diff --git a/docs/src/related-work.md b/docs/src/related-work.md index 615f1203..74d5c215 100644 --- a/docs/src/related-work.md +++ b/docs/src/related-work.md @@ -20,7 +20,7 @@ on my (limited) experience with these packages. * [Ripser.jl](https://github.com/mtsch/Ripser.jl) my deprecated wrapper of the original C++ program. Very bare-bones and outdated. Runs a bit slower than Ripserer. -* [Sparips.jl](https://github.com/mtsch/Ripser.jl) this is a preprocessor that comes with +* [Sparips.jl](https://github.com/bbrehm/Sparips.jl) this is a preprocessor that comes with a different wrapper of Ripser. The preprocessor allows you to compute persistent homology of very large datasets. Integrating it with Ripserer is on my TODO list. diff --git a/test/extra/cycles.jl b/test/extra/cycles.jl index c353d880..f76d5d0d 100644 --- a/test/extra/cycles.jl +++ b/test/extra/cycles.jl @@ -6,16 +6,14 @@ using Ripserer: distance_matrix, OneSkeleton @testset "OneSkeleton respects the Graphs interface" begin @testset "no threshold or removed simplices" begin - flt = Rips( - [ - 0 1 2 3 2 1 - 1 0 1 2 3 2 - 2 1 0 1 2 3 - 3 2 1 0 1 2 - 2 3 2 1 0 1 - 1 2 3 2 1 0 - ] - ) + flt = Rips([ + 0 1 2 3 2 1 + 1 0 1 2 3 2 + 2 1 0 1 2 3 + 3 2 1 0 1 2 + 2 3 2 1 0 1 + 1 2 3 2 1 0 + ]) g = OneSkeleton(flt) @test eltype(g) ≡ Int @@ -127,16 +125,14 @@ end @testset "Cycle reconstruction" begin @testset "small cycle" begin - flt = Rips( - [ - 0 1 2 3 2 1 - 1 0 1 2 3 2 - 2 1 0 1 2 3 - 3 2 1 0 1 2 - 2 3 2 1 0 1 - 1 2 3 2 1 0 - ] - ) + flt = Rips([ + 0 1 2 3 2 1 + 1 0 1 2 3 2 + 2 1 0 1 2 3 + 3 2 1 0 1 2 + 2 3 2 1 0 1 + 1 2 3 2 1 0 + ]) interval = ripserer(flt; reps=true)[2][1] cyc1 = reconstruct_cycle(flt, interval) @@ -282,16 +278,14 @@ end end @testset "Errors" begin - flt = Rips( - [ - 0 1 2 3 2 1 - 1 0 1 2 3 2 - 2 1 0 1 2 3 - 3 2 1 0 1 2 - 2 3 2 1 0 1 - 1 2 3 2 1 0 - ] - ) + flt = Rips([ + 0 1 2 3 2 1 + 1 0 1 2 3 2 + 2 1 0 1 2 3 + 3 2 1 0 1 2 + 2 3 2 1 0 1 + 1 2 3 2 1 0 + ]) _, d1, d2 = ripserer(flt; reps=2, dim_max=2) @test_throws ArgumentError reconstruct_cycle(flt, d1[1]) diff --git a/test/filtrations/custom.jl b/test/filtrations/custom.jl index 4a1717dc..aa6db34f 100644 --- a/test/filtrations/custom.jl +++ b/test/filtrations/custom.jl @@ -73,16 +73,14 @@ end end @testset "Custom filtration vs sparse Rips" begin - spdist = sparse( - [ - 0 1 0 0 0 1 - 1 0 1 0 0 0 - 0 1 0 1 0 0 - 0 0 1 0 1 0 - 0 0 0 1 0 1 - 1 0 0 0 1 0 - ] - ) + spdist = sparse([ + 0 1 0 0 0 1 + 1 0 1 0 0 0 + 0 1 0 1 0 0 + 0 0 1 0 1 0 + 0 0 0 1 0 1 + 1 0 0 0 1 0 + ]) cf = Custom([ (1,) => 0, (2,) => 0,