popy_run¶
The most important command in the suite of Command Line Tools is popy_run. It processes PoPy scripts.
Running a script¶
To run a PoPy script Open a PoPy Command Prompt and type:-
$ popy_run my_script.pyml
What happens with the script depends on its type. There are many script formats:-
- fit - Fit a model to data
- gen - Generate data from a model
- sim - Simulate PK/PD curves
- tut - gen data and fit and compare the results
- comp - Compare gen and fit results
- mfit - Fit a model to multiple data sets
- mgen - Generate multiple data from a model
- msim - Simulate multiple PK/PD curves
- mtut - mgen multiple data and mfit and compare
- mcomp - Compare mgen and mfit results
- grph - Plot graphs
- vpc - Plot VPCs
- fitsum - HTML summary of fit results
- gensum - HTML summary of gen results
- tutsum - HTML summary of tut results
- n2pdat - converts Nonmem to PoPy data
- p2ndat - converts PoPy to Nonmem data
See Script File Formats for more information.
Note a common switch to use with popy_run is:-
$ popy_run -o my_script.pyml
Here the ‘-o’ option overwrites previous output automatically. If the script has already been run and you do not use the ‘-o’ option, you will be asked to confirm you want to overwrite any previous output.
For other command line options see Command line options.
Running multiple scripts¶
Note you can also run all scripts in a directory using:-
$ popy_run *.pyml
This runs all files with the ‘.pyml’ extension in serial.
Log files created by popy_run¶
When popy_run processes a script file, it creates a log file:-
my_script.pyml.run.main.log
as a record of the output. If a runtime error occurs during processing, a stack trace is sent to:-
my_script.pyml.run.error.log
as a record of what went wrong.
Command line options¶
usage: popy_run [-h] [-a] [-c] [-f] [-i] [-l] [-m] [-o] [-r] [-s] [-t]
[-v {noset,info,debug,warning,error,critical}]
input_file
Runs a PoPy script
positional arguments:
input_file Required path to input configuration file.
optional arguments:
-h, --help show this help message and exit
-a, --all_config Optionally output all possible config file entries in
output script files. If set to false, the default
entries with default values are suppressed for the
sake of brevity.
-c, --comment_scripts
Optionally add explanatory comments to all entries in
output script files.
-f, --format_on_fly Optionally attempt to format the input config file
during run. And switch to the new formatted verison of
the file. Note this re-formatting is only useful if
the input config is a valid version of an older PoPy
format.
-i, --i_am_feeling_lucky
Optionally do NOT run the PoPy script checking i.e
silence the warnings and errors output at the start
this option is not recommended, but you can use if you
do not believe the warnings/errors and want to run
your script regardless.
-l, --line_breaks Optionally enforce line breaks in the config file.
This increases the length of files, but may improve
clarity. If set to False, short dictionary lines are
compacted instead using {} notation.
-m, --manual_mode Optionally do NOT run output scripts automatically,
even if 'output_mode: run' set in config file.
Effectively uses 'output_mode: create' instead. Then
user has to run output scripts manually.
-o, --overwrite Optionally overwrite existing output files without
asking.
-r, --replicate_scripts
Optionally replicate input config files in log files.
-s, --spaces Optionally add more spaces to the output config file
for greater clarity, but longer config files. Off by
default.
-t, --timestamp Optionally included timestamp string in log file name
and output folder name.
-v {noset,info,debug,warning,error,critical}, --verbosity {noset,info,debug,warning,error,critical}
verbosity of output in log file