)
 
-## Example: Spin dynamics
+## [Example: Dissipative Spin dynamics](@id doc-TE:Example:Dissipative-Spin-dynamics)
 
 Using the example with the dynamics of spin-``\frac{1}{2}`` from the previous section ([Schrödinger Equation Solver](@ref doc-TE:Schrödinger-Equation-Solver)), we can easily add a relaxation process (describing the dissipation of energy from the spin to the environment), by adding `[sqrt(γ) * sigmax()]` in the fourth parameter of the [`mesolve`](@ref) function.
 
@@ -143,7 +143,7 @@ axislegend(ax, position = :rt)
 fig
 ```
 
-## Example: Harmonic oscillator in thermal bath
+## [Example: Harmonic oscillator in thermal bath](@id doc-TE:Example:Harmonic-oscillator-in-thermal-bath)
 
 Consider a harmonic oscillator (single-mode cavity) couples to a thermal bath. If the single-mode cavity initially is in a `10`-photon [`fock`](@ref) state, the dynamics is calculated with the following code:
 
@@ -181,7 +181,7 @@ lines!(ax, tlist, Num)
 fig
 ```
 
-## Example: Two-level atom coupled to dissipative single-mode cavity
+## [Example: Two-level atom coupled to dissipative single-mode cavity](@id doc-TE:Example:Two-level-atom-coupled-to-dissipative-single-mode-cavity)
 
 Consider a two-level atom coupled to a dissipative single-mode cavity through a dipole-type interaction, which supports a coherent exchange of quanta between the two systems. If the atom initially is in its ground state and the cavity in a `5`-photon [`fock`](@ref) state, the dynamics is calculated with the following code:
 
diff --git a/docs/src/users_guide/time_evolution/sesolve.md b/docs/src/users_guide/time_evolution/sesolve.md
@@ -1,6 +1,6 @@
 # [Schrödinger Equation Solver](@id doc-TE:Schrödinger-Equation-Solver)
 
-## Unitary evolution
+## [Unitary evolution](@id doc-TE:Unitary-evolution)
 
 The dynamics of a closed (pure) quantum system is governed by the Schrödinger equation
 
@@ -19,7 +19,7 @@ where ``|\psi(t)\rangle`` is the state vector, and the Hamiltonian ``\hat{H}`` i
 
 The Schrödinger equation, which governs the time-evolution of closed quantum systems, is defined by its Hamiltonian and state vector. In the previous sections, [Manipulating States and Operators](@ref doc:Manipulating-States-and-Operators) and [Tensor Products and Partial Traces](@ref doc:Tensor-products-and-Partial-Traces), we showed how Hamiltonians and state vectors are constructed in `QuantumToolbox.jl`. Given a Hamiltonian, we can calculate the unitary (non-dissipative) time-evolution of an arbitrary initial state vector ``|\psi(0)\rangle`` using the `QuantumToolbox` time evolution problem [`sesolveProblem`](@ref) or directly call the function [`sesolve`](@ref). It evolves the state vector ``|\psi(t)\rangle`` and evaluates the expectation values for a set of operators `e_ops` at each given time points, using an ordinary differential equation solver provided by the powerful julia package [`DifferentialEquation.jl`](https://docs.sciml.ai/DiffEqDocs/stable/).
 
-## Example: Spin dynamics
+## [Example: Spin dynamics](@id doc-TE:Example:Spin-dynamics)
 
 ```@setup sesolve
 using QuantumToolbox
diff --git a/docs/src/users_guide/time_evolution/solution.md b/docs/src/users_guide/time_evolution/solution.md
@@ -4,7 +4,7 @@
 using QuantumToolbox
 ```
 
-## Solution
+## [Solution](@id doc-TE:Solution)
 `QuantumToolbox` utilizes the powerful [`DifferentialEquation.jl`](https://docs.sciml.ai/DiffEqDocs/stable/) to simulate different kinds of quantum system dynamics. Thus, we will first look at the data structure used for returning the solution (`sol`) from [`DifferentialEquation.jl`](https://docs.sciml.ai/DiffEqDocs/stable/). The solution stores all the crucial data needed for analyzing and plotting the results of a simulation. A generic structure [`TimeEvolutionSol`](@ref) contains the following properties for storing simulation data:
 
 | **Fields (Attributes)** | **Description** |
@@ -17,7 +17,7 @@ using QuantumToolbox
 | `sol.reltol` | The relative tolerance which is used during the solving process. |
 | `sol.retcode` (or `sol.converged`) | The returned status from the solver. |
 
-## Accessing data in solutions
+## [Accessing data in solutions](@id doc-TE:Accessing-data-in-solutions)
 
 To understand how to access the data in solution, we will use an example as a guide, although we do not worry about the simulation details at this stage. The Schrödinger equation solver ([`sesolve`](@ref)) used in this example returns [`TimeEvolutionSol`](@ref):
 
@@ -86,6 +86,6 @@ Here, the solution contains only one (final) state. Because the `states` will be
 
 Some other solvers can have other output.
 
-## Multiple trajectories solution
+## [Multiple trajectories solution](@id doc-TE:Multiple-trajectories-solution)
 
 This part is still under construction, please visit [API](@ref doc-API) first.
