migrated namespace from TimothyStiles/poly to bebop/poly

TimothyStiles · TimothyStiles · commit 05cdd6d14978 · 2023-12-11T12:48:30.000-08:00
diff --git a/CONTRIBUTING.md b/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/bebop/poly/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/bebop/poly/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/bebop/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!
 
 ### Working on your first Pull Request? 
 
@@ -106,11 +106,11 @@ 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/bebop/poly/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/bebop/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/bebop/poly/labels/enhancement)
 
 # How add a recommended VSCode Plugin
 
diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
 # (Poly)merase <img align="right" src="https://cdn.discordapp.com/attachments/766785755305213953/777596834734145546/ProfileFrameArtboard_1.png" width="100">
 
-[![PkgGoDev](https://pkg.go.dev/badge/github.com/TimothyStiles/poly)](https://pkg.go.dev/github.com/TimothyStiles/poly)
-[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/TimothyStiles/poly/blob/main/LICENSE) 
-![Tests](https://github.com/TimothyStiles/poly/workflows/Test/badge.svg)
+[![PkgGoDev](https://pkg.go.dev/badge/github.com/bebop/poly)](https://pkg.go.dev/github.com/bebop/poly)
+[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/bebop/poly/blob/main/LICENSE) 
+![Tests](https://github.com/bebop/poly/workflows/Test/badge.svg)
 ![Test Coverage](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/TimothyStiles/e58f265655ac0acacdd1a38376ccd32a/raw/coverage.json)
 
 Poly is a Go package for engineering organisms.
@@ -18,14 +18,14 @@ Poly is a Go package for engineering organisms.
 
 ## Install
 
-`go get github.com/TimothyStiles/poly@latest`
+`go get github.com/bebop/poly@latest`
 
 ## Documentation
 
 
-* **[Library](https://pkg.go.dev/github.com/TimothyStiles/poly#pkg-examples)**
+* **[Library](https://pkg.go.dev/github.com/bebop/poly#pkg-examples)**
 
-* **[Tutorials](https://github.com/TimothyStiles/poly/tree/main/tutorials)**
+* **[Tutorials](https://github.com/bebop/poly/tree/main/tutorials)**
 
 * **[Learning Synbio](https://github.com/TimothyStiles/how-to-synbio)**
 
diff --git a/align/align.go b/align/align.go
@@ -66,7 +66,7 @@ Tim
 package align
 
 import (
-	"github.com/TimothyStiles/poly/align/matrix"
+	"github.com/bebop/poly/align/matrix"
 )
 
 // Scoring is a struct that holds the scoring matrix for match, mismatch, and gap penalties.
diff --git a/align/align_test.go b/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/bebop/poly/align"
+	"github.com/bebop/poly/align/matrix"
+	"github.com/bebop/poly/alphabet"
 )
 
 func TestNeedlemanWunsch(t *testing.T) {
diff --git a/align/example_test.go b/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/bebop/poly/align"
+	"github.com/bebop/poly/align/matrix"
+	"github.com/bebop/poly/alphabet"
 )
 
 func ExampleNeedlemanWunsch() {
diff --git a/align/matrix/matrix.go b/align/matrix/matrix.go
@@ -6,7 +6,7 @@ package matrix
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/alphabet"
+	"github.com/bebop/poly/alphabet"
 )
 
 // SubstitutionMatrix is a struct that holds a substitution matrix and the two alphabets that the matrix is defined over.
diff --git a/align/matrix/matrix_test.go b/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/bebop/poly/align/matrix"
+	"github.com/bebop/poly/alphabet"
 	"github.com/stretchr/testify/assert"
 )
 
diff --git a/alphabet/alphabet_test.go b/alphabet/alphabet_test.go
@@ -4,7 +4,7 @@ import (
 	"reflect"
 	"testing"
 
-	"github.com/TimothyStiles/poly/alphabet"
+	"github.com/bebop/poly/alphabet"
 )
 
 func TestAlphabet(t *testing.T) {
diff --git a/checks/checks.go b/checks/checks.go
@@ -6,7 +6,7 @@ package checks
 import (
 	"strings"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/transform"
 )
 
 // IsPalindromic accepts a sequence of even length and returns if it is
diff --git a/checks/checks_test.go b/checks/checks_test.go
@@ -3,7 +3,7 @@ package checks_test
 import (
 	"testing"
 
-	"github.com/TimothyStiles/poly/checks"
+	"github.com/bebop/poly/checks"
 )
 
 // This also needs an example test.
diff --git a/clone/clone.go b/clone/clone.go
@@ -47,9 +47,9 @@ import (
 	"sort"
 	"strings"
 
-	"github.com/TimothyStiles/poly/checks"
-	"github.com/TimothyStiles/poly/seqhash"
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/checks"
+	"github.com/bebop/poly/seqhash"
+	"github.com/bebop/poly/transform"
 )
 
 // Part is a simple struct that can carry a circular or linear DNA sequence.
diff --git a/clone/example_test.go b/clone/example_test.go
@@ -4,8 +4,8 @@ import (
 	"fmt"
 	"log"
 
-	"github.com/TimothyStiles/poly/clone"
-	"github.com/TimothyStiles/poly/seqhash"
+	"github.com/bebop/poly/clone"
+	"github.com/bebop/poly/seqhash"
 )
 
 func ExampleGoldenGate() {
diff --git a/doc.go b/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/bebop/poly#section-directories
 */
 package poly
diff --git a/fold/dna.go b/fold/dna.go
@@ -1,6 +1,6 @@
 package fold
 
-import "github.com/TimothyStiles/poly/transform"
+import "github.com/bebop/poly/transform"
 
 var dnaComplement = transform.ComplementBase
 
diff --git a/fold/example_test.go b/fold/example_test.go
@@ -3,7 +3,7 @@ package fold_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/fold"
+	"github.com/bebop/poly/fold"
 )
 
 func ExampleZuker() {
diff --git a/fold/fold.go b/fold/fold.go
@@ -33,7 +33,7 @@ import (
 	"math"
 	"strings"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/transform"
 )
 
 // Zuker folds the DNA sequence and return the lowest free energy score.
diff --git a/fold/rna.go b/fold/rna.go
@@ -1,6 +1,6 @@
 package fold
 
-import "github.com/TimothyStiles/poly/transform"
+import "github.com/bebop/poly/transform"
 
 var rnaComplement = transform.ComplementBaseRNA
 
diff --git a/fold/seqfold.go b/fold/seqfold.go
@@ -5,7 +5,7 @@ import (
 	"math"
 	"strings"
 
-	"github.com/TimothyStiles/poly/checks"
+	"github.com/bebop/poly/checks"
 )
 
 const (
diff --git a/go.mod b/go.mod
@@ -1,4 +1,4 @@
-module github.com/TimothyStiles/poly
+module github.com/bebop/poly
 
 go 1.18
 
diff --git a/io/example_test.go b/io/example_test.go
@@ -1,10 +1,10 @@
 package io_test
 
 import (
-	"github.com/TimothyStiles/poly/io/fasta"
-	"github.com/TimothyStiles/poly/io/genbank"
-	"github.com/TimothyStiles/poly/io/gff"
-	"github.com/TimothyStiles/poly/io/polyjson"
+	"github.com/bebop/poly/io/fasta"
+	"github.com/bebop/poly/io/genbank"
+	"github.com/bebop/poly/io/gff"
+	"github.com/bebop/poly/io/polyjson"
 )
 
 // This is where the integration tests that make effed up cyclic dependencies go.
diff --git a/io/fasta/example_test.go b/io/fasta/example_test.go
@@ -7,7 +7,7 @@ import (
 	"os"
 	"strings"
 
-	"github.com/TimothyStiles/poly/io/fasta"
+	"github.com/bebop/poly/io/fasta"
 )
 
 //go:embed data/base.fasta
diff --git a/io/fastq/example_test.go b/io/fastq/example_test.go
@@ -6,7 +6,7 @@ import (
 	"os"
 	"strings"
 
-	"github.com/TimothyStiles/poly/io/fastq"
+	"github.com/bebop/poly/io/fastq"
 )
 
 //go:embed data/nanosavseq.fastq
diff --git a/io/genbank/example_test.go b/io/genbank/example_test.go
@@ -6,7 +6,7 @@ import (
 	"os"
 	"path/filepath"
 
-	"github.com/TimothyStiles/poly/io/genbank"
+	"github.com/bebop/poly/io/genbank"
 )
 
 // This example shows how to open a genbank file and search for a gene given
diff --git a/io/genbank/genbank.go b/io/genbank/genbank.go
@@ -20,7 +20,7 @@ import (
 	"strconv"
 	"strings"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/transform"
 	"github.com/lunny/log"
 	"github.com/mitchellh/go-wordwrap"
 )
diff --git a/io/genbank/genbank_test.go b/io/genbank/genbank_test.go
@@ -12,7 +12,7 @@ import (
 
 	"reflect"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/transform"
 	"github.com/google/go-cmp/cmp"
 	"github.com/google/go-cmp/cmp/cmpopts"
 	"github.com/stretchr/testify/assert"
diff --git a/io/gff/example_test.go b/io/gff/example_test.go
@@ -7,8 +7,8 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/TimothyStiles/poly/io/gff"
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/io/gff"
+	"github.com/bebop/poly/transform"
 )
 
 // This example shows how to open a gff file and search for a gene given its
diff --git a/io/gff/gff.go b/io/gff/gff.go
@@ -22,7 +22,7 @@ import (
 
 	"lukechampine.com/blake3"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/transform"
 )
 
 var (
diff --git a/io/polyjson/example_test.go b/io/polyjson/example_test.go
@@ -6,8 +6,8 @@ import (
 	"path/filepath"
 	"time"
 
-	"github.com/TimothyStiles/poly/io/polyjson"
-	"github.com/TimothyStiles/poly/seqhash"
+	"github.com/bebop/poly/io/polyjson"
+	"github.com/bebop/poly/seqhash"
 )
 
 func Example() {
diff --git a/io/polyjson/polyjson.go b/io/polyjson/polyjson.go
@@ -13,7 +13,7 @@ import (
 	"os"
 	"time"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/transform"
 )
 
 /******************************************************************************
diff --git a/io/polyjson/polyjson_test.go b/io/polyjson/polyjson_test.go
@@ -6,7 +6,7 @@ import (
 	"strings"
 	"testing"
 
-	"github.com/TimothyStiles/poly/transform"
+	"github.com/bebop/poly/transform"
 	"github.com/stretchr/testify/assert"
 )
 
diff --git a/io/rebase/example_test.go b/io/rebase/example_test.go
@@ -3,7 +3,7 @@ package rebase_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/io/rebase"
+	"github.com/bebop/poly/io/rebase"
 )
 
 // This example reads rebase into an enzymeMap and returns the AarI recognition
diff --git a/io/slow5/example_test.go b/io/slow5/example_test.go
@@ -4,7 +4,7 @@ import (
 	"fmt"
 	"os"
 
-	"github.com/TimothyStiles/poly/io/slow5"
+	"github.com/bebop/poly/io/slow5"
 )
 
 func ExampleNewParser() {
diff --git a/io/slow5/slow5.go b/io/slow5/slow5.go
@@ -300,7 +300,7 @@ func (parser *Parser) ParseNext() (Read, error) {
 			// For whatever reason, this is a string.
 			newRead.ChannelNumber = values[valueIndex]
 		default:
-			newRead.Error = fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/TimothyStiles/poly", fieldValue, parser.line)
+			newRead.Error = fmt.Errorf("Unknown field to parser '%s' found on line %d. Please report to github.com/bebop/poly", fieldValue, parser.line)
 		}
 	}
 	return newRead, nil
diff --git a/io/uniprot/example_test.go b/io/uniprot/example_test.go
@@ -3,7 +3,7 @@ package uniprot_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/io/uniprot"
+	"github.com/bebop/poly/io/uniprot"
 )
 
 // This example shows how to open a uniprot data dump file and read the results
diff --git a/mash/example_test.go b/mash/example_test.go
@@ -3,7 +3,7 @@ package mash_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/mash"
+	"github.com/bebop/poly/mash"
 )
 
 func ExampleMash() {
diff --git a/mash/mash_test.go b/mash/mash_test.go
@@ -3,7 +3,7 @@ package mash_test
 import (
 	"testing"
 
-	"github.com/TimothyStiles/poly/mash"
+	"github.com/bebop/poly/mash"
 )
 
 func TestMash(t *testing.T) {
diff --git a/primers/pcr/example_test.go b/primers/pcr/example_test.go
@@ -3,7 +3,7 @@ package pcr_test
 import (
 	"fmt"
 
-	"github.com/TimothyStiles/poly/primers/pcr"
+	"github.com/bebop/poly/primers/pcr"
 )
 
 // This example shows how to design a sequence.
diff --git a/primers/pcr/pcr.go b/primers/pcr/pcr.go
diff --git a/primers/primers.go b/primers/primers.go
diff --git a/primers/primers_test.go b/primers/primers_test.go
diff --git a/seqhash/example_test.go b/seqhash/example_test.go
diff --git a/seqhash/seqhash.go b/seqhash/seqhash.go
diff --git a/seqhash/seqhash_test.go b/seqhash/seqhash_test.go
diff --git a/synthesis/codon/codon.go b/synthesis/codon/codon.go
diff --git a/synthesis/codon/codon_test.go b/synthesis/codon/codon_test.go
diff --git a/synthesis/codon/example_test.go b/synthesis/codon/example_test.go
diff --git a/synthesis/fix/example_test.go b/synthesis/fix/example_test.go
diff --git a/synthesis/fix/synthesis.go b/synthesis/fix/synthesis.go
diff --git a/synthesis/fix/synthesis_test.go b/synthesis/fix/synthesis_test.go
diff --git a/synthesis/fragment/example_test.go b/synthesis/fragment/example_test.go
diff --git a/synthesis/fragment/fragment.go b/synthesis/fragment/fragment.go
diff --git a/transform/examples_test.go b/transform/examples_test.go
diff --git a/transform/transform_test.go b/transform/transform_test.go
diff --git a/tutorials/001_input_output_test.go b/tutorials/001_input_output_test.go
diff --git a/tutorials/README.md b/tutorials/README.md

Original file line number	Diff line number	Diff line change
`@@ -66,7 +66,7 @@ Tim`
`66`	`66`	`package align`
`67`	`67`
`68`	`68`	`import (`
`69`		`- "github.com/TimothyStiles/poly/align/matrix"`
	`69`	`+ "github.com/bebop/poly/align/matrix"`
`70`	`70`	`)`
`71`	`71`
`72`	`72`	`// Scoring is a struct that holds the scoring matrix for match, mismatch, and gap penalties.`
Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@ package matrix`
`6`	`6`	`import (`
`7`	`7`	`"fmt"`
`8`	`8`
`9`		`- "github.com/TimothyStiles/poly/alphabet"`
	`9`	`+ "github.com/bebop/poly/alphabet"`
`10`	`10`	`)`
`11`	`11`
`12`	`12`	`// SubstitutionMatrix is a struct that holds a substitution matrix and the two alphabets that the matrix is defined over.`
Original file line number	Diff line number	Diff line change
`@@ -3,8 +3,8 @@ package matrix_test`
`3`	`3`	`import (`
`4`	`4`	`"testing"`
`5`	`5`
`6`		`- "github.com/TimothyStiles/poly/align/matrix"`
`7`		`- "github.com/TimothyStiles/poly/alphabet"`
	`6`	`+ "github.com/bebop/poly/align/matrix"`
	`7`	`+ "github.com/bebop/poly/alphabet"`
`8`	`8`	`"github.com/stretchr/testify/assert"`
`9`	`9`	`)`
`10`	`10`
Original file line number	Diff line number	Diff line change
`@@ -4,7 +4,7 @@ import (`
`4`	`4`	`"reflect"`
`5`	`5`	`"testing"`
`6`	`6`
`7`		`- "github.com/TimothyStiles/poly/alphabet"`
	`7`	`+ "github.com/bebop/poly/alphabet"`
`8`	`8`	`)`
`9`	`9`
`10`	`10`	`func TestAlphabet(t *testing.T) {`
Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@ package checks`
`6`	`6`	`import (`
`7`	`7`	`"strings"`
`8`	`8`
`9`		`- "github.com/TimothyStiles/poly/transform"`
	`9`	`+ "github.com/bebop/poly/transform"`
`10`	`10`	`)`
`11`	`11`
`12`	`12`	`// IsPalindromic accepts a sequence of even length and returns if it is`
Original file line number	Diff line number	Diff line change
`@@ -3,7 +3,7 @@ package checks_test`
`3`	`3`	`import (`
`4`	`4`	`"testing"`
`5`	`5`
`6`		`- "github.com/TimothyStiles/poly/checks"`
	`6`	`+ "github.com/bebop/poly/checks"`
`7`	`7`	`)`
`8`	`8`
`9`	`9`	`// This also needs an example test.`