cmd: rework some flag descriptions

cmd/init.go

@@ -61,7 +61,7 @@ func NewInitCmd() *cobra.Command {
 	}
 
 	const directory string = "dir"
-	cmd.Flags().StringSlice(directory, []string{}, "A directory in which to look for NONMEM Installations")
+	cmd.Flags().StringSlice(directory, []string{}, "directory in which to look for NONMEM installations")
 
 	return cmd
 }

cmd/local.go

@@ -354,8 +354,8 @@ func NewLocalCmd() *cobra.Command {
 	}
 
 	childDirIdentifier := "create_child_dirs"
-	cmd.PersistentFlags().Bool(childDirIdentifier, true, "Indicates whether or not local branch execution"+
-		"should create a new subdirectory with the output_dir variable as its name and execute in that directory")
+	cmd.PersistentFlags().Bool(childDirIdentifier, true,
+		"create a new subdirectory, named based on the output_dir option, for execution")
 	errpanic(viper.BindPFlag("local."+childDirIdentifier, cmd.PersistentFlags().Lookup(childDirIdentifier)))
 
 	return cmd

cmd/nonmem.go

@@ -180,63 +180,63 @@ func NewNonmemCmd() *cobra.Command {
 
 	// NM Selector
 	const nmVersionIdentifier string = "nm_version"
-	cmd.PersistentFlags().String(nmVersionIdentifier, "", "Version of NONMEM from the configuration list to use")
+	cmd.PersistentFlags().String(nmVersionIdentifier, "", "version of NONMEM from the configuration list to use")
 	errpanic(viper.BindPFlag(nmVersionIdentifier, cmd.PersistentFlags().Lookup(nmVersionIdentifier)))
 
 	// Parallelization Components
 	const parallelIdentifier string = "parallel"
-	cmd.PersistentFlags().Bool(parallelIdentifier, false, "Whether or not to run NONMEM in parallel mode")
+	cmd.PersistentFlags().Bool(parallelIdentifier, false, "whether to run NONMEM in parallel mode")
 	errpanic(viper.BindPFlag(parallelIdentifier, cmd.PersistentFlags().Lookup(parallelIdentifier)))
 
 	const parallelCompletionTimeoutIdentifier string = "parallel_timeout"
-	cmd.PersistentFlags().Int(parallelCompletionTimeoutIdentifier, 2147483647, "The amount of time to wait for parallel operations in NONMEM before timing out")
+	cmd.PersistentFlags().Int(parallelCompletionTimeoutIdentifier, 2147483647, "amount of time to wait for parallel operations in NONMEM before timing out")
 	errpanic(viper.BindPFlag(parallelCompletionTimeoutIdentifier, cmd.PersistentFlags().Lookup(parallelCompletionTimeoutIdentifier)))
 
 	const mpiExecPathIdentifier string = "mpi_exec_path"
-	cmd.PersistentFlags().String(mpiExecPathIdentifier, "/usr/local/mpich3/bin/mpiexec", "The fully qualified path to mpiexec. Used for NONMEM parallel operations")
+	cmd.PersistentFlags().String(mpiExecPathIdentifier, "/usr/local/mpich3/bin/mpiexec", "fully qualified path to mpiexec to use for NONMEM parallel operations")
 	errpanic(viper.BindPFlag(mpiExecPathIdentifier, cmd.PersistentFlags().Lookup(mpiExecPathIdentifier)))
 
 	const parafileIdentifier string = "parafile"
-	cmd.PersistentFlags().String(parafileIdentifier, "", "Location of a user-provided parafile to use for parallel execution")
+	cmd.PersistentFlags().String(parafileIdentifier, "", "location of a user-provided parafile to use for parallel execution")
 	errpanic(viper.BindPFlag(parafileIdentifier, cmd.PersistentFlags().Lookup(parafileIdentifier)))
 
 	const nmQualIdentifier string = "nmqual"
-	cmd.PersistentFlags().Bool(nmQualIdentifier, false, "Whether or not to execute with nmqual (autolog.pl)")
+	cmd.PersistentFlags().Bool(nmQualIdentifier, false, "whether to execute with nmqual (autolog.pl)")
 	errpanic(viper.BindPFlag(nmQualIdentifier, cmd.PersistentFlags().Lookup(nmQualIdentifier)))
 
 	// NMFE Options
 	const nmfeGroup string = "nmfe_options"
 	const licFileIdentifier string = "licfile"
-	cmd.PersistentFlags().String(licFileIdentifier, "", "RAW NMFE OPTION - Specify a license file to use with NMFE (NONMEM)")
+	cmd.PersistentFlags().String(licFileIdentifier, "", "RAW NMFE OPTION - NONMEM license file to use")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+licFileIdentifier, cmd.PersistentFlags().Lookup(licFileIdentifier)))
 
 	const prSameIdentifier string = "prsame"
-	cmd.PersistentFlags().Bool(prSameIdentifier, false, "RAW NMFE OPTION - Indicates to NONMEM that the PREDPP compilation step should be skipped")
+	cmd.PersistentFlags().Bool(prSameIdentifier, false, "RAW NMFE OPTION - tell NONMEM to skip the PREDPP compilation step")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+prSameIdentifier, cmd.PersistentFlags().Lookup(prSameIdentifier)))
 
 	const backgroundIdentifier string = "background"
-	cmd.PersistentFlags().Bool(backgroundIdentifier, false, "RAW NMFE OPTION - Tells NONMEM not to scan StdIn for control characters")
+	cmd.PersistentFlags().Bool(backgroundIdentifier, false, "RAW NMFE OPTION - tell NONMEM not to scan stdin for control characters")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+backgroundIdentifier, cmd.PersistentFlags().Lookup(backgroundIdentifier)))
 
 	const prCompileIdentifier string = "prcompile"
-	cmd.PersistentFlags().Bool(prCompileIdentifier, false, "RAW NMFE OPTION - Forces PREDPP compilation")
+	cmd.PersistentFlags().Bool(prCompileIdentifier, false, "RAW NMFE OPTION - forces PREDPP compilation")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+prCompileIdentifier, cmd.PersistentFlags().Lookup(prCompileIdentifier)))
 
 	const prDefaultIdentifier string = "prdefault"
-	cmd.PersistentFlags().Bool(prDefaultIdentifier, false, "RAW NMFE OPTION - Do not recompile any routines other than FSUBS")
+	cmd.PersistentFlags().Bool(prDefaultIdentifier, false, "RAW NMFE OPTION - do not recompile any routines other than FSUBS")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+prDefaultIdentifier, cmd.PersistentFlags().Lookup(prDefaultIdentifier)))
 
 	const tprDefaultIdentifier string = "tprdefault"
-	cmd.PersistentFlags().Bool(tprDefaultIdentifier, false, "RAW NMFE OPTION - Test if is okay to do -prdefault")
+	cmd.PersistentFlags().Bool(tprDefaultIdentifier, false, "RAW NMFE OPTION - test if is okay to do -prdefault")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+tprDefaultIdentifier, cmd.PersistentFlags().Lookup(tprDefaultIdentifier)))
 
 	const noBuildIdentifier string = "nobuild"
-	cmd.PersistentFlags().Bool(noBuildIdentifier, false, "RAW NMFE OPTION - Skips recompiling and rebuilding on NONMEM executable")
+	cmd.PersistentFlags().Bool(noBuildIdentifier, false, "RAW NMFE OPTION - do not build a new NONMEM executable")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+noBuildIdentifier, cmd.PersistentFlags().Lookup(noBuildIdentifier)))
 
 	const maxLimIdentifier string = "maxlim"
 	cmd.PersistentFlags().Int(maxLimIdentifier, 2,
-		"RAW NMFE OPTION - Set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe)")
+		"RAW NMFE OPTION - set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe)")
 	errpanic(viper.BindPFlag(nmfeGroup+"."+maxLimIdentifier, cmd.PersistentFlags().Lookup(maxLimIdentifier)))
 
 	cmd.AddCommand(NewCleanCmd())

cmd/root.go

@@ -91,7 +91,7 @@ func NewRootCmd() *cobra.Command {
 	cmd.PersistentFlags().IntVar(&threads, "threads", 4, "number of threads to execute with locally or nodes to execute on in parallel")
 	errpanic(viper.BindPFlag("threads", cmd.PersistentFlags().Lookup("threads"))) // Update to make sure viper binds to the flag
 
-	cmd.PersistentFlags().BoolVar(&Json, "json", false, "json tree of output, if possible")
+	cmd.PersistentFlags().BoolVar(&Json, "json", false, "show JSON output, if possible")
 	errpanic(viper.BindPFlag("json", cmd.PersistentFlags().Lookup("json"))) // Bind to viper
 
 	cmd.PersistentFlags().BoolVarP(&preview, "preview", "p", false, "preview action, but don't actually run command")

cmd/run.go

@@ -80,12 +80,12 @@ func NewRunCmd() *cobra.Command {
 	viper.SetDefault("output_dir", "{{ .Name }}")
 
 	// Int Variables
-	cmd.PersistentFlags().Int("clean_lvl", 1, "clean level used for file output from a given (set of) runs")
+	cmd.PersistentFlags().Int("clean_lvl", 1, "clean level used for output")
 	errpanic(viper.BindPFlag("clean_lvl", cmd.PersistentFlags().Lookup("clean_lvl")))
 	// TODO: these are likely not meangingful as should be set in configlib, but want to configm
 	viper.SetDefault("clean_lvl", 1)
 
-	cmd.PersistentFlags().Int("copy_lvl", 0, "copy level used for file output from a given (set of) runs")
+	cmd.PersistentFlags().Int("copy_lvl", 0, "copy level used for output")
 	errpanic(viper.BindPFlag("copy_lvl", cmd.PersistentFlags().Lookup("copy_lvl")))
 	viper.SetDefault("copy_lvl", 0)
 
@@ -98,32 +98,32 @@ func NewRunCmd() *cobra.Command {
 	errpanic(viper.BindPFlag("git", cmd.PersistentFlags().Lookup("git")))
 	viper.SetDefault("git", true)
 
-	cmd.PersistentFlags().Bool("overwrite", false, "Whether or not to remove existing output directories if they are present")
+	cmd.PersistentFlags().Bool("overwrite", false, "whether to remove existing output directories")
 	errpanic(viper.BindPFlag("overwrite", cmd.PersistentFlags().Lookup("overwrite")))
 	viper.SetDefault("overwrite", false)
 
 	const configIdentifier string = "config"
-	cmd.PersistentFlags().String(configIdentifier, "", "Path (relative or absolute) to another bbi.yaml to load")
+	cmd.PersistentFlags().String(configIdentifier, "", "path to another bbi.yaml to load")
 	errpanic(viper.BindPFlag(configIdentifier, cmd.PersistentFlags().Lookup(configIdentifier)))
 
 	const saveconfig string = "save_config"
-	cmd.PersistentFlags().Bool(saveconfig, true, "Whether or not to save the existing configuration to a file with the model")
+	cmd.PersistentFlags().Bool(saveconfig, true, "whether to save the existing configuration to the output directory")
 	errpanic(viper.BindPFlag(saveconfig, cmd.PersistentFlags().Lookup(saveconfig)))
 
 	const delayIdentifier string = "delay"
 	cmd.PersistentFlags().Int(delayIdentifier, 0, "Selects a random number of seconds between 1 and this value to stagger / jitter job execution. Assists in dealing with large volumes of work dealing with the same data set. May avoid NMTRAN issues about not being able read / close files")
 	errpanic(viper.BindPFlag(delayIdentifier, cmd.PersistentFlags().Lookup(delayIdentifier)))
 
 	const logFileIdentifier string = "log_file"
-	cmd.PersistentFlags().String(logFileIdentifier, "", "If populated, specifies the file into which to store the output / logging details from bbi")
+	cmd.PersistentFlags().String(logFileIdentifier, "", "file into which to store the output / logging details from bbi")
 	errpanic(viper.BindPFlag(logFileIdentifier, cmd.PersistentFlags().Lookup(logFileIdentifier)))
 
 	const postExecutionHookIdentifier string = "post_work_executable"
-	cmd.PersistentFlags().String(postExecutionHookIdentifier, "", "A script or binary to run when job execution completes or fails")
+	cmd.PersistentFlags().String(postExecutionHookIdentifier, "", "script or binary to run when job execution completes or fails")
 	errpanic(viper.BindPFlag(postExecutionHookIdentifier, cmd.PersistentFlags().Lookup(postExecutionHookIdentifier)))
 
 	const additionalEnvIdentifier string = "additional_post_work_envs"
-	cmd.PersistentFlags().StringSlice(additionalEnvIdentifier, []string{}, "Any additional values (as ENV KEY=VALUE) to provide for the post execution environment")
+	cmd.PersistentFlags().StringSlice(additionalEnvIdentifier, []string{}, "additional values (as ENV KEY=VALUE) to provide for the post execution environment")
 	errpanic(viper.BindPFlag(additionalEnvIdentifier, cmd.PersistentFlags().Lookup(additionalEnvIdentifier)))
 
 	cmd.AddCommand(NewLocalCmd())

docs/commands/bbi.md

@@ -7,7 +7,7 @@ manage and execute models
 ```
   -d, --debug           debug mode
   -h, --help            help for bbi
-      --json            json tree of output, if possible
+      --json            show JSON output, if possible
   -o, --output string   output file
   -p, --preview         preview action, but don't actually run command
       --threads int     number of threads to execute with locally or nodes to execute on in parallel (default 4)

docs/commands/bbi_init.md

@@ -14,15 +14,15 @@ bbi init [flags]
 ### Options
 
 ```
-      --dir strings   A directory in which to look for NONMEM Installations
+      --dir strings   directory in which to look for NONMEM installations
   -h, --help          help for init
 ```
 
 ### Options inherited from parent commands
 
 ```
   -d, --debug           debug mode
-      --json            json tree of output, if possible
+      --json            show JSON output, if possible
   -o, --output string   output file
   -p, --preview         preview action, but don't actually run command
       --threads int     number of threads to execute with locally or nodes to execute on in parallel (default 4)

docs/commands/bbi_nonmem.md

@@ -32,28 +32,28 @@ bbi nonmem [flags]
 ### Options
 
 ```
-      --background             RAW NMFE OPTION - Tells NONMEM not to scan StdIn for control characters
+      --background             RAW NMFE OPTION - tell NONMEM not to scan stdin for control characters
   -h, --help                   help for nonmem
-      --licfile string         RAW NMFE OPTION - Specify a license file to use with NMFE (NONMEM)
-      --maxlim int             RAW NMFE OPTION - Set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe) (default 2)
-      --mpi_exec_path string   The fully qualified path to mpiexec. Used for NONMEM parallel operations (default "/usr/local/mpich3/bin/mpiexec")
-      --nm_version string      Version of NONMEM from the configuration list to use
-      --nmqual                 Whether or not to execute with nmqual (autolog.pl)
-      --nobuild                RAW NMFE OPTION - Skips recompiling and rebuilding on NONMEM executable
-      --parafile string        Location of a user-provided parafile to use for parallel execution
-      --parallel               Whether or not to run NONMEM in parallel mode
-      --parallel_timeout int   The amount of time to wait for parallel operations in NONMEM before timing out (default 2147483647)
-      --prcompile              RAW NMFE OPTION - Forces PREDPP compilation
-      --prdefault              RAW NMFE OPTION - Do not recompile any routines other than FSUBS
-      --prsame                 RAW NMFE OPTION - Indicates to NONMEM that the PREDPP compilation step should be skipped
-      --tprdefault             RAW NMFE OPTION - Test if is okay to do -prdefault
+      --licfile string         RAW NMFE OPTION - NONMEM license file to use
+      --maxlim int             RAW NMFE OPTION - set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe) (default 2)
+      --mpi_exec_path string   fully qualified path to mpiexec to use for NONMEM parallel operations (default "/usr/local/mpich3/bin/mpiexec")
+      --nm_version string      version of NONMEM from the configuration list to use
+      --nmqual                 whether to execute with nmqual (autolog.pl)
+      --nobuild                RAW NMFE OPTION - do not build a new NONMEM executable
+      --parafile string        location of a user-provided parafile to use for parallel execution
+      --parallel               whether to run NONMEM in parallel mode
+      --parallel_timeout int   amount of time to wait for parallel operations in NONMEM before timing out (default 2147483647)
+      --prcompile              RAW NMFE OPTION - forces PREDPP compilation
+      --prdefault              RAW NMFE OPTION - do not recompile any routines other than FSUBS
+      --prsame                 RAW NMFE OPTION - tell NONMEM to skip the PREDPP compilation step
+      --tprdefault             RAW NMFE OPTION - test if is okay to do -prdefault
 ```
 
 ### Options inherited from parent commands
 
 ```
   -d, --debug           debug mode
-      --json            json tree of output, if possible
+      --json            show JSON output, if possible
   -o, --output string   output file
   -p, --preview         preview action, but don't actually run command
       --threads int     number of threads to execute with locally or nodes to execute on in parallel (default 4)

docs/commands/bbi_nonmem_clean.md

@@ -51,25 +51,25 @@ bbi nonmem clean [flags]
 ### Options inherited from parent commands
 
 ```
-      --background             RAW NMFE OPTION - Tells NONMEM not to scan StdIn for control characters
+      --background             RAW NMFE OPTION - tell NONMEM not to scan stdin for control characters
   -d, --debug                  debug mode
-      --json                   json tree of output, if possible
-      --licfile string         RAW NMFE OPTION - Specify a license file to use with NMFE (NONMEM)
-      --maxlim int             RAW NMFE OPTION - Set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe) (default 2)
-      --mpi_exec_path string   The fully qualified path to mpiexec. Used for NONMEM parallel operations (default "/usr/local/mpich3/bin/mpiexec")
-      --nm_version string      Version of NONMEM from the configuration list to use
-      --nmqual                 Whether or not to execute with nmqual (autolog.pl)
-      --nobuild                RAW NMFE OPTION - Skips recompiling and rebuilding on NONMEM executable
+      --json                   show JSON output, if possible
+      --licfile string         RAW NMFE OPTION - NONMEM license file to use
+      --maxlim int             RAW NMFE OPTION - set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe) (default 2)
+      --mpi_exec_path string   fully qualified path to mpiexec to use for NONMEM parallel operations (default "/usr/local/mpich3/bin/mpiexec")
+      --nm_version string      version of NONMEM from the configuration list to use
+      --nmqual                 whether to execute with nmqual (autolog.pl)
+      --nobuild                RAW NMFE OPTION - do not build a new NONMEM executable
   -o, --output string          output file
-      --parafile string        Location of a user-provided parafile to use for parallel execution
-      --parallel               Whether or not to run NONMEM in parallel mode
-      --parallel_timeout int   The amount of time to wait for parallel operations in NONMEM before timing out (default 2147483647)
-      --prcompile              RAW NMFE OPTION - Forces PREDPP compilation
-      --prdefault              RAW NMFE OPTION - Do not recompile any routines other than FSUBS
+      --parafile string        location of a user-provided parafile to use for parallel execution
+      --parallel               whether to run NONMEM in parallel mode
+      --parallel_timeout int   amount of time to wait for parallel operations in NONMEM before timing out (default 2147483647)
+      --prcompile              RAW NMFE OPTION - forces PREDPP compilation
+      --prdefault              RAW NMFE OPTION - do not recompile any routines other than FSUBS
   -p, --preview                preview action, but don't actually run command
-      --prsame                 RAW NMFE OPTION - Indicates to NONMEM that the PREDPP compilation step should be skipped
+      --prsame                 RAW NMFE OPTION - tell NONMEM to skip the PREDPP compilation step
       --threads int            number of threads to execute with locally or nodes to execute on in parallel (default 4)
-      --tprdefault             RAW NMFE OPTION - Test if is okay to do -prdefault
+      --tprdefault             RAW NMFE OPTION - test if is okay to do -prdefault
   -v, --verbose                verbose output
 ```