From 05cdd6d1497899492736430ad36937c44c4d0c62 Mon Sep 17 00:00:00 2001 From: Timothy Stiles Date: Mon, 11 Dec 2023 12:48:30 -0800 Subject: [PATCH] migrated namespace from TimothyStiles/poly to bebop/poly --- CONTRIBUTING.md | 10 +++++----- README.md | 12 ++++++------ align/align.go | 2 +- align/align_test.go | 6 +++--- align/example_test.go | 6 +++--- align/matrix/matrix.go | 2 +- align/matrix/matrix_test.go | 4 ++-- alphabet/alphabet_test.go | 2 +- checks/checks.go | 2 +- checks/checks_test.go | 2 +- clone/clone.go | 6 +++--- clone/example_test.go | 4 ++-- doc.go | 2 +- fold/dna.go | 2 +- fold/example_test.go | 2 +- fold/fold.go | 2 +- fold/rna.go | 2 +- fold/seqfold.go | 2 +- go.mod | 2 +- io/example_test.go | 8 ++++---- io/fasta/example_test.go | 2 +- io/fastq/example_test.go | 2 +- io/genbank/example_test.go | 2 +- io/genbank/genbank.go | 2 +- io/genbank/genbank_test.go | 2 +- io/gff/example_test.go | 4 ++-- io/gff/gff.go | 2 +- io/polyjson/example_test.go | 4 ++-- io/polyjson/polyjson.go | 2 +- io/polyjson/polyjson_test.go | 2 +- io/rebase/example_test.go | 2 +- io/slow5/example_test.go | 2 +- io/slow5/slow5.go | 2 +- io/uniprot/example_test.go | 2 +- mash/example_test.go | 2 +- mash/mash_test.go | 2 +- primers/pcr/example_test.go | 2 +- primers/pcr/pcr.go | 4 ++-- primers/primers.go | 4 ++-- primers/primers_test.go | 4 ++-- seqhash/example_test.go | 4 ++-- seqhash/seqhash.go | 2 +- seqhash/seqhash_test.go | 2 +- synthesis/codon/codon.go | 2 +- synthesis/codon/codon_test.go | 2 +- synthesis/codon/example_test.go | 4 ++-- synthesis/fix/example_test.go | 4 ++-- synthesis/fix/synthesis.go | 6 +++--- synthesis/fix/synthesis_test.go | 4 ++-- synthesis/fragment/example_test.go | 2 +- synthesis/fragment/fragment.go | 4 ++-- transform/examples_test.go | 2 +- transform/transform_test.go | 2 +- tutorials/001_input_output_test.go | 2 +- tutorials/README.md | 2 +- 55 files changed, 87 insertions(+), 87 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index df7b9f9ae..5b378ab3c 100644 --- 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 index 97abd1a36..4d2c24370 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,8 @@ # (Poly)merase -[![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 index fc4edef92..0eaddae70 100644 --- 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 index aca3a7de5..547d1c086 100644 --- 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 index 1cab08e86..3d455a108 100644 --- 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 index 5c5bb2f19..c36e93334 100644 --- 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 index f05c63f84..d1e5d0027 100644 --- 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 index 81dd70ad0..ca09a0a7a 100644 --- 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 index 23a797405..572cb1257 100644 --- 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 index d1862d978..7588b231e 100644 --- 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 index e7f1c3eee..25d8754bb 100644 --- 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 index 85d12dc60..3e0158873 100644 --- 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 index a75059514..dd9762733 100644 --- 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 index 4ed2c4162..c132102a7 100644 --- 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 index 7ed6c9178..87e5a4e0c 100644 --- 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 index 34ca7998b..6e810c262 100644 --- 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 index a718b50af..3d166d642 100644 --- 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 index f5a39fb3c..52b94ca83 100644 --- 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 index 418924651..db54fa954 100644 --- 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 index 08fd21f4a..620d3d758 100644 --- 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 index e1bb6eeb5..26587b8c2 100644 --- 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 index 498b1e38e..2b50efa48 100644 --- 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 index 0bc8433ea..89b128b85 100644 --- 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 index 468e17cf6..6ef8cb43e 100644 --- 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 index 9466c6b1f..a0ac784cc 100644 --- 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 index 040e9403a..8f747bd7a 100644 --- 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 index afc688df1..3cd4809dd 100644 --- 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 index eb65a1906..9d79dd2df 100644 --- 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 index 813704802..9c2631265 100644 --- 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 index eaee25b19..6584f073d 100644 --- 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 index 313da658f..82f4c98bf 100644 --- 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 index f51d44b29..b96776552 100644 --- 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 index 3d43f0cd9..d56abe5cd 100644 --- 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 index 5b1af1390..a5446e5db 100644 --- 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 index 48743a721..76a5db618 100644 --- 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 index ccf20ce49..f22f4715a 100644 --- 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 index aefa8147f..cee08ea05 100644 --- 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 index 8546f59c4..648bc8ac6 100644 --- a/primers/pcr/pcr.go +++ b/primers/pcr/pcr.go @@ -27,8 +27,8 @@ import ( "sort" "strings" - "github.com/TimothyStiles/poly/primers" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/primers" + "github.com/bebop/poly/transform" ) // https://doi.org/10.1089/dna.1994.13.75 diff --git a/primers/primers.go b/primers/primers.go index b10d8988f..ef730c424 100644 --- a/primers/primers.go +++ b/primers/primers.go @@ -24,8 +24,8 @@ import ( "math" "strings" - "github.com/TimothyStiles/poly/checks" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/checks" + "github.com/bebop/poly/transform" ) // For reference: https://www.sigmaaldrich.com/technical-documents/articles/biology/oligos-melting-temp.html diff --git a/primers/primers_test.go b/primers/primers_test.go index f6c498f01..75857d8c1 100644 --- a/primers/primers_test.go +++ b/primers/primers_test.go @@ -6,8 +6,8 @@ import ( "strings" "testing" - "github.com/TimothyStiles/poly/primers" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/primers" + "github.com/bebop/poly/transform" ) func ExampleMarmurDoty() { diff --git a/seqhash/example_test.go b/seqhash/example_test.go index 02629c857..2d2633ed4 100644 --- a/seqhash/example_test.go +++ b/seqhash/example_test.go @@ -3,8 +3,8 @@ package seqhash_test import ( "fmt" - "github.com/TimothyStiles/poly/io/genbank" - "github.com/TimothyStiles/poly/seqhash" + "github.com/bebop/poly/io/genbank" + "github.com/bebop/poly/seqhash" ) // This example shows how to seqhash a sequence. diff --git a/seqhash/seqhash.go b/seqhash/seqhash.go index 335a92545..215f94e30 100644 --- a/seqhash/seqhash.go +++ b/seqhash/seqhash.go @@ -61,7 +61,7 @@ import ( "sort" "strings" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/transform" "lukechampine.com/blake3" ) diff --git a/seqhash/seqhash_test.go b/seqhash/seqhash_test.go index 5787cc36b..1abd279d7 100644 --- a/seqhash/seqhash_test.go +++ b/seqhash/seqhash_test.go @@ -5,7 +5,7 @@ import ( "fmt" "testing" - "github.com/TimothyStiles/poly/io/genbank" + "github.com/bebop/poly/io/genbank" "github.com/sergi/go-diff/diffmatchpatch" ) diff --git a/synthesis/codon/codon.go b/synthesis/codon/codon.go index db3c4fc11..2f7fdf82f 100644 --- a/synthesis/codon/codon.go +++ b/synthesis/codon/codon.go @@ -26,7 +26,7 @@ import ( "strings" "time" - "github.com/TimothyStiles/poly/io/genbank" + "github.com/bebop/poly/io/genbank" weightedRand "github.com/mroth/weightedrand" ) diff --git a/synthesis/codon/codon_test.go b/synthesis/codon/codon_test.go index a73fb8a74..8d34e7cd6 100644 --- a/synthesis/codon/codon_test.go +++ b/synthesis/codon/codon_test.go @@ -6,7 +6,7 @@ import ( "strings" "testing" - "github.com/TimothyStiles/poly/io/genbank" + "github.com/bebop/poly/io/genbank" "github.com/google/go-cmp/cmp" weightedRand "github.com/mroth/weightedrand" "github.com/stretchr/testify/assert" diff --git a/synthesis/codon/example_test.go b/synthesis/codon/example_test.go index 6d7aee668..0fae9bbb9 100644 --- a/synthesis/codon/example_test.go +++ b/synthesis/codon/example_test.go @@ -4,8 +4,8 @@ import ( "fmt" "os" - "github.com/TimothyStiles/poly/io/genbank" - "github.com/TimothyStiles/poly/synthesis/codon" + "github.com/bebop/poly/io/genbank" + "github.com/bebop/poly/synthesis/codon" ) func ExampleTranslationTable_Translate() { diff --git a/synthesis/fix/example_test.go b/synthesis/fix/example_test.go index acda11d47..41825039e 100644 --- a/synthesis/fix/example_test.go +++ b/synthesis/fix/example_test.go @@ -4,8 +4,8 @@ import ( "fmt" "sync" - "github.com/TimothyStiles/poly/synthesis/codon" - "github.com/TimothyStiles/poly/synthesis/fix" + "github.com/bebop/poly/synthesis/codon" + "github.com/bebop/poly/synthesis/fix" ) var dataDir string = "../../data/" diff --git a/synthesis/fix/synthesis.go b/synthesis/fix/synthesis.go index ad4e16631..b1f4989f6 100644 --- a/synthesis/fix/synthesis.go +++ b/synthesis/fix/synthesis.go @@ -28,9 +28,9 @@ import ( "strings" "sync" - "github.com/TimothyStiles/poly/checks" - "github.com/TimothyStiles/poly/synthesis/codon" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/checks" + "github.com/bebop/poly/synthesis/codon" + "github.com/bebop/poly/transform" ) // DnaSuggestion is a suggestion of a fixer, generated by a diff --git a/synthesis/fix/synthesis_test.go b/synthesis/fix/synthesis_test.go index e86deb8c4..6ca7ea088 100644 --- a/synthesis/fix/synthesis_test.go +++ b/synthesis/fix/synthesis_test.go @@ -6,8 +6,8 @@ import ( "sync" "testing" - "github.com/TimothyStiles/poly/synthesis/codon" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/synthesis/codon" + "github.com/bebop/poly/transform" ) /****************************************************************************** diff --git a/synthesis/fragment/example_test.go b/synthesis/fragment/example_test.go index 2f726adac..ab30e0fc1 100644 --- a/synthesis/fragment/example_test.go +++ b/synthesis/fragment/example_test.go @@ -3,7 +3,7 @@ package fragment_test import ( "fmt" - "github.com/TimothyStiles/poly/synthesis/fragment" + "github.com/bebop/poly/synthesis/fragment" ) // This example shows how to use the fragmenter to fragment a gene in diff --git a/synthesis/fragment/fragment.go b/synthesis/fragment/fragment.go index ab01d06ec..ba4e9536c 100644 --- a/synthesis/fragment/fragment.go +++ b/synthesis/fragment/fragment.go @@ -15,8 +15,8 @@ import ( "fmt" "strings" - "github.com/TimothyStiles/poly/checks" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/checks" + "github.com/bebop/poly/transform" ) // SetEfficiency gets the estimated fidelity rate of a given set of diff --git a/transform/examples_test.go b/transform/examples_test.go index 266bcfcdc..e374ef7fc 100644 --- a/transform/examples_test.go +++ b/transform/examples_test.go @@ -3,7 +3,7 @@ package transform_test import ( "fmt" - "github.com/TimothyStiles/poly/transform" + "github.com/bebop/poly/transform" ) func ExampleReverseComplement() { diff --git a/transform/transform_test.go b/transform/transform_test.go index fdcf51e61..f534f62d4 100644 --- a/transform/transform_test.go +++ b/transform/transform_test.go @@ -4,7 +4,7 @@ import ( "math/rand" "testing" - "github.com/TimothyStiles/poly/random" + "github.com/bebop/poly/random" ) func TestReverse(t *testing.T) { diff --git a/tutorials/001_input_output_test.go b/tutorials/001_input_output_test.go index c44eee482..e205c1bf8 100644 --- a/tutorials/001_input_output_test.go +++ b/tutorials/001_input_output_test.go @@ -7,7 +7,7 @@ import ( "path/filepath" "testing" - "github.com/TimothyStiles/poly/io/genbank" + "github.com/bebop/poly/io/genbank" "github.com/google/go-cmp/cmp" "github.com/google/go-cmp/cmp/cmpopts" ) diff --git a/tutorials/README.md b/tutorials/README.md index b6d5ae8d1..589c31c3c 100644 --- a/tutorials/README.md +++ b/tutorials/README.md @@ -1,5 +1,5 @@ # Poly Tutorials -This directory holds a set of always up to date tutorials for Poly that be run can run, edited, and explored in the browser via this [gitpod deployment](https://gitpod.io/#tutorial=true/https://github.com/TimothyStiles/poly) +This directory holds a set of always up to date tutorials for Poly that be run can run, edited, and explored in the browser via this [gitpod deployment](https://gitpod.io/#tutorial=true/https://github.com/bebop/poly) Many tutorials in this directory haven't been started yet. Please feel free to write one and add it to our main repo via pull request! \ No newline at end of file