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migrated namespace from TimothyStiles/poly to bebop/poly
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TimothyStiles committed Dec 11, 2023
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10 changes: 5 additions & 5 deletions CONTRIBUTING.md
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Expand Up @@ -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?

Expand Down Expand Up @@ -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

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12 changes: 6 additions & 6 deletions README.md
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@@ -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.
Expand All @@ -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)**

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2 changes: 1 addition & 1 deletion align/align.go
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Expand Up @@ -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.
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6 changes: 3 additions & 3 deletions align/align_test.go
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Expand Up @@ -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) {
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6 changes: 3 additions & 3 deletions align/example_test.go
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Expand Up @@ -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() {
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2 changes: 1 addition & 1 deletion align/matrix/matrix.go
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Expand Up @@ -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.
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4 changes: 2 additions & 2 deletions align/matrix/matrix_test.go
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Expand Up @@ -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"
)

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2 changes: 1 addition & 1 deletion alphabet/alphabet_test.go
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Expand Up @@ -4,7 +4,7 @@ import (
"reflect"
"testing"

"github.com/TimothyStiles/poly/alphabet"
"github.com/bebop/poly/alphabet"
)

func TestAlphabet(t *testing.T) {
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2 changes: 1 addition & 1 deletion checks/checks.go
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion checks/checks_test.go
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Expand Up @@ -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.
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6 changes: 3 additions & 3 deletions clone/clone.go
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Expand Up @@ -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.
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4 changes: 2 additions & 2 deletions clone/example_test.go
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Expand Up @@ -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() {
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2 changes: 1 addition & 1 deletion doc.go
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Expand Up @@ -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
2 changes: 1 addition & 1 deletion fold/dna.go
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@@ -1,6 +1,6 @@
package fold

import "github.com/TimothyStiles/poly/transform"
import "github.com/bebop/poly/transform"

var dnaComplement = transform.ComplementBase

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2 changes: 1 addition & 1 deletion fold/example_test.go
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Expand Up @@ -3,7 +3,7 @@ package fold_test
import (
"fmt"

"github.com/TimothyStiles/poly/fold"
"github.com/bebop/poly/fold"
)

func ExampleZuker() {
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2 changes: 1 addition & 1 deletion fold/fold.go
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion fold/rna.go
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@@ -1,6 +1,6 @@
package fold

import "github.com/TimothyStiles/poly/transform"
import "github.com/bebop/poly/transform"

var rnaComplement = transform.ComplementBaseRNA

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2 changes: 1 addition & 1 deletion fold/seqfold.go
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Expand Up @@ -5,7 +5,7 @@ import (
"math"
"strings"

"github.com/TimothyStiles/poly/checks"
"github.com/bebop/poly/checks"
)

const (
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2 changes: 1 addition & 1 deletion go.mod
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@@ -1,4 +1,4 @@
module github.com/TimothyStiles/poly
module github.com/bebop/poly

go 1.18

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8 changes: 4 additions & 4 deletions io/example_test.go
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@@ -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.
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2 changes: 1 addition & 1 deletion io/fasta/example_test.go
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Expand Up @@ -7,7 +7,7 @@ import (
"os"
"strings"

"github.com/TimothyStiles/poly/io/fasta"
"github.com/bebop/poly/io/fasta"
)

//go:embed data/base.fasta
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2 changes: 1 addition & 1 deletion io/fastq/example_test.go
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Expand Up @@ -6,7 +6,7 @@ import (
"os"
"strings"

"github.com/TimothyStiles/poly/io/fastq"
"github.com/bebop/poly/io/fastq"
)

//go:embed data/nanosavseq.fastq
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2 changes: 1 addition & 1 deletion io/genbank/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion io/genbank/genbank.go
Original file line number Diff line number Diff line change
Expand Up @@ -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"
)
Expand Down
2 changes: 1 addition & 1 deletion io/genbank/genbank_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
4 changes: 2 additions & 2 deletions io/gff/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion io/gff/gff.go
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ import (

"lukechampine.com/blake3"

"github.com/TimothyStiles/poly/transform"
"github.com/bebop/poly/transform"
)

var (
Expand Down
4 changes: 2 additions & 2 deletions io/polyjson/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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() {
Expand Down
2 changes: 1 addition & 1 deletion io/polyjson/polyjson.go
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Expand Up @@ -13,7 +13,7 @@ import (
"os"
"time"

"github.com/TimothyStiles/poly/transform"
"github.com/bebop/poly/transform"
)

/******************************************************************************
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2 changes: 1 addition & 1 deletion io/polyjson/polyjson_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ import (
"strings"
"testing"

"github.com/TimothyStiles/poly/transform"
"github.com/bebop/poly/transform"
"github.com/stretchr/testify/assert"
)

Expand Down
2 changes: 1 addition & 1 deletion io/rebase/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion io/slow5/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ import (
"fmt"
"os"

"github.com/TimothyStiles/poly/io/slow5"
"github.com/bebop/poly/io/slow5"
)

func ExampleNewParser() {
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2 changes: 1 addition & 1 deletion io/slow5/slow5.go
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion io/uniprot/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion mash/example_test.go
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Expand Up @@ -3,7 +3,7 @@ package mash_test
import (
"fmt"

"github.com/TimothyStiles/poly/mash"
"github.com/bebop/poly/mash"
)

func ExampleMash() {
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2 changes: 1 addition & 1 deletion mash/mash_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ package mash_test
import (
"testing"

"github.com/TimothyStiles/poly/mash"
"github.com/bebop/poly/mash"
)

func TestMash(t *testing.T) {
Expand Down
2 changes: 1 addition & 1 deletion primers/pcr/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
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