A pipeline framework for python
Documentation | ChangeLog | Examples | API
- Easy to use
- Nearly zero-configuration
- Nice logging
- Highly extendable
pip install -U pipenexample.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.py06-09 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: 0.14.5
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 v0.11.0
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 3See more examples at examples/ and a more realcase example at:
https://github.com/pwwang/pipen-report/tree/master/example
Plugins make pipen even better.
pipen-annotate: Use docstring to annotate pipen processespipen-args: Command line argument parser for pipenpipen-board: Visualize configuration and running of pipen pipelines on the webpipen-diagram: Draw pipeline diagrams for pipenpipen-dry: Dry runner for pipen pipelinespipen-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 pipenpipen-poplog: Populate logs from jobs to running log of the pipelinepipen-report: Generate report for pipenpipen-runinfo: Save running information to file for pipenpipen-verbose: Add verbosal information in logs for pipen.pipen-cli-init: A pipen CLI plugin to create a pipen project (pipeline)pipen-cli-ref: Make reference documentation for processespipen-cli-require: A pipen cli plugin check the requirements of a pipelinepipen-cli-run: A pipen cli plugin to run a process or a pipeline
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