Update go.mod

CHANGELOG.md

@@ -13,28 +13,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added statistics to the `synthesis/codon` package (keeping track of the observed start codon occurrences in a translation table) (#350)
 - Added option to fragmenter to fragment with only certain overhangs (#387)
 - GoldenGates with methylated sequences using lowercase letters (#391)
-- Generic parser is now implemented across all parsers for consistent interactions. [(#339)](https://github.com/TimothyStiles/poly/issues/339)
-- Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package [(#305)](https://github.com/TimothyStiles/poly/issues/305)
-- Added a parser and writer for the `pileup` sequence alignment format [(#329)](https://github.com/TimothyStiles/poly/issues/329)
-- Created copy methods for Feature and Location to address concerns raised by [(#342)](https://github.com/TimothyStiles/poly/issues/342)
+- Generic parser is now implemented across all parsers for consistent interactions. [(#339)](https://github.com/koeng101/dnadesign/issues/339)
+- Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package [(#305)](https://github.com/koeng101/dnadesign/issues/305)
+- Added a parser and writer for the `pileup` sequence alignment format [(#329)](https://github.com/koeng101/dnadesign/issues/329)
+- Created copy methods for Feature and Location to address concerns raised by [(#342)](https://github.com/koeng101/dnadesign/issues/342)
 - Created new methods to convert polyjson -> genbank.
-- Created new `Feature.StoreSequence` method to enable [(#388)](https://github.com/TimothyStiles/poly/issues/388)
+- Created new `Feature.StoreSequence` method to enable [(#388)](https://github.com/koeng101/dnadesign/issues/388)
 - Added seqhash v2 (#398)
 
 ### Changed
-- **Breaking**: Genbank parser uses new custom multimap for `Feature.Attributes`, which allows for duplicate keys. This changes the type of Features.Attributes from `map[string]string` to `MultiMap[string, string]`, an alias for `map[string]string` defined in `multimap.go`. [(#383)](https://github.com/TimothyStiles/poly/issues/383)
+- **Breaking**: Genbank parser uses new custom multimap for `Feature.Attributes`, which allows for duplicate keys. This changes the type of Features.Attributes from `map[string]string` to `MultiMap[string, string]`, an alias for `map[string]string` defined in `multimap.go`. [(#383)](https://github.com/koeng101/dnadesign/issues/383)
 - Improves error reporting for genbank parse errors via a new `ParseError` struct.
 
 ### Fixed
-- `fastq` parser no longer becomes de-aligned when reading [(#325)](https://github.com/TimothyStiles/poly/issues/325)
-- `fastq` now handles optionals correctly [(#323)](https://github.com/TimothyStiles/poly/issues/323)
-- Adds functional test and fix for [(#313)](https://github.com/TimothyStiles/poly/issues/313).
+- `fastq` parser no longer becomes de-aligned when reading [(#325)](https://github.com/koeng101/dnadesign/issues/325)
+- `fastq` now handles optionals correctly [(#323)](https://github.com/koeng101/dnadesign/issues/323)
+- Adds functional test and fix for [(#313)](https://github.com/koeng101/dnadesign/issues/313).
 - In addition to expanding the set of genbank files which can be validly parsed, the parser is more vocal when it encounters unusual syntax in the "feature" section. This "fail fast" approach is better as there were cases where inputs triggered a codepath which would neither return a valid Genbank object nor an error, and should help with debugging.
 -  Fixed bug that produced wrong overhang in linear, non-directional, single cut reactions. #408
 >>>>>>> main
 
 ## [0.26.0] - 2023-07-22
 Oops, we weren't keeping a changelog before this tag!
 
-[unreleased]: https://github.com/TimothyStiles/poly/compare/v0.26.0...main
-[0.26.0]: https://github.com/TimothyStiles/poly/releases/tag/v0.26.0
+[unreleased]: https://github.com/koeng101/dnadesign/compare/v0.26.0...main
+[0.26.0]: https://github.com/koeng101/dnadesign/releases/tag/v0.26.0

CONTRIBUTING.md

@@ -60,11 +60,11 @@ As one final guideline please be welcoming to newcomers and encourage new contri
 
 Unsure where to begin contributing to Poly? You can start by looking through these beginner and help-wanted issues:
 
-[Good first issues](https://github.com/TimothyStiles/poly/contribute) - issues which are good for first time contributors.
+[Good first issues](https://github.com/koeng101/dnadesign/contribute) - issues which are good for first time contributors.
 
-[Help wanted issues](https://github.com/TimothyStiles/poly/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
+[Help wanted issues](https://github.com/koeng101/dnadesign/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22+) - issues which should be a bit more involved than beginner issues.
 
-[Feature requests](https://github.com/TimothyStiles/poly/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag!
+[Feature requests](https://github.com/koeng101/dnadesign/labels/enhancement) - before requesting a new feature search through previous feature requests to see if it's already been requested. If not then feel free to submit a request and tag it with the enhancement tag!
 
 ### Working on your first Pull Request? 
 
@@ -118,11 +118,11 @@ If the answer to either of those two questions are "yes", then you're probably d
 
 ### Non-security related bugs
 
-For non-security bug reports please [submit it using this template!](https://github.com/TimothyStiles/poly/issues/new?assignees=&labels=&template=bug_report.md&title=)
+For non-security bug reports please [submit it using this template!](https://github.com/koeng101/dnadesign/issues/new?assignees=&labels=&template=bug_report.md&title=)
 
 # How to suggest a feature or enhancement
 
-If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/TimothyStiles/poly/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/TimothyStiles/poly/labels/enhancement)
+If you want to suggest a feature it's as easy as filling out this [issue template](https://github.com/koeng101/dnadesign/issues/new?assignees=&labels=&template=feature_request.md&title=), but before you do please [check to see if it's already been suggested!](https://github.com/koeng101/dnadesign/labels/enhancement)
 
 # How add a recommended VSCode Plugin
 

align/align.go

@@ -66,7 +66,7 @@ Tim
 package align
 
 import (
-	"github.com/TimothyStiles/poly/align/matrix"
+	"github.com/koeng101/dnadesign/align/matrix"
 )
 
 // Scoring is a struct that holds the scoring matrix for match, mismatch, and gap penalties.

align/align_test.go

@@ -3,9 +3,9 @@ package align_test
 import (
 	"testing"
 
-	"github.com/TimothyStiles/poly/align"
-	"github.com/TimothyStiles/poly/align/matrix"
-	"github.com/TimothyStiles/poly/alphabet"
+	"github.com/koeng101/dnadesign/align"
+	"github.com/koeng101/dnadesign/align/matrix"
+	"github.com/koeng101/dnadesign/alphabet"
 )
 
 func TestNeedlemanWunsch(t *testing.T) {

align/example_test.go

@@ -4,9 +4,9 @@ package align_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/align"
-	"github.com/TimothyStiles/poly/align/matrix"
-	"github.com/TimothyStiles/poly/alphabet"
+	"github.com/koeng101/dnadesign/align"
+	"github.com/koeng101/dnadesign/align/matrix"
+	"github.com/koeng101/dnadesign/alphabet"
 )
 
 func ExampleNeedlemanWunsch() {

align/matrix/matrix.go

@@ -6,7 +6,7 @@ package matrix
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/alphabet"
+	"github.com/koeng101/dnadesign/alphabet"
 )
 
 // SubstitutionMatrix is a struct that holds a substitution matrix and the two alphabets that the matrix is defined over.

align/matrix/matrix_test.go

@@ -3,8 +3,8 @@ package matrix_test
 import (
 	"testing"
 
-	"github.com/TimothyStiles/poly/align/matrix"
-	"github.com/TimothyStiles/poly/alphabet"
+	"github.com/koeng101/dnadesign/align/matrix"
+	"github.com/koeng101/dnadesign/alphabet"
 	"github.com/stretchr/testify/assert"
 )
 

alphabet/alphabet_test.go

@@ -4,7 +4,7 @@ import (
 	"reflect"
 	"testing"
 
-	"github.com/TimothyStiles/poly/alphabet"
+	"github.com/koeng101/dnadesign/alphabet"
 )
 
 func TestAlphabet(t *testing.T) {

bio/bio.go

@@ -16,11 +16,11 @@ import (
 	"io"
 	"math"
 
-	"github.com/TimothyStiles/poly/bio/fasta"
-	"github.com/TimothyStiles/poly/bio/fastq"
-	"github.com/TimothyStiles/poly/bio/genbank"
-	"github.com/TimothyStiles/poly/bio/pileup"
-	"github.com/TimothyStiles/poly/bio/slow5"
+	"github.com/koeng101/dnadesign/bio/fasta"
+	"github.com/koeng101/dnadesign/bio/fastq"
+	"github.com/koeng101/dnadesign/bio/genbank"
+	"github.com/koeng101/dnadesign/bio/pileup"
+	"github.com/koeng101/dnadesign/bio/slow5"
 	"golang.org/x/sync/errgroup"
 )
 

bio/example_test.go

@@ -8,8 +8,8 @@ import (
 	"os"
 	"strings"
 
-	"github.com/TimothyStiles/poly/bio"
-	"github.com/TimothyStiles/poly/bio/fasta"
+	"github.com/koeng101/dnadesign/bio"
+	"github.com/koeng101/dnadesign/bio/fasta"
 )
 
 // Example_read shows an example of reading a file from disk.

bio/fasta/example_test.go

@@ -8,7 +8,7 @@ import (
 	"os"
 	"strings"
 
-	"github.com/TimothyStiles/poly/bio/fasta"
+	"github.com/koeng101/dnadesign/bio/fasta"
 )
 
 // This example shows how to open a file with the fasta parser. The sequences

bio/fastq/example_test.go

@@ -5,7 +5,7 @@ import (
 	"fmt"
 	"strings"
 
-	"github.com/TimothyStiles/poly/bio/fastq"
+	"github.com/koeng101/dnadesign/bio/fastq"
 )
 
 //go:embed data/nanosavseq.fastq

bio/genbank/genbank.go

@@ -20,7 +20,7 @@ import (
 	"strconv"
 	"strings"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/transform"
 	"github.com/lunny/log"
 	"github.com/mitchellh/go-wordwrap"
 )

bio/genbank/genbank_test.go

@@ -12,7 +12,7 @@ import (
 
 	"reflect"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/transform"
 	"github.com/google/go-cmp/cmp"
 	"github.com/google/go-cmp/cmp/cmpopts"
 	"github.com/stretchr/testify/assert"

bio/gff/example_test.go

@@ -7,8 +7,8 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/TimothyStiles/poly/bio/gff"
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/bio/gff"
+	"github.com/koeng101/dnadesign/transform"
 )
 
 // This example shows how to open a gff file and search for a gene given its

bio/gff/gff.go

@@ -22,7 +22,7 @@ import (
 
 	"lukechampine.com/blake3"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/transform"
 )
 
 var (

bio/polyjson/example_test.go

@@ -6,8 +6,8 @@ import (
 	"path/filepath"
 	"time"
 
-	"github.com/TimothyStiles/poly/bio/polyjson"
-	"github.com/TimothyStiles/poly/seqhash"
+	"github.com/koeng101/dnadesign/bio/polyjson"
+	"github.com/koeng101/dnadesign/seqhash"
 )
 
 func Example() {

bio/polyjson/polyjson.go

@@ -13,8 +13,8 @@ import (
 	"os"
 	"time"
 
-	"github.com/TimothyStiles/poly/bio/genbank"
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/bio/genbank"
+	"github.com/koeng101/dnadesign/transform"
 )
 
 /******************************************************************************

bio/polyjson/polyjson_test.go

@@ -6,7 +6,7 @@ import (
 	"strings"
 	"testing"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/transform"
 	"github.com/stretchr/testify/assert"
 )
 

bio/rebase/example_test.go

@@ -3,7 +3,7 @@ package rebase_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/bio/rebase"
+	"github.com/koeng101/dnadesign/bio/rebase"
 )
 
 // This example reads rebase into an enzymeMap and returns the AarI recognition

bio/slow5/example_test.go

@@ -4,7 +4,7 @@ import (
 	"fmt"
 	"os"
 
-	"github.com/TimothyStiles/poly/bio/slow5"
+	"github.com/koeng101/dnadesign/bio/slow5"
 )
 
 func ExampleNewParser() {

bio/slow5/slow5.go

@@ -328,7 +328,7 @@ func (parser *Parser) Next() (*Read, error) {
 			// For whatever reason, this is a string.
 			newRead.ChannelNumber = values[valueIndex]
 		default:
-			return nil, fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/TimothyStiles/poly", fieldValue, parser.line)
+			return nil, fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/koeng101/dnadesign", fieldValue, parser.line)
 		}
 	}
 	return &newRead, nil

bio/uniprot/example_test.go

@@ -3,7 +3,7 @@ package uniprot_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/bio/uniprot"
+	"github.com/koeng101/dnadesign/bio/uniprot"
 )
 
 // This example shows how to open a uniprot data dump file and read the results

checks/checks.go

@@ -6,7 +6,7 @@ package checks
 import (
 	"strings"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/transform"
 )
 
 // IsPalindromic accepts a sequence of even length and returns if it is

checks/checks_test.go

@@ -3,7 +3,7 @@ package checks_test
 import (
 	"testing"
 
-	"github.com/TimothyStiles/poly/checks"
+	"github.com/koeng101/dnadesign/checks"
 )
 
 // This also needs an example test.

clone/clone.go

@@ -52,9 +52,9 @@ import (
 	"sort"
 	"strings"
 
-	"github.com/TimothyStiles/poly/checks"
-	"github.com/TimothyStiles/poly/seqhash"
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/checks"
+	"github.com/koeng101/dnadesign/seqhash"
+	"github.com/koeng101/dnadesign/transform"
 )
 
 // Part is a simple struct that can carry a circular or linear DNA sequence.

clone/clone_test.go

@@ -109,7 +109,7 @@ func TestCutWithEnzymeRegression(t *testing.T) {
 	}
 
 	// cut with BsaI
-	fragments := CutWithEnzyme(part, false, bsa1)
+	fragments := CutWithEnzyme(part, false, bsa1, false)
 
 	// check that the fragments are correct
 	if len(fragments) != 2 {

clone/example_test.go

@@ -4,8 +4,8 @@ import (
 	"fmt"
 	"log"
 
-	"github.com/TimothyStiles/poly/clone"
-	"github.com/TimothyStiles/poly/seqhash"
+	"github.com/koeng101/dnadesign/clone"
+	"github.com/koeng101/dnadesign/seqhash"
 )
 
 func ExampleGoldenGate() {

doc.go

@@ -29,6 +29,6 @@ Throw money at Tim's github sponsors page:
 https://github.com/sponsors/TimothyStiles
 
 Browse our subpackages to find the functionality and documentation you need:
-https://pkg.go.dev/github.com/TimothyStiles/poly#section-directories
+https://pkg.go.dev/github.com/koeng101/dnadesign#section-directories
 */
 package poly

fold/dna.go

@@ -1,6 +1,6 @@
 package fold
 
-import "github.com/TimothyStiles/poly/transform"
+import "github.com/koeng101/dnadesign/transform"
 
 var dnaComplement = transform.ComplementBase
 

fold/example_test.go

@@ -3,7 +3,7 @@ package fold_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/fold"
+	"github.com/koeng101/dnadesign/fold"
 )
 
 func ExampleZuker() {

fold/fold.go

@@ -33,7 +33,7 @@ import (
 	"math"
 	"strings"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/koeng101/dnadesign/transform"
 )
 
 // Zuker folds the DNA sequence and return the lowest free energy score.

fold/rna.go

@@ -1,6 +1,6 @@
 package fold
 
-import "github.com/TimothyStiles/poly/transform"
+import "github.com/koeng101/dnadesign/transform"
 
 var rnaComplement = transform.ComplementBaseRNA
 

fold/seqfold.go

@@ -5,7 +5,7 @@ import (
 	"math"
 	"strings"
 
-	"github.com/TimothyStiles/poly/checks"
+	"github.com/koeng101/dnadesign/checks"
 )
 
 const (

go.mod

@@ -1,4 +1,4 @@
-module github.com/TimothyStiles/poly
+module github.com/koeng101/dnadesign
 
 go 1.18