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README.md

compomics.github.io

Overview and documentation of CompOmics GitHub repositories.

Run website locally

  • Install Jekyll requirements
  • Install webpage dependencies: bundle install
  • Run Jekyll web server: bundle exec jekyll serve
  • The website is now hosted at http://localhost:4000

Create pages for GitHub repositories

The entire pages folder can be generated automatically by generate_docs.py. This script can be configured trough a YAML config file or the command line interface (run python generate_docs.py -h). See requirements.txt for the required Python packages.

Folder structure

Requires the following folder structure for projects:

pages/
|-- sample_project/
    |-- sample_project.md
    |-- wiki/
        |-- sample_wikipage.md
        |-- sample_wikipage2.md

where every GitHub repository has one folder with in its root the README file and a subfolder containing all wiki pages of that repository.

Jekyll file headers

The project markdown files need to contain the following items in their header:

README file

---
name: "simple"
description: "A simple tool"
layout: default
tags: project_home, simple
permalink: /projects/simple
project: simple
github_project: "https://github.com/compomics/simple"
---

Wiki page

---
name: docs
title: docs
layout: default
permalink: "/projects/simple/wiki/docs"
tags: wiki, simple
project: simple
github_project: https://github.com/compomics/simple
---

Jenkins post-build Groovy script

def projectName = manager.build.project.name
 
// replace with command of your choice for OS of your choice
def processBuilder=new ProcessBuilder('/home/compomics/miniconda3/bin/python', 'generate_docs.py', '-c', 'generate_docs_token.yaml', '-u', 'compomics', '-p', projectName, '-g')
manager.listener.logger.println(processBuilder.command())
processBuilder.redirectErrorStream(true)
processBuilder.directory(new File('/home/compomics/compomics.github.io'))
def process = processBuilder.start()

process.inputStream.eachLine {manager.listener.logger.println it}

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