Merge branch 'master' into kellertuer/modularize-tests-I

# Conflicts: # test/runtests.jl
JuliaManifolds · Jan 27, 2024 · 6a155f1 · 6a155f1
2 parents beaaf8b + e46a864
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diff --git a/.github/workflows/documenter.yml b/.github/workflows/documenter.yml
@@ -9,7 +9,7 @@ jobs:
   docs:
     name: Documentation
     runs-on: ubuntu-latest
-    if: "contains( github.event.pull_request.labels.*.name, 'preview docs') || github.ref == 'refs/heads/master' || contains(github.ref, 'refs/tags/')"
+    if: contains( github.event.pull_request.labels.*.name, 'preview docs') || github.ref == 'refs/heads/master' || contains(github.ref, 'refs/tags/')
     steps:
       - uses: actions/checkout@v4
       - uses: quarto-dev/quarto-actions/setup@v2
@@ -22,7 +22,7 @@ jobs:
         uses: julia-actions/cache@v1
       - name: Cache Quarto
         id: cache-quarto
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-name: cache-quarto
         with:
@@ -32,7 +32,7 @@ jobs:
             ${{ runner.os }}-${{ env.cache-name }}-
       - name: Cache Documenter
         id: cache-documenter
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-name: cache-documenter
         with:
@@ -42,7 +42,7 @@ jobs:
             ${{ runner.os }}-${{ env.cache-name }}-
       - name: Cache CondaPkg
         id: cache-condaPkg
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-name: cache-condapkg
         with:

diff --git a/NEWS.md b/NEWS.md
@@ -5,119 +5,172 @@ 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).
 
+## [0.9.13] – 2024-01-24
+
+### Added
+
+* added the real symplectic Grassmann manifold `SymplecticGrassmann`
+* Introduce the manifold of `HamiltonianMatrices` and a wrapper for `Hamiltonian` matrices
+* introduce `rand(:HamiltonianMatrices)`
+* extend `rand` to also `rand!` for `HamiltonianMatrices`, `SymplecticMatrices` and `SymplecticStiefel`
+* implement `riemannian_gradient` conversion for `SymplecticMatrices` and `SymplecticGrassmann`
+* the new manifold of `MultinomialSymmetricPositiveDefinite` matrices
+* `rand!` for `MultinomialDoublyStochastic` and `MultinomialSymmetric`
+
+### Deprecated
+
+* Rename `Symplectic` to `SimplecticMatrices` in order to have a `Symplectic` wrapper for such matrices as well in the future for the next breaking change.
+* Rename `SymplecticMatrix` to `SymplecticElement` to clarify that it is the special matrix ``J_{2n}`` and not an arbitrary symplectic matrix.
+
+### Fixed
+
+* a bug that cause `project` for tangent vectors to return wrong results on `MultinomialDoublyStochastic`
+
+## [0.9.12] – 2024-01-21
+
+### Fixed
+
+* Fixed `var` on `TranslationGroup`.
+
+## [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
 
-- Improved distribution of random vector generation for rotation matrices and complex circle.
+* Improved distribution of random vector generation for rotation matrices and complex circle.
 
-## [0.9.7] - 2023-11-14
+## [0.9.7] – 2023-11-14
 
 ### Fixed
 
-- Fixed `is_flat` for `CholeskySpace` and `SymmetricPositiveDefinite` with `LogCholeskyMetric` [https://github.com/JuliaManifolds/Manifolds.jl/issues/684](https://github.com/JuliaManifolds/Manifolds.jl/issues/684).
+* Fixed `is_flat` for `CholeskySpace` and `SymmetricPositiveDefinite` with `LogCholeskyMetric` [https://github.com/JuliaManifolds/Manifolds.jl/issues/684](https://github.com/JuliaManifolds/Manifolds.jl/issues/684).
 
 ## [0.9.6] - 2023-11-09
 
 ### Fixed
 
-- Fixed real coefficient basis for complex circle (an issue exposed by [https://github.com/JuliaManifolds/ManifoldsBase.jl/pull/173](https://github.com/JuliaManifolds/ManifoldsBase.jl/pull/173)).
-- Fixed `VeeOrthogonalBasis` test for non-real manifolds.
+* Fixed real coefficient basis for complex circle (an issue exposed by [https://github.com/JuliaManifolds/ManifoldsBase.jl/pull/173](https://github.com/JuliaManifolds/ManifoldsBase.jl/pull/173)).
+* Fixed `VeeOrthogonalBasis` test for non-real manifolds.
 
 ## [0.9.5] - 2023-11-08
 
 ### Changed
 
-- `identity_element` now returns a complex matrix for unitary group.
-- `number_of_coordinates` is now exported.
+* `identity_element` now returns a complex matrix for unitary group.
+* `number_of_coordinates` is now exported.
 
 ## [0.9.4] - 2023-11-06
 
 ### Added
 
-- Functions `inv_diff`, `inv_diff!`, `adjoint_inv_diff` and `adjoint_inv_diff!` that correspond to differentials and pullbacks of group inversion.
-- Julia 1.10-rc CI workflow.
+* Functions `inv_diff`, `inv_diff!`, `adjoint_inv_diff` and `adjoint_inv_diff!` that correspond to differentials and pullbacks of group inversion.
+* Julia 1.10-rc CI workflow.
 
 ### Changed
 
-- Documentation project files are marked as compatible with `BoundaryValueDiffEq` v5.
+* Documentation project files are marked as compatible with `BoundaryValueDiffEq` v5.
 
 ### Fixed
 
-- Fixed issue with incorrect implementation of `apply_diff_group` in `GroupOperationAction` with left backward and right forward action [#669](https://github.com/JuliaManifolds/Manifolds.jl/issues/669).
+* Fixed issue with incorrect implementation of `apply_diff_group` in `GroupOperationAction` with left backward and right forward action [#669](https://github.com/JuliaManifolds/Manifolds.jl/issues/669).
 
 ## [0.9.3] - 2023-10-28
 
 ### Added
 
-- Support for `BoundaryValueDiffEq` v5.
+* Support for `BoundaryValueDiffEq` v5.
 
 ## [0.9.2] - 2023-10-27
 
 ### Added
 
-- `rand(G; vector_at=Identity(G))` now works for translation, special orthogonal and special Euclidean groups `G` (issue [#665](https://github.com/JuliaManifolds/Manifolds.jl/issues/665)).
-- `get_embedding` now works for `GeneralUnitaryMultiplicationGroup`.
-- Github action that checks for NEWS.md changes.
+* `rand(G; vector_at=Identity(G))` now works for translation, special orthogonal and special Euclidean groups `G` (issue [#665](https://github.com/JuliaManifolds/Manifolds.jl/issues/665)).
+* `get_embedding` now works for `GeneralUnitaryMultiplicationGroup`.
+* Github action that checks for NEWS.md changes.
 
 ## [0.9.1] - 2023-10-25
 
 ### Added
 
-- a new retraction and its inverse for the fixed Rank Manifolds, the orthographic retraction.
+* a new retraction and its inverse for the fixed Rank Manifolds, the orthographic retraction.
 
 ## [0.9.0] - 2023-10-24
 
 ### Added
 
-- Vector bundles are generalized to fiber bundles. Old `BundleFibers` functionality was reworked to better match mathematical abstractions. Fiber bundle functionality is experimental and minor changes may happen without a breaking release, with the exception of `TangentBundle` which is considered to be stable.
-- `RotationTranslationAction` is introduced.
+* Vector bundles are generalized to fiber bundles. Old `BundleFibers` functionality was reworked to better match mathematical abstractions. Fiber bundle functionality is experimental and minor changes may happen without a breaking release, with the exception of `TangentBundle` which is considered to be stable.
+* `RotationTranslationAction` is introduced.
 
 ### Changed
 
-- Sizes of all manifolds can now be either encoded in type or stored in a field to avoid over-specialization.
+* Sizes of all manifolds can now be either encoded in type or stored in a field to avoid over-specialization.
   The default is set to store the size in type parameter (except for `PowerManifold` and its variants), replicating the previous behavior.
   For field storage, pass the `parameter=:field` keyword argument to manifold constructor.
   For example statically sized `CenteredMatrices{m,n}` is now `CenteredMatrices{TypeParameter{Tuple{m,n}}}`, whereas the type of special Euclidean group with field-stored size is `CenteredMatrices{Tuple{Int,Int}}`. Similar change applies to:
-  - `CenteredMatrices{m,n}`,
-  - `CholeskySpace{N}`,
-  - `Elliptope{N,K}`,
-  - `Euclidean`,
-  - `FixedRankMatrices{m,n,k}`,
-  - `KendallsPreShapeSpace{n,k}`,
-  - `KendallsShapeSpace{n,k}`,
-  - `GeneralLinear{n}`,
-  - `GeneralUnitaryMultiplicationGroup{n}`,
-  - `GeneralizedGrassmann{n,k}`,
-  - `GeneralizedStiefel{n,k}`,
-  - `Grassmann{n,k}`,
-  - `Heisenberg{n}`,
-  - `Hyperbolic{n}`,
-  - `MultinomialMatrices{N,M}`,
-  - `MultinomialDoublyStochastic{n}`,
-  - `MultinomialSymmetric{n}`,
-  - `Orthogonal{n}`,
-  - `PowerManifold`,
-  - `PositiveArrays`,
-  - `PositiveMatrices`,
-  - `PositiveNumbers`,
-  - `ProbabilitySimplex{n}`,
-  - `SPDFixedDeterminant{n}`,
-  - `SpecialLinear{n}`,
-  - `SpecialOrthogonal{n}`,
-  - `SpecialUnitary{n}`,
-  - `SpecialEuclidean{n}`,
-  - `SpecialEuclideanManifold{n}`,
-  - `Spectrahedron{n,k}`,
-  - `SphereSymmetricMatrices{N}`,
-  - `Stiefel{n,k}`,
-  - `SymmetricMatrices{N}`,
-  - `SymmetricPositiveDefinite{n}`,
-  - `SymmetricPositiveSemidefiniteFixedRank{n,k}`,
-  - `Symplectic{n}`,
-  - `SymplecticStiefel{n,k}`,
-  - `TranslationGroup`,
-  - `Tucker`.
+  * `CenteredMatrices{m,n}`,
+  * `CholeskySpace{N}`,
+  * `Elliptope{N,K}`,
+  * `Euclidean`,
+  * `FixedRankMatrices{m,n,k}`,
+  * `KendallsPreShapeSpace{n,k}`,
+  * `KendallsShapeSpace{n,k}`,
+  * `GeneralLinear{n}`,
+  * `GeneralUnitaryMultiplicationGroup{n}`,
+  * `GeneralizedGrassmann{n,k}`,
+  * `GeneralizedStiefel{n,k}`,
+  * `Grassmann{n,k}`,
+  * `Heisenberg{n}`,
+  * `Hyperbolic{n}`,
+  * `MultinomialMatrices{N,M}`,
+  * `MultinomialDoublyStochastic{n}`,
+  * `MultinomialSymmetric{n}`,
+  * `Orthogonal{n}`,
+  * `PowerManifold`,
+  * `PositiveArrays`,
+  * `PositiveMatrices`,
+  * `PositiveNumbers`,
+  * `ProbabilitySimplex{n}`,
+  * `SPDFixedDeterminant{n}`,
+  * `SpecialLinear{n}`,
+  * `SpecialOrthogonal{n}`,
+  * `SpecialUnitary{n}`,
+  * `SpecialEuclidean{n}`,
+  * `SpecialEuclideanManifold{n}`,
+  * `Spectrahedron{n,k}`,
+  * `SphereSymmetricMatrices{N}`,
+  * `Stiefel{n,k}`,
+  * `SymmetricMatrices{N}`,
+  * `SymmetricPositiveDefinite{n}`,
+  * `SymmetricPositiveSemidefiniteFixedRank{n,k}`,
+  * `Symplectic{n}`,
+  * `SymplecticStiefel{n,k}`,
+  * `TranslationGroup`,
+  * `Tucker`.
 
   For example
 
@@ -157,12 +210,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   end
   ```
 
-- Argument order for type aliases `RotationActionOnVector` and `RotationTranslationActionOnVector`: most often dispatched on argument is now first.
-- A more consistent handling of action direction was introduced. 4-valued `ActionDirection` was split into 2-valued `ActionDirection` (either left or right action) and `GroupActionSide` (action acting from the left or right side). See [https://github.com/JuliaManifolds/Manifolds.jl/issues/637](https://github.com/JuliaManifolds/Manifolds.jl/issues/637) for a design discussion.
+* Argument order for type aliases `RotationActionOnVector` and `RotationTranslationActionOnVector`: most often dispatched on argument is now first.
+* A more consistent handling of action direction was introduced. 4-valued `ActionDirection` was split into 2-valued `ActionDirection` (either left or right action) and `GroupActionSide` (action acting from the left or right side). See [https://github.com/JuliaManifolds/Manifolds.jl/issues/637](https://github.com/JuliaManifolds/Manifolds.jl/issues/637) for a design discussion.
 
 ### Removed
 
-- `ProductRepr` is removed; please use `ArrayPartition` instead.
-- Default methods throwing "not implemented" `ErrorException` for some group-related operations. Standard `MethodError` is now thrown instead.
-- `LinearAffineMetric` was deprecated in a previous release and the symbol is now removed.
+* `ProductRepr` is removed; please use `ArrayPartition` instead.
+* Default methods throwing "not implemented" `ErrorException` for some group-related operations. Standard `MethodError` is now thrown instead.
+* `LinearAffineMetric` was deprecated in a previous release and the symbol is now removed.
   Please use `AffineInvariantMetric` instead.
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 = "0.9.13"
 
 [deps]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
@@ -43,7 +43,7 @@ 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"
@@ -52,15 +52,15 @@ 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/make.jl b/docs/make.jl
@@ -113,11 +113,13 @@ makedocs(;
                 "Generalized Stiefel" => "manifolds/generalizedstiefel.md",
                 "Generalized Grassmann" => "manifolds/generalizedgrassmann.md",
                 "Grassmann" => "manifolds/grassmann.md",
+                "Hamiltonian" => "manifolds/hamiltonian.md",
                 "Hyperbolic space" => "manifolds/hyperbolic.md",
                 "Lorentzian manifold" => "manifolds/lorentz.md",
                 "Multinomial doubly stochastic matrices" => "manifolds/multinomialdoublystochastic.md",
                 "Multinomial matrices" => "manifolds/multinomial.md",
                 "Multinomial symmetric matrices" => "manifolds/multinomialsymmetric.md",
+                "Multinomial symmetric positive definite matrices" => "manifolds/multinomialsymmetricpositivedefinite.md",
                 "Oblique manifold" => "manifolds/oblique.md",
                 "Probability simplex" => "manifolds/probabilitysimplex.md",
                 "Positive numbers" => "manifolds/positivenumbers.md",
@@ -133,7 +135,8 @@ makedocs(;
                 "Symmetric positive definite" => "manifolds/symmetricpositivedefinite.md",
                 "SPD, fixed determinant" => "manifolds/spdfixeddeterminant.md",
                 "Symmetric positive semidefinite fixed rank" => "manifolds/symmetricpsdfixedrank.md",
-                "Symplectic" => "manifolds/symplectic.md",
+                "Symplectic Grassmann" => "manifolds/symplecticgrassmann.md",
+                "Symplectic matrices" => "manifolds/symplectic.md",
                 "Symplectic Stiefel" => "manifolds/symplecticstiefel.md",
                 "Torus" => "manifolds/torus.md",
                 "Tucker" => "manifolds/tucker.md",