Remove PersistenceDiagramsBase dependency, update Julia version (#53)

* Remove PersistenceDiagramsBase dependency, update Julia version

* Update doctests and formatting

* fix Test.yml

Author: mtsch

Project.toml

@@ -1,35 +1,34 @@
 name = "PersistenceDiagrams"
 uuid = "90b4794c-894b-4756-a0f8-5efeb5ddf7ae"
 authors = ["mtsch <matijacufar@gmail.com>"]
-version = "0.9.6"
+version = "0.9.7"
 
 [deps]
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 Hungarian = "e91730f6-4275-51fb-a7a0-7064cfbd3b39"
 MLJModelInterface = "e80e1ace-859a-464e-9ed9-23947d8ae3ea"
-PersistenceDiagramsBase = "b1ad91c1-539c-4ace-90bd-ea06abc420fa"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 ScientificTypes = "321657f4-b219-11e9-178b-2701a2544e81"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [compat]
-Compat = "^3.10.0"
+Compat = "^3.10, 4"
 Hungarian = "0.6"
 MLJModelInterface = "1"
-PersistenceDiagramsBase = "^0.1.1"
 RecipesBase = "1"
 ScientificTypes = "3"
 Tables = "1"
 julia = "1"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Aqua", "Documenter", "MLJBase", "SafeTestsets", "Suppressor", "Test"]
+test = ["Aqua", "DataFrames", "Documenter", "MLJBase", "SafeTestsets", "Suppressor", "Test"]

src/PersistenceDiagrams.jl

@@ -40,12 +40,14 @@ export PersistenceDiagram,
 
 using Compat
 using Hungarian
-using PersistenceDiagramsBase
 using RecipesBase
 using ScientificTypes
 using Statistics
 using Tables
 
+include("intervals.jl")
+include("diagrams.jl")
+include("tables.jl")
 include("matching.jl")
 
 include("persistencecurves.jl")

src/diagrams.jl

@@ -0,0 +1,137 @@
+"""
+    PersistenceDiagram <: AbstractVector{PersistenceInterval}
+
+Type for representing persistence diagrams. Behaves exactly like a vector of
+`PersistenceInterval`s, but can have additional metadata attached to it. It supports pretty
+printing and plotting.
+
+Can be used as a table with any function that uses the
+[`Tables.jl`](https://github.com/JuliaData/Tables.jl) interface. Note that using it as a
+table will only keep interval endpoints and the `dim` and `threshold` attributes.
+
+# Example
+
+```jldoctest
+julia> diagram = PersistenceDiagram([(1, 3), (3, 4), (1, Inf)]; dim=1, custom_metadata=:a)
+3-element 1-dimensional PersistenceDiagram:
+ [1.0, 3.0)
+ [3.0, 4.0)
+ [1.0, ∞)
+
+julia> diagram[1]
+[1.0, 3.0)
+
+julia> sort(diagram; by=persistence, rev=true)
+3-element 1-dimensional PersistenceDiagram:
+ [1.0, ∞)
+ [1.0, 3.0)
+ [3.0, 4.0)
+
+julia> propertynames(diagram)
+(:intervals, :dim, :custom_metadata)
+
+julia> dim(diagram)
+1
+
+julia> diagram.custom_metadata
+:a
+```
+"""
+struct PersistenceDiagram <: AbstractVector{PersistenceInterval}
+    intervals::Vector{PersistenceInterval}
+    meta::NamedTuple
+end
+
+function PersistenceDiagram(intervals::Vector{PersistenceInterval}; kwargs...)
+    meta = (; kwargs...)
+    return PersistenceDiagram(intervals, meta)
+end
+function PersistenceDiagram(intervals::AbstractVector{PersistenceInterval}; kwargs...)
+    return PersistenceDiagram(collect(intervals); kwargs...)
+end
+function PersistenceDiagram(pairs::AbstractVector{<:Tuple}; kwargs...)
+    return PersistenceDiagram(PersistenceInterval.(pairs); kwargs...)
+end
+function PersistenceDiagram(table)
+    rows = Tables.rows(table)
+    if isempty(rows)
+        return PersistenceDiagram(PersistenceInterval[])
+    else
+        firstrow = first(rows)
+        dim = hasproperty(firstrow, :dim) ? firstrow.dim : missing
+        threshold = hasproperty(firstrow, :threshold) ? firstrow.threshold : missing
+        intervals = map(rows) do row
+            d = hasproperty(row, :dim) ? row.dim : missing
+            t = hasproperty(row, :threshold) ? row.threshold : missing
+            if !isequal(d, dim)
+                error("different `dim`s detected. Try splitting the table first.")
+            end
+            if !isequal(t, threshold)
+                error("different `threshold`s detected. Try splitting the table first.")
+            end
+            PersistenceInterval(row.birth, row.death)
+        end
+        return PersistenceDiagram(intervals; dim=dim, threshold=threshold)
+    end
+end
+
+function Base.show(io::IO, diag::PersistenceDiagram)
+    return summary(io, diag)
+end
+function Base.summary(io::IO, diag::PersistenceDiagram)
+    if haskey(diag.meta, :dim)
+        print(io, length(diag), "-element ", dim(diag), "-dimensional PersistenceDiagram")
+    else
+        print(io, length(diag), "-element PersistenceDiagram")
+    end
+end
+
+###
+### Array interface
+###
+Base.size(diag::PersistenceDiagram) = size(diag.intervals)
+Base.getindex(diag::PersistenceDiagram, i::Integer) = diag.intervals[i]
+Base.setindex!(diag::PersistenceDiagram, x, i::Integer) = diag.intervals[i] = x
+Base.firstindex(diag::PersistenceDiagram) = 1
+Base.lastindex(diag::PersistenceDiagram) = length(diag.intervals)
+
+function Base.similar(diag::PersistenceDiagram)
+    return PersistenceDiagram(similar(diag.intervals); diag.meta...)
+end
+function Base.similar(diag::PersistenceDiagram, dims::Tuple)
+    return PersistenceDiagram(similar(diag.intervals, dims); diag.meta...)
+end
+
+###
+### Meta
+###
+function Base.getproperty(diag::PersistenceDiagram, key::Symbol)
+    if hasfield(typeof(diag), key)
+        return getfield(diag, key)
+    elseif haskey(diag.meta, key)
+        return diag.meta[key]
+    else
+        error("$diag has no $key")
+    end
+end
+function Base.propertynames(diag::PersistenceDiagram, private::Bool=false)
+    if private
+        return tuple(:intervals, :meta, propertynames(diag.meta)...)
+    else
+        return tuple(:intervals, propertynames(diag.meta)...)
+    end
+end
+
+"""
+    threshold(diagram::PersistenceDiagram)
+
+Get the threshold of persistence diagram. Equivalent to `diagram.threshold`.
+"""
+threshold(diag::PersistenceDiagram) = diag.threshold
+
+"""
+    dim(diagram::PersistenceDiagram)
+
+Get the dimension of persistence diagram. Equivalent to `diagram.dim`.
+"""
+dim(diag::PersistenceDiagram) = diag.dim

src/intervals.jl

@@ -0,0 +1,182 @@
+"""
+    PersistenceInterval
+
+Type for representing persistence intervals. It behaves exactly like a `Tuple{Float64,
+Float64}`, but can have meta data attached to it. The metadata is accessible with
+`getproperty` or the dot syntax.
+
+# Example
+
+```jldoctest
+julia> interval = PersistenceInterval(1, Inf; meta1=:a, meta2=:b)
+[1.0, ∞) with:
+ meta1: Symbol
+ meta2: Symbol
+
+julia> birth(interval), death(interval), persistence(interval)
+(1.0, Inf, Inf)
+
+julia> isfinite(interval)
+false
+
+julia> propertynames(interval)
+(:birth, :death, :meta1, :meta2)
+
+julia> interval.meta1
+:a
+```
+"""
+struct PersistenceInterval
+    birth::Float64
+    death::Float64
+    meta::NamedTuple
+end
+function PersistenceInterval(birth, death; kwargs...)
+    meta = (; kwargs...)
+    return PersistenceInterval(Float64(birth), Float64(death), meta)
+end
+function PersistenceInterval(t::Tuple{<:Any,<:Any}; kwargs...)
+    meta = (; kwargs...)
+    return PersistenceInterval(Float64(t[1]), Float64(t[2]), meta)
+end
+function PersistenceInterval(int::PersistenceInterval; kwargs...)
+    meta = (; kwargs...)
+    return PersistenceInterval(Float64(int[1]), Float64(int[2]), meta)
+end
+
+"""
+    birth(interval)
+
+Get the birth time of `interval`.
+"""
+birth(int::PersistenceInterval) = getfield(int, 1)
+"""
+    death(interval)
+
+Get the death time of `interval`.
+"""
+death(int::PersistenceInterval) = getfield(int, 2)
+"""
+    persistence(interval)
+
+Get the persistence of `interval`, which is equal to `death - birth`.
+"""
+persistence(int::PersistenceInterval) = death(int) - birth(int)
+
+"""
+    midlife(interval)
+
+Get the midlife of the `interval`, which is equal to `(birth + death) / 2`.
+"""
+midlife(int::PersistenceInterval) = (birth(int) + death(int)) / 2
+
+Base.isfinite(int::PersistenceInterval) = isfinite(death(int))
+
+###
+### Iteration
+###
+function Base.iterate(int::PersistenceInterval, i=1)
+    if i == 1
+        return birth(int), i + 1
+    elseif i == 2
+        return death(int), i + 1
+    else
+        return nothing
+    end
+end
+
+Base.length(::PersistenceInterval) = 2
+Base.IteratorSize(::Type{<:PersistenceInterval}) = Base.HasLength()
+Base.IteratorEltype(::Type{<:PersistenceInterval}) = Base.HasEltype()
+Base.eltype(::Type{<:PersistenceInterval}) = Float64
+
+function Base.getindex(int::PersistenceInterval, i)
+    if i == 1
+        return birth(int)
+    elseif i == 2
+        return death(int)
+    else
+        throw(BoundsError(int, i))
+    end
+end
+
+Base.firstindex(int::PersistenceInterval) = 1
+Base.lastindex(int::PersistenceInterval) = 2
+
+###
+### Equality and ordering
+###
+function Base.:(==)(int1::PersistenceInterval, int2::PersistenceInterval)
+    return birth(int1) == birth(int2) && death(int1) == death(int2)
+end
+Base.:(==)(int::PersistenceInterval, (b, d)::Tuple) = birth(int) == b && death(int) == d
+Base.:(==)((b, d)::Tuple, int::PersistenceInterval) = birth(int) == b && death(int) == d
+
+function Base.isless(int1::PersistenceInterval, int2::PersistenceInterval)
+    return (birth(int1), death(int1)) < (birth(int2), death(int2))
+end
+
+###
+### Printing
+###
+function Base.show(io::IO, int::PersistenceInterval)
+    b = round(birth(int); sigdigits=3)
+    d = isfinite(death(int)) ? round(death(int); sigdigits=3) : "∞"
+    return print(io, "[$b, $d)")
+end
+
+function Base.show(io::IO, ::MIME"text/plain", int::PersistenceInterval)
+    b = round(birth(int); sigdigits=3)
+    d = isfinite(death(int)) ? round(death(int); sigdigits=3) : "∞"
+    print(io, "[$b, $d)")
+    if !isempty(int.meta)
+        print(io, " with:")
+        for (k, v) in zip(keys(int.meta), int.meta)
+            print(io, "\n ", k, ": ", summary(v))
+        end
+    end
+end
+
+###
+### Metadata
+###
+function Base.getproperty(int::PersistenceInterval, key::Symbol)
+    if hasfield(typeof(int), key)
+        return getfield(int, key)
+    elseif haskey(int.meta, key)
+        return int.meta[key]
+    else
+        error("interval $int has no $key")
+    end
+end
+function Base.propertynames(int::PersistenceInterval, private::Bool=false)
+    if private
+        return tuple(:birth, :death, propertynames(int.meta)..., :meta)
+    else
+        return (:birth, :death, propertynames(int.meta)...)
+    end
+end
+
+"""
+    representative(interval::PersistenceInterval)
+
+Get the representative (co)cycle attached to `interval`, if it has one.
+"""
+representative(int::PersistenceInterval) = int.representative
+
+"""
+    birth_simplex(interval::PersistenceInterval)
+
+Get the critical birth simplex of `interval`, if it has one.
+"""
+birth_simplex(int::PersistenceInterval) = int.birth_simplex
+
+"""
+    death_simplex(interval::PersistenceInterval)
+
+Get the critical death simplex of `interval`, if it has one.
+
+!!! note
+    An infinite interval's death simplex is `nothing`.
+"""
+death_simplex(int::PersistenceInterval) = int.death_simplex

src/persistencecurves.jl

@@ -272,7 +272,7 @@ persistence diagrams. [arXiv preprint arXiv:1904.07768](https://arxiv.org/abs/19
 function Midlife(args...; kwargs...)
     return PersistenceCurve(midlife, sum, args...; kwargs...)
 end
-PersistenceDiagramsBase.midlife((b, d), _, _) = (b + d) / 2
+midlife((b, d), _, _) = (b + d) / 2
 
 """
     LifeEntropy