CLI¶
flepimop2¶
flepimop2 - Flexible Epidemic Modeling Pipeline (version 2).
Usage:
Options:
flepimop2 build¶
Compile and build a model defined in a configuration file.
Usage:
Options:
--dry-run Should this command be run using dry run?
-v, --verbosity The verbosity level to use for this command.
--help Show this message and exit.
flepimop2 format¶
Format a configuration file into flepimop2's normalized YAML style.
By default this command rewrites the input file in place. Use --check to
validate formatting without modifying the file, or --dry-run to print the
formatted configuration to stdout.
Usage:
Options:
--dry-run Should this command be run using dry run?
--check Check whether the configuration is already formatted.
-v, --verbosity The verbosity level to use for this command.
--help Show this message and exit.
flepimop2 job¶
Dispatch a flepimop2 command to a configured job backend.
Usage:
Options:
flepimop2 job list¶
List submitted jobs and their current status.
Reads jobs cached under .flepimop2_cache/job/ (recorded when they were
submitted via flepimop2 job <subcommand>) and prints a line per job.
Finished jobs are retained, so this is also a record of recently completed
work.
To stay fast, the command only re-queries the backend for jobs whose
last-known status (read from summary.json) was unfinished - i.e. never
checked, pending, or running. Jobs already known to be finished are reported
from the cached summary without contacting the backend again.
Usage:
Options:
flepimop2 job process¶
Execute a processing step based on a configuration file.
The CONFIG argument should point to a valid configuration file.
Usage:
Options:
-j, --job-target TEXT The configured job module to dispatch this command
to.
--no-cache Do not record the submitted job handle in the local
job cache. Useful for one-off or debugging
submissions that should not appear in `flepimop2 job
list`.
--dry-run Should this command be run using dry run?
-t, --target TEXT The target to use for this command.
-v, --verbosity The verbosity level to use for this command.
--help Show this message and exit.
flepimop2 job simulate¶
Run simulations based on a configuration file.
This command runs epidemic simulations specified from a provided configuration file.
The CONFIG argument should point to a valid configuration file.
Usage:
Options:
-j, --job-target TEXT The configured job module to dispatch this command
to.
--no-cache Do not record the submitted job handle in the local
job cache. Useful for one-off or debugging
submissions that should not appear in `flepimop2 job
list`.
--dry-run Should this command be run using dry run?
-t, --target TEXT The target to use for this command.
-v, --verbosity The verbosity level to use for this command.
--help Show this message and exit.
flepimop2 job status¶
Show the status of a single submitted job.
Looks up a job cached under .flepimop2_cache/job/ by its identifier,
rebuilds the exact job backend that launched it from the cached
configuration, queries the backend, and prints the job's current status
along with any backend-specific detail.
Usage:
Options:
flepimop2 patch¶
Patch one or more configuration files together.
This command applies configuration files from left to right. The first file is used as the base configuration, and each subsequent file is patched onto the accumulated result.
Usage:
Options:
--dry-run Should this command be run using dry run?
-o, --output FILE Write the patched configuration to this file
instead of stdout.
--patch-mode [error|merge|replace]
How to handle duplicate configuration keys
while patching. [default: error]
-v, --verbosity The verbosity level to use for this command.
--help Show this message and exit.
flepimop2 process¶
Execute a processing step based on a configuration file.
The CONFIG argument should point to a valid configuration file.
Usage:
Options:
--dry-run Should this command be run using dry run?
-t, --target TEXT The target to use for this command.
-v, --verbosity The verbosity level to use for this command.
--help Show this message and exit.
flepimop2 simulate¶
Run simulations based on a configuration file.
This command runs epidemic simulations specified from a provided configuration file.
The CONFIG argument should point to a valid configuration file.
Usage:
Options:
--dry-run Should this command be run using dry run?
-t, --target TEXT The target to use for this command.
-v, --verbosity The verbosity level to use for this command.
--help Show this message and exit.
flepimop2 skeleton¶
Create a project skeleton with directory structure and template files.
This command scaffolds a new flepimop2 project by creating the necessary directory structure and populating it with template configuration files, environment specifications, and other boilerplate files needed to get started.
The PATH argument specifies where to create the project. If omitted, the
skeleton will be created in the current working directory.
Examples: # Create an empty project in a new directory $ flepimop2 skeleton foobar # Create a project in the current directory $ mkdir fizzbuzz && cd fizzbuzz $ flepimop2 skeleton
Usage:
Options: