micropype 0.1

Very basic pipelining toolbox

MicroPype

A tiny package to create very basic pipeline executing command lines and/or calling python functions.

Install

pip install micropype

API

Here are the two mains functions you need:

cached_run

Use it to execute a cammand line.

Arguments:

• cmd: Command line
• out_files: One or a list of file path(s) that are created by the command.
• title:(str, default: None) - A title
• log: (str, default: None) - A path to a log file (text file)
• versions: (dict, default: None) - A dictionnary giving all the versions that must be logged
• raise_errors: (bool, default: True) - Wether to raise python error if the command failed (if True) or just print error in the console and continue (if False)

cached_function_call

Use it to call a python function.

Arguments:

• func: A callable python object (function)
• args: List of the arguments
• out_files: One or a list of file path(s) that are created by the command.
• title:(str, default: None) - A title
• log: (str, default: None) - A path to a log file (text file)
• versions: (dict, default: None) - A dictionnary giving all the versions that must be logged
• raise_errors: (bool, default: True) - Wether to raise python error if the command failed (if True) or just print error in the console and continue (if False)

Configuration file

Example

Here is an example of simple configuration file:

steps:
    do_ls: true
    do_myfunction: false

And then the pipeline:

from micropipe import cached_run, cached_function_call

log = "mylog.txt"

out_f = "lsOutput.log"
cached_run(
    f"ls -lrt >> {out_f}",
    out_f,
    "Listing current folder items",
    log_f
)

cached_function_call(
    myfuntion,
    [arg1, arg2],
    [file_1, file_2],
    title=f"Executing a python function",
    log=log_f
)