Merge pull request #324 from metrumresearchgroup/ci-lint-update

ci: update lint workflow
metrumresearchgroup · Aug 14, 2024 · 94c9262 · 94c9262
2 parents 5e1f919 + f044cb9
commit 94c9262
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Showing 23 changed files with 78 additions and 89 deletions.
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -6,28 +6,15 @@ on:
       - 'scratch/**'
   pull_request:
 
-# Note: this avoids golangci/golangci-lint-action to work around an
-# error triggered by us pinning to a golangci-lint version built with
-# an older Go.  Revisit when moving from golangci-lint v1.47.2.
-#
-# https://github.com/golangci/golangci-lint-action/issues/442#issuecomment-1203786890
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-go@v5
         with:
-          go-version-file: go.mod
-      - name: Install golangci-lint
-        shell: bash
-        run: |
-          bin=$(mktemp -d)
-          curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | \
-            sh -s -- -b "$bin" v1.47.2
-          echo "$bin" >>$GITHUB_PATH
+          go-version: stable
       - name: Run golangci-lint
-        shell: bash
-        run: |
-          command -v golangci-lint
-          golangci-lint run --out-format=github-actions
+        uses: golangci/golangci-lint-action@v6
+        with:
+          version: v1.59
diff --git a/.golangci.yml b/.golangci.yml
@@ -7,12 +7,14 @@ issues:
         - gocyclo
         - dupl
         - gosec
+  exclude-dirs:
+    - (^|/)mock($|/)
 
 linters-settings:
   errcheck:
     check-type-assertions: true
   govet:
-    check-shadowing: true
+    shadow: true
   unparam:
     check-exported: true
   unused:
@@ -31,22 +33,17 @@ linters-settings:
 
 run:
   skip-dirs-use-default: true
-  skip-dirs:
-    - (^|/)mock($|/)
   timeout: 3m
 
 linters:
   enable:
-    - deadcode
     - errcheck
     - gosimple
     - govet
     - ineffassign
     - staticcheck
-    - structcheck
     - typecheck
     - unused
-    - varcheck
 #    - gosec
     - unparam
     - unconvert
@@ -58,5 +55,4 @@ linters:
     - whitespace
     - rowserrcheck
     - godot
-    - ifshort
     - nakedret
diff --git a/cmd/bbi/main.go b/cmd/bbi/main.go
@@ -8,6 +8,7 @@ import (
 var buildTime string
 
 // if want to generate docs
+//
 //	import "github.com/spf13/cobra/doc"
 //	err := doc.GenMarkdownTree(cmd.RootCmd, "../../docs/bbi")
 //	if err != nil {

diff --git a/cmd/sge.go b/cmd/sge.go
@@ -30,7 +30,7 @@ type sgeOperation struct {
 	Models []SGEModel `json:"models"`
 }
 
-//SGEModel is the struct used for SGE operations containing the NonMemModel.
+// SGEModel is the struct used for SGE operations containing the NonMemModel.
 type SGEModel struct {
 	Nonmem               *NonMemModel
 	Cancel               chan bool
@@ -66,12 +66,12 @@ func (s *SGEModel) GetWorkingPath() string {
 	return s.Nonmem.OutputDir
 }
 
-//Begin Scalable method definitions.
+// Begin Scalable method definitions.
 func (l SGEModel) CancellationChannel() chan bool {
 	return l.Cancel
 }
 
-//Prepare is basically the old EstimateModel function. Responsible for creating directories and preparation.
+// Prepare is basically the old EstimateModel function. Responsible for creating directories and preparation.
 func (l SGEModel) Prepare(channels *turnstile.ChannelMap) {
 	log.Debugf("%s Beginning Prepare phase of SGE Work", l.Nonmem.LogIdentifier())
 
@@ -122,7 +122,7 @@ func (l SGEModel) Prepare(channels *turnstile.ChannelMap) {
 	}
 }
 
-//Work describes the Turnstile execution phase -> IE What heavy lifting should be done.
+// Work describes the Turnstile execution phase -> IE What heavy lifting should be done.
 func (l SGEModel) Work(channels *turnstile.ChannelMap) {
 	cerr := executeNonMemJob(executeSGEJob, l.Nonmem)
 
@@ -139,12 +139,12 @@ func (l SGEModel) Work(channels *turnstile.ChannelMap) {
 	channels.Completed <- 1
 }
 
-//Monitor is the 3rd phase of turnstile (not implemented here).
+// Monitor is the 3rd phase of turnstile (not implemented here).
 func (l SGEModel) Monitor(_ *turnstile.ChannelMap) {
 	//Do nothing for this implementation
 }
 
-//Cleanup is the last phase of execution, in which computation / hard work is done and we're cleaning up leftover files, copying results around et all.
+// Cleanup is the last phase of execution, in which computation / hard work is done and we're cleaning up leftover files, copying results around et all.
 func (l SGEModel) Cleanup(_ *turnstile.ChannelMap) {
 	//err := configlib.WriteViperConfig(l.Nonmem.OutputDir, true)
 	//
@@ -352,7 +352,7 @@ func sgeModelsFromArguments(args []string, config configlib.Config) ([]SGEModel,
 	return output, nil
 }
 
-//Generate the command line script to execute bbi on the grid.
+// Generate the command line script to execute bbi on the grid.
 func generateBbiScript(fileTemplate string, l NonMemModel) ([]byte, error) {
 	t, err := template.New("file").Parse(fileTemplate)
 	buf := new(bytes.Buffer)

diff --git a/integration/nonmem/bbi_expansion_test.go b/integration/nonmem/bbi_expansion_test.go
@@ -8,7 +8,7 @@ import (
 	"strings"
 	"testing"
 
-	. "github.com/metrumresearchgroup/bbi/integration"
+	bi "github.com/metrumresearchgroup/bbi/integration"
 	"github.com/metrumresearchgroup/bbi/utils"
 
 	"github.com/metrumresearchgroup/wrapt"
@@ -39,7 +39,7 @@ func TestBBIExpandsWithoutPrefix(tt *testing.T) {
 			filepath.Join(scenario.Workpath, "model", targets),
 		}
 
-		output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
+		output, err := bi.ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 		t.R.NoError(err)
 		t.R.NotEmpty(output)
@@ -108,7 +108,7 @@ func TestBBIExpandsWithPrefix(tt *testing.T) {
 			filepath.Join(scenario.Workpath, "model", targets),
 		}
 
-		output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
+		output, err := bi.ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 		t.R.NoError(err)
 		t.R.NotEmpty(output)
@@ -178,7 +178,7 @@ func TestBBIExpandsWithPrefixToPartialMatch(tt *testing.T) {
 				filepath.Join(scenario.Workpath, "model", targets),
 			}
 
-			output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
+			output, err := bi.ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 			t.R.NoError(err)
 			t.R.NotEmpty(output)

diff --git a/integration/nonmem/bbi_local_test.go b/integration/nonmem/bbi_local_test.go
@@ -8,7 +8,7 @@ import (
 	"testing"
 	"time"
 
-	. "github.com/metrumresearchgroup/bbi/integration"
+	bi "github.com/metrumresearchgroup/bbi/integration"
 	"github.com/metrumresearchgroup/bbi/utils"
 
 	"github.com/metrumresearchgroup/wrapt"
@@ -136,7 +136,7 @@ func TestNMFEOptionsEndInScript(tt *testing.T) {
 
 					// Now let's run the script that was generated
 					t.R.NoError(os.Chdir(filepath.Join(scenario.Workpath, m.identifier)))
-					_, err = ExecuteCommand(ctx, filepath.Join(scenario.Workpath, m.identifier, m.identifier+".sh"))
+					_, err = bi.ExecuteCommand(ctx, filepath.Join(scenario.Workpath, m.identifier, m.identifier+".sh"))
 					t.R.NoError(os.Chdir(whereami))
 					t.R.NoError(err)
 

diff --git a/integration/nonmem/init_test.go b/integration/nonmem/init_test.go
@@ -10,7 +10,7 @@ import (
 	"runtime"
 	"testing"
 
-	. "github.com/metrumresearchgroup/bbi/integration"
+	bi "github.com/metrumresearchgroup/bbi/integration"
 	"github.com/metrumresearchgroup/bbi/utils"
 
 	"github.com/metrumresearchgroup/wrapt"
@@ -35,7 +35,7 @@ func TestInitialization(tt *testing.T) {
 			scenario.Prepare(t, context.Background())
 
 			t.Run(fmt.Sprintf("init_%s", scenario.identifier), func(t *wrapt.T) {
-				_, err := ExecuteCommand(context.Background(), "bbi", "init", "--dir", os.Getenv("NONMEMROOT"))
+				_, err := bi.ExecuteCommand(context.Background(), "bbi", "init", "--dir", os.Getenv("NONMEMROOT"))
 				t.R.NoError(err)
 
 				t.A.FileExists(filepath.Join(scenario.Workpath, "bbi.yaml"))

diff --git a/integration/nonmem/setup.go b/integration/nonmem/setup.go
@@ -13,7 +13,7 @@ import (
 	"strconv"
 	"strings"
 
-	. "github.com/metrumresearchgroup/bbi/integration"
+	bi "github.com/metrumresearchgroup/bbi/integration"
 
 	"github.com/metrumresearchgroup/wrapt"
 	log "github.com/sirupsen/logrus"
@@ -61,7 +61,7 @@ func (m Model) Execute(scenario *Scenario, args ...string) (string, error) {
 		filepath.Join(scenario.Workpath, m.filename),
 	}...)
 
-	return ExecuteCommand(scenario.ctx, "bbi", cmdArguments...)
+	return bi.ExecuteCommand(scenario.ctx, "bbi", cmdArguments...)
 }
 
 var ErrNoModelsLocated = errors.New("no model directories were located in the provided scenario")
@@ -431,7 +431,7 @@ func findModelFiles(path string) []string {
 func (scenario *Scenario) Prepare(t *wrapt.T, ctx context.Context) {
 	t.Helper()
 
-	_, err := ExecuteCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT"))
+	_, err := bi.ExecuteCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT"))
 	t.R.NoError(err)
 
 	fs := afero.NewOsFs()
@@ -451,7 +451,7 @@ func (scenario *Scenario) Prepare(t *wrapt.T, ctx context.Context) {
 
 	t.R.NoError(os.Chdir(scenario.Workpath))
 
-	_, err = ExecuteCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT"))
+	_, err = bi.ExecuteCommand(ctx, "bbi", "init", "--dir", os.Getenv("NONMEMROOT"))
 	t.R.NoError(err)
 
 	t.R.NoError(os.Chdir(whereami))

diff --git a/integration/postrun/bbi_covcor_test.go b/integration/postrun/bbi_covcor_test.go
@@ -7,7 +7,7 @@ import (
 	"regexp"
 	"testing"
 
-	. "github.com/metrumresearchgroup/bbi/integration"
+	bi "github.com/metrumresearchgroup/bbi/integration"
 	"github.com/metrumresearchgroup/bbi/utils"
 
 	"github.com/metrumresearchgroup/wrapt"
@@ -33,7 +33,7 @@ func TestCovCorHappyPath(tt *testing.T) {
 				filepath.Join(SUMMARY_TEST_DIR, mod.name, mod.name),
 			}
 
-			output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
+			output, err := bi.ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 			t.R.NoError(err)
 			t.R.NotEmpty(output)
@@ -75,7 +75,7 @@ func TestCovCorErrors(tt *testing.T) {
 
 			// try without flag and get error
 			var output string
-			output, err := ExecuteCommandNoErrorCheck(context.Background(), "bbi", commandAndArgs...)
+			output, err := bi.ExecuteCommandNoErrorCheck(context.Background(), "bbi", commandAndArgs...)
 			t.R.Error(err)
 
 			errorMatch := rgx.MatchString(output)

diff --git a/integration/postrun/bbi_params_test.go b/integration/postrun/bbi_params_test.go
@@ -6,7 +6,7 @@ import (
 	"path/filepath"
 	"testing"
 
-	. "github.com/metrumresearchgroup/bbi/integration"
+	bi "github.com/metrumresearchgroup/bbi/integration"
 	"github.com/metrumresearchgroup/bbi/utils"
 	"github.com/metrumresearchgroup/wrapt"
 )
@@ -39,7 +39,7 @@ func TestParamsSingleModel(tt *testing.T) {
 				commandAndArgs = append(commandAndArgs, tc.bbiOption)
 			}
 
-			output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
+			output, err := bi.ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 			t.R.NoError(err)
 			t.R.NotEmpty(output)
@@ -75,7 +75,7 @@ func TestParamsDir(tt *testing.T) {
 				commandAndArgs = append(commandAndArgs, tc.bbiOption)
 			}
 
-			output, err := ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
+			output, err := bi.ExecuteCommand(context.Background(), "bbi", commandAndArgs...)
 
 			t.R.NoError(err)
 			t.R.NotEmpty(output)

diff --git a/integration/postrun/bbi_reclean_test.go b/integration/postrun/bbi_reclean_test.go
@@ -7,7 +7,7 @@ import (
 	"regexp"
 	"testing"
 
-	. "github.com/metrumresearchgroup/bbi/integration"
+	bi "github.com/metrumresearchgroup/bbi/integration"
 	"github.com/metrumresearchgroup/wrapt"
 )
 
@@ -23,7 +23,7 @@ func TestBBIRecleanBasic(tt *testing.T) {
 	_ = os.WriteFile(fdataCSV, []byte("fake"), 0644)
 	t.A.FileExists(fdataCSV)
 
-	output, err := ExecuteCommand(context.Background(),
+	output, err := bi.ExecuteCommand(context.Background(),
 		"bbi", "nonmem", "reclean", "--recleanLvl=1", "-v", dir)
 	t.R.NoError(err)
 	t.R.NotEmpty(output)
@@ -34,7 +34,7 @@ func TestBBIRecleanBasic(tt *testing.T) {
 func TestBBIRecleanError(tt *testing.T) {
 	t := wrapt.WrapT(tt)
 
-	output, err := ExecuteCommandNoErrorCheck(context.Background(),
+	output, err := bi.ExecuteCommandNoErrorCheck(context.Background(),
 		"bbi", "nonmem", "reclean")
 
 	t.R.NotNil(err)