Fix documentation on master (#694)

* Fix most of the docs. * Update news entry.
JuliaManifolds · Dec 25, 2023 · 631e8b4 · 631e8b4 · kellertuer · Dec 25, 2023
1 parent deede80
commit 631e8b4
Show file tree

Hide file tree

Showing 24 changed files with 38 additions and 38 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -5,7 +5,7 @@ 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).
 
-## [0.9.9] – 2023-12-24
+## [0.9.9] – 2023-12-25
 
 ### Fixed
 

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},
@@ -108,7 +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},
@@ -117,9 +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,
@@ -588,7 +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/GeneralUnitaryMatrices.jl b/src/manifolds/GeneralUnitaryMatrices.jl
@@ -946,7 +946,7 @@ end
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of `x` using
-[`GeodesicInterpolationWithinRadius`](@ref).
+[`GeodesicInterpolationWithinRadius`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolationWithinRadius).
 """
 mean(::GeneralUnitaryMatrices{<:Any,ℝ}, ::Any)
 

diff --git a/src/manifolds/GeneralizedGrassmann.jl b/src/manifolds/GeneralizedGrassmann.jl
@@ -276,7 +276,7 @@ end
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of `x` using
-[`GeodesicInterpolationWithinRadius`](@ref).
+[`GeodesicInterpolationWithinRadius`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolationWithinRadius).
 """
 mean(::GeneralizedGrassmann, ::Any...)
 

diff --git a/src/manifolds/Grassmann.jl b/src/manifolds/Grassmann.jl
@@ -167,7 +167,7 @@ end
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of `x` using
-[`GeodesicInterpolationWithinRadius`](@ref).
+[`GeodesicInterpolationWithinRadius`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolationWithinRadius).
 """
 mean(::Grassmann, ::Any...)
 

diff --git a/src/manifolds/Hyperbolic.jl b/src/manifolds/Hyperbolic.jl
@@ -328,7 +328,7 @@ manifold_volume(::Hyperbolic) = Inf
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of `x` on the
-[`Hyperbolic`](@ref) space using [`CyclicProximalPointEstimation`](@ref).
+[`Hyperbolic`](@ref) space using [`CyclicProximalPointEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.CyclicProximalPointEstimation).
 """
 mean(::Hyperbolic, ::Any...)
 

diff --git a/src/manifolds/ProbabilitySimplex.jl b/src/manifolds/ProbabilitySimplex.jl
@@ -342,7 +342,7 @@ end
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of `x` using
-[`GeodesicInterpolation`](@ref).
+[`GeodesicInterpolation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolation).
 """
 mean(::ProbabilitySimplex, ::Any...)
 

diff --git a/src/manifolds/ProjectiveSpace.jl b/src/manifolds/ProjectiveSpace.jl
@@ -393,7 +393,7 @@ end
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of points in vector `x`
-using [`GeodesicInterpolationWithinRadius`](@ref).
+using [`GeodesicInterpolationWithinRadius`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolationWithinRadius).
 """
 mean(::AbstractProjectiveSpace, ::Any...)
 

diff --git a/src/manifolds/Sphere.jl b/src/manifolds/Sphere.jl
@@ -415,7 +415,7 @@ end
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of `x` using
-[`GeodesicInterpolationWithinRadius`](@ref).
+[`GeodesicInterpolationWithinRadius`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolationWithinRadius).
 """
 mean(::AbstractSphere, ::Any...)
 

diff --git a/src/manifolds/SymmetricPositiveDefinite.jl b/src/manifolds/SymmetricPositiveDefinite.jl
@@ -285,7 +285,7 @@ end
     )
 
 Compute the Riemannian [`mean`](@ref mean(M::AbstractManifold, args...)) of `x` using
-[`GeodesicInterpolation`](@ref).
+[`GeodesicInterpolation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolation).
 """
 mean(::SymmetricPositiveDefinite, ::Any)
 

diff --git a/src/statistics.jl b/src/statistics.jl
@@ -87,7 +87,7 @@ as the point that satisfies the minimizer
 ````
 where $\mathrm{d}_{\mathcal M}$ denotes the Riemannian [`distance`](@ref).
 
-In the general case, the [`GradientDescentEstimation`](@ref) is used to compute the mean.
+In the general case, the [`GradientDescentEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GradientDescentEstimation) is used to compute the mean.
     mean(
         M::AbstractManifold,
         x::AbstractVector,
@@ -110,7 +110,7 @@ Compute the mean using the specified `method`.
         kwargs...,
     )
 
-Compute the mean using the gradient descent scheme [`GradientDescentEstimation`](@ref).
+Compute the mean using the gradient descent scheme [`GradientDescentEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GradientDescentEstimation).
 
 Optionally, provide `p0`, the starting point (by default set to the first data
 point). `stop_iter` denotes the maximal number of iterations to perform and the
@@ -243,7 +243,7 @@ end
 
 Estimate the Riemannian center of mass of `x` in an online fashion using
 repeated weighted geodesic interpolation. See
-[`GeodesicInterpolation`](@ref) for details.
+[`GeodesicInterpolation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolation) for details.
 
 If `shuffle_rng` is provided, it is used to shuffle the order in which the
 points are considered for computing the mean.
@@ -305,7 +305,7 @@ end
     )
 
 Estimate the Riemannian center of mass of `x` using
-[`GeodesicInterpolationWithinRadius`](@ref).
+[`GeodesicInterpolationWithinRadius`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolationWithinRadius).
 
 See [`mean`](@ref mean(::AbstractManifold, ::AbstractVector, ::AbstractVector, ::GeodesicInterpolation))
 for a description of `kwargs`.
@@ -388,7 +388,7 @@ end
     )
 
 Estimate the Riemannian center of mass of `x` using
-[`ExtrinsicEstimation`](@ref), i.e. by computing the mean in the embedding and projecting
+[`ExtrinsicEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.ExtrinsicEstimation), i.e. by computing the mean in the embedding and projecting
 the result back.
 
 See [`mean`](@ref mean(::AbstractManifold, ::AbstractVector, ::AbstractVector, ::GeodesicInterpolation))
@@ -448,7 +448,7 @@ Compute the (optionally weighted) Riemannian median of the vector `x` of points
 where $\mathrm{d}_{\mathcal M}$ denotes the Riemannian [`distance`](@ref).
 This function is nonsmooth (i.e nondifferentiable).
 
-In the general case, the [`CyclicProximalPointEstimation`](@ref) is used to compute the
+In the general case, the [`CyclicProximalPointEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.CyclicProximalPointEstimation) is used to compute the
 median. However, this default may be overloaded for specific manifolds.
 
 Compute the median using the specified `method`.
@@ -479,7 +479,7 @@ end
         kwargs...,
     )
 
-Compute the median using [`CyclicProximalPointEstimation`](@ref).
+Compute the median using [`CyclicProximalPointEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.CyclicProximalPointEstimation).
 
 Optionally, provide `p0`, the starting point (by default set to the first
 data point). `stop_iter` denotes the maximal number of iterations to perform
@@ -510,7 +510,7 @@ Statistics.median(
         kwargs...,
     )
 
-Estimate the median of `x` using [`ExtrinsicEstimation`](@ref), i.e. by computing the median
+Estimate the median of `x` using [`ExtrinsicEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.ExtrinsicEstimation), i.e. by computing the median
 in the embedding and projecting the result back.
 
 See [`median`](@ref median(::AbstractManifold, ::AbstractVector, ::AbstractVector, ::CyclicProximalPointEstimation))
@@ -537,7 +537,7 @@ Statistics.median(
         kwargs...,
     )
 
-Compute the median using [`WeiszfeldEstimation`](@ref).
+Compute the median using [`WeiszfeldEstimation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.WeiszfeldEstimation).
 
 Optionally, provide `p0`, the starting point (by default set to the first
 data point). `stop_iter` denotes the maximal number of iterations to perform
@@ -888,7 +888,7 @@ If `shuffle_rng` is provided, it is used to shuffle the order in which the
 points are considered. Optionally, pass `retraction` and `inverse_retraction`
 method types to specify the (inverse) retraction.
 
-See [`GeodesicInterpolation`](@ref) for details on the geodesic
+See [`GeodesicInterpolation`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolation) for details on the geodesic
 interpolation method.
 
 !!! note
@@ -954,7 +954,7 @@ end
 Use repeated weighted geodesic interpolation to estimate the mean.
 Simultaneously, use a Welford-like recursion to estimate the variance.
 
-See [`GeodesicInterpolationWithinRadius`](@ref) and
+See [`GeodesicInterpolationWithinRadius`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions/#ManifoldsBase.GeodesicInterpolationWithinRadius) and
 [`mean_and_var`](@ref mean_and_var(::AbstractManifold, ::AbstractVector, ::AbstractWeights, ::GeodesicInterpolation))
 for more information.
 """

diff --git a/tutorials/getstarted.qmd b/tutorials/getstarted.qmd
@@ -429,7 +429,7 @@ Again, for all of these, the concrete types only have to be used if you want to
 
 ````{=commonmark}
 ```@bibliography
-Pages = ["tutorials/getstarted.md"]
+Pages = ["getstarted.md"]
 Canonical=false
 ```
 ````
diff --git a/tutorials/integration.qmd b/tutorials/integration.qmd
@@ -175,6 +175,6 @@ See [BoyaSudarshanTilma:2003](@cite) for some considerations on symmetric spaces
 ## Literature
 
 ```@bibliography
-Pages = ["tutorials/integration.md"]
+Pages = ["integration.md"]
 Canonical=false
 ```