Port functionality from gml to GeometricOptimizers

.githooks/pre-push

@@ -0,0 +1,19 @@
+# pre-push git hook that runs all tests before pushing
+
+red='\033[0;31m'
+green='\033[0;32m'
+no_color='\033[0m'
+
+reponame=$(basename `git rev-parse --show-toplevel`)
+
+
+echo "\nRunning pre-push hook\n"
+echo "Testing $reponame"
+julia --project=@.  -e "using Pkg; Pkg.test(\"GeometricOptimizers\")"
+
+if [[ $? -ne 0 ]]; then
+        echo "\n${red}ERROR - Tests must pass before push!\n${no_color}"
+  exit 1
+fi
+
+echo "\n${green}Git hook was SUCCESSFUL!${no_color}\n"

.github/workflows/CI.yml

@@ -19,9 +19,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
-          - '1.9'
-          - '^1.10.0-0'
+          - '1.10'
+          - '1.11'
         os:
           - ubuntu-latest
           - macOS-latest

.github/workflows/Documenter.yml

@@ -0,0 +1,24 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Make docs (call julia documenter)
+        run: |
+          julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+          julia --project=docs --color=yes --threads=2 docs/make.jl
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

AUTHORS.md

@@ -1,6 +1,6 @@
 # Authors
 
-GeometricOptimizers' development is coordinated by a group of *principal developers*, who are also its main contributors and who can be contacted in case of questions about GeometricOptimizers. In addition, there are *contributors* who have provided substantial additions or modifications. Together, these two groups form "The GeometricOptimizers Authors" as mentioned in the [LICENSE](LICENSE.md) file.
+`GeometricOptimizers`' development is coordinated by a group of *principal developers*, who are also its main contributors and who can be contacted in case of questions about `GeometricOptimizers`. In addition, there are *contributors* who have provided substantial additions or modifications. Together, these two groups form "The GeometricOptimizers Authors" as mentioned in the [LICENSE](LICENSE.md) file.
 
 ## Principal Developers
 
@@ -11,7 +11,7 @@ GeometricOptimizers' development is coordinated by a group of *principal develop
 
 ## Contributors
 
-The following people contributed to SymbolicNetworks and are listed in alphabetical order:
+The following people contributed to `GeometricOptimizers` and are listed in alphabetical order:
 
 * Benedikt Brantner
 * Michael Kraus

Project.toml

@@ -1,13 +1,27 @@
 name = "GeometricOptimizers"
 uuid = "fc236c15-5557-4942-aa65-b650f329279e"
-authors = ["Michael Kraus"]
+authors = ["Michael Kraus", "Benedikt Brantner"]
 version = "1.0.0-DEV"
 
+[deps]
+ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
+LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
 [compat]
+ChainRulesCore = "1.25.0"
+KernelAbstractions = "0.9.31"
+LazyArrays = "2.3.1"
+SafeTestsets = "0.1.0"
+Zygote = "0.7.1"
 julia = "1.6"
 
 [extras]
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Test"]
+test = ["Test", "SafeTestsets", "Zygote"]

README.md

@@ -5,3 +5,15 @@
 [![Build Status](https://github.com/JuliaGNI/GeometricOptimizers.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaGNI/GeometricOptimizers.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/JuliaGNI/GeometricOptimizers.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaGNI/GeometricOptimizers.jl)
 [![PkgEval](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/G/GeometricOptimizers.svg)](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/G/GeometricOptimizers.html)
+
+
+## References
+- Brantner B. Generalizing Adam To Manifolds For Efficiently Training Transformers. arXiv preprint arXiv:2305.16901, 2023.
+
+## Development
+
+We are using git hooks, e.g., to enforce that all tests pass before pushing.
+In order to activate these hooks, the following command must be executed once:
+```
+git config core.hooksPath .githooks
+```

docs/Project.toml

@@ -1,3 +1,5 @@
 [deps]
+Bibliography = "f1be7e48-bf82-45af-a471-ae754a193061"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 GeometricOptimizers = "fc236c15-5557-4942-aa65-b650f329279e"

docs/make.jl

@@ -1,9 +1,15 @@
 using GeometricOptimizers
 using Documenter
+using DocumenterCitations
+import Bibliography
+
+bib = CitationBibliography(joinpath(@__DIR__, "src", "GeometricOptimizers.bib"))
+Bibliography.sort_bibliography!(bib.entries, :nyt)  # name-year-title
 
 DocMeta.setdocmeta!(GeometricOptimizers, :DocTestSetup, :(using GeometricOptimizers); recursive=true)
 
 makedocs(;
+    plugins = [bib],
     modules=[GeometricOptimizers],
     authors="Michael Kraus",
     repo="https://github.com/JuliaGNI/GeometricOptimizers.jl/blob/{commit}{path}#{line}",
@@ -16,6 +22,7 @@ makedocs(;
     ),
     pages=[
         "Home" => "index.md",
+        "References" => "references.md",
     ],
 )
 

docs/src/GeometricOptimizers.bib

@@ -0,0 +1,61 @@
+@book{goodfellow2016deep,
+  title={Deep learning},
+  author={Goodfellow, Ian and Bengio, Yoshua and Courville, Aaron},
+  year={2016},
+  publisher={MIT press},
+  address={Cambridge, MA}
+}
+
+@article{brantner2023generalizing,
+  title={Generalizing Adam To Manifolds For Efficiently Training Transformers},
+  author={Brantner, Benedikt},
+  journal={arXiv preprint arXiv:2305.16901},
+  year={2023}
+}
+
+@book{hairer2006geometric,
+  title={Geometric Numerical integration: structure-preserving algorithms for ordinary differential equations},
+  author={Hairer, Ernst and Lubich, Christian and Wanner, Gerhard},
+  year={2006},
+  publisher={Springer},
+  address={Heidelberg}
+}
+
+@article{mezzadri2006generate,
+  title={How to generate random matrices from the classical compact groups},
+  author={Mezzadri, Francesco},
+  journal={arXiv preprint math-ph/0609050},
+  year={2006}
+}
+
+@article{absil2004riemannian,
+  title={Riemannian geometry of Grassmann manifolds with a view on algorithmic computation},
+  author={Absil, Pierre-Antoine and Mahony, Robert and Sepulchre, Rodolphe},
+  journal={Acta Applicandae Mathematica},
+  volume={80},
+  pages={199--220},
+  year={2004},
+  publisher={Springer}
+}
+
+@book{absil2008optimization,
+  title={Optimization algorithms on matrix manifolds},
+  author={Absil, Pierre-Antoine and Mahony, Robert and Sepulchre, Rodolphe},
+  publisher={Princeton University Press},
+  address={Princeton, New Jersey},
+  year={2008}
+}
+
+@article{bendokat2020grassmann,
+  title={A Grassmann manifold handbook: Basic geometry and computational aspects},
+  author={Bendokat, Thomas and Zimmermann, Ralf and Absil, Pierre-Antoine},
+  journal={arXiv preprint arXiv:2011.13699},
+  year={2020}
+}
+
+@article{bendokat2021real,
+  title={The real symplectic Stiefel and Grassmann manifolds: metrics, geodesics and applications},
+  author={Bendokat, Thomas and Zimmermann, Ralf},
+  journal={arXiv preprint arXiv:2108.12447},
+  year={2021}
+}

docs/src/references.md

@@ -0,0 +1,9 @@
+# References 
+
+```@raw latex
+\thispagestyle{empty}
+```
+
+```@bibliography
+*
+```

src/GeometricOptimizers.jl

@@ -1,5 +1,61 @@
 module GeometricOptimizers
 
-# Write your package code here.
+    using KernelAbstractions
+    using Random
+    using LinearAlgebra: Adjoint, qr!, norm, I, mul!, rmul!
+    import LinearAlgebra
+    import ChainRulesCore
+    using ChainRulesCore: ProjectTo
+    # we use the Vcat function from LazyArrays
+    import LazyArrays
 
+    include("utils.jl")
+
+    export Manifold, StiefelManifold, GrassmannManifold
+    export rgrad
+    include("manifolds/abstract_manifold.jl")
+    include("manifolds/stiefel_manifold.jl")
+    include("manifolds/grassmann_manifold.jl")
+
+    export SkewSymMatrix, SymmetricMatrix, LowerTriangular, UpperTriangular
+    include("special_matrices/skew_symmetric.jl")
+    include("special_matrices/symmetric.jl")
+    include("special_matrices/stiefel_projection.jl")
+    include("special_matrices/triangular.jl")
+    include("special_matrices/lower_triangular.jl")
+    include("special_matrices/upper_triangular.jl")
+
+    export StiefelLieAlgHorMatrix, GrassmannLieAlgHorMatrix
+    include("lie_algebras/abstract_lie_algebra_horizontal.jl")
+    include("lie_algebras/stiefel_lie_algebra_horizontal.jl")
+    include("lie_algebras/grassmann_lie_algebra_horizontal.jl")
+    include("lie_algebras/stiefel_projection.jl")
+
+    export GlobalSection, global_rep
+    include("global_sections/global_sections.jl")
+    include("global_sections/omega_functions.jl")
+
+    include("retractions/modified_exponential.jl")
+    include("retractions/retraction_types.jl")
+    include("retractions/retractions.jl")
+
+    # optimizer methods I
+    include("optimizers/optimizer_method.jl")
+
+    # optimizer caches
+    include("optimizers/optimizer_caches.jl")
+    include("optimizers/bfgs_cache.jl")
+
+    # optimizer
+    export Optimizer
+    include("optimizers/optimizer.jl")
+
+    # optimizer methods II
+    include("optimizers/gradient_optimizer.jl")
+    include("optimizers/momentum_optimizer.jl")
+    include("optimizers/adam_optimizer.jl")
+    include("optimizers/adam_optimizer_with_decay.jl")
+    include("optimizers/bfgs_optimizer.jl")
+
+    include("optimizers/init_optimizer_cache.jl")
 end