rex.utilities.execution.SubprocessManager

class SubprocessManager

Bases: object

Base class to handle subprocess execution.

Methods

format_walltime(hours)	Get the SLURM walltime string in format "HH:MM:SS"
make_path(d)	Make a directory tree if it doesn't exist.
make_sh(fname, script)	Make a shell script (.sh file) to execute a subprocess.
rm(fname)	Remove a file.
s(s)	Format input as str w/ appropriate quote types for python cli entry.
submit(cmd[, background, background_stdout])	Open a subprocess and submit a command.

static make_path(d)

Make a directory tree if it doesn’t exist.

Parameters:

d (str) – Directory tree to check and potentially create.

static make_sh(fname, script)

Make a shell script (.sh file) to execute a subprocess.

Parameters:

• fname (str) – Name of the .sh file to create.

• script (str) – Contents to be written into the .sh file.

static rm(fname)

Remove a file.

Parameters:

fname (str) – Filename (with path) to remove.

static submit(cmd, background=False, background_stdout=False)

Open a subprocess and submit a command.

Parameters:

• cmd (str) – Command to be submitted using python subprocess.

• background (bool) – Flag to submit subprocess in the background. stdout stderr will be empty strings if this is True.

• background_stdout (bool) – Flag to capture the stdout/stderr from the background process in a nohup.out file.

Returns:

• stdout (str) – Subprocess standard output. This is decoded from the subprocess stdout with rstrip.

• stderr (str) – Subprocess standard error. This is decoded from the subprocess stderr with rstrip. After decoding/rstrip, this will be empty if the subprocess doesn’t return an error.

static s(s)

Format input as str w/ appropriate quote types for python cli entry.

Examples

list, tuple -> “[‘one’, ‘two’]” dict -> “{‘key’: ‘val’}” int, float, None -> ‘0’ str, other -> ‘string’

static format_walltime(hours)

Get the SLURM walltime string in format “HH:MM:SS”

Parameters:

hours (float | int) – Requested number of job hours.

Returns:

walltime (str) – SLURM walltime request in format “HH:MM:SS”