Update Compat dependency, general maintenance (#156)

* Update julia compat, fix doctests

* Apply formatting

* Drop compat v3

* Fix Test.yml, restore compat allowed versions

* Fix docstrings so they work on CI

* appease aqua

* Remove mentions of PersistenceDiagramsBase

.github/workflows/Test.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        julia-version: ['1.6', '1', 'nightly']
+        julia-version: ['1', '1.6', 'nightly']
     name: ${{ matrix.julia-version }}
     steps:
       - uses: actions/checkout@v2

Project.toml

@@ -1,7 +1,7 @@
 name = "Ripserer"
 uuid = "aa79e827-bd0b-42a8-9f10-2b302677a641"
 authors = ["mtsch <matijacufar@gmail.com>"]
-version = "0.16.9"
+version = "0.16.10"
 
 [deps]
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
@@ -21,7 +21,7 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 TupleTools = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6"
 
 [compat]
-Compat = "3.10.0"
+Compat = "^3.10, 4"
 DataStructures = "0.17, 0.18"
 Distances = "0.8, 0.9, 0.10"
 Graphs = "1"
@@ -33,7 +33,7 @@ ProgressMeter = "1"
 RecipesBase = "1"
 StaticArrays = "0.12, 1"
 TupleTools = "1"
-julia = "1"
+julia = "1.6"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

README.md

@@ -45,7 +45,7 @@ matrices.
 
 ```julia
 julia> ripserer(data)
-# 2-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+# 2-element Vector{PersistenceDiagrams.PersistenceDiagram}:
 #  200-element 0-dimensional PersistenceDiagram
 #  84-element 1-dimensional PersistenceDiagram
 ```
@@ -56,7 +56,7 @@ tell `ripserer` to use them by passing them as the first argument.
 
 ```julia
 julia> ripserer(EdgeCollapsedRips, data)
-# 2-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+# 2-element Vector{PersistenceDiagrams.PersistenceDiagram}:
 #  200-element 0-dimensional PersistenceDiagram
 #  84-element 1-dimensional PersistenceDiagram
 ```
@@ -69,7 +69,7 @@ julia> rips = EdgeCollapsedRips(data, threshold=1)
 ```
 ```julia
 julia> ripserer(rips, dim_max=2)
-# 3-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+# 3-element Vector{PersistenceDiagrams.PersistenceDiagram}:
 #  200-element 0-dimensional PersistenceDiagram
 #  84-element 1-dimensional PersistenceDiagram
 #  16-element 2-dimensional PersistenceDiagram

src/base/chain.jl

@@ -22,39 +22,95 @@ julia> data = [(rand(), rand(), rand()) for _ in 1:100];
 julia> result = ripserer(data; reps=true, modulus=7);
 
 julia> chain = result[end][end].representative
-6-element Chain{Mod{7},Simplex{1, Float64, Int64}}:
- +Simplex{1}((87, 59), 0.23148225999797645) => 6 mod 7
- +Simplex{1}((59, 46), 0.3054281021426286) => 1 mod 7
- +Simplex{1}((87, 14), 0.32453294355760326) => 6 mod 7
- +Simplex{1}((87, 1), 0.34642558062390577) => 6 mod 7
- +Simplex{1}((100, 87), 0.3480194268484163) => 1 mod 7
- +Simplex{1}((79, 1), 0.36519064466525686) => 6 mod 7
+28-element Chain{Ripserer.Mod{7},Ripserer.Simplex{1, Float64, Int64}}:
+ +Simplex{1}((68, 54), 0.25178097927369875) => 6 mod 7
+ +Simplex{1}((54, 46), 0.2575262844682746) => 1 mod 7
+ +Simplex{1}((88, 56), 0.25936896586973557) => 1 mod 7
+ +Simplex{1}((79, 22), 0.26690101517910964) => 6 mod 7
+ +Simplex{1}((53, 13), 0.27161939814693414) => 6 mod 7
+ +Simplex{1}((24, 13), 0.28686687771884056) => 6 mod 7
+ +Simplex{1}((56, 54), 0.2869400047523196) => 6 mod 7
+ +Simplex{1}((50, 42), 0.29274772369750884) => 6 mod 7
+ +Simplex{1}((93, 50), 0.3022995886824861) => 1 mod 7
+ +Simplex{1}((73, 54), 0.30771273548368216) => 6 mod 7
+ ⋮
+ +Simplex{1}((70, 34), 0.3412250751087395) => 6 mod 7
+ +Simplex{1}((49, 42), 0.3414959312908324) => 6 mod 7
+ +Simplex{1}((49, 7), 0.35568373080560794) => 6 mod 7
+ +Simplex{1}((88, 46), 0.35629002982624475) => 1 mod 7
+ +Simplex{1}((95, 88), 0.3566986102316938) => 6 mod 7
+ +Simplex{1}((95, 54), 0.363029725360828) => 6 mod 7
+ +Simplex{1}((50, 13), 0.3648936036309352) => 6 mod 7
+ +Simplex{1}((24, 3), 0.3653704317993549) => 6 mod 7
+ +Simplex{1}((85, 42), 0.369953146904745) => 6 mod 7
 
 julia> simplex.(chain)
-6-element Vector{Simplex{1, Float64, Int64}}:
- +Simplex{1}((87, 59), 0.23148225999797645)
- +Simplex{1}((59, 46), 0.3054281021426286)
- +Simplex{1}((87, 14), 0.32453294355760326)
- +Simplex{1}((87, 1), 0.34642558062390577)
- +Simplex{1}((100, 87), 0.3480194268484163)
- +Simplex{1}((79, 1), 0.36519064466525686)
+28-element Vector{Simplex{1, Float64, Int64}}:
+ +Simplex{1}((68, 54), 0.25178097927369875)
+ +Simplex{1}((54, 46), 0.2575262844682746)
+ +Simplex{1}((88, 56), 0.25936896586973557)
+ +Simplex{1}((79, 22), 0.26690101517910964)
+ +Simplex{1}((53, 13), 0.27161939814693414)
+ +Simplex{1}((24, 13), 0.28686687771884056)
+ +Simplex{1}((56, 54), 0.2869400047523196)
+ +Simplex{1}((50, 42), 0.29274772369750884)
+ +Simplex{1}((93, 50), 0.3022995886824861)
+ +Simplex{1}((73, 54), 0.30771273548368216)
+ ⋮
+ +Simplex{1}((70, 34), 0.3412250751087395)
+ +Simplex{1}((49, 42), 0.3414959312908324)
+ +Simplex{1}((49, 7), 0.35568373080560794)
+ +Simplex{1}((88, 46), 0.35629002982624475)
+ +Simplex{1}((95, 88), 0.3566986102316938)
+ +Simplex{1}((95, 54), 0.363029725360828)
+ +Simplex{1}((50, 13), 0.3648936036309352)
+ +Simplex{1}((24, 3), 0.3653704317993549)
+ +Simplex{1}((85, 42), 0.369953146904745)
 
 julia> vertices.(chain)
-6-element Vector{Tuple{Int64, Int64}}:
- (87, 59)
- (59, 46)
- (87, 14)
- (87, 1)
- (100, 87)
- (79, 1)
+28-element Vector{Tuple{Int64, Int64}}:
+ (68, 54)
+ (54, 46)
+ (88, 56)
+ (79, 22)
+ (53, 13)
+ (24, 13)
+ (56, 54)
+ (50, 42)
+ (93, 50)
+ (73, 54)
+ ⋮
+ (70, 34)
+ (49, 42)
+ (49, 7)
+ (88, 46)
+ (95, 88)
+ (95, 54)
+ (50, 13)
+ (24, 3)
+ (85, 42)
 
 julia> coefficient.(chain)
-6-element Vector{Mod{7}}:
+28-element Vector{Mod{7}}:
  6 mod 7
  1 mod 7
+ 1 mod 7
+ 6 mod 7
+ 6 mod 7
+ 6 mod 7
  6 mod 7
  6 mod 7
  1 mod 7
+ 6 mod 7
+       ⋮
+ 6 mod 7
+ 6 mod 7
+ 6 mod 7
+ 1 mod 7
+ 6 mod 7
+ 6 mod 7
+ 6 mod 7
+ 6 mod 7
  6 mod 7
 
 ```

src/computation/ripserer.jl

@@ -98,17 +98,17 @@ julia> ts = range(0, 2π; length=20)[1:(end - 1)];
 julia> X = [((2 + cos(θ)) * cos(φ), (2 + cos(θ)) * sin(φ), sin(θ)) for θ in ts for φ in ts];
 
 julia> ripserer(X)
-2-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+2-element Vector{PersistenceDiagrams.PersistenceDiagram}:
  361-element 0-dimensional PersistenceDiagram
  362-element 1-dimensional PersistenceDiagram
 
 julia> ripserer(EdgeCollapsedRips, X; modulus=7, threshold=2)
-2-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+2-element Vector{PersistenceDiagrams.PersistenceDiagram}:
  361-element 0-dimensional PersistenceDiagram
  362-element 1-dimensional PersistenceDiagram
 
 julia> ripserer(Rips(X; threshold=1); alg=:involuted)
-2-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+2-element Vector{PersistenceDiagrams.PersistenceDiagram}:
  361-element 0-dimensional PersistenceDiagram
  362-element 1-dimensional PersistenceDiagram
 

src/computation/zerodimensional.jl

@@ -85,7 +85,7 @@ function interval(dset::DisjointSetsWithBirth, filtration, vertex, edge, cutoff,
             rep = (;
                 representative=sort!([
                     simplex(filtration, Val(0), (v,)) for v in find_leaves!(dset, vertex)
-                ]),
+                ])
             )
         else
             rep = NamedTuple()

src/extra/circularcoordinates.jl

@@ -192,7 +192,7 @@ CircularCoordinates(
   radius=(0.9510565162951535,),
   n_landmarks=10,
   partition=linear,
-  metric=Euclidean(0.0),
+  metric=Distances.Euclidean(0.0),
 )
 
 julia> summary(cc(data))

src/filtrations/alpha.jl

@@ -180,13 +180,13 @@ julia> length(Ripserer.edges(rips))
 
 julia> sort(ripserer(alpha)[2], by=persistence)[end]
 [0.375, 2.01) with:
- birth_simplex: Simplex{1, Float64, Int64}
- death_simplex: Simplex{2, Float64, Int64}
+ birth_simplex: Ripserer.Simplex{1, Float64, Int64}
+ death_simplex: Ripserer.Simplex{2, Float64, Int64}
 
 julia> sort(ripserer(rips)[2], by=persistence)[end]
 [0.375, 2.01) with:
- birth_simplex: Simplex{1, Float64, Int64}
- death_simplex: Simplex{2, Float64, Int64}
+ birth_simplex: Ripserer.Simplex{1, Float64, Int64}
+ death_simplex: Ripserer.Simplex{2, Float64, Int64}
 ```
 """
 struct Alpha{I,P<:SVector} <: AbstractCustomFiltration{I,Float64}

src/filtrations/edgecollapse.jl

@@ -164,24 +164,24 @@ julia> rips = Rips(data)
 Rips{Int64, Float64}(nv=100, sparse=false)
 
 julia> length(Ripserer.edges(rips))
-3906
+3934
 
 julia> collapsed = EdgeCollapsedRips(data) # or EdgeCollapsedRips(rips)
 EdgeCollapsedRips{Int64, Float64}(nv=100)
 
 julia> length(Ripserer.edges(collapsed))
-1419
+1324
 
 julia> ripserer(rips) == ripserer(collapsed)
 true
 
 julia> ripserer(collapsed; dim_max=4)
-5-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+5-element Vector{PersistenceDiagrams.PersistenceDiagram}:
  100-element 0-dimensional PersistenceDiagram
- 75-element 1-dimensional PersistenceDiagram
- 37-element 2-dimensional PersistenceDiagram
- 14-element 3-dimensional PersistenceDiagram
- 1-element 4-dimensional PersistenceDiagram
+ 58-element 1-dimensional PersistenceDiagram
+ 35-element 2-dimensional PersistenceDiagram
+ 10-element 3-dimensional PersistenceDiagram
+ 4-element 4-dimensional PersistenceDiagram
 
 ```
 

src/filtrations/rips.jl

@@ -13,7 +13,7 @@ julia> struct MyRips <: Ripserer.AbstractRipsFiltration{Int, Float16} end
 julia> Ripserer.adjacency_matrix(::MyRips) = [0 1 1; 1 0 1; 1 1 0]
 
 julia> ripserer(MyRips())
-2-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+2-element Vector{PersistenceDiagrams.PersistenceDiagram}:
  3-element 0-dimensional PersistenceDiagram
  0-element 1-dimensional PersistenceDiagram
 
@@ -185,7 +185,7 @@ faster.
 julia> data = [(sin(t), cos(t)) for t in range(0, 2π, length=101)][1:end-1];
 
 julia> ripserer(Rips(data))
-2-element Vector{PersistenceDiagramsBase.PersistenceDiagram}:
+2-element Vector{PersistenceDiagrams.PersistenceDiagram}:
  100-element 0-dimensional PersistenceDiagram
  1-element 1-dimensional PersistenceDiagram
 

test/aqua.jl

@@ -1,4 +1,7 @@
 using Aqua
 using Ripserer
 
-Aqua.test_all(Ripserer; ambiguities=false)
+if VERSION < v"1.8-DEV"
+    # Note: will have to change Project.toml for 1.8
+    Aqua.test_all(Ripserer; ambiguities=false)
+end

test/doctests.jl

@@ -2,11 +2,11 @@ using Documenter
 using Distances
 using Ripserer
 
-if VERSION ≥ v"1.7-DEV" || VERSION < v"1.6-DEV" || !Sys.islinux()
-    @warn "Doctests only run on Linux and Julia 1.6"
+if VERSION ≥ v"1.8-DEV" || VERSION < v"1.7-DEV" || !Sys.islinux()
+    @warn "Doctests only run on Linux and Julia 1.7"
 else
     DocMeta.setdocmeta!(
         Ripserer, :DocTestSetup, :(using Ripserer; using Distances); recursive=true
     )
-    doctest(Ripserer; fix=true)
+    doctest(Ripserer)
 end