Merge branch 'master' into kellertuer/more-grassmann

# Conflicts: # NEWS.md
JuliaManifolds · Dec 29, 2023 · c4f69c3 · c4f69c3
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diff --git a/NEWS.md b/NEWS.md
@@ -11,7 +11,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 * added the real symplectic Grassmann manifold `SymplecticGrassmann`
 
-## [0.9.8] * 2023-11-17
+## [0.9.11] – 2023-12-27
+
+### Fixed
+
+* Fixed mixed array index number in-place `parallel_transport_to!` on zero-index `Euclidean`, on Julia 1.6.
+
+## [0.9.10] – 2023-12-27
+
+### Added
+
+* Compatibility with `RecursiveArrayTools` v3.
+
+### Fixed
+
+* Fixed mixed array index number in-place `parallel_transport_to!` on real `Circle`, on Julia 1.6.
+* Violations of MD004 lint rule in this file.
+
+## [0.9.9] – 2023-12-25
+
+### Fixed
+
+* introduced a nonzero `atol` for all point and vector checks that compre to zero.
+  This makes those checks a bit more relaxed by default and resolves [#630](https://github.com/JuliaManifolds/Manifolds.jl/issues/630).
+* `default_estimation_method(M, f)` is deprecated, use `default_approximation_method(M, f)` for your specific method `f` on the manifold `M`.
+* `AbstractEstimationMethod` is deprecated, use `AbstractApproximationMethod` instead.
+
+## [0.9.8] - 2023-11-17
 
 ### Fixed
 

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Manifolds"
 uuid = "1cead3c2-87b3-11e9-0ccd-23c62b72b94e"
 authors = ["Seth Axen <[email protected]>", "Mateusz Baran <[email protected]>", "Ronny Bergmann <[email protected]>", "Antoine Levitt <[email protected]>"]
-version = "0.9.8"
+version = "0.9.11"
 
 [deps]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
@@ -42,7 +42,7 @@ ManifoldsRecipesBaseExt = ["Colors", "RecipesBase"]
 ManifoldsTestExt = "Test"
 
 [compat]
-BoundaryValueDiffEq = "4, 5"
+BoundaryValueDiffEq = "4, 5.6.1"
 Colors = "0.12"
 Distributions = "0.22.6, 0.23, 0.24, 0.25"
 Einsum = "0.4"
@@ -51,15 +51,15 @@ HybridArrays = "0.4"
 Kronecker = "0.4, 0.5"
 LinearAlgebra = "1.6"
 ManifoldDiff = "0.3.7"
-ManifoldsBase = "0.15.0"
+ManifoldsBase = "0.15.6"
 Markdown = "1.6"
 MatrixEquations = "2.2"
 OrdinaryDiffEq = "6.31"
 Plots = "1"
 Quaternions = "0.5, 0.6, 0.7"
 Random = "1.6"
 RecipesBase = "1.1"
-RecursiveArrayTools = "2"
+RecursiveArrayTools = "2, 3"
 Requires = "0.5, 1"
 SimpleWeightedGraphs = "1.2"
 SpecialFunctions = "0.8, 0.9, 0.10, 1.0, 2"

diff --git a/README.md b/README.md
@@ -53,17 +53,19 @@ If you have any questions regarding the Manifolds.jl ecosystem feel free to reac
 
 ## Citation
 
-If you use `Manifolds.jl` in your work, please cite the following
+If you use `Manifolds.jl` in your work, please cite the following open access article
 
 ```biblatex
 @article{AxenBaranBergmannRzecki:2023,
-    AUTHOR     = {Seth D. Axen and Mateusz Baran and Ronny Bergmann and Krzysztof Rzecki},
-    EPRINT     = {2021.08777},
-    EPRINTTYPE = {arXiv},
-    JOURNAL    = {AMS Transactions on Mathematical Software},
-    NOTE       = {accepted for publication},
-    TITLE      = {Manifolds.jl: An Extensible {J}ulia Framework for Data Analysis on Manifolds},
-    YEAR       = {2023}
+    AUTHOR    = {Axen, Seth D. and Baran, Mateusz and Bergmann, Ronny and Rzecki, Krzysztof},
+    ARTICLENO = {33},
+    DOI       = {10.1145/3618296},
+    JOURNAL   = {ACM Transactions on Mathematical Software},
+    MONTH     = {dec},
+    NUMBER    = {4},
+    TITLE     = {Manifolds.Jl: An Extensible Julia Framework for Data Analysis on Manifolds},
+    VOLUME    = {49},
+    YEAR      = {2023}
 }
 ```
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -25,7 +25,7 @@ CondaPkg = "0.2"
 DiffEqCallbacks = "2"
 Distributions = "0.22.6, 0.23, 0.24, 0.25"
 Documenter = "1"
-DocumenterCitations = "1.2.1"
+DocumenterCitations = "1.3"
 FiniteDifferences = "0.12"
 Graphs = "1.4"
 HybridArrays = "0.4"

diff --git a/docs/src/features/statistics.md b/docs/src/features/statistics.md
@@ -9,6 +9,6 @@ Order = [:type, :function]
 ## Literature
 
 ```@bibliography
-Pages = ["features/statistics.md"]
+Pages = ["statistics.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/fixedrankmatrices.md b/docs/src/manifolds/fixedrankmatrices.md
@@ -9,6 +9,6 @@ Order = [:type, :function]
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/fixedrankmatrices.md"]
+Pages = ["fixedrankmatrices.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/grassmann.md b/docs/src/manifolds/grassmann.md
@@ -10,7 +10,7 @@ Order = [:type,:function]
 
 ```@autodocs
 Modules = [Manifolds]
-Pages = ["manifolds/GrassmannStiefel.jl"]
+Pages = ["GrassmannStiefel.jl"]
 Order = [:type,:function]
 ```
 
@@ -26,6 +26,6 @@ Order = [:type,:function]
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/grassmann.md"]
+Pages = ["grassmann.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/hyperbolic.md b/docs/src/manifolds/hyperbolic.md
@@ -180,6 +180,6 @@ plot!(scene, M, [pts[2], origin], geodesic_interpolation=100)
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/hyperbolic.md"]
+Pages = ["hyperbolic.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/probabilitysimplex.md b/docs/src/manifolds/probabilitysimplex.md
@@ -43,6 +43,6 @@ Public=false
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/probabilitysimplex.md"]
+Pages = ["probabilitysimplex.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/rotations.md b/docs/src/manifolds/rotations.md
@@ -39,6 +39,6 @@ Order = [:type, :function]
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/rotations.md"]
+Pages = ["rotations.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/sphere.md b/docs/src/manifolds/sphere.md
@@ -66,6 +66,6 @@ plot!(scene, M, pts2, vecs; wireframe = false, linewidth=1.5)
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/sphere.md"]
+Pages = ["sphere.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/stiefel.md b/docs/src/manifolds/stiefel.md
@@ -67,6 +67,6 @@ Private = true
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/stiefel.md"]
+Pages = ["stiefel.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/symplectic.md b/docs/src/manifolds/symplectic.md
@@ -40,6 +40,6 @@ Order = [:type, :function]
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/symplectic.md"]
+Pages = ["symplectic.md"]
 Canonical=false
 ```
diff --git a/docs/src/manifolds/symplecticstiefel.md b/docs/src/manifolds/symplecticstiefel.md
@@ -31,6 +31,6 @@ Order = [:type, :function]
 ## Literature
 
 ```@bibliography
-Pages = ["manifolds/symplecticstiefel.md"]
+Pages = ["symplecticstiefel.md"]
 Canonical=false
 ```
diff --git a/docs/src/references.bib b/docs/src/references.bib
@@ -10,7 +10,7 @@
 @book{AbsilMahonySepulchre:2008,
     AUTHOR    = {Absil, P.-A. and Mahony, R. and Sepulchre, R.},
     DOI       = {10.1515/9781400830244},
-    NOTE      = {available online at [press.princeton.edu/chapters/absil/](http://press.princeton.edu/chapters/absil/)},
+    NOTE      = {available online at \href{http://press.princeton.edu/chapters/absil/}{press.princeton.edu/chapters/absil/}},
     PUBLISHER = {Princeton University Press},
     TITLE     = {Optimization Algorithms on Matrix Manifolds},
     YEAR      = {2008},
@@ -89,13 +89,15 @@ @book{AyJostLeSchwachhoefer:2017
     PUBLISHER = {Springer Cham}
 }
 @article{AxenBaranBergmannRzecki:2023,
-    AUTHOR     = {Seth D. Axen and Mateusz Baran and Ronny Bergmann and Krzysztof Rzecki},
-    EPRINT     = {2021.08777},
-    EPRINTTYPE = {arXiv},
-    JOURNAL    = {AMS Transactions on Mathematical Software},
-    NOTE       = {accepted for publication},
-    TITLE      = {Manifolds.jl: An Extensible {J}ulia Framework for Data Analysis on Manifolds},
-    YEAR       = {2023}
+    AUTHOR    = {Axen, Seth D. and Baran, Mateusz and Bergmann, Ronny and Rzecki, Krzysztof},
+    ARTICLENO = {33},
+    DOI       = {10.1145/3618296},
+    JOURNAL   = {ACM Transactions on Mathematical Software},
+    MONTH     = {dec},
+    NUMBER    = {4},
+    TITLE     = {Manifolds.Jl: An Extensible Julia Framework for Data Analysis on Manifolds},
+    VOLUME    = {49},
+    YEAR      = {2023}
 }
 #
 # B
@@ -106,7 +108,6 @@ @article{Bacak:2014
     EPRINT     = {1210.2145},
     EPRINTTYPE = {arXiv},
     JOURNAL    = {SIAM Journal on Optimization},
-    NOTE       = {arXiv: [1210.2145](https://arxiv.org/abs/1210.2145)},
     NUMBER     = {3},
     PAGES      = {1542--1566},
     TITLE      = {Computing medians and means in Hadamard spaces},
@@ -115,9 +116,10 @@ @article{Bacak:2014
 }
 @article{BendokatZimmermann:2021,
     AUTHOR = {Bendokat, Thomas and Zimmermann, Ralf},
+    EPRINT     = {2108.12447},
+    EPRINTTYPE = {arXiv},
     Journal = {arXiv Preprint, 2108.12447},
     TITLE = {The real symplectic Stiefel and Grassmann manifolds: metrics, geodesics and applications},
-    URL = {https://arxiv.org/abs/2108.12447},
     YEAR = {2021}
 }
 @article{BendokatZimmermannAbsil:2020,
@@ -586,7 +588,7 @@ @article{MassartAbsil:2020
     DOI     = {10.1137/18m1231389},
     YEAR    = {2020},
     VOLUME  = {41},
-    NOTE = {Preprint: [sites.uclouvain.be/absil/2018.06](https://sites.uclouvain.be/absil/2018.06)},
+    NOTE    = {Preprint: \href{https://sites.uclouvain.be/absil/2018.06}{sites.uclouvain.be/absil/2018.06}},
     NUMBER  = {1},
     PAGES   = {171--198},
     AUTHOR  = {Estelle Massart and P.-A. Absil},

diff --git a/src/Manifolds.jl b/src/Manifolds.jl
@@ -48,6 +48,7 @@ import ManifoldsBase:
     check_vector,
     copy,
     copyto!,
+    default_approximation_method,
     default_inverse_retraction_method,
     default_retraction_method,
     default_vector_transport_method,
@@ -149,19 +150,14 @@ import ManifoldsBase:
     submanifold_component,
     submanifold_components,
     vector_space_dimension,
-    vector_transport_along, # just specified in Euclidean - the next 5 as well
-    vector_transport_along_diff,
-    vector_transport_along_project,
+    vector_transport_along,           # just specified in Euclidean - the next 5 as well
     vector_transport_along!,
-    vector_transport_along_diff!,
-    vector_transport_along_project!,
+    vector_transport_along_diff!,     # For consistency these are imported, but for now not
+    vector_transport_along_project!,  # overwritten with new definitons.
     vector_transport_direction,
-    vector_transport_direction_diff,
     vector_transport_direction!,
     vector_transport_direction_diff!,
     vector_transport_to,
-    vector_transport_to_diff,
-    vector_transport_to_project,
     vector_transport_to!,
     vector_transport_to_diff!,
     vector_transport_to_project!, # some overwrite layer 2
@@ -186,6 +182,9 @@ import ManifoldDiff:
     riemannian_Hessian,
     riemannian_Hessian!
 
+import Statistics: mean, mean!, median, median!, cov, var
+import StatsBase: mean_and_var
+
 using Base.Iterators: repeated
 using Distributions
 using Einsum: @einsum
@@ -198,6 +197,7 @@ using ManifoldsBase:
     ℝ,
     ℂ,
     ℍ,
+    AbstractApproximationMethod,
     AbstractBasis,
     AbstractDecoratorManifold,
     AbstractInverseRetractionMethod,
@@ -225,20 +225,26 @@ using ManifoldsBase:
     CotangentSpaceType,
     CoTFVector,
     CoTVector,
+    CyclicProximalPointEstimation,
     DefaultBasis,
     DefaultOrthogonalBasis,
     DefaultOrthonormalBasis,
     DefaultOrDiagonalizingBasis,
     DiagonalizingBasisData,
     DiagonalizingOrthonormalBasis,
     DifferentiatedRetractionVectorTransport,
+    EfficientEstimator,
     EmbeddedManifold,
     EmptyTrait,
     EuclideanMetric,
     ExponentialRetraction,
+    ExtrinsicEstimation,
     Fiber,
     FiberType,
     FVector,
+    GeodesicInterpolation,
+    GeodesicInterpolationWithinRadius,
+    GradientDescentEstimation,
     InverseProductRetraction,
     IsIsometricEmbeddedManifold,
     IsEmbeddedManifold,
@@ -295,6 +301,7 @@ using ManifoldsBase:
     VectorSpaceFiber,
     VectorSpaceType,
     VeeOrthogonalBasis,
+    WeiszfeldEstimation,
     @invoke_maker,
     _euclidean_basis_vector,
     combine_allocation_promotion_functions,
@@ -607,8 +614,9 @@ include("deprecated.jl")
 export test_manifold
 export test_group, test_action
 
-#
+# Abstract main types
 export CoTVector, AbstractManifold, AbstractManifoldPoint, TVector
+# Manifolds
 export AbstractSphere, AbstractProjectiveSpace
 export Euclidean,
     ArrayProjectiveSpace,
@@ -748,9 +756,10 @@ export AbstractInverseRetractionMethod,
     ShootingInverseRetraction,
     SoftmaxInverseRetraction
 # Estimation methods for median and mean
-export AbstractEstimationMethod,
+export AbstractApproximationMethod,
     GradientDescentEstimation,
     CyclicProximalPointEstimation,
+    EfficientEstimator,
     GeodesicInterpolation,
     GeodesicInterpolationWithinRadius,
     ExtrinsicEstimation
@@ -788,9 +797,10 @@ export ×,
     convert,
     complex_dot,
     decorated_manifold,
-    default_vector_transport_method,
+    default_approximation_method,
     default_inverse_retraction_method,
     default_retraction_method,
+    default_vector_transport_method,
     det_local_metric,
     differential_canonical_project,
     differential_canonical_project!,

diff --git a/src/deprecated.jl b/src/deprecated.jl
@@ -1 +1,6 @@
 
+@deprecate default_estimation_method(M::AbstractManifold, f) default_approximation_method(
+    M,
+    f,
+)
+@deprecate ExtrinsicEstimation() ExtrinsicEstimation(EfficientEstimator())