pipen 0.15.3

A pipeline framework for python

A pipeline framework for python

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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, run

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()
    run("MyPipeline", starts=P1)

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

06-09 23:15:29 I core                  _____________________________________   __
06-09 23:15:29 I core                  ___  __ \___  _/__  __ \__  ____/__  | / /
06-09 23:15:29 I core                  __  /_/ /__  / __  /_/ /_  __/  __   |/ /
06-09 23:15:29 I core                  _  ____/__/ /  _  ____/_  /___  _  /|  /
06-09 23:15:29 I core                  /_/     /___/  /_/     /_____/  /_/ |_/
06-09 23:15:29 I core
06-09 23:15:29 I core                              version: 0.15.3
06-09 23:15:29 I core
06-09 23:15:29 I core    ╔══════════════════════════════════════════════════════════════════╗
06-09 23:15:29 I core    ║                            MYPIPELINE                            ║
06-09 23:15:29 I core    ╚══════════════════════════════════════════════════════════════════╝
06-09 23:15:29 I core    plugins         : verbose v0.12.0
06-09 23:15:29 I core    # procs         : 2
06-09 23:15:29 I core    profile         : default
06-09 23:15:29 I core    outdir          : /home/pwwang/github/pipen/MyPipeline-output
06-09 23:15:29 I core    cache           : True
06-09 23:15:29 I core    dirsig          : 1
06-09 23:15:29 I core    error_strategy  : ignore
06-09 23:15:29 I core    forks           : 1
06-09 23:15:29 I core    lang            : bash
06-09 23:15:29 I core    loglevel        : info
06-09 23:15:29 I core    num_retries     : 3
06-09 23:15:29 I core    scheduler       : local
06-09 23:15:29 I core    submission_batch: 8
06-09 23:15:29 I core    template        : liquid
06-09 23:15:29 I core    workdir         : /home/pwwang/github/pipen/.pipen/MyPipeline
06-09 23:15:29 I core    plugin_opts     :
06-09 23:15:29 I core    template_opts   :
06-09 23:15:31 I core
06-09 23:15:31 I core    ╭─────────────────────────────── P1 ───────────────────────────────╮
06-09 23:15:31 I core    │ Sort input file                                                  │
06-09 23:15:31 I core    ╰──────────────────────────────────────────────────────────────────╯
06-09 23:15:31 I core    P1: Workdir: '/home/pwwang/github/pipen/.pipen/MyPipeline/P1'
06-09 23:15:31 I core    P1: <<< [START]
06-09 23:15:31 I core    P1: >>> ['P2']
06-09 23:15:31 I verbose P1: size: 1
06-09 23:15:31 I verbose P1: [0/0] in.infile: /tmp/data.txt
06-09 23:15:31 I verbose P1: [0/0] out.outfile:
                 /home/pwwang/github/pipen/.pipen/MyPipeline/P1/0/output/intermediate.txt
06-09 23:15:33 I verbose P1: Time elapsed: 00:00:02.018s
06-09 23:15:33 I core
06-09 23:15:33 I core    ╭═══════════════════════════════ P2 ═══════════════════════════════╮
06-09 23:15:33 I core    ║ Paste line number                                                ║
06-09 23:15:33 I core    ╰══════════════════════════════════════════════════════════════════╯
06-09 23:15:33 I core    P2: Workdir: '/home/pwwang/github/pipen/.pipen/MyPipeline/P2'
06-09 23:15:33 I core    P2: <<< ['P1']
06-09 23:15:33 I core    P2: >>> [END]
06-09 23:15:33 I verbose P2: size: 1
06-09 23:15:33 I verbose P2: [0/0] in.infile:
                 /home/pwwang/github/pipen/.pipen/MyPipeline/P1/0/output/intermediate.txt
06-09 23:15:33 I verbose P2: [0/0] out.outfile:
                 /home/pwwang/github/pipen/MyPipeline-output/P2/result.txt
06-09 23:15:35 I verbose P2: Time elapsed: 00:00:02.009s
06-09 23:15:35 I core

              MYPIPELINE: 100%|█████████████████████████████| 2/2 [00:06<00:00, 0.36 procs/s]

> cat ./MyPipeline-output/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-annotate: Use docstring to annotate pipen processes
• pipen-args: Command line argument parser for pipen
• pipen-board: Visualize configuration and running of pipen pipelines on the web
• pipen-diagram: Draw pipeline diagrams for pipen
• pipen-dry: Dry runner for pipen pipelines
• pipen-filters: Add a set of useful filters for pipen templates.
• pipen-lock: Process lock for pipen to prevent multiple runs at the same time.
• pipen-log2file: Save running logs to file for pipen
• pipen-poplog: Populate logs from jobs to running log of the pipeline
• pipen-report: Generate report for pipen
• pipen-runinfo: Save running information to file for pipen
• pipen-verbose: Add verbosal information in logs for pipen.
• pipen-gcs: A plugin for pipen to handle files in Google Cloud Storage.
• pipen-cli-init: A pipen CLI plugin to create a pipen project (pipeline)
• pipen-cli-ref: Make reference documentation for processes
• pipen-cli-require: A pipen cli plugin check the requirements of a pipeline
• pipen-cli-run: A pipen cli plugin to run a process or a pipeline