sup3r.utilities.cli.BaseCLI

sup3r.utilities.cli.BaseCLI#

class BaseCLI[source]#

Bases: object

Base CLI class used to create CLI for modules in ModuleName

Methods

add_status_cmd(config, pipeline_step, cmd)

Append status file command to command for executing given module

check_module_name(module_name)

Make sure module_name is a valid member of the ModuleName class

from_config(module_name, module_class, ctx, ...)

Run sup3r module from a config file.

from_config_preflight(module_name, ctx, ...)

Parse conifg file prior to running sup3r module.

kickoff_local_job(module_name, ctx, cmd[, ...])

Run sup3r module locally.

kickoff_slurm_job(module_name, ctx, cmd[, ...])

Run sup3r module on HPC via SLURM job submission.
classmethod from_config(module_name, module_class, ctx, config_file, verbose, pipeline_step=None)[source]#

Run sup3r module from a config file.

Parameters:

  • module_name (str) – Module name string from sup3r.utilities.ModuleName.

  • module_class (Object) – Class object used to call get_node_cmd(config). e.g. Sup3rQa.get_node_cmd(config)

  • ctx (click.pass_context) – Click context object where ctx.obj is a dictionary

  • config_file (str) – Path to config file provided all needed inputs to module_class

  • verbose (bool) – Whether to run in verbose mode.

  • pipeline_step (str, optional) – Name of the pipeline step being run. If None, the pipeline_step will be set to the module_name, mimicking old reV behavior. By default, None.

classmethod from_config_preflight(module_name, ctx, config_file, verbose)[source]#

Parse conifg file prior to running sup3r module.

Parameters:

  • module_name (str) – Module name string from sup3r.utilities.ModuleName.

  • module_class (Object) – Class object used to call get_node_cmd(config). e.g. Sup3rQa.get_node_cmd(config)

  • ctx (click.pass_context) – Click context object where ctx.obj is a dictionary

  • config_file (str) – Path to config file provided all needed inputs to module_class

  • verbose (bool) – Whether to run in verbose mode.

Returns:

config (dict) – Dictionary corresponding to config_file

classmethod check_module_name(module_name)[source]#

Make sure module_name is a valid member of the ModuleName class

classmethod kickoff_slurm_job(module_name, ctx, cmd, alloc='sup3r', memory=None, walltime=4, feature=None, stdout_path='./stdout/', pipeline_step=None)[source]#

Run sup3r module on HPC via SLURM job submission.

Parameters:

  • module_name (str) – Module name string from sup3r.utilities.ModuleName.

  • ctx (click.pass_context) – Click context object where ctx.obj is a dictionary

  • cmd (str) –

    Command to be submitted in SLURM shell script. Example:

    ‘python -m sup3r.cli <module_name> -c <config_file>’

  • alloc (str) – HPC project (allocation) handle. Example: ‘sup3r’.

  • memory (int) – Node memory request in GB.

  • walltime (float) – Node walltime request in hours.

  • feature (str) – Additional flags for SLURM job. Format is “–qos=high” or “–depend=[state:job_id]”. Default is None.

  • stdout_path (str) – Path to print .stdout and .stderr files.

  • pipeline_step (str, optional) – Name of the pipeline step being run. If None, the pipeline_step will be set to the module_name, mimicking old reV behavior. By default, None.

classmethod kickoff_local_job(module_name, ctx, cmd, pipeline_step=None)[source]#

Run sup3r module locally.

Parameters:

  • module_name (str) – Module name string from sup3r.utilities.ModuleName.

  • ctx (click.pass_context) – Click context object where ctx.obj is a dictionary

  • cmd (str) –

    Command to be submitted in shell script. Example:

    ‘python -m sup3r.cli <module_name> -c <config_file>’

  • pipeline_step (str, optional) – Name of the pipeline step being run. If None, the pipeline_step will be set to the module_name, mimicking old reV behavior. By default, None.

classmethod add_status_cmd(config, pipeline_step, cmd)[source]#

Append status file command to command for executing given module

Parameters:

  • config (dict) – sup3r config with all necessary args and kwargs to run given module.

  • pipeline_step (str) – Name of the pipeline step being run.

  • cmd (str) – String including command to execute given module.

Returns:

cmd (str) – Command string with status file command included if job_name is not None