Merge pull request #331 from metrumresearchgroup/clean-fix

clean: fix handling of files from *_copied.json

cmd/clean.go

@@ -110,16 +110,28 @@ func clean(cmd *cobra.Command, args []string) error {
 
 	if !filesOnly {
 		for _, f := range matchedFolders {
+			if !filepath.IsAbs(f) {
+				f = filepath.Join(dir, f)
+			}
 			// explicitly ignoring errors here, as this is not critical
 			// and it's more important to try than to succeed
-			_ = AppFs.RemoveAll(filepath.Join(dir, f))
+			err = AppFs.RemoveAll(f)
+			if err != nil {
+				log.Printf("failed to remove directory %s: %v", f, err)
+			}
 		}
 	}
 	if !dirsOnly {
 		for _, f := range matchedFiles {
+			if !filepath.IsAbs(f) {
+				f = filepath.Join(dir, f)
+			}
 			// explicitly ignoring errors here, as this is not critical
 			// and it's more important to try than to succeed
-			_ = AppFs.Remove(filepath.Join(dir, f))
+			err = AppFs.Remove(f)
+			if err != nil {
+				log.Printf("failed to remove file %s: %v", f, err)
+			}
 		}
 	}
 

cmd/nonmem.go

@@ -645,8 +645,6 @@ func extrapolateCopyFilesFromExtensions(filename string, level int) []string {
 	}
 
 	extensions[2] = []string{
-		".clt",
-		".coi",
 		".clt",
 		".coi",
 		".cpu",

integration/nmless/bbi_clean_test.go

@@ -230,7 +230,7 @@ func TestCleanCopiedRuns(tt *testing.T) {
 	writeCopied(t, filepath.Join(dir, "run10"),
 		[]runner.TargetedFile{
 			{
-				File: "run10.baz",
+				File: filepath.Join(dir, "run10.baz"),
 			},
 		},
 	)

runner/consts.go

@@ -102,8 +102,6 @@ func EstOutputFilesByRun(r string) map[string]int {
 		"_RMAT.msf",
 	}
 	fileExtsLvl2 := []string{
-		".clt",
-		".coi",
 		".clt",
 		".coi",
 		".cpu",