GitHub - pwwang/pipen: A pipeline framework for python (original) (raw)
A pipeline framework for python
Documentation | ChangeLog | Examples | API
Features
- Easy to use
- Nearly zero-configuration
- Nice logging
- Highly extendable
- Cloud support naively
Installation
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:file" 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
04-17 16:19:35 I core _____________________________________ __
04-17 16:19:35 I core ___ __ \___ _/__ __ \__ ____/__ | / /
04-17 16:19:35 I core __ /_/ /__ / __ /_/ /_ __/ __ |/ /
04-17 16:19:35 I core _ ____/__/ / _ ____/_ /___ _ /| /
04-17 16:19:35 I core /_/ /___/ /_/ /_____/ /_/ |_/
04-17 16:19:35 I core
04-17 16:19:35 I core version: 0.17.3
04-17 16:19:35 I core
04-17 16:19:35 I core ╔═══════════════════════════ MYPIPELINE ════════════════════════════╗
04-17 16:19:35 I core ║ My pipeline ║
04-17 16:19:35 I core ╚═══════════════════════════════════════════════════════════════════╝
04-17 16:19:35 I core plugins : verbose v0.14.1
04-17 16:19:35 I core # procs : 2
04-17 16:19:35 I core profile : default
04-17 16:19:35 I core outdir :
/home/pwwang/github/pipen/examples/MyPipeline-output
04-17 16:19:35 I core cache : True
04-17 16:19:35 I core dirsig : 1
04-17 16:19:35 I core error_strategy : ignore
04-17 16:19:35 I core forks : 1
04-17 16:19:35 I core lang : bash
04-17 16:19:35 I core loglevel : info
04-17 16:19:35 I core num_retries : 3
04-17 16:19:35 I core scheduler : local
04-17 16:19:35 I core submission_batch: 8
04-17 16:19:35 I core template : liquid
04-17 16:19:35 I core workdir :
/home/pwwang/github/pipen/examples/.pipen/MyPipeline
04-17 16:19:35 I core plugin_opts :
04-17 16:19:35 I core template_opts : filters={'realpath': <function realpath at
0x7fc3eba12...
04-17 16:19:35 I core : globals={'realpath': <function realpath at
0x7fc3eba12...
04-17 16:19:35 I core Initializing plugins ...
04-17 16:19:36 I core
04-17 16:19:36 I core ╭─────────────────────────────── P1 ────────────────────────────────╮
04-17 16:19:36 I core │ Sort input file │
04-17 16:19:36 I core ╰───────────────────────────────────────────────────────────────────╯
04-17 16:19:36 I core P1: Workdir:
'/home/pwwang/github/pipen/examples/.pipen/MyPipeline/P1'
04-17 16:19:36 I core P1: <<< [START]
04-17 16:19:36 I core P1: >>> ['P2']
04-17 16:19:36 I verbose P1: in.infile: /tmp/data.txt
04-17 16:19:36 I verbose P1: out.outfile:
/home/pwwang/github/pipen/examples/.pipen/MyPipeline/P1/0/output/intermediate
.txt
04-17 16:19:38 I verbose P1: Time elapsed: 00:00:02.051s
04-17 16:19:38 I core
04-17 16:19:38 I core ╭═══════════════════════════════ P2 ════════════════════════════════╮
04-17 16:19:38 I core ║ Paste line number ║
04-17 16:19:38 I core ╰═══════════════════════════════════════════════════════════════════╯
04-17 16:19:38 I core P2: Workdir:
'/home/pwwang/github/pipen/examples/.pipen/MyPipeline/P2'
04-17 16:19:38 I core P2: <<< ['P1']
04-17 16:19:38 I core P2: >>> [END]
04-17 16:19:38 I verbose P2: in.infile:
/home/pwwang/github/pipen/examples/.pipen/MyPipeline/P1/0/output/intermediate
.txt
04-17 16:19:38 I verbose P2: out.outfile:
/home/pwwang/github/pipen/examples/MyPipeline-output/P2/result.txt
04-17 16:19:41 I verbose P2: Time elapsed: 00:00:02.051s
04-17 16:19:41 I core
MYPIPELINE: 100%|██████████████████████████████| 2/2 [00:06<00:00, 0.35 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