The Clifford Lab website

This is the source code for gdclifford.info, which is run on GitHub Pages.

Bibliography

The Publications page on this site is automatically generated from a collection of BibTeX files under bibliography/. Entries are organized into category by file, and sorted chronologically within each category.

Most of the citations come from Gari Clifford's Google Scholar profile, with many additions and corrections. The scholar page is checked routinely via a GitHub Action, which calls ./download_bibliography.py to download new entries using SerpAPI. Citations are never downloaded twice, so this makes fewer than 10 API queries a month, unless the Clifford Lab is extraordinarily prolific that month.

Then another GitHub Action generates a publications page from the BibTeX entries that were just downloaded.

You can

• wait for the page to update every month,
• update the bibliography yourself by running two GitHub Actions, or
• edit the bibliography yourself and regenerate the publications page on your local machine.

How to update the bibliography manually

1. Update Bibliography: Actions -> Update Bibliography -> Run workflow -> Run workflow.
2. Make Publications Page: Actions -> Make Publications Page -> Run workflow -> Run workflow.

Dependencies (for updating the bibliography locally)

With Python 3 installed:

pip3 install --requirements requirements.txt

On Mac OS X, you will also have to install setuptools:

pip3 install setuptools

Initial setup on a local machine

Run ./init.sh before the first time you commit.

This script adds a commit hook to the local repository, at .git/hooks/pre-commit. You don't need to interact with this file at all; this will simply ensure that pre-commit gets executed before committing changes.

Wait, but what does pre-commit do?

pre-commit does the following actions:

1. Attempt to generate publications.md from the bibliography files.
2. If the publications list was successfully created, add it to the commit.

The effect of this is that you don't have to touch the publications page, even to add it when it's changed. Both updating it and adding it are automated. All you need to do is edit the bibliography files, add those files, commit them, and presto! the publications page is also generated and included in the commit.

Currently supported citation types

Currently, these will be cited:

Journal Articles

• article. Required fields: author, title, journal, and either date or year.

Conference Papers

• conference. Required fields: author, title, either journal or booktitle, and either date or year.
• inproceedings. This is currently treated the same as conference.

Books and Chapters

• book. Required fields: author, title, publisher, and either date or year.
• inbook. Required fields: author, title, booktitle, and either date or year.
• incollection. This is currently treated the same as inbook.

Other Material (including Patents)

• misc. Required fields: author, title, howpublished, and either date or year.

Theses

• thesis. Required fields: author, title, school, type, year.

How to add a publication

• Get a BibTeX citation for the publication. These can be downloaded from Google Scholar, the library website, the journal, or another academic database. Optionally, you can edit the url, doi, and date fields.

  • url: ideally, link to a publicly available full-text source for the publication.
  • doi: give it either in the form number/number, or https://doi.org/number/number.
  • date: by default, most of these sources just give year. If you know the exact date, you can specify it in year-month-day format in a date field: e.g., replace year={2023} with date={2023-06-23}. If you know the year and the month, you can add it in a month field, e.g., month=Jun. Entries are sorted by the available date information in the bibtex file.

• Add this citation to the bibliography. Also, make sure it doesn't use the same key as another entry already in the bibliography.

• Try running make_publications_page.py. If it can't parse the file, it will crash and hopefully give a useful error message.

How to fix a wrong citation

To fix a wrong citation, you can edit the BibTeX entry directly. Since this entry will not be redownloaded, your changes will persist.

To find the BibTeX entry:

• On the site, click “[show BibTeX]” and note the BibTeX key (the string xyz in @article{xyz,).
• Search for the BibTeX key in the .bib file under bibliography corresponding to the section.

Or if you're very impatient, you can enter bibliography in the command line and run

grep -br "<some words from the citation>" --ignore-case

(with no angle-brackets), and you should see which file and where it is.

How to remove a citation entirely

Delete the citation from its BibTeX file. If it was automatically downloaded from Google Scholar, make sure that its Google Scholar citation ID is still listed in bibliography/do_not_download_these_citations.txt. Its BibTeX key will be included in the comment:

<citation_id> # <BibTeX key>

You may want to move it to the MANUALLY SKIPPED section, just to avoid confusing anyone else down the line (including yourself).

How to restore a citation to the version in Google Scholar

Delete the citation's Google Scholar citation ID from bibliography/do_not_download_these_citations.txt.

How to change the citation style

In make_publications_page.py, edit the function render_citation.

Theme

The theme of this website is Minima, with customizations. Minima is distributed with the MIT License:

The MIT License (MIT)

Copyright (c) 2016-present Parker Moore and the minima contributors

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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