Link to external examples

.github/workflows/CI.yml

@@ -25,12 +25,12 @@ jobs:
             version: '1'
             arch: x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
       - run: |
           # Instantiate Pkg
           wget https://raw.githubusercontent.com/JuliaQuantumControl/JuliaQuantumControl/master/scripts/installorg.jl
@@ -49,7 +49,8 @@ jobs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+      - uses: julia-actions/cache@v1
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
@@ -90,7 +91,7 @@ jobs:
     name: Codestyle
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1'

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Michael Goerz <[email protected]> and contributors
+Copyright (c) 2024 Michael Goerz <[email protected]> and contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

docs/make.jl

@@ -1,4 +1,5 @@
 using QuantumControlBase
+using QuantumPropagators
 using Krotov
 using Documenter
 using DocumenterCitations
@@ -9,25 +10,44 @@ using Plots
 gr()
 ENV["GKSwstype"] = "100"
 
-include(joinpath("..", "test", "download_dumps.jl"))
-
-# Generate examples
-include("generate.jl")
-
-DocMeta.setdocmeta!(Krotov, :DocTestSetup, :(using Krotov); recursive=true)
 
 PROJECT_TOML = Pkg.TOML.parsefile(joinpath(@__DIR__, "..", "Project.toml"))
 VERSION = PROJECT_TOML["version"]
 NAME = PROJECT_TOML["name"]
 AUTHORS = join(PROJECT_TOML["authors"], ", ") * " and contributors"
 GITHUB = "https://github.com/JuliaQuantumControl/Krotov.jl"
 
+DEV_OR_STABLE = "stable/"
+if endswith(VERSION, "dev")
+    DEV_OR_STABLE = "dev/"
+end
+
+links = InterLinks(
+    "TimerOutputs" => (
+        "https://github.com/KristofferC/TimerOutputs.jl",
+        joinpath(@__DIR__, "src", "inventories", "TimerOutputs.toml")
+    ),
+    "QuantumPropagators" => "https://juliaquantumcontrol.github.io/QuantumPropagators.jl/$DEV_OR_STABLE",
+    "QuantumControl" => "https://juliaquantumcontrol.github.io/QuantumControl.jl/$DEV_OR_STABLE",
+    "GRAPE" => "https://juliaquantumcontrol.github.io/GRAPE.jl/$DEV_OR_STABLE",
+    "Examples" => "https://juliaquantumcontrol.github.io/QuantumControlExamples.jl/$DEV_OR_STABLE",
+)
+
 println("Starting makedocs")
 
 bib = CitationBibliography(joinpath(@__DIR__, "src", "refs.bib"); style=:numeric)
 
+PAGES = [
+    "Home" => "index.md",
+    "Overview" => "overview.md",
+    "Examples" => "examples.md",
+    "API" => "api.md",
+    "References" => "references.md",
+    hide("externals.md"),
+]
+
 makedocs(;
-    plugins=[bib],
+    plugins=[bib, links],
     modules=[Krotov],
     authors=AUTHORS,
     sitename="Krotov.jl",
@@ -43,27 +63,14 @@ makedocs(;
                 "https://juliaquantumcontrol.github.io/QuantumControl.jl/dev/assets/topbar/topbar.js"
             ),
         ],
+        size_threshold_ignore=["externals.md"],
         mathengine=KaTeX(),
         footer="[$NAME.jl]($GITHUB) v$VERSION docs powered by [Documenter.jl](https://github.com/JuliaDocs/Documenter.jl).",
     ),
-    pages=[
-        "Home" => "index.md",
-        "Overview" => "overview.md",
-        "Examples" => [
-            "List of Examples" => "examples/index.md",
-            "Example 1 (TLS)" => "examples/simple_state_to_state.md",
-            "Example 2 (Diss. Gate)" => "examples/rho_3states.md",
-            "Example 3 (Parametrization)" => "examples/state_to_state_parametrizations.md",
-            "Example 4 (PE)" => "examples/perfect_entanglers.md",
-        ],
-        "API" => "api.md",
-        "References" => "references.md",
-    ],
+    pages=PAGES,
     warnonly=true,
 )
 
 println("Finished makedocs")
 
-rm(joinpath(@__DIR__, "build", "examples", ".gitignore"))
-
 deploydocs(; repo="github.com/JuliaQuantumControl/Krotov.jl", devbranch="master")

docs/src/api.md

@@ -1,6 +1,7 @@
 # API
 
 ```@index
+Pages = ["api.md"]
 ```
 
 ```@autodocs

docs/src/examples.md

@@ -0,0 +1,7 @@
+# Examples
+
+The following examples illustrate the use of Krotov's method:
+
+* Example: [Entangling quantum gates for coupled transmon qubits](@extref Examples). Written for [GRAPE](@extref GRAPE :doc:`index`), but could use Krotov's method interchangeably.
+* Example: [Optimization of a Dissipative Quantum Gate](@extref Examples)
+* Tutorial: [Pulse Parametrization for Krotov's Method](@extref Examples)

docs/src/externals.md

@@ -0,0 +1,39 @@
+```@autodocs
+Modules = [QuantumControlBase]
+```
+
+```@autodocs
+Modules = [QuantumPropagators]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.Generators]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.Arnoldi]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.Interfaces]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.Controls]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.Storage]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.SpectralRange]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.Newton]
+```
+
+```@autodocs
+Modules = [QuantumPropagators.Cheby]
+```

docs/src/index.md

@@ -17,7 +17,7 @@ version_badge = "![v$VERSION](https://img.shields.io/badge/version-v$VERSION-gre
 Markdown.parse("$github_badge $version_badge")
 ```
 
-Implementation of [Krotov's method of optimal control](https://arxiv.org/abs/1008.5126) enhanced with automatic differentiation.
+Implementation of Krotov's method of optimal control [Krotov1996,SomloiCP1993,BartanaJCP1997,PalaoPRA2003,ReichJCP2012,GoerzSPP2019](@cite) enhanced with automatic differentiation [GoerzQ2022](@cite).
 
 Part of [`QuantumControl.jl`](https://github.com/JuliaQuantumControl/QuantumControl.jl#readme) and the [JuliaQuantumControl](https://github.com/JuliaQuantumControl) organization.
 
@@ -26,44 +26,12 @@ Part of [`QuantumControl.jl`](https://github.com/JuliaQuantumControl/QuantumCont
 
 ## Contents
 
-### Overview
-
 ```@contents
-Pages = [
-    "overview.md",
-]
-Depth = 1
+Depth = 2
+Pages = [pair[2] for pair in Main.PAGES[2:end-1]]
 ```
 
-### Examples
-
-```@contents
-Pages = [
-    "examples/simple_state_to_state.md",
-    "examples/rho_3states.md",
-    "examples/state_to_state_parametrizations.md",
-    "examples/perfect_entanglers.md",
-]
-Depth = 1
-```
-
-See also the [general examples](https://juliaquantumcontrol.github.io/QuantumControl.jl/stable/examples/) of the [QuantumControl](https://juliaquantumcontrol.github.io/QuantumControl.jl/stable/) package.
-
-
-### API
-
-```@contents
-Pages = [
-    "api.md",
-]
-Depth = 1
-```
 
 ## History
 
 See the [Releases](https://github.com/JuliaQuantumControl/Krotov.jl/releases) on Github.
-
-## References
-
-```@bibliography
-```

docs/src/inventories/TimerOutputs.toml

@@ -0,0 +1,84 @@
+[Inventory]
+format = "DocInventories v0"
+project = "TimerOutputs.jl"
+version = "0.5.23"
+
+[[std.doc]]
+name = "readme"
+uri = ""
+dispname = "TimerOutputs"
+
+[[std.label]]
+name = "timeroutputs"
+uri = "#$"
+dispname = "TimerOutputs"
+[[std.label]]
+name = "example-output"
+uri = "#$"
+dispname = "Example output"
+[[std.label]]
+name = "usage"
+uri = "#$"
+dispname = "Usage"
+[[std.label]]
+name = "settings-for-printing"
+uri = "#$"
+dispname = "Settings for printing"
+[[std.label]]
+name = "flattening"
+uri = "#$"
+dispname = "Flattening"
+[[std.label]]
+name = "merging"
+uri = "#$"
+dispname = "Merging"
+[[std.label]]
+name = "resetting"
+uri = "#$"
+dispname = "Resetting"
+[[std.label]]
+name = "indexing-into-a-table"
+uri = "#$"
+dispname = "Indexing into a table"
+[[std.label]]
+name = "querying-data"
+uri = "#$"
+dispname = "Querying data"
+[[std.label]]
+name = "default-timer"
+uri = "#$"
+dispname = "Default Timer"
+[[std.label]]
+name = "measuring-time-consumed-outside-timeit-blocks"
+uri = "#$"
+dispname = "Measuring time consumed outside @timeit blocks"
+[[std.label]]
+name = "shared-timers"
+uri = "#$"
+dispname = "Shared Timers"
+[[std.label]]
+name = "serialization"
+uri = "#$"
+dispname = "Serialization"
+[[std.label]]
+name = "overhead"
+uri = "#$"
+dispname = "Overhead"
+[[std.label]]
+name = "author"
+uri = "#$"
+dispname = "Autor"
+[[std.label]]
+name = "acknowledgments"
+uri = "#$"
+dispname = "Acknowledgments"
+
+[[jl.type]]
+name = "TimerOutputs.TimerOutput"
+uri = "#usage"
+[[jl.function]]
+name = "TimerOutputs.print_timer"
+uri = "#settings-for-printing"
+[[jl.function]]
+name = "TimerOutputs.reset_timer!"
+uri = "#resetting"