Update ValidationManifold (#217)

* A first commit updating doc strings, adding the point. * allow for AbstractMPoints to be in the validation scheme not only arrays. * Start with the ignores dictionary. * Unify _msg, add functions from the interface file. * make _msg also handle errors, hence tests pass again, where two errors gut a bit more precise. * Debugging and Test coverage. * Follow the same scheme as Manifolds.jl and make LTS (1.10) the lower bound. * Remove dependency on Requires.jl, since we raised LTS. * promote base points on new TVectors. * also update existing base points if a vector is mutated. * improve test cov. --------- Co-authored-by: Mateusz Baran <[email protected]>
JuliaManifolds · Dec 9, 2024 · 76d6a5f · 76d6a5f · kellertuer · Dec 9, 2024
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: ["1.6", "1.10", "~1.11.0-0"]
+        julia-version: ["lts", "1", "pre"]
         os: [ubuntu-latest, macOS-latest, windows-latest]
     steps:
       - uses: actions/checkout@v4

diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,21 @@ All notable changes to this project will be documented in this file.
 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).
 
+## [0.15.23] 09/12/2024
+
+### Added
+
+* a field `point` to `ValidationFibreVector` to potentially store the point of the vector.
+* a field `store_base_point` to `ValidationManifold` to indicate whether for new fibre vectors the base point should be stored.
+* a keyword `ignore_contexts` to `ValidationManifold` to ignore certain contexts from validation, such as `:Input`, `:Output`, `:Point`, or `:Vector`.
+* a keyword `ignore_functions` to `ValidationFibreVector` to ignore certain contexts within a single function. This is provided as a dictionary with the key being the (allocating) function and the value is a context or vector of contexts.
+
+### Changed
+
+* the internal function `array_value` was renamed to `internal_value` and is now exported, since it can be also used on elements that store values different from arrays,
+e.g. a `ValidationMPoint` storing a subtype of a `ManifoldPoint`. `array_value` is hence deprecated.
+* Minimum Julia version is now 1.10 (the LTS which replaced 1.6)
+
 ## [0.15.22] 15/11/2024
 
 ### Added

diff --git a/Project.toml b/Project.toml
@@ -1,14 +1,13 @@
 name = "ManifoldsBase"
 uuid = "3362f125-f0bb-47a3-aa74-596ffd7ef2fb"
 authors = ["Seth Axen <[email protected]>", "Mateusz Baran <[email protected]>", "Ronny Bergmann <[email protected]>", "Antoine Levitt <[email protected]>"]
-version = "0.15.22"
+version = "0.15.23"
 
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 
 [weakdeps]
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
@@ -33,13 +32,12 @@ Plots = "1"
 Printf = "1.6"
 Random = "1.6"
 RecursiveArrayTools = "2, 3"
-Requires = "1"
 ReverseDiff = "1"
 StaticArrays = "1"
 Statistics = "1.6"
 Quaternions = "0.7"
 Test = "1.6"
-julia = "1.6"
+julia = "1.10"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

diff --git a/docs/make.jl b/docs/make.jl
@@ -60,7 +60,7 @@ makedocs(;
     # for development, we disable prettyurls
     format = Documenter.HTML(;
         prettyurls = (get(ENV, "CI", nothing) == "true") || ("--prettyurls" ∈ ARGS),
-        assets = ["assets/favicon.ico", "assets/citations.css"],
+        assets = ["assets/favicon.ico", "assets/citations.css", "assets/link-icons.css"],
         size_threshold_warn = 200 * 2^10, # raise slightly from 100 to 200 KiB
         size_threshold = 300 * 2^10,      # raise slightly 200 to to 300 KiB
     ),

diff --git a/docs/src/assets/link-icons.css b/docs/src/assets/link-icons.css
@@ -0,0 +1,41 @@
+a[href^="https://juliamanifolds.github.io/Manifolds.jl/"]::before {
+    content: "";
+    background-image: url('logo-manifolds.png');
+    background-size: contain;
+    background-repeat: no-repeat;
+    display: inline-block;
+    height: 1em;
+    width: 1em;
+    margin-right: 4px;
+    vertical-align: middle;
+}
+
+a[href^="https://manoptjl.org/"]::before {
+    content: "";
+    background-image: url('logo-manopt.png');
+    background-size: contain;
+    background-repeat: no-repeat;
+    display: inline-block;
+    height: 1em;
+    width: 1em;
+    margin-right: 4px;
+    vertical-align: middle;
+}
+
+a[href^="https://en.wikipedia.org/"]::before {
+    content: "";
+    background-image: url('wikipedia.png');
+    background-size: contain;
+    background-repeat: no-repeat;
+    display: inline-block;
+    height: 1em;
+    width: 1em;
+    margin-right: 4px;
+    vertical-align: middle;
+}
+
+@media (prefers-color-scheme: dark) {
+    a[href^="https://juliamanifolds.github.io/Manifolds.jl/"]::before {
+        background-image: url('logo-manifolds-dark.png');
+    }
+}
diff --git a/docs/src/assets/logo-manifolds-dark.png b/docs/src/assets/logo-manifolds-dark.png
diff --git a/docs/src/assets/logo-manifolds.png b/docs/src/assets/logo-manifolds.png
diff --git a/docs/src/assets/logo-manopt.png b/docs/src/assets/logo-manopt.png
diff --git a/docs/src/assets/wikipedia.png b/docs/src/assets/wikipedia.png
diff --git a/ext/ManifoldsBasePlotsExt.jl b/ext/ManifoldsBasePlotsExt.jl
@@ -1,18 +1,9 @@
 module ManifoldsBasePlotsExt
 
-if isdefined(Base, :get_extension)
-    using ManifoldsBase
-    using Plots
-    using Printf: @sprintf
-    import ManifoldsBase: plot_slope
-else
-    # imports need to be relative for Requires.jl-based workflows:
-    # https://github.com/JuliaArrays/ArrayInterface.jl/pull/387
-    using ..ManifoldsBase
-    using ..Plots
-    using ..ManifoldsBase: @sprintf # is from Printf, but loaded in ManifoldsBase, and since Printf loading works here only on full moon days between 12 and noon, this trick might do it?
-    import ..ManifoldsBase: plot_slope
-end
+using ManifoldsBase
+using Plots
+using Printf: @sprintf
+import ManifoldsBase: plot_slope
 
 function ManifoldsBase.plot_slope(
     x,

diff --git a/ext/ManifoldsBaseQuaternionsExt.jl b/ext/ManifoldsBaseQuaternionsExt.jl
@@ -1,16 +1,8 @@
 module ManifoldsBaseQuaternionsExt
 
-if isdefined(Base, :get_extension)
-    using ManifoldsBase
-    using ManifoldsBase: ℍ, QuaternionNumbers
-    using Quaternions
-else
-    # imports need to be relative for Requires.jl-based workflows:
-    # https://github.com/JuliaArrays/ArrayInterface.jl/pull/387
-    using ..ManifoldsBase
-    using ..ManifoldsBase: ℍ, QuaternionNumbers
-    using ..Quaternions
-end
+using ManifoldsBase
+using ManifoldsBase: ℍ, QuaternionNumbers
+using Quaternions
 
 @inline function ManifoldsBase.allocate_result_type(
     ::AbstractManifold{ℍ},

diff --git a/ext/ManifoldsBaseRecursiveArrayToolsExt/ManifoldsBaseRecursiveArrayToolsExt.jl b/ext/ManifoldsBaseRecursiveArrayToolsExt/ManifoldsBaseRecursiveArrayToolsExt.jl
@@ -1,69 +1,34 @@
 module ManifoldsBaseRecursiveArrayToolsExt
 
-if isdefined(Base, :get_extension)
-    using ManifoldsBase
-    using RecursiveArrayTools
-    using ManifoldsBase: AbstractBasis, ProductBasisData, TangentSpaceType
-    using ManifoldsBase: number_of_components
-    using Random
+using ManifoldsBase
+using RecursiveArrayTools
+using ManifoldsBase: AbstractBasis, ProductBasisData, TangentSpaceType
+using ManifoldsBase: number_of_components
+using Random
 
-    import ManifoldsBase:
-        allocate,
-        allocate_on,
-        allocate_result,
-        default_inverse_retraction_method,
-        default_retraction_method,
-        default_vector_transport_method,
-        _get_dim_ranges,
-        get_vector,
-        get_vectors,
-        inverse_retract,
-        parallel_transport_direction,
-        parallel_transport_to,
-        project,
-        riemann_tensor,
-        submanifold_component,
-        submanifold_components,
-        vector_transport_direction,
-        _vector_transport_direction,
-        _vector_transport_to,
-        vector_transport_to,
-        ziptuples
-    import Base: copyto!, getindex, setindex!, view
-else
-    # imports need to be relative for Requires.jl-based workflows:
-    # https://github.com/JuliaArrays/ArrayInterface.jl/pull/387
-    using ..ManifoldsBase
-    using ..RecursiveArrayTools
-    using ..ManifoldsBase: AbstractBasis, ProductBasisData, TangentSpaceType
-    using ..ManifoldsBase: number_of_components
-    using ..Random
-
-    import ..ManifoldsBase:
-        allocate,
-        allocate_on,
-        allocate_result,
-        default_inverse_retraction_method,
-        default_retraction_method,
-        default_vector_transport_method,
-        _get_dim_ranges,
-        get_vector,
-        get_vectors,
-        inverse_retract,
-        parallel_transport_direction,
-        parallel_transport_to,
-        project,
-        _retract,
-        riemann_tensor,
-        submanifold_component,
-        submanifold_components,
-        vector_transport_direction,
-        _vector_transport_direction,
-        _vector_transport_to,
-        vector_transport_to,
-        ziptuples
-    import ..Base: copyto!, getindex, setindex!, view
-end
+import ManifoldsBase:
+    allocate,
+    allocate_on,
+    allocate_result,
+    default_inverse_retraction_method,
+    default_retraction_method,
+    default_vector_transport_method,
+    _get_dim_ranges,
+    get_vector,
+    get_vectors,
+    inverse_retract,
+    parallel_transport_direction,
+    parallel_transport_to,
+    project,
+    riemann_tensor,
+    submanifold_component,
+    submanifold_components,
+    vector_transport_direction,
+    _vector_transport_direction,
+    _vector_transport_to,
+    vector_transport_to,
+    ziptuples
+import Base: copyto!, getindex, setindex!, view
 
 include("ProductManifoldRecursiveArrayToolsExt.jl")
 

diff --git a/ext/ManifoldsBaseStatisticsExt.jl b/ext/ManifoldsBaseStatisticsExt.jl
@@ -1,16 +1,8 @@
 module ManifoldsBaseStatisticsExt
 
-if isdefined(Base, :get_extension)
-    using Statistics
-    using ManifoldsBase
-    import ManifoldsBase: find_best_slope_window
-else
-    # imports need to be relative for Requires.jl-based workflows:
-    # https://github.com/JuliaArrays/ArrayInterface.jl/pull/387
-    using ..Statistics
-    using ..ManifoldsBase
-    import ..ManifoldsBase: find_best_slope_window
-end
+using Statistics
+using ManifoldsBase
+import ManifoldsBase: find_best_slope_window
 
 function ManifoldsBase.find_best_slope_window(
     X,

diff --git a/src/ManifoldsBase.jl b/src/ManifoldsBase.jl
@@ -26,7 +26,6 @@ using LinearAlgebra
 using Markdown: @doc_str
 using Printf: @sprintf
 using Random
-using Requires
 
 include("maintypes.jl")
 include("numbers.jl")
@@ -1171,6 +1170,7 @@ include("DefaultManifold.jl")
 include("ProductManifold.jl")
 include("PowerManifold.jl")
 
+include("deprecated.jl")
 #
 #
 # Init
@@ -1207,23 +1207,6 @@ function __init__()
             end
         end
     end
-    # Extensions in the pre 1.9 fallback using Requires.jl
-    @static if !isdefined(Base, :get_extension)
-        @require RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" begin
-            include(
-                "../ext/ManifoldsBaseRecursiveArrayToolsExt/ManifoldsBaseRecursiveArrayToolsExt.jl",
-            )
-        end
-        @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin
-            include("../ext/ManifoldsBasePlotsExt.jl")
-        end
-        @require Quaternions = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0" begin
-            include("../ext/ManifoldsBaseQuaternionsExt.jl")
-        end
-        @require Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" begin
-            include("../ext/ManifoldsBaseStatisticsExt.jl")
-        end
-    end
 end
 #
 #
@@ -1368,6 +1351,7 @@ export ×,
     hat!,
     injectivity_radius,
     inner,
+    internal_value,
     inverse_retract,
     inverse_retract!,
     isapprox,