update for core 0.5.0

Project.toml

@@ -1,7 +1,7 @@
 name = "PopGenSims"
 uuid = "e670a858-c023-4621-870e-30d0f49b8322"
 authors = ["Pavel Dimens <[email protected]>"]
-version = "0.3.0"
+version = "0.3.1"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -15,7 +15,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 DataFrames = "1.0, 1.1"
 InvertedIndices = "1.0"
 PooledArrays = "1.0, 1.1"
-PopGenCore = "0.4, 0.5"
+PopGenCore = "0.5"
 StaticArrays = "1.2"
 StatsBase = "0.33"
 julia = "1.5, 1.6"

src/Cross.jl

@@ -58,8 +58,8 @@ function cross(data::PopData, parent1::String, parent2::String; n::Int = 100, ge
     p2_ploidy isa AbstractVector && error("Parent $parent2 has mixed ploidy, which is unsupported")
 
     # get parental genotypes
-    p1 = get_genotypes(data, parent1)
-    p2 = get_genotypes(data, parent2)
+    p1 = genotypes(data, parent1)
+    p2 = genotypes(data, parent2)
 
     loci = data.locusinfo.locus
 
@@ -133,8 +133,8 @@ function cross(parent_1::Pair, parent_2::Pair; n::Int = 100, generation::String
     p2_ploidy isa AbstractVector && error("Parent $parent2 has mixed ploidy, which is unsupported")
 
     # get parental genotypes
-    p1 = get_genotypes(parent_1_data, parent1)
-    p2 = get_genotypes(parent_2_data, parent2)
+    p1 = genotypes(parent_1_data, parent1)
+    p2 = genotypes(parent_2_data, parent2)
 
     # pre-allocate all output information
     out_loci_names = repeat(loci, outer = n)

src/PopGenSims.jl

@@ -26,11 +26,11 @@ using DataFrames, PooledArrays, StaticArrays
 using StatsBase: sample, Weights
 import PopGenCore: read, write
 using PopGenCore:
-    allele_freq,
+    allelefreq,
     copy,
     Genotype,
     GenoArray,
-    get_genotypes,
+    genotypes,
     PopData, 
     sort
 

src/Samples.jl

@@ -98,7 +98,7 @@ function simulate(data::PopData; n::Int = 100)
     gdf = groupby(data.genodata, [:population, :locus])
     freqs = DataFrames.combine(
         gdf,
-        :genotype => allele_freq => :frq
+        :genotype => allelefreq => :frq
     )
     # create new genotypes
     transform!(freqs, :frq => (i -> sample_locus.(i,n,ploidy)) => :frq)

test/runtests.jl

@@ -1,6 +1,6 @@
 fatalerrors = length(ARGS) > 0 && ARGS[1] == "-f"
 quiet = length(ARGS) > 0 && ARGS[1] == "-q"
-anyerrors = false
+anyerrors = 0
 
 using PopGenCore
 using PopGenSims
@@ -15,22 +15,22 @@ all_tests = [
 
 println("Running tests:")
 
-for a_test in all_tests
-    try
-        include(a_test)
-        println("\t\033[1m\033[32mPASSED\033[0m: $(a_test)")
-    catch e
-        global anyerrors = true
-        println("\t\033[1m\033[31mFAILED\033[0m: $(a_test)")
-        if fatalerrors
-            rethrow(e)
-        elseif !quiet
-            showerror(stdout, e, backtrace())
-            println()
+@testset "All Tests" begin
+    for a_test in all_tests
+        try
+            include(a_test)
+            println("\t\033[1m\033[32mPASSED\033[0m: $(a_test)")
+        catch e
+            global anyerrors += 1
+            println("\t\033[1m\033[31mFAILED\033[0m: $(a_test)")
+            if fatalerrors
+                rethrow(e)
+            elseif !quiet
+                showerror(stdout, e, backtrace())
+                println()
+            end
         end
     end
 end
 
-if anyerrors
-    throw("Tests failed :(")
-end
+anyerrors > 0 && throw("$anyerrors files of tests failed :(")