[wip] go fmt

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)

parsers/nmparser/diagonal_elements.go

@@ -7,18 +7,20 @@ import (
 
 // lowerDiagonalLengthToDimension takes l which is
 // the number of total elements in the lower diagonal
-//  matrix, and calculates the dimension (aka number of
+// matrix, and calculates the dimension (aka number of
 // diagonal elements) for the matrix.
 // Additionally, this function can be used to pass
 // a specific index from the array of lower diagonal
 // elements (as l). In that case, it will return one
 // of the following:
 // * If the index is a diagonal element:
-//   * The number of that diagonal element
-//   * true
+//   - The number of that diagonal element
+//   - true
+//
 // * If the index is not a diagonal element:
-//   * 0
-//   * false
+//   - 0
+//   - false
+//
 // For example, there are 6 elements in the lower
 // diagonal of a 3x3 matrix, the 1st, 3rd, and 6th
 // being diagonals. Calling this function on 1-6

parsers/nmparser/parse_initial_estimates_test.go

@@ -1,15 +1,17 @@
 package parser
 
 // example omega initial estimates given complex omega structure
-// IOV = EXP(ETA(3))
-// IF(VISI.EQ.6) IOV=EXP(ETA(4))
-// IF(VISI.EQ.8) IOV=EXP(ETA(5))
-// $OMEGA  0.14  ; 1 IIV BASE
-// $OMEGA  0.8  ; 2 IIV EC50
-// $OMEGA  BLOCK(1)
-//  0.03  ; 1 IOV BASE
-// $OMEGA  BLOCK(1) SAME
-// $OMEGA  BLOCK(1) SAME.
+//
+//	IOV = EXP(ETA(3))
+//	IF(VISI.EQ.6) IOV=EXP(ETA(4))
+//	IF(VISI.EQ.8) IOV=EXP(ETA(5))
+//	$OMEGA  0.14  ; 1 IIV BASE
+//	$OMEGA  0.8  ; 2 IIV EC50
+//	$OMEGA  BLOCK(1)
+//	 0.03  ; 1 IOV BASE
+//	$OMEGA  BLOCK(1) SAME
+//	$OMEGA  BLOCK(1) SAME
+//
 // TODO: remove omegaBlock01 if we find no use.
 var _ = /*omegaBlock01*/ []string{
 	"0INITIAL ESTIMATE OF OMEGA:",

parsers/nmparser/read_ext.go

@@ -40,7 +40,7 @@ func ParseExtLines(lines []string) ExtData {
 	}
 }
 
-//ParseParamsExt returns the ExtData in the structure of final parameter estimates
+// ParseParamsExt returns the ExtData in the structure of final parameter estimates
 // the parameter names correspond to the names per the ext file (THETA1, THETA2, etc)
 // per nonmem 7.4 the following information will be grabbed
 // 1) Theburn-in iterations of the MCMCBayesian analysis are given negative values,starting at –NBURN, the number of burn-in iterations requested by the user. These are followed by positive iterations of the stationary phase.
@@ -149,7 +149,7 @@ func ParseParamsExt(ed ExtData) ([]ParametersData, ParameterNames) {
 	}
 }
 
-//ParseConditionNumberExt returns the condition number for each estimation method from ExtData
+// ParseConditionNumberExt returns the condition number for each estimation method from ExtData
 // per nonmem 7.4 the following information will be grabbed
 // Iteration -1000000003 indicates that this line contains the condition number , lowest, highest, Eigenvalues of the correlation matrix of the variances of the final parameters.
 // NONMEM Users Guide: Introduction to NONMEM 7.4.1.

parsers/nmparser/read_grd.go

@@ -39,7 +39,7 @@ func ParseGrdLines(lines []string) ExtData {
 	}
 }
 
-//ParseGrdData returns the ExtData in the structure of final parameter estimates.
+// ParseGrdData returns the ExtData in the structure of final parameter estimates.
 func ParseGrdData(ed ExtData) ([]ParametersData, ParameterNames) {
 	var allParametersData []ParametersData
 	var thetas []string

runner/consts.go

@@ -82,7 +82,7 @@ func EstOutputFileCleanLevels(r string) map[string]int {
 	return EstOutputFiles
 }
 
-//CleanFilesByRun sets clean levels for files by run.
+// CleanFilesByRun sets clean levels for files by run.
 func CleanFilesByRun(r string) map[string]int {
 	var EstOutputFiles = make(map[string]int)
 	// fileExtLvls are based on 1 = lowest priority -> n = highest priority

runner/estimate_model.go

@@ -17,7 +17,8 @@ import (
 // EstimateModel prepares, runs and cleans up a model estimation run
 // modelPath is the relative path of the model from where Estimate model is called from
 // cacheDir is the location of the cache dir, relative to the baseDir,
-//		for nonmem executable for version 7.4 for use in precompilation
+// for nonmem executable for version 7.4 for use in precompilation
+//
 // exeNameInCache is the name of the nonmem executable in the cache dir.
 func EstimateModel(
 	fs afero.Fs,

runner/estimate_model_test.go

@@ -40,7 +40,7 @@ func TestCustomEstimateModel(tt *testing.T) {
 	})
 }
 
-//Should just get back the provided output dir.
+// Should just get back the provided output dir.
 func TestLogiclessTemplateForEstimateModel(tt *testing.T) {
 	testId := "UNIT-RUN-005"
 	tt.Run(utils.AddTestId("", testId), func(tt *testing.T) {

runner/prepare_to_execute.go

@@ -6,7 +6,7 @@ import (
 	parser "github.com/metrumresearchgroup/bbi/parsers/nmparser"
 )
 
-//PrepareForExecution parses and prepares strings from a file for execution in a different context
+// PrepareForExecution parses and prepares strings from a file for execution in a different context
 // for example, replacing the $DATA path.
 func PrepareForExecution(s []string) []string {
 	for i, line := range s {

runner/structs.go

@@ -24,7 +24,7 @@ type ReturnStatus struct {
 	Error  error  `json:"error,omitempty"`
 }
 
-//NextDirSuggestion provides a struct for the recommended next
+// NextDirSuggestion provides a struct for the recommended next
 // directory name, and whether there should be a project reorganization
 // based on directory modifications, and whether this will be the first dir in the sequence.
 type NextDirSuggestion struct {

utils/expand_sequence.go

@@ -8,7 +8,8 @@ import (
 )
 
 // ExpandNameSequence takes a full name pattern with a sequence and returns all values
-//  run[001:004].mod --> run001.mod run002.mod run003.mod run004.mod
+//
+//	run[001:004].mod --> run001.mod run002.mod run003.mod run004.mod
 func ExpandNameSequence(fnp string) ([]string, error) {
 	var output []string
 	r := regexp.MustCompile(`(.*)?\[(.*)](.*)?`)

utils/io.go

@@ -11,9 +11,8 @@ import (
 	"github.com/spf13/afero"
 )
 
-//ReadParamsAndOutputFromExt returns the lines associated
+// ReadParamsAndOutputFromExt returns the lines associated
 // with either parameter table outputs or output lines (-100xxx lines).
-//
 func ReadParamsAndOutputFromExt(path string) ([]string, error) {
 	inFile, err := os.Open(path)
 	if err != nil {
@@ -61,7 +60,7 @@ func ReadParamsAndOutputFromExt(path string) ([]string, error) {
 	return lines, nil
 }
 
-//ReadLines reads lines for a file at a given path.
+// ReadLines reads lines for a file at a given path.
 func ReadLines(path string) ([]string, error) {
 	inFile, err := os.Open(path)
 	if err != nil {
@@ -78,7 +77,7 @@ func ReadLines(path string) ([]string, error) {
 	return lines, nil
 }
 
-//ReadLinesFS reads lines for a file at a given path.
+// ReadLinesFS reads lines for a file at a given path.
 func ReadLinesFS(fs afero.Fs, path string) ([]string, error) {
 	inFile, err := fs.Open(path)
 	if err != nil {
@@ -95,7 +94,7 @@ func ReadLinesFS(fs afero.Fs, path string) ([]string, error) {
 	return lines, nil
 }
 
-//WriteLines writes lines to a file at a given path given a filesystem.
+// WriteLines writes lines to a file at a given path given a filesystem.
 func WriteLines(lines []string, path string) error {
 	file, err := os.Create(path)
 	if err != nil {
@@ -111,7 +110,7 @@ func WriteLines(lines []string, path string) error {
 	return w.Flush()
 }
 
-//WriteLinesFS writes lines to a file at a given path given a filesystem.
+// WriteLinesFS writes lines to a file at a given path given a filesystem.
 func WriteLinesFS(fs afero.Fs, lines []string, path string) error {
 	file, err := fs.Create(path)
 	if err != nil {