Documentation
Commands
nonmem clean

bbi nonmem clean

Clean files and folders

Synopsis

Clean the files and directories that match the specified patterns. Whether the pattern is interpreted as a glob or regex is controlled by the --regex flag.

If files were copied to the parent directory automatically after model execution (via the copy_lvl configuration), the original files in the run directory can be cleaned up by selecting the run with the --copiedRuns option.

bbi nonmem clean [flags] <pattern> [<pattern>...]

Examples 

  # Remove items in the current directory that end with ".mod"
  bbi nonmem clean *.mod
  # The same as above but ensure only files are removed
  bbi nonmem clean --filesOnly *.mod

  # Remove files in the current directory that start with "run" and end with
  # ".mod" or ".lst"
  bbi nonmem clean --filesOnly --regex "run.*\.(mod|lst)$"
  # Report what the above would remove but don't actually do it
  bbi nonmem clean --preview --filesOnly --regex "run.*\.(mod|lst)$"

  # Remove copied files (recorded in '{run}_copied.json' by 'bbi run') for
  # run001, run002, run003, and run100
  bbi nonmem clean --copiedRuns='run[001:003],run100'

Flags

  • --copiedRuns string: run names

  • --dirsOnly: only match and clean directories

  • --filesOnly: only match and clean files

  • -h, --help: help for clean

  • --inverse: inverse selection from the given regex match criteria

  • --regex: use regular expression to match instead of glob

Inherited

  • --background: RAW NMFE OPTION - tell NONMEM not to scan stdin for control characters

  • -d, --debug: debug mode

  • --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 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 - 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

  • -v, --verbose: verbose output

See also

  • bbi nonmem - Entry point for NONMEM-related subcommands
nonmemnonmem covcor