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
mfit - Fit a model to multiple data sets
mgen - Generate multiple data from a model
msim - Simulate multiple PK/PD curves
grph - Plot graphs
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
Note: "popy_run ..." will be deprecated in favour of "popy run ..." from v1.3
usage: popy_run [-h] [-t] [-a] [-c] [-l] [-s]
[-v {noset,info,debug,warning,error,critical}] [-o]
[--no_check] [-r] [-w N] [--log_folder LOG_FOLDER]
script_path
Runs a PoPy script.
positional arguments:
script_path Required path to configuration file.
optional arguments:
-h, --help show this help message and exit
-t, --timestamp Optionally included timestamp string in log file name
and output folder name.
-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.
-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.
-s, --spaces Optionally add more spaces to the output config file
for greater clarity, but longer config files. Off by
default.
-v {noset,info,debug,warning,error,critical}, --verbosity {noset,info,debug,warning,error,critical}
verbosity of output in log file
-o, --overwrite Optionally overwrite existing output files without
asking.
--no_check 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.
-r, --replicate_scripts
Suppress replicating input config files in log files.
-w N, --worker_index N
Optionally provide a worker index, so get separate log
files for each worker
--log_folder LOG_FOLDER
Optional path to worker log folder.