CHANGELOG.md

@@ -7,12 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [0.2.0] - 2023-01-10
-
 ### Added
 
 - Tutorial-type documentation ([#28](https://github.com/BioJulia/SequenceVariation.jl/pull/28))
-- `Base.isless` implementation for `Edit` and `Variation` ([#31](https://github.com/BioJulia/SequenceVariation.jl/pull/31))
 
 ### Changed
 
@@ -63,8 +60,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `Variant` constructor to automatically detect mutations from a `BioAlignments.PairwiseAlignment`
 - Methods to get reference and alternate bases from a `Variation`
 
-[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.0...HEAD
+[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.4...HEAD
-[0.2.0]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.4...v0.2.0
 [0.1.4]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.3...v0.1.4
 [0.1.3]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.2...v0.1.3
 [0.1.2]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.1...v0.1.2

Project.toml

@@ -1,7 +1,7 @@
 name = "SequenceVariation"
 uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
 authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>", "Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>"]
-version = "0.2.0"
+version = "0.1.4"
 
 [deps]
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"

README.md

@@ -5,7 +5,6 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/SequenceVariation.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/stable)
 [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/dev/)
-[![DOI](https://zenodo.org/badge/343847382.svg)](https://zenodo.org/badge/latestdoi/343847382)
 
 > This project follows the [semver](https://semver.org) _pro forma_ and uses the [OneFlow branching model](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow).
 
@@ -24,7 +23,7 @@ add SequenceVariation
 
 ## Testing
 
-SequenceVariation is tested against Julia `1.6` (LTS), `1.X` (release) and nightly on Linux.
+SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 

docs/src/index.md

@@ -23,7 +23,7 @@ add SequenceVariation
 
 ## Testing
 
-SequenceVariation is tested against Julia `1.6` (LTS), `1.X` (release) and nightly on Linux.
+SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 

src/Edit.jl

@@ -17,13 +17,6 @@ end
 Base.length(e::Edit) = length(_mutation(e))
 Base.:(==)(e1::Edit, e2::Edit) = e1.pos == e2.pos && e1.x == e2.x
 Base.hash(x::Edit, h::UInt) = hash(Edit, hash((x.x, x.pos), h))
-function Base.isless(x::Edit, y::Edit)
-    if leftposition(x) == leftposition(y)
-        return length(x) < length(y)
-    end
-
-    return leftposition(x) < leftposition(y)
-end
 
 function Base.parse(::Type{T}, s::AbstractString) where {T<:Edit{Se,Sy}} where {Se,Sy}
     return parse(T, String(s))

src/Variation.jl

@@ -75,11 +75,6 @@ BioGenerics.leftposition(v::Variation) = leftposition(_edit(v))
 BioGenerics.rightposition(v::Variation) = rightposition(_edit(v))
 Base.:(==)(x::Variation, y::Variation) = x.ref == y.ref && x.edit == y.edit
 Base.hash(x::Variation, h::UInt) = hash(Variation, hash((x.ref, x.edit), h))
-function Base.isless(x::Variation, y::Variation)
-    reference(x) == reference(y) ||
-        error("Variations cannot be compared if their reference sequences aren't equal")
-    return leftposition(x) < leftposition(y)
-end
 
 """
     _is_valid(v::Variation)

test/runtests.jl

@@ -36,15 +36,6 @@ seq1 = ungap!(dna"--ATGCGTGTTAGCAAC--TTATCGCG")
 seq2 = ungap!(dna"TGATGCGTGT-AGCAACACTTATAGCG")
 var = Haplotype(align(seq1, seq2))
 
-@testset "EditSorting" begin
-    S = typeof(seq1)
-    T = eltype(seq1)
-    @test SequenceVariation.Edit{S,T}(Deletion(1), 1) <
-        SequenceVariation.Edit{S,T}(Deletion(1), 2)
-    @test SequenceVariation.Edit{S,T}(Deletion(1), 1) <
-        SequenceVariation.Edit{S,T}(Deletion(2), 1)
-end
-
 @testset "HaplotypeRoundtrip" begin
     for v in variations(var)
         @test v in var
@@ -56,10 +47,6 @@ end
     @test reconstruct(var) == seq1
 end
 
-@testset "VariationSorting" begin
-    @test Variation(seq2, "A3T") < Variation(seq2, "T4A")
-end
-
 @testset "VariationPosition" begin
     refseq = dna"ACAACTTTATCT"
     mutseq = dna"ACATCTTTATCT"