Bump Golang version

go.mod

@@ -1,6 +1,6 @@
 module github.com/TimothyStiles/poly
 
-go 1.18
+go 1.21
 
 require (
 	github.com/google/go-cmp v0.5.8
@@ -9,14 +9,14 @@ require (
 	github.com/mroth/weightedrand v0.4.1
 	github.com/pmezard/go-difflib v1.0.0
 	github.com/sergi/go-diff v1.2.0
+	github.com/spaolacci/murmur3 v1.1.0
 	golang.org/x/exp v0.0.0-20230310171629-522b1b587ee0
 	lukechampine.com/blake3 v1.1.5
 )
 
 require (
 	github.com/davecgh/go-spew v1.1.1 // indirect
 	github.com/mattn/go-sqlite3 v1.14.13 // indirect
-	github.com/spaolacci/murmur3 v1.1.0 // indirect
 )
 
 require (

io/slow5/slow5_test.go

@@ -3,7 +3,6 @@ package slow5
 import (
 	"errors"
 	"io"
-	"io/ioutil"
 	"os"
 	"testing"
 )
@@ -190,11 +189,11 @@ func TestWrite(t *testing.T) {
 	}
 
 	// Compare both files
-	example, err := ioutil.ReadFile("data/example.slow5")
+	example, err := os.ReadFile("data/example.slow5")
 	if err != nil {
 		t.Errorf("Failed to read example file: %s", err)
 	}
-	testWrite, err := ioutil.ReadFile("data/test_write.slow5")
+	testWrite, err := os.ReadFile("data/test_write.slow5")
 	if err != nil {
 		t.Errorf("Failed to read test file: %s", err)
 	}

random/random.go

@@ -19,7 +19,7 @@
 
 	// https://en.wikipedia.org/wiki/Amino_acid#Table_of_standard_amino_acid_abbreviations_and_properties
 	var aminoAcidsAlphabet = []rune("ACDEFGHIJLMNPQRSTVWY")
-	rand.Seed(seed)
+	randomSource := rand.New(rand.NewSource(seed))
 
 	randomSequence := make([]rune, length)
 
@@ -31,7 +31,7 @@
 			//* is the standard abbreviation for the stop codon. That's a signal for the ribosome to stop the translation and because of that a protein sequence is finished with *
 			randomSequence[peptide] = '*'
 		} else {
-			randomIndex := rand.Intn(len(aminoAcidsAlphabet))
+			randomIndex := randomSource.Intn(len(aminoAcidsAlphabet))
 			randomSequence[peptide] = aminoAcidsAlphabet[randomIndex]
 		}
 	}
@@ -51,7 +51,7 @@
 
 func randomNucelotideSequence(length int, seed int64, alphabet []rune) string {
 	alphabetLength := len(alphabet)
 	rand.Seed(seed)
 
 	randomSequence := make([]rune, length)
 	for basepair := range randomSequence {

synthesis/codon/codon.go

@@ -149,11 +149,13 @@ func (table *TranslationTable) OptimizeSequence(aminoAcids string, randomState .
 	}
 
 	// weightedRand library insisted setting seed like this. Not sure what environmental side effects exist.
+	var randomSource rand.Source
 	if len(randomState) > 0 {
-		rand.Seed(int64(randomState[0]))
+		randomSource = rand.NewSource(int64(randomState[0]))
 	} else {
-		rand.Seed(time.Now().UTC().UnixNano())
+		randomSource = rand.NewSource(time.Now().UTC().UnixNano())
 	}
+	rand := rand.New(randomSource)
 
 	var codons strings.Builder
 	codonChooser := table.Choosers
@@ -163,6 +165,7 @@ func (table *TranslationTable) OptimizeSequence(aminoAcids string, randomState .
 		if !ok {
 			return "", invalidAminoAcidError{aminoAcid}
 		}
+		chooser.PickSource(rand)
 
 		codons.WriteString(chooser.Pick().(string))
 	}