Replaced the Seqhash sequencetype with Struct type argument instead o…

…f a plain string.. (#264) * Replaced the Seqhash sequencetype with Struct type argument instead of a plain string.. * Cleared the linting errors for Go > 1.16 where ioutils package has been depreciated Co-authored-by: Tim <[email protected]>
bebop · Sep 11, 2022 · eba6b72 · eba6b72
1 parent 07afbb6
commit eba6b72
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Showing 16 changed files with 143 additions and 144 deletions.
diff --git a/.github/workflows/golangci-lint.yml b/.github/workflows/golangci-lint.yml
@@ -1,22 +1,23 @@
 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/[email protected]
-#         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
+
+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/[email protected]
+        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

diff --git a/.github/workflows/notify.yml b/.github/workflows/notify.yml
@@ -4,9 +4,8 @@ on:
   release: 
   issues: 
   pull_request:
-  issue_comment: 
-  pull_request_review:
-  pull_request_review_comment: 
+    types: [opened]
+  issue_comment:
   discussion: 
   discussion_comment:
   push:
@@ -23,4 +22,4 @@ jobs:
       - name: Actions for Discord
         env:
           DISCORD_WEBHOOK: ${{ secrets.DISCORD_WEBHOOK }}
-        uses: Ilshidur/[email protected]
+        uses: Ilshidur/[email protected]
diff --git a/io/fasta/fasta.go b/io/fasta/fasta.go
@@ -16,7 +16,6 @@ import (
 	"bytes"
 	"compress/gzip"
 	"io"
-	"io/ioutil"
 	"os"
 	"strings"
 )
@@ -193,5 +192,5 @@ func Write(fastas []Fasta, path string) error {
 	if err != nil {
 		return err
 	}
-	return ioutil.WriteFile(path, fastaBytes, 0644)
+	return os.WriteFile(path, fastaBytes, 0644)
 }
diff --git a/io/genbank/example_test.go b/io/genbank/example_test.go
@@ -3,7 +3,6 @@ package genbank_test
 import (
 	"bytes"
 	"fmt"
-	"io/ioutil"
 	"os"
 	"path/filepath"
 
@@ -29,7 +28,7 @@ func ExampleRead() {
 }
 
 func ExampleWrite() {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		fmt.Println(err.Error())
 	}
@@ -74,7 +73,7 @@ func ExampleReadMulti() {
 }
 
 func ExampleWriteMulti() {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		fmt.Println(err.Error())
 	}

diff --git a/io/genbank/genbank.go b/io/genbank/genbank.go
@@ -15,7 +15,6 @@ import (
 	"bytes"
 	"fmt"
 	"io"
-	"io/ioutil"
 	"os"
 	"regexp"
 	"strconv"
@@ -33,7 +32,7 @@ GBK specific IO related things begin here.
 ******************************************************************************/
 
 var (
-	readFileFn        = ioutil.ReadFile
+	readFileFn        = os.ReadFile
 	parseMultiNthFn   = ParseMultiNth
 	parseReferencesFn = parseReferences
 )
@@ -187,7 +186,7 @@ func Write(sequences Genbank, path string) error {
 	// add error handling in the future.
 	gbk, _ := Build(sequences)
 
-	err := ioutil.WriteFile(path, gbk, 0644)
+	err := os.WriteFile(path, gbk, 0644)
 	return err
 }
 
@@ -198,7 +197,7 @@ func WriteMulti(sequences []Genbank, path string) error {
 	// add error handling in the future.
 	gbk, _ := BuildMulti(sequences)
 
-	err := ioutil.WriteFile(path, gbk, 0644)
+	err := os.WriteFile(path, gbk, 0644)
 	return err
 }
 

diff --git a/io/genbank/genbank_test.go b/io/genbank/genbank_test.go
@@ -3,7 +3,6 @@ package genbank
 import (
 	"errors"
 	"io"
-	"io/ioutil"
 	"os"
 	"path/filepath"
 	"strings"
@@ -34,7 +33,7 @@ var singleGbkPaths = []string{
 }
 
 func TestGbkIO(t *testing.T) {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		t.Error(err)
 	}
@@ -68,7 +67,7 @@ func TestMultiLineFeatureParse(t *testing.T) {
 }
 
 func TestMultiGenbankIO(t *testing.T) {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		t.Error(err)
 	}
@@ -89,7 +88,7 @@ func TestMultiGenbankIO(t *testing.T) {
 }
 
 func TestGbkLocationStringBuilder(t *testing.T) {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		t.Error(err)
 	}
@@ -117,7 +116,7 @@ func TestGbkLocationStringBuilder(t *testing.T) {
 }
 
 func TestGbLocationStringBuilder(t *testing.T) {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		t.Error(err)
 	}

diff --git a/io/gff/example_test.go b/io/gff/example_test.go
@@ -3,7 +3,6 @@ package gff_test
 import (
 	"bytes"
 	"fmt"
-	"io/ioutil"
 	"os"
 	"path/filepath"
 	"testing"
@@ -49,7 +48,7 @@ func ExampleBuild() {
 }
 
 func ExampleWrite() {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		fmt.Println(err.Error())
 	}

diff --git a/io/gff/gff.go b/io/gff/gff.go
@@ -14,7 +14,6 @@ package gff
 import (
 	"bytes"
 	"io"
-	"io/ioutil"
 	"os"
 	"sort"
 	"strconv"
@@ -26,7 +25,7 @@ import (
 )
 
 var (
-	readAllFn = ioutil.ReadAll
+	readAllFn = io.ReadAll
 	atoiFn    = strconv.Atoi
 	openFn    = os.Open
 )
@@ -305,5 +304,5 @@ func Read(path string) (Gff, error) {
 // Write takes an poly.Sequence struct and a path string and writes out a gff to that path.
 func Write(sequence Gff, path string) error {
 	gff, _ := Build(sequence)
-	return ioutil.WriteFile(path, gff, 0644)
+	return os.WriteFile(path, gff, 0644)
 }
diff --git a/io/gff/gff_test.go b/io/gff/gff_test.go
@@ -4,7 +4,6 @@ import (
 	"bytes"
 	"errors"
 	"io"
-	"io/ioutil"
 	"os"
 	"path/filepath"
 	"strings"
@@ -24,7 +23,7 @@ Gff related tests and benchmarks begin here.
 // TODO should delete output files.
 
 func TestGffIO(t *testing.T) {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		t.Error(err)
 	}
@@ -42,8 +41,8 @@ func TestGffIO(t *testing.T) {
 		t.Errorf("Parsing the output of Build() does not produce the same output as parsing the original file read with ReadGff(). Got this diff:\n%s", diff)
 	}
 
-	original, _ := ioutil.ReadFile(testInputPath)
-	builtOutput, _ := ioutil.ReadFile(tmpGffFilePath)
+	original, _ := os.ReadFile(testInputPath)
+	builtOutput, _ := os.ReadFile(tmpGffFilePath)
 	gffDiff := difflib.UnifiedDiff{
 		A:        difflib.SplitLines(string(original)),
 		B:        difflib.SplitLines(string(builtOutput)),

diff --git a/io/polyjson/example_test.go b/io/polyjson/example_test.go
@@ -2,7 +2,6 @@ package polyjson_test
 
 import (
 	"fmt"
-	"io/ioutil"
 	"os"
 	"path/filepath"
 	"time"
@@ -14,7 +13,7 @@ import (
 func Example() {
 
 	// this example also is run by the poly's test suite so this just sets up a temporary directory for writing files
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		fmt.Println(err.Error())
 	}
@@ -74,7 +73,7 @@ func ExampleParse() {
 }
 
 func ExampleWrite() {
-	tmpDataDir, err := ioutil.TempDir("", "data-*")
+	tmpDataDir, err := os.MkdirTemp("", "data-*")
 	if err != nil {
 		fmt.Println(err.Error())
 	}

diff --git a/io/polyjson/polyjson.go b/io/polyjson/polyjson.go
@@ -10,7 +10,6 @@ import (
 	"bytes"
 	"encoding/json"
 	"io"
-	"io/ioutil"
 	"os"
 	"time"
 
@@ -151,7 +150,7 @@ func Write(sequence Poly, path string) error {
 	if err != nil {
 		return err
 	}
-	return ioutil.WriteFile(path, file, 0644)
+	return os.WriteFile(path, file, 0644)
 }
 
 /******************************************************************************