Fix iterator constructor and other failing tests (#32)

* Fix iterator constructor and other failing tests * Update test/access.jl Co-authored-by: Kevin Bonham <[email protected]> * Update test/access.jl Co-authored-by: Kevin Bonham <[email protected]> * Update the compat * Update test/access.jl Co-authored-by: Kevin Bonham <[email protected]> --------- Co-authored-by: Kevin Bonham <[email protected]> Co-authored-by: Sabrina J. Ward <[email protected]>
BioJulia · Apr 11, 2023 · 0bdf3a8 · 0bdf3a8
1 parent 5dd8f8f
commit 0bdf3a8
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Showing 6 changed files with 14 additions and 9 deletions.
diff --git a/Project.toml b/Project.toml
@@ -7,7 +7,7 @@ version = "0.1.0"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 
 [compat]
-BioSequences = "3"
+BioSequences = "3.1.3"
 julia = "1.5"
 
 [extras]

diff --git a/src/kmer.jl b/src/kmer.jl
@@ -156,7 +156,8 @@ function Kmer{A,K,N}(itr) where {A,K,N}
     # Construct the head.
     head = zero(UInt64)
     @inbounds for i in 1:n_head
-        sym = convert(eltype(Kmer{A,K,N}), itr[i])
+        (x, next_i) = iterate(itr, i)
+        sym = convert(eltype(Kmer{A,K,N}), x)
         # Encode will throw if it cant encode an element.
         head = (head << bits_per_sym) | UInt64(BioSequences.encode(A(), sym))
     end
@@ -167,7 +168,8 @@ function Kmer{A,K,N}(itr) where {A,K,N}
         Base.@_inline_meta
         body = zero(UInt64)
         @inbounds for i in 1:n_per_chunk
-            sym = convert(eltype(Kmer{A,K,N}), itr[idx[]])
+            (x, next_idx) = iterate(itr, idx[])
+            sym = convert(eltype(Kmer{A,K,N}), x)
             # Encode will throw  if it cant encode an element.
             body = (body << bits_per_sym) | UInt64(BioSequences.encode(A(), sym))
             idx[] += 1

diff --git a/src/revtrans.jl b/src/revtrans.jl
@@ -1,5 +1,3 @@
-struct Unsafe end
-
 const N_AA = length(AminoAcidAlphabet())
 
 """

diff --git a/test/access.jl b/test/access.jl
@@ -31,7 +31,8 @@
         @test iterate(DNAKmer("ACTG"), 1)  !== nothing
         @test iterate(DNAKmer("ACTG"), 4)  !== nothing
         @test iterate(DNAKmer("ACTG"), 5)  === nothing
-        @test_throws BoundsError iterate(DNAKmer("ACTG"), -1)
+        @test isnothing(iterate(DNAKmer("ACTG"), -1))
+        @test iterate(DNAKmer("ACTG"), 0) === nothing
 
         dna_vec = [DNA_A, DNA_C, DNA_T, DNA_G]
         @test all([nt === dna_vec[i] for (i, nt) in enumerate(dna_kmer)])
@@ -64,10 +65,11 @@
         @test iterate(RNAKmer("ACUG"), 4) == (RNA_G, 5)
 
 
-        @test iterate(RNAKmer("ACUG"), 1)  !== nothing
+        @test iterate(RNAKmer("ACUG"), 1) !== nothing
         @test iterate(RNAKmer("ACUG"), 4)  !== nothing
         @test iterate(RNAKmer("ACUG"), 5)  === nothing
-        @test_throws BoundsError iterate(RNAKmer("ACUG"), -1)
+        @test iterate(RNAKmer("ACUG"), -1) === nothing
+        @test iterate(RNAKmer("ACUG"), 0) === nothing
 
         rna_vec = [RNA_A, RNA_C, RNA_U, RNA_G]
         @test all([nt === rna_vec[i] for (i, nt) in enumerate(rna_kmer)])

diff --git a/test/conversion.jl → test/construction_and_conversion.jl b/test/conversion.jl → test/construction_and_conversion.jl
@@ -8,6 +8,9 @@ global reps = 10
     @test DNAKmer(DNA_G, DNA_C, DNA_T) == Kmer("GCT")
     @test RNAKmer(RNA_G, RNA_U, RNA_C, RNA_U) == Kmer("GUCU")
 
+    # creation from iterator
+    @test Kmers.kmertype(Kmer{DNAAlphabet{2},31})((i for i in rand(ACGT, 31))) isa Kmers.kmertype(Kmer{DNAAlphabet{2},31})
+
     # Check that kmers in strings survive round trip conversion:
     #   String → Kmer → String
     function check_string_construction(::Type{T}, seq::AbstractString) where {T<:Kmer}

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -10,7 +10,7 @@ include("utils.jl")
 
 if GROUP == "BioSequences" || GROUP == "All"
     include("biosequences_interface.jl")
-    include("conversion.jl")
+    include("construction_and_conversion.jl")
     include("comparisons.jl")
     include("length.jl")
     include("access.jl")