Bump dependencies. (#309)

* Bump dependencies.
* Move ARC CG subsolver to the main module
* Update Changelog.md
* Add a workflow that makes sure we do not forget to add an entry to Changelog.md on PRs.
* Apply suggestions from code review
* Add Changelog to docs.

---------

Co-authored-by: Mateusz Baran <[email protected]>

Author: kellertuer

.github/workflows/changelog.yml

@@ -0,0 +1,12 @@
+name: Check Changelog
+on:
+  pull_request:
+
+jobs:
+  Check-Changelog:
+    name: Check Changelog Action
+    runs-on: ubuntu-latest
+    steps:
+      - uses: tarides/changelog-check-action@v2
+        with:
+          changelog: Changelog.md

.gitignore

@@ -20,3 +20,4 @@ docs/src/tutorials/*.md
 docs/.CondaPkg
 docs/src/tutorials/Optimize!_files
 docs/src/tutorials/*.html
+docs/src/changelog.md

Changelog.md

@@ -5,6 +5,68 @@ All notable Changes to the Julia package `Manopt.jl` will be documented in this
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.40] – 24/10/2023
+
+### Added
+
+* add a `--help` argument to `docs/make.jl` to document all availabel command line arguments
+* add a `--exclude-tutorials` argument to `docs/make.jl`. This way, when quarto is not available
+  on a computer, the docs can still be build with the tutorials not being added to the menu
+  such that documenter does not expect them to exist.
+
+### Changes
+
+* Bump dependencies to `ManifoldsBase.jl` 0.15 and `Manifolds.jl` 0.9
+* move the ARC CG subsolver to the main package, since `TangentSpace` is now already
+  available from `ManifoldsBase`.
+
+## [0.4.39] – 09/10/2023
+
+### Changes
+
+* also use the pair of a retraction and the inverse retraction (see last update)
+  to perform the relaxation within the Douglas-Rachford algorithm.
+
+## [0.4.38] – 08/10/2023
+
+### Changes
+
+* avoid allocations when calling `get_jacobian!` within the Levenberg-Marquard Algorithm.
+
+### Fixed
+
+* Fix a lot of typos in the documentation
+
+## [0.4.37] – 28/09/2023
+
+### Changes
+
+* add more of the Riemannian Levenberg-Marquard algorithms parameters as keywords, so they
+  can be changed on call
+* generalize the internal reflection of Douglas-Rachford, such that is also works with an
+  arbitrary pair of a reflection and an inverse reflection.
+
+## [0.4.36] – 20/09/2023
+
+### Fixed
+
+* Fixed a bug that caused non-matrix points and vectors to fail when working with approcimate
+
+## [0.4.35] – 14/09/2023
+
+### Added
+
+* The access to functions of the objective is now unified and encapsulated in proper `get_`
+  functions.
+
+## [0.4.34] – 02/09/2023
+
+### Added
+
+* an `ManifoldEuclideanGradientObjetive` to allow the cost, gradient, and Hessian and other
+  first or second derivative based elements to be Euclidean and converted when needed.
+* a keyword `objective_type=:Euclidean` for all solvers, that specifies that an Objective shall be created of the above type
+
 ## [0.4.33] - 24/08/2023
 
 ### Added
@@ -282,7 +344,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * a `max_stepsize` per manifold to avoid leaving the injectivity radius,
   which it also defaults to
 
-## {0.4.0] - 10/01/2023
+## [0.4.0] - 10/01/2023
 
 ### Added
 

Project.toml

@@ -1,7 +1,7 @@
 name = "Manopt"
 uuid = "0fc0a36d-df90-57f3-8f93-d78a9fc72bb5"
 authors = ["Ronny Bergmann <[email protected]>"]
-version = "0.4.39"
+version = "0.4.40"
 
 [deps]
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
@@ -40,8 +40,8 @@ Colors = "0.11.2, 0.12"
 DataStructures = "0.17, 0.18"
 LRUCache = "1.4"
 ManifoldDiff = "0.2, 0.3.3"
-Manifolds = "0.8.75"
-ManifoldsBase = "0.14.10"
+Manifolds = "0.9"
+ManifoldsBase = "0.15"
 PolynomialRoots = "1"
 Requires = "0.5, 1"
 julia = "1.6"

docs/Project.toml

@@ -22,6 +22,6 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 [compat]
 BenchmarkTools = "1.3"
 CondaPkg = "0.2"
-Documenter = "0.27"
-Manifolds = "0.8.75"
-ManifoldsBase = "0.13, 0.14"
+Documenter = "1"
+Manifolds = "0.8.81, 0.9"
+ManifoldsBase = "0.14.12, 0.15"

docs/make.jl

@@ -2,6 +2,28 @@
 #
 #
 
+if "--help" ∈ ARGS
+    println(
+        """
+docs/make.jl
+
+Render the `Manopt.jl` documenation with optinal arguments
+
+Arguments
+* `--exclude-docs` - exclude the tutorials from the menu of Documenter,
+  this can be used if you do not have Quarto installed to still be able to render the docs
+  locally on this machine. This option should not be set on CI.
+* `--help`         - print this help and exit without rendering the documentation
+* `--quarto`       – run the Quarto notebooks from the `tutorials/` folder before generating the documentation
+  this has to be run locally at least once for the `tutorials/*.md` files to exist that are included in
+  the documentation (see `--exclude-tutorials`) for the alternative.
+  If they are generated ones they are cached accordingly.
+  Then you can spare time in the rendering by not passing this argument.
+""",
+    )
+    exit(0)
+end
+
 #
 # (a) if docs is not the current active environment, switch to it
 # (from https://github.com/JuliaIO/HDF5.jl/pull/1020/) 
@@ -29,6 +51,17 @@ if "--quarto" ∈ ARGS
     end
 end
 
+tutorials_in_menu = true
+if "--exclude-tutorials" ∈ ARGS
+    @warn """
+    You are excluding the tutorials from the Menu,
+    which might be done if you can not render them locally.
+
+    Remember that this should never be done on CI for the full documentation.
+    """
+    tutorials_in_menu = false
+end
+
 # (c) load necessary packages for the docs
 using Documenter
 using DocumenterCitations
@@ -38,26 +71,42 @@ using LineSearches, LRUCache, Manopt, Manifolds, Plots
 generated_path = joinpath(@__DIR__, "src")
 base_url = "https://github.com/JuliaManifolds/Manopt.jl/blob/master/"
 isdir(generated_path) || mkdir(generated_path)
-open(joinpath(generated_path, "contributing.md"), "w") do io
-    # Point to source license file
-    println(
-        io,
-        """
-        ```@meta
-        EditURL = "$(base_url)CONTRIBUTING.md"
-        ```
-        """,
-    )
-    # Write the contents out below the meta block
-    for line in eachline(joinpath(dirname(@__DIR__), "CONTRIBUTING.md"))
-        println(io, line)
+for (md_file, doc_file) in
+    [("CONTRIBUTING.md", "contributing.md"), ("Changelog.md", "changelog.md")]
+    open(joinpath(generated_path, doc_file), "w") do io
+        # Point to source license file
+        println(
+            io,
+            """
+            ```@meta
+            EditURL = "$(base_url)$(md_file)"
+            ```
+            """,
+        )
+        # Write the contents out below the meta block
+        for line in eachline(joinpath(dirname(@__DIR__), md_file))
+            println(io, line)
+        end
     end
 end
 
+## Build titorials menu
+tutorials_menu =
+    "How to..." => [
+        "Get started: Optimize!" => "tutorials/Optimize!.md",
+        "Speedup using Inplace computations" => "tutorials/InplaceGradient.md",
+        "Use Automatic Differentiation" => "tutorials/AutomaticDifferentiation.md",
+        "Define Objectives in the Embedding" => "tutorials/EmbeddingObjectives.md",
+        "Count and use a Cache" => "tutorials/CountAndCache.md",
+        "Print Debug Output" => "tutorials/HowToDebug.md",
+        "Record values" => "tutorials/HowToRecord.md",
+        "Implement a Solver" => "tutorials/ImplementASolver.md",
+        "Do Constrained Optimization" => "tutorials/ConstrainedOptimization.md",
+        "Do Geodesic Regression" => "tutorials/GeodesicRegression.md",
+    ]
 # (e) ...finally! make docs
 bib = CitationBibliography(joinpath(@__DIR__, "src", "references.bib"); style=:alpha)
-makedocs(
-    bib;
+makedocs(;
     format=Documenter.HTML(;
         mathengine=MathJax3(), prettyurls=get(ENV, "CI", nothing) == "true"
     ),
@@ -86,36 +135,10 @@ makedocs(
     ],
     authors="Ronny Bergmann and contributors.",
     sitename="Manopt.jl",
-    strict=[
-        :doctest,
-        :linkcheck,
-        :parse_error,
-        :example_block,
-        :autodocs_block,
-        :cross_references,
-        :docs_block,
-        :eval_block,
-        :example_block,
-        :footnote,
-        :meta_block,
-        :missing_docs,
-        :setup_block,
-    ],
     pages=[
         "Home" => "index.md",
         "About" => "about.md",
-        "How to..." => [
-            "Get started: Optimize!" => "tutorials/Optimize!.md",
-            "Speedup using Inplace computations" => "tutorials/InplaceGradient.md",
-            "Use Automatic Differentiation" => "tutorials/AutomaticDifferentiation.md",
-            "Define Objectives in the Embedding" => "tutorials/EmbeddingObjectives.md",
-            "Count and use a Cache" => "tutorials/CountAndCache.md",
-            "Print Debug Output" => "tutorials/HowToDebug.md",
-            "Record values" => "tutorials/HowToRecord.md",
-            "Implement a Solver" => "tutorials/ImplementASolver.md",
-            "Do Constrained Optimization" => "tutorials/ConstrainedOptimization.md",
-            "Do Geodesic Regression" => "tutorials/GeodesicRegression.md",
-        ],
+        (tutorials_in_menu ? [tutorials_menu] : [])...,
         "Solvers" => [
             "Introduction" => "solvers/index.md",
             "Adaptive Regularization with Cubics" => "solvers/adaptive-regularization-with-cubics.md",
@@ -168,8 +191,10 @@ makedocs(
         "Contributing to Manopt.jl" => "contributing.md",
         "Extensions" => "extensions.md",
         "Notation" => "notation.md",
+        "Changelog" => "changelog.md",
         "References" => "references.md",
     ],
+    plugins=[bib],
 )
 deploydocs(; repo="github.com/JuliaManifolds/Manopt.jl", push_preview=true)
 #back to main env

docs/src/notation.md

@@ -2,10 +2,8 @@
 
 In this package, we follow the notation introduced in [Manifolds.jl – Notation](https://juliamanifolds.github.io/Manifolds.jl/latest/misc/notation.html)
 
-with the following additional or slightly changed notation
+with the following additional notation
 
 | Symbol | Description | Also used | Comment |
 |:--:|:--------------- |:--:|:-- |
 | ``∇`` | The [Levi-Cevita connection](https://en.wikipedia.org/wiki/Levi-Civita_connection) | | |
-| ``\operatorname{grad}f`` | The Riemannian gradient | ``∇f``| due to possible confusion with the connection, we try to avoid ``∇f`` |
-| ``\operatorname{Hess}f``| The Riemannian Hessian | |

docs/src/solvers/ChambollePock.md

@@ -3,7 +3,7 @@
 The Riemannian Chambolle–Pock is a generalization of the Chambolle–Pock algorithm [ChambollePock:2011](@citet*)
 It is also known as primal-dual hybrid gradient (PDHG) or primal-dual proximal splitting (PDPS) algorithm.
 
-In order to minimize over $p∈\mathcal M§ the cost function consisting of
+In order to minimize over $p∈\mathcal M$ the cost function consisting of
 
 ```math
 F(p) + G(Λ(p)),

ext/ManoptManifoldsExt/ARC_CG.jl

@@ -30,5 +30,4 @@ include("nonmutating_manifolds_functions.jl")
 include("artificialDataFunctionsManifolds.jl")
 include("ChambollePockManifolds.jl")
 include("alternating_gradient.jl")
-include("ARC_CG.jl")
 end

ext/ManoptManifoldsExt/ManoptManifoldsExt.jl

@@ -69,8 +69,10 @@ using ManifoldsBase:
     NestedPowerRepresentation,
     ParallelTransport,
     PowerManifold,
+    ProductManifold,
     ProjectionTransport,
     QRRetraction,
+    TangentSpace,
     ^,
     _read,
     _write,
@@ -123,6 +125,7 @@ using ManifoldsBase:
     set_component!,
     shortest_geodesic,
     shortest_geodesic!,
+    submanifold_components,
     vector_transport_to,
     vector_transport_to!,
     zero_vector,