Scripts

This folder contains some utility scripts that might be useful on a day-to-day basis to create elements for this website.

NB: This file was copied from our compbio website repo - it was created by Nelle Varoquaux

Converting bibtex files to publication “formatted markdown” files

The script convert_bibtex_to_md.py takes as input a bibtex file and outputs in a directory a markdown file per publication formatted as required by our website. It solely requires the python package bibtextparser, which can be installed via anaconda with conda install -c conda-forge bibtexparser. You can then use this script as following:

python convert_bibtex_to_md.py filename.bib results/

Because I (Nelle…) is very lazy, I’ve added in my bibtex files a note entry containing any additional information useful for the creation of the markdown file that isn’t typically in a bibtex file. In zotero, it consists in adding the information in the extra entry of each citation.

A bibtex file of the format:

@article{cauer_inferring_2019,
        title = {Inferring {Diploid} {3D} {Chromatin} {Structures} from {Hi}-{C} {Data}},
        copyright = {Creative Commons Attribution 3.0 Unported license (CC-BY 3.0)},
        url = {http://drops.dagstuhl.de/opus/volltexte/2019/11041/},
        doi = {10.4230/LIPICS.WABI.2019.11},
        language = {en},
        urldate = {2021-10-19},
        author = {Cauer, Alexandra Gesine and Yardimci, Gürkan and Vert, Jean-Philippe and Varoquaux, Nelle and Noble, William Stafford},
        collaborator = {Wagner, Michael},
        year = {2019},
        note = {oa\_paperurl: 'http://doi.org/10.1101/2020.08.13.249110'
githuburl: 'https://tree-timc.github.io/circhic/'},
        keywords = {000 Computer science, knowledge, general works, Computer Science},
        pages = {13 pages},
}

will be written to a markdown file as follows:

---
title: "Inferring Diploid 3D Chromatin Structures from Hi-C Data"
collection: publications
permalink: /publication/2019-cauer_yardimci_vert_varoquaux
venue: ''
citation: '<a href="http://drops.dagstuhl.de/opus/volltexte/2019/11041/">A. G. Cauer, G. Yardimci, J.-P. Vert, N. Varoquaux <i>et al.</i>. <b>Inferring Diploid 3D Chromatin Structures from Hi-C Data</b>, <i></i> 2019</a>'
oa_paperurl: 'http://doi.org/10.1101/2020.08.13.249110'
githuburl: 'https://tree-timc.github.io/circhic/'
---

and the two icons for Open Access papers and github URL will be displayed properly. Note that no check is currently done on what this note entry contains. It could possible cause problems.

To only export the publications associated to one authors, use the following command:

python convert_bibtex_to_md.py test-data.bib results -f Varoquaux,\ Nelle

Sophie Abby

Scripts

Converting bibtex files to publication “formatted markdown” files