Re-enable golangci-lint.yml, turn on linters, and lint. (#343)

.github/workflows/golangci-lint.yml

@@ -0,0 +1,38 @@
+name: golangci-lint
+
+on:
+  push:
+    tags:
+      - v*
+    branches:
+      - main
+  pull_request:
+jobs:
+  golangci:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run golangci-lint
+        uses: golangci/golangci-lint-action@v2.5.2
+        with:
+          # Optional: version of golangci-lint to use in form of v1.2 or v1.2.3 or `latest` to use the latest version
+          version: latest
+
+          # Optional: working directory, useful for monorepos
+          # working-directory: somedir
+
+          # Optional: golangci-lint command line arguments.
+          # args: --issues-exit-code=0
+
+          # Optional: show only new issues if it's a pull request. The default value is `false`.
+          # only-new-issues: true
+
+          # Optional: if set to true then the action will use pre-installed Go.
+          # skip-go-installation: true
+
+          # Optional: if set to true then the action don't cache or restore ~/go/pkg.
+          # skip-pkg-cache: true
+
+          # Optional: if set to true then the action don't cache or restore ~/.cache/go-build.
+          # skip-build-cache: true

.golangci.yml

@@ -5,31 +5,25 @@ run:
 linters:
   enable:
     - bodyclose
-    ##- dogsled
     - dupl
-    #- exhaustivestruct
     - exportloopref
-    #- funlen
     - gochecknoinits
-    ##- goconst
-    ##- gocritic
-    ##- gocyclo
-    ##- gofmt
-    ##- goimports
-    #- gomnd
+    # - goconst # TODO: Enable this and fix the errors.
+    - gofmt
+    - goimports
     - goprintffuncname
-    ##- gosec
-    #- lll
-    ##- misspell
+    - misspell
     - nakedret
     - nilnil
     - noctx
     - nolintlint
-    ##- stylecheck
-    ##- unconvert
-    ##- unparam
-    ##- whitespace
-#linters-settings:
-#  stylecheck:
-#    # https://staticcheck.io/docs/options#checks
-#    checks: ["all", "-ST1005"]
+    - stylecheck
+    - unconvert
+    - unparam
+    - whitespace
+linters-settings:
+  stylecheck:
+    # https://staticcheck.io/docs/options#checks
+    checks:
+      - "all"
+      - "-ST1005" # Disable "Incorrectly formatted error string" errors. TODO: Enable this and fix the errors.

align/align.go

@@ -77,7 +77,6 @@ type Scoring struct {
 
 // NewScoring returns a new Scoring struct with default values for DNA.
 func NewScoring(substitutionMatrix *matrix.SubstitutionMatrix, gapPenalty int) (Scoring, error) {
-
 	if substitutionMatrix == nil {
 		substitutionMatrix = matrix.Default
 	}
@@ -99,7 +98,6 @@ func (s Scoring) Score(a, b byte) (int, error) {
 // It returns the final score and the optimal alignments of the two strings in O(nm) time and O(nm) space.
 // https://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm
 func NeedlemanWunsch(stringA string, stringB string, scoring Scoring) (int, string, string, error) {
-
 	// Get the M and N dimensions of the matrix. The M x N matrix is standard linear algebra notation.
 	// But I added columns and rows to the variable name to make it more clear what the dimensions are.
 	columnLengthM, rowLengthN := len(stringA), len(stringB)
@@ -171,7 +169,6 @@ func NeedlemanWunsch(stringA string, stringB string, scoring Scoring) (int, stri
 // It returns the max score and optimal local alignments between two strings alignments of the two strings in O(nm) time and O(nm) space.
 // https://en.wikipedia.org/wiki/Smith-Waterman_algorithm
 func SmithWaterman(stringA string, stringB string, scoring Scoring) (int, string, string, error) {
-
 	columnLengthM, rowLengthN := len(stringA), len(stringB)
 
 	// Initialize the alignment matrix

align/align_test.go

@@ -9,7 +9,6 @@ import (
 )
 
 func TestNeedlemanWunsch(t *testing.T) {
-
 	mat := [][]int{
 		/*       A C G T U */
 		/* A */ {1, -1, -1, -1, -1},
@@ -138,7 +137,6 @@ func TestNeedlemanWunsch(t *testing.T) {
 }
 
 func TestSmithWaterman(t *testing.T) {
-
 	mat := [][]int{
 		/*       - A C G T */
 		/* - */ {0, 0, 0, 0, 0},
@@ -291,5 +289,4 @@ func TestSmithWaterman(t *testing.T) {
 	if alignN != "G" {
 		t.Errorf("Alignment is %s, expected G", alignN)
 	}
-
 }

align/example_test.go

@@ -1,3 +1,4 @@
+//nolint:dupl
 package align_test
 
 import (

align/matrix/matrices.go

@@ -5,7 +5,7 @@
 // license that can be found in the LICENSE file.
 
 /*
-Package matrix provides a variety of alignment scoring matrices for sequence alignment. 
+Package matrix provides a variety of alignment scoring matrices for sequence alignment.
 These matrices have been lovingly borrowed from biogo/align.
 
 https://github.com/biogo/biogo/blob/master/align/matrix/matrices.go

align/matrix/matrix_test.go

@@ -11,7 +11,7 @@ import (
 func TestSubstitutionMatrix(t *testing.T) {
 	alpha1 := alphabet.NewAlphabet([]string{"-", "A", "C", "G", "T"})
 	alpha2 := alphabet.NewAlphabet([]string{"-", "A", "C", "G", "T"})
-	NUC_4 := [][]int{
+	NUC_4 := [][]int{ //nolint:stylecheck
 		/*       - A C G T */
 		/* - */ {0, 0, 0, 0, 0},
 		/* A */ {0, 5, -4, -4, -4},

alphabet/alphabet_test.go

@@ -64,7 +64,6 @@ func TestAlphabet(t *testing.T) {
 }
 
 func TestAlphabet_Symbols(t *testing.T) {
-
 	// Test Symbols
 	symbols := []string{"A", "C", "G", "T"}
 	a := alphabet.NewAlphabet(symbols)

clone/clone_test.go

@@ -141,7 +141,6 @@ func ExampleGoldenGate() {
 
 	fmt.Println(seqhash.RotateSequence(Clones[0]))
 	// Output: AAAAAAAGGATCTCAAGAAGGCCTACTATTAGCAACAACGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACCTGCACCAGTCAGTAAAACGACGGCCAGTAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTTGGTTCAGGTGGAGTGGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGAGGTGTCAATCGTCGGAGCCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCATGGTCATAGCTGTTTCCTGAGAGCTTGGCAGGTGATGACACACATTAACAAATTTCGTGAGGAGTCTCCAGAAGAATGCCATTAATTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAG
-
 }
 
 func TestSignalKilledGoldenGate(t *testing.T) {

fold/fold.go

@@ -480,7 +480,6 @@ func multibranch(start, mid, end int, foldContext context, helix bool) (nucleicA
 			}
 			summedEnergy += w.energy
 		}
-
 	}
 
 	if unpaired < 0 {
@@ -539,7 +538,6 @@ func internalLoop(start, rightOfStart, end, leftOfEnd int, foldContext context)
 
 	if loopLeftIndex < 1 {
 		return 0, fmt.Errorf("internal loop: subsequence (%d, %d, %d, %d): missing left part of the loop", start, rightOfStart, end, leftOfEnd)
-
 	}
 	if loopRightIndex < 1 {
 		return 0, fmt.Errorf("internal loop: subsequence (%d, %d, %d, %d): missing right part of the loop", start, rightOfStart, end, leftOfEnd)

fold/seqfold.go

@@ -41,7 +41,7 @@ A - number of helices in the loop
 B - number of unpaired nucleotides in the loop
 C - coxial stacking in the loop
 D - terminal mismatch contributions
-E - base composition of the unpaired nucleotides (probably neglible?)
+E - base composition of the unpaired nucleotides (probably negligible?)
 Inferred from:
 Supplemental Material: Annu.Rev.Biophs.Biomol.Struct.33:415-40
 doi: 10.1146/annurev.biophys.32.110601.141800
@@ -189,7 +189,6 @@ func newFoldingContext(seq string, temp float64) (context, error) {
 		return context{}, fmt.Errorf("error filling the caches for the FoldingContext: %w", err)
 	}
 	return ret, nil
-
 }
 
 // Result holds the resulting structures of the folded s

io/example_test.go

@@ -10,7 +10,6 @@ import (
 // This is where the integration tests that make effed up cyclic dependencies go.
 
 func Example() {
-
 	// Poly can take in basic gff, gbk, fasta, and JSON.
 	// We call the json package "pson" (poly JSON) to prevent namespace collision with Go's standard json package.
 

io/fasta/fasta.go

@@ -363,7 +363,6 @@ func Build(fastas []Fasta) ([]byte, error) {
 		lineCount := 0
 		// write the fasta sequence 80 characters at a time
 		for _, character := range fasta.Sequence {
-
 			fastaString.WriteRune(character)
 			lineCount++
 			if lineCount == 80 {

io/genbank/example_test.go

@@ -111,7 +111,6 @@ func ExampleParseMulti() {
 }
 
 func ExampleGenbank_AddFeature() {
-
 	// Sequence for greenflourescent protein (GFP) that we're using as test data for this example.
 	gfpSequence := "ATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA"
 
@@ -123,7 +122,7 @@ func ExampleGenbank_AddFeature() {
 	sequence.Sequence = gfpSequence
 
 	// Set the initialized feature name and sequence location.
-	feature.Description = "Green Flourescent Protein"
+	feature.Description = "Green Fluorescent Protein"
 	feature.Location = genbank.Location{}
 	feature.Location.Start = 0
 	feature.Location.End = len(sequence.Sequence)
@@ -141,7 +140,6 @@ func ExampleGenbank_AddFeature() {
 }
 
 func ExampleFeature_GetSequence() {
-
 	// Sequence for greenflourescent protein (GFP) that we're using as test data for this example.
 	gfpSequence := "ATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA"
 
@@ -153,7 +151,7 @@ func ExampleFeature_GetSequence() {
 	sequence.Sequence = gfpSequence
 
 	// Set the initialized feature name and sequence location.
-	feature.Description = "Green Flourescent Protein"
+	feature.Description = "Green Fluorescent Protein"
 	feature.Location.Start = 0
 	feature.Location.End = len(sequence.Sequence)
 
@@ -167,5 +165,4 @@ func ExampleFeature_GetSequence() {
 	fmt.Println(gfpSequence == featureSequence)
 
 	// Output: true
-
 }