pipen 0.7.0

A pipeline framework for python

A pipeline framework for python

---

Documentation | ChangeLog | Examples | API

Features

• Easy to use
• Nearly zero-configuration
• Nice logging
• Highly extendable

Installation

pip install -U pipen

Quickstart

example.py

from pipen import Proc, Pipen

class P1(Proc):
    """Sort input file"""
    input = "infile"
    input_data = ["/tmp/data.txt"]
    output = "outfile:file:intermediate.txt"
    script = "cat {{in.infile}} | sort > {{out.outfile}}"

class P2(Proc):
    """Paste line number"""
    requires = P1
    input = "infile"
    output = "outfile:file:result.txt"
    script = "paste <(seq 1 3) {{in.infile}} > {{out.outfile}}"

class MyPipeline(Pipen):
    starts = P1

if __name__ == "__main__":
    MyPipeline().run()

> echo -e "3\n2\n1" > /tmp/data.txt
> python example.py

[09/13/21 04:23:37] I main                    _____________________________________   __
[09/13/21 04:23:37] I main                    ___  __ \___  _/__  __ \__  ____/__  | / /
[09/13/21 04:23:37] I main                    __  /_/ /__  / __  /_/ /_  __/  __   |/ /
[09/13/21 04:23:37] I main                    _  ____/__/ /  _  ____/_  /___  _  /|  /
[09/13/21 04:23:37] I main                    /_/     /___/  /_/     /_____/  /_/ |_/
[09/13/21 04:23:37] I main
[09/13/21 04:23:37] I main                                 version: 0.7.0
[09/13/21 04:23:37] I main
[09/13/21 04:23:37] I main    ╭═════════════════════════════ MYPIPELIN ═══════════════════════════════╮
[09/13/21 04:23:37] I main    ║  # procs          = 2                                                 ║
[09/13/21 04:23:37] I main    ║  plugins          = ['main', 'verbose-0.0.1']                         ║
[09/13/21 04:23:37] I main    ║  profile          = default                                           ║
[09/13/21 04:23:37] I main    ║  outdir           = mypipeline_results                                ║
[09/13/21 04:23:37] I main    ║  cache            = True                                              ║
[09/13/21 04:23:37] I main    ║  dirsig           = 1                                                 ║
[09/13/21 04:23:37] I main    ║  error_strategy   = ignore                                            ║
[09/13/21 04:23:37] I main    ║  forks            = 1                                                 ║
[09/13/21 04:23:37] I main    ║  lang             = bash                                              ║
[09/13/21 04:23:37] I main    ║  loglevel         = info                                              ║
[09/13/21 04:23:37] I main    ║  num_retries      = 3                                                 ║
[09/13/21 04:23:37] I main    ║  plugin_opts      = {}                                                ║
[09/13/21 04:23:37] I main    ║  plugins          = None                                              ║
[09/13/21 04:23:37] I main    ║  scheduler        = local                                             ║
[09/13/21 04:23:37] I main    ║  scheduler_opts   = {}                                                ║
[09/13/21 04:23:37] I main    ║  submission_batch = 8                                                 ║
[09/13/21 04:23:37] I main    ║  template         = liquid                                            ║
[09/13/21 04:23:37] I main    ║  template_opts    = {}                                                ║
[09/13/21 04:23:37] I main    ║  workdir          = ./.pipen                                          ║
[09/13/21 04:23:37] I main    ╰═══════════════════════════════════════════════════════════════════════╯
[09/13/21 04:23:37] I main
[09/13/21 04:23:37] I main    ╭───────────────────────────────── P1 ──────────────────────────────────╮
[09/13/21 04:23:37] I main    │ Sort input file                                                       │
[09/13/21 04:23:37] I main    ╰───────────────────────────────────────────────────────────────────────╯
[09/13/21 04:23:37] I main    P1: Workdir: '.pipen/mypipeline/p1'
[09/13/21 04:23:37] I main    P1: <<< [START]
[09/13/21 04:23:37] I main    P1: >>> ['P2']
[09/13/21 04:23:37] I verbose P1: size: 1
[09/13/21 04:23:37] I verbose P1: [0/0] in.infile: /tmp/data.txt
[09/13/21 04:23:37] I verbose P1: [0/0] out.outfile:
                      /home/pwwang/github/pipen/.pipen/mypipeline/p1/0/output/intermediate.txt
[09/13/21 04:23:38] I verbose P1: Time elapsed: 00:00:01.039s
[09/13/21 04:23:38] I main
[09/13/21 04:23:38] I main    ╭═════════════════════════════════ P2 ══════════════════════════════════╮
[09/13/21 04:23:38] I main    ║ Paste line number                                                     ║
[09/13/21 04:23:38] I main    ╰═══════════════════════════════════════════════════════════════════════╯
[09/13/21 04:23:38] I main    P2: Workdir: '.pipen/mypipeline/p2'
[09/13/21 04:23:38] I main    P2: <<< ['P1']
[09/13/21 04:23:38] I main    P2: >>> [END]
[09/13/21 04:23:38] I verbose P2: size: 1
[09/13/21 04:23:38] I verbose P2: [0/0] in.infile:
                      /home/pwwang/github/pipen/.pipen/mypipeline/p1/0/output/intermediate.txt
[09/13/21 04:23:38] I verbose P2: [0/0] out.outfile:
                      /home/pwwang/github/pipen/mypipeline_results/P2/result.txt
[09/13/21 04:23:40] I verbose P2: Time elapsed: 00:00:02.074s
[09/13/21 04:23:40] I main

                PIPEN-0: 100%|████████████████████████████████████████| 2/2 [00:04<00:00, 0.56 procs/s]

> cat ./mypipeline_results/P2/result.txt
1       1
2       2
3       3

Examples

See more examples at examples/ and a more realcase example at: https://github.com/pwwang/pipen-report/tree/master/example

Plugin gallery

Plugins make pipen even better.

• pipen-verbose: Add verbosal information in logs for pipen.
• pipen-lock: Process lock for pipen to prevent multiple runs at the same time.
• pipen-report: Generate report for pipen
• pipen-filters: Add a set of useful filters for pipen templates.
• pipen-diagram: Draw pipeline diagrams for pipen
• pipen-annotate: Use docstring to annotate pipen processes
• pipen-args: Command line argument parser for pipen
• pipen-dry: Dry runner for pipen pipelines
• pipen-cli-init: A pipen CLI plugin to create a pipen project (pipeline)
• pipen-cli-run: A pipen cli plugin to run a process or a pipeline
• pipen-cli-require: A pipen cli plugin check the requirements of a pipeline