Remove unneeded dependencies (#28)

* Removed many deps, integrated svb and wordwrap

* removed svb submodule

* added svb back

* add cpuid, murmur, remove testify

* change around workflows

* Fix linting problems except weightedrand

* Added go.mod to lib, removed weightedRand

* fix import problems

* update directories

* Updated readme and seqhash.go for clarity

.github/workflows/coverage.yml

@@ -13,11 +13,11 @@ jobs:
       - name: Install Go
         uses: actions/setup-go@v2
         with:
-          go-version: 1.18
+          go-version: 1.21
       - name: Checkout code
         uses: actions/checkout@v2
       - name: Generate coverage report
-        run: go test -v  -coverprofile=profile.cov ./...
+        run: go test -v  -coverprofile=profile.cov ./lib/...
       - name: Parse overall coverage
         run: coverage=$(go tool cover -func profile.cov | tail -1 | rev | cut -f 1 | rev) && echo "COVERAGE=$coverage" >> $GITHUB_ENV 
       - name: Create the Badge

.github/workflows/golangci-lint.yml

@@ -20,7 +20,7 @@ jobs:
           version: latest
 
           # Optional: working directory, useful for monorepos
-          # working-directory: somedir
+          working-directory: lib
 
           # Optional: golangci-lint command line arguments.
           # args: --issues-exit-code=0

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
   test:
     strategy:
       matrix:
-        go-version: [1.18.x,]
+        go-version: [1.21.x,]
         platform: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.platform }}
     steps:
@@ -21,4 +21,4 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v2
     - name: Test
-      run: go test -v ./...
+      run: go test -v ./lib/...

.golangci.yml

@@ -3,6 +3,7 @@ run:
   skip-dirs:
     - data
     - api/gen
+    - lib/bio/slow5/svb
 linters:
   enable:
     - bodyclose

README.md

@@ -26,6 +26,14 @@ Write good, useful code. Open a pull request, and we'll see if it fits!
 
 * Copyright (c) 2023 Keoni Gandall
 
+### Sources
+
+There are a few pieces of "complete" software that we have directly integrated into the source tree (with their associated licenses). These projects don't receive updates anymore (or just bug fixes with years between). In particular, `lib` has most of these, since we intend to have as few dependencies as possible in `lib`. The integrated projects include the following.
+- [svb](https://github.com/rleiwang/svb) in `lib/bio/slow5/svb`
+- [intel-cpuid](https://github.com/aregm/cpuid) in `lib/bio/slow5/svb/intel-cpuid`
+- [murmur3](https://github.com/spaolacci/murmur3) in `lib/mash/murmur3`
+- [wordwrap](https://github.com/mitchellh/go-wordwrap) in `lib/bio/genbank`
+
 ### Other
 
 DnaDesign is a fork of [Poly](https://github.com/TimothyStiles/poly) at commit f76bf05 with a different mission focus. 

go.work

@@ -0,0 +1,3 @@
+go 1.21.5
+
+use ./lib

lib/align/matrix/matrix_test.go

@@ -5,7 +5,6 @@ import (
 
 	"github.com/koeng101/dnadesign/lib/align/matrix"
 	"github.com/koeng101/dnadesign/lib/alphabet"
-	"github.com/stretchr/testify/assert"
 )
 
 func TestSubstitutionMatrix(t *testing.T) {
@@ -21,7 +20,9 @@ func TestSubstitutionMatrix(t *testing.T) {
 	}
 	subMat, err := matrix.NewSubstitutionMatrix(alpha1, alpha2, NUC_4)
 
-	assert.Nil(t, err)
+	if err != nil {
+		t.Error(err)
+	}
 
 	testCases := []struct {
 		symbol1 string
@@ -39,8 +40,12 @@ func TestSubstitutionMatrix(t *testing.T) {
 		sym2, _ := alpha2.Encode(tc.symbol2)
 		score, err := subMat.Score(tc.symbol1, tc.symbol2)
 
-		assert.Nil(t, err)
-		assert.Equal(t, NUC_4[sym1][sym2], score)
+		if err != nil {
+			t.Error(err)
+		}
+		if NUC_4[sym1][sym2] != score {
+			t.Errorf("NUC_4[sym1][sym2] and score should be equivalent, but are not.")
+		}
 
 		if score != tc.score {
 			t.Errorf("Expected score %d for symbols %s and %s, but got %d", tc.score, tc.symbol1, tc.symbol2, score)

lib/bio/genbank/genbank.go

@@ -21,8 +21,6 @@ import (
 	"strings"
 
 	"github.com/koeng101/dnadesign/lib/transform"
-	"github.com/lunny/log"
-	"github.com/mitchellh/go-wordwrap"
 )
 
 /******************************************************************************
@@ -787,8 +785,7 @@ func (parser *Parser) Next() (*Genbank, error) {
 				parser.parameters.sequenceBuilder.WriteString(sequenceRegex.ReplaceAllString(line, ""))
 			}
 		default:
-			log.Warnf("Unknown parse step: %s", parser.parameters.parseStep)
-			parser.parameters.genbankStarted = false
+			return &Genbank{}, fmt.Errorf("Unknown parse step: %s", parser.parameters.parseStep)
 		}
 	}
 	return &Genbank{}, io.EOF
@@ -1100,7 +1097,8 @@ func buildMetaString(name string, data string) string {
 		keyWhitespaceTrail += " "
 	}
 	name += keyWhitespaceTrail
-	wrappedData := wordwrap.WrapString(data, 68)
+
+	wrappedData := wrapString(data, 68)
 	splitData := strings.Split(wrappedData, "\n")
 	var returnData string
 	for index, datum := range splitData {

lib/bio/genbank/genbank_test.go

@@ -15,7 +15,6 @@ import (
 	"github.com/google/go-cmp/cmp"
 	"github.com/google/go-cmp/cmp/cmpopts"
 	"github.com/koeng101/dnadesign/lib/transform"
-	"github.com/stretchr/testify/assert"
 )
 
 /******************************************************************************
@@ -673,7 +672,9 @@ func TestRead_error(t *testing.T) {
 		readFileFn = oldreadFileFn
 	}()
 	_, err := read("/tmp/file")
-	assert.EqualError(t, err, readErr.Error())
+	if err.Error() != readErr.Error() {
+		t.Errorf("err should equal readErr")
+	}
 }
 
 func TestBuildFeatureString(t *testing.T) {
@@ -685,7 +686,9 @@ func TestBuildFeatureString(t *testing.T) {
 		},
 	}
 	str := BuildFeatureString(feature)
-	assert.Equal(t, str, "     test type       gbk location\n")
+	if str != "     test type       gbk location\n" {
+		t.Errorf("BuildFeatureString did not produce proper string")
+	}
 }
 
 func TestParse_error(t *testing.T) {
@@ -698,10 +701,14 @@ func TestParse_error(t *testing.T) {
 		parseMultiNthFn = oldParseMultiNthFn
 	}()
 	_, err := parse(strings.NewReader(""))
-	assert.Equal(t, err, parseMultiErr.wraps)
+	if err != parseMultiErr.wraps {
+		t.Errorf("err should equal parseMultiErr.wraps")
+	}
 
 	_, err = parseMultiNth(strings.NewReader(""), 10000)
-	assert.Equal(t, err, parseMultiErr)
+	if err.Error() != parseMultiErr.Error() {
+		t.Errorf("err should equal parseMultiErr")
+	}
 }
 
 func TestParseReferences_error(t *testing.T) {
@@ -714,7 +721,9 @@ func TestParseReferences_error(t *testing.T) {
 	}()
 	file, _ := os.Open("data/puc19.gbk")
 	_, err := parseMultiNthFn(file, 1)
-	assert.Equal(t, err.info, "failed in parsing reference")
+	if err.info != "failed in parsing reference" {
+		t.Errorf("err.info should have failed to parse reference")
+	}
 }
 
 func TestIssue303Regression(t *testing.T) {

lib/bio/genbank/wordwrap.go

@@ -0,0 +1,93 @@
+package genbank
+
+import (
+	"bytes"
+	"unicode"
+)
+
+/*
+The MIT License (MIT)
+
+Copyright (c) 2014 Mitchell Hashimoto
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+const nbsp = 0xA0
+
+// wrapString wraps the given string within lim width in characters.
+//
+// Wrapping is currently naive and only happens at white-space. A future
+// version of the library will implement smarter wrapping. This means that
+// pathological cases can dramatically reach past the limit, such as a very
+// long word.
+func wrapString(s string, lim uint) string {
+	// Initialize a buffer with a slightly larger size to account for breaks
+	init := make([]byte, 0, len(s))
+	buf := bytes.NewBuffer(init)
+
+	var current uint
+	var wordBuf, spaceBuf bytes.Buffer
+	var wordBufLen, spaceBufLen uint
+
+	for _, char := range s {
+		if char == '\n' {
+			if wordBuf.Len() == 0 {
+				if current+spaceBufLen > lim {
+
+				} else {
+					_, _ = spaceBuf.WriteTo(buf)
+				}
+				spaceBuf.Reset()
+				spaceBufLen = 0
+			} else {
+				_, _ = spaceBuf.WriteTo(buf)
+				spaceBuf.Reset()
+				spaceBufLen = 0
+				_, _ = wordBuf.WriteTo(buf)
+				wordBuf.Reset()
+				wordBufLen = 0
+			}
+			buf.WriteRune(char)
+			current = 0
+		} else if unicode.IsSpace(char) && char != nbsp {
+			if spaceBuf.Len() == 0 || wordBuf.Len() > 0 {
+				current += spaceBufLen + wordBufLen
+				_, _ = spaceBuf.WriteTo(buf)
+				spaceBuf.Reset()
+				spaceBufLen = 0
+				_, _ = wordBuf.WriteTo(buf)
+				wordBuf.Reset()
+				wordBufLen = 0
+			}
+
+			spaceBuf.WriteRune(char)
+			spaceBufLen++
+		} else {
+			wordBuf.WriteRune(char)
+			wordBufLen++
+
+			if current+wordBufLen+spaceBufLen > lim && wordBufLen < lim {
+				buf.WriteRune('\n')
+				current = 0
+				spaceBuf.Reset()
+				spaceBufLen = 0
+			}
+		}
+	}
+
+	if wordBuf.Len() == 0 {
+		if current+spaceBufLen <= lim {
+			_, _ = spaceBuf.WriteTo(buf)
+		}
+	} else {
+		_, _ = spaceBuf.WriteTo(buf)
+		_, _ = wordBuf.WriteTo(buf)
+	}
+
+	return buf.String()
+}