Upgrade Manifolds.jl to ManifoldsBase 0.13 (#468)

* Sphere tests work. * Lost in Default Metric Dispatch. * move parallel transport to Level 3 * is_default_metric set; and `inner` forwarding * Grassmann and Stiefel updates * Adapt Grassmann and Elliptope. * test IsExplicitDecorator. * imports one further function * finish fixed rank. * Adapt Circle to the new validation scheme. * Symmetric update * Fix DoublyStochastic and ProbSimplex. * Fix Hyperbolic. * Fix Spectrahedron * Fix SphereSymmetricMatrices * Fix SymPosSemidefFR. * fix SkewHermitian. * add the power dimension to Oblique. * fix ProductManifold * return ArrayPartition/ProductRepr more consistently * Fix symplectic Stiefel. * Work on the interaction between Validation and group. * fixed group-metric interaction * Finish Circle Group. * towards an explicit handling of GroupManifold (and IsGroupManifold has automatic passthrough/transparency) * rewrite transparency. * Extract the explicit group decorator – GroupManifold – to its own file. * ...just has_approx_invariant_metric missing for general linear. * finish most (up to has_approx_invariant_metric) of SE. * ExplicitManifold should reduce this but it still errors. * fixing some group<->metric interactions * Fix fallbacks and special/general linear groups. * Introduce (and document) layer2 log_lie * some improvements to FixedRank coverage * two small tricks to test ConnectionManifolds * FiniteDiff and Zygote backends are moved entirely to ManifoldDiff.jl * ForwardDiff and ReverseDiff moved to ManifoldDiff Co-authored-by: Mateusz Baran <[email protected]>
JuliaManifolds · May 10, 2022 · 01c62dd · 01c62dd · kellertuer · May 10, 2022
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -7,12 +7,15 @@ on:
 
 jobs:
   test:
-    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }}
+    name: Julia ${{ matrix.julia-version }} - ${{ matrix.group }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: ["1.5", "1.6", "~1.7.0-0"]
+        julia-version: ["1.6", "1.7"]
         os: [ubuntu-latest, macOS-latest]
+        group:
+          - 'test_manifolds'
+          - 'test_lie_groups'
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -23,8 +26,9 @@ jobs:
       - uses: julia-actions/julia-runtest@latest
         env:
           PYTHON: ""
+          MANIFOLDS_TEST_GROUP: ${{ matrix.group }}
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v2
         with:
           fail_ci_if_error: false
-        if: ${{ matrix.julia-version == '1.6' && matrix.os =='ubuntu-latest' }}
+        if: ${{ matrix.julia-version == '1.7' && matrix.os =='ubuntu-latest' }}
diff --git a/.github/workflows/clear_preview.yml b/.github/workflows/clear_preview.yml
@@ -1,4 +1,4 @@
-name: Documentation Preview Cleanup
+name: Doc Preview Cleanup
 
 on:
   pull_request:
@@ -12,17 +12,15 @@ jobs:
         uses: actions/checkout@v2
         with:
           ref: gh-pages
-
-      - name: Delete preview and history
+      - name: Delete preview and history + push changes
         run: |
-            git config user.name "Documenter.jl"
-            git config user.email "[email protected]"
-            git rm -rf "previews/PR$PRNUM"
-            git commit -m "delete preview"
-            git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
         env:
-            PRNUM: ${{ github.event.number }}
-
-      - name: Push changes
-        run: |
-            git push --force origin gh-pages-new:gh-pages
+            PRNUM: ${{ github.event.number }}
diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
@@ -4,12 +4,15 @@ on:
 
 jobs:
   test:
-    name: Julia nightly - ${{ matrix.os }}
+    name: Julia nightly - ${{ matrix.group }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macOS-latest, windows-latest]
+        group:
+          - 'test_manifolds'
+          - 'test_lie_groups'
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -20,3 +23,4 @@ jobs:
       - uses: julia-actions/julia-runtest@latest
         env:
           PYTHON: ""
+          MANIFOLDS_TEST_GROUP: ${{ matrix.group }}
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -38,7 +38,7 @@ Even providing a single new method is a good contribution.
 
 A main contribution you can provide is another manifold that is not yet included in the
 package.
-A manifold is a concrete type of [`AbstractManifold`](https://juliamanifolds.github.io/Manifolds.jl/latest/interface.html#ManifoldsBase.AbstractManifold) from [`ManifoldsBase.jl`](https://juliamanifolds.github.io/Manifolds.jl/latest/interface.html).
+A manifold is a concrete type of [`AbstractManifold`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/types.html#ManifoldsBase.AbstractManifold) from [`ManifoldsBase.jl`](https://juliamanifolds.github.io/Manifolds.jl/latest/interface.html).
 This package also provides the main set of functions a manifold can/should implement.
 Don't worry if you can only implement some of the functions.
 If the application you have in mind only requires a subset of these functions, implement those.
@@ -49,7 +49,7 @@ See for example [exp!](https://juliamanifolds.github.io/Manifolds.jl/latest/inte
 The non-mutating one (e.g. `exp`) always falls back to use the mutating one, so in most cases it should
 suffice to implement the mutating one (e.g. `exp!`).
 
-Note that since the first argument is _always_ the [`AbstractManifold`](https://juliamanifolds.github.io/Manifolds.jl/latest/interface.html#ManifoldsBase.AbstractManifold), the mutated argument is always the second one in the signature.
+Note that since the first argument is _always_ the [`AbstractManifold`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/types.html#ManifoldsBase.AbstractManifold), the mutated argument is always the second one in the signature.
 In the example we have `exp(M, p, X)` for the exponential map and `exp!(M, q, X, p)` for the mutating one, which stores the result in `q`.
 
 On the other hand, the user will most likely look for the documentation of the non-mutating version, so we recommend adding the docstring for the non-mutating one, where all different signatures should be collected in one string when reasonable.

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 = "0.7.8"
+version = "0.8.0"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
@@ -27,11 +27,10 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Colors = "0.12"
 Distributions = "0.22.6, 0.23, 0.24, 0.25"
 Einsum = "0.4"
-FiniteDiff = "2"
 Graphs = "1.4"
 HybridArrays = "0.4"
 Kronecker = "0.4, 0.5"
-ManifoldsBase = "0.12.13"
+ManifoldsBase = "0.13"
 Plots = "1"
 RecipesBase = "1.1"
 RecursiveArrayTools = "2"
@@ -40,14 +39,12 @@ SimpleWeightedGraphs = "1.2"
 SpecialFunctions = "0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "1.0"
 StatsBase = "0.32, 0.33"
-julia = "1.5"
+julia = "1.6"
 
 [extras]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 DoubleFloats = "497a8b3b-efae-58df-a0af-a86822472b78"
-FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
 FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
-ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Gtk = "4c0ca9eb-093a-5379-98c5-f87ac0bbbf44"
 ImageIO = "82e4d734-157c-48bb-816b-45c225c6df19"
 ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
@@ -58,10 +55,8 @@ PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 QuartzImageIO = "dca85d43-d64c-5e67-8c65-017450d5d020"
 Quaternions = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 VisualRegressionTests = "34922c18-7c2a-561c-bac1-01e79b2c4c92"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Test", "Colors", "DoubleFloats", "FiniteDiff", "FiniteDifferences", "ForwardDiff", "Gtk", "ImageIO", "ImageMagick", "OrdinaryDiffEq", "NLsolve", "Plots", "PyPlot", "Quaternions", "QuartzImageIO", "RecipesBase", "ReverseDiff", "Zygote"]
+test = ["Test", "Colors", "DoubleFloats", "FiniteDifferences", "Gtk", "ImageIO", "ImageMagick", "OrdinaryDiffEq", "NLsolve", "Plots", "PyPlot", "Quaternions", "QuartzImageIO", "RecipesBase"]
diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 <div align="center">
-    <img src="https://github.com/JuliaManifolds/Manifolds.jl/blob/master/docs/src/assets/logo-text-readme.png" alt="Manifolds.jl" width="526">
+    <img src="https://github.com/JuliaManifolds/Manifolds.jl/blob/master/docs/src/assets/logo-text-readme.png" alt="Manifolds.jl Logo with text" width="526">
 </div>
 
 | **Documentation** | **Source** | **Citation** |
@@ -21,8 +21,8 @@ To install the package just type
 ] add Manifolds
 ```
 
-Then you can directly start, for example to stop half way from the north pole on the [`Sphere`](https://juliamanifolds.github.io/Manifolds.jl/stable/manifolds/sphere.html) to a point on the equator, you can generate the [`shortest_geodesic`](https://juliamanifolds.github.io/Manifolds.jl/stable/interface.html#ManifoldsBase.shortest_geodesic-Tuple{AbstractManifold,Any,Any}).
-It internally employs [`exp`](https://juliamanifolds.github.io/Manifolds.jl/latest/interface.html#Base.exp-Tuple{AbstractManifold,Any,Any}) and [`log`](https://juliamanifolds.github.io/Manifolds.jl/latest/interface.html#Base.log-Tuple{AbstractManifold,Any,Any}).
+Then you can directly start, for example to stop half way from the north pole on the [`Sphere`](https://juliamanifolds.github.io/Manifolds.jl/stable/manifolds/sphere.html) to a point on the equator, you can generate the [`shortest_geodesic`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions.html#ManifoldsBase.shortest_geodesic-Tuple{AbstractManifold,%20Any,%20Any}).
+It internally employs [`exp`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions.html#Base.exp-Tuple{AbstractManifold,%20Any,%20Any}) and [`log`](https://juliamanifolds.github.io/ManifoldsBase.jl/stable/functions.html#Base.log-Tuple{AbstractManifold,%20Any,%20Any}).
 
 ```julia
 using Manifolds

diff --git a/REQUIRE b/REQUIRE
diff --git a/assets/retraction_illustration.jl b/assets/retraction_illustration.jl
@@ -95,7 +95,7 @@ push!(
 )
 push!(
     tp,
-    raw"\node[label ={[label distance=.05cm]below:{\color{gray}$q=\exp_pX$}}] at (axis cs:" *
+    raw"\node[label ={[label distance=.05cm]left:{\color{gray}$q=\exp_pX$}}] at (axis cs:" *
     "$(real(qE)),$(imag(qE))) {};",
 )
 

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -2,24 +2,22 @@
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
-ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 HybridArrays = "1baab800-613f-4b0a-84e4-9cd3431bfbb9"
 Manifolds = "1cead3c2-87b3-11e9-0ccd-23c62b72b94e"
 ManifoldsBase = "3362f125-f0bb-47a3-aa74-596ffd7ef2fb"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-Documenter = "0.24, 0.25, 0.26, 0.27"
+Documenter = "0.27"
 FiniteDifferences = "0.12"
 Graphs = "1.4"
 HybridArrays = "0.4"
-ManifoldsBase = "0.12.9"
+ManifoldsBase = "0.13"
 Plots = "1"
 PyPlot = "2.9"
 StaticArrays = "1.0"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,6 +1,6 @@
 using Plots, RecipesBase, Manifolds, ManifoldsBase, Documenter, PyPlot
 # required for loading the manifold tests functios
-using Test, ForwardDiff, ReverseDiff, FiniteDifferences
+using Test, FiniteDifferences
 ENV["GKSwstype"] = "100"
 
 generated_path = joinpath(@__DIR__, "src", "misc")
@@ -26,13 +26,11 @@ end
 makedocs(
     # for development, we disable prettyurls
     format=Documenter.HTML(prettyurls=false, assets=["assets/favicon.ico"]),
-    modules=[Manifolds, ManifoldsBase],
+    modules=[Manifolds],
     authors="Seth Axen, Mateusz Baran, Ronny Bergmann, and contributors.",
     sitename="Manifolds.jl",
     pages=[
         "Home" => "index.md",
-        "ManifoldsBase.jl" => "interface.md",
-        "Examples" => ["How to implement a Manifold" => "examples/manifold.md"],
         "Manifolds" => [
             "Basic manifolds" => [
                 "Centered matrices" => "manifolds/centeredmatrices.md",

diff --git a/docs/src/assets/images/projection_illustration.png b/docs/src/assets/images/projection_illustration.png
diff --git a/docs/src/assets/images/projection_illustration_600.png b/docs/src/assets/images/projection_illustration_600.png
diff --git a/docs/src/assets/images/retraction_illustration.png b/docs/src/assets/images/retraction_illustration.png
diff --git a/docs/src/assets/images/retraction_illustration_600.png b/docs/src/assets/images/retraction_illustration_600.png