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Updating the "Projects using XGI" Page

This page is automatically generated from structured YAML files. Do not edit the .rst file directly because any changes will be overwritten the next time the generator is run. Note that you'll need the docs dependencies to run the generate_using_xgi.py script.

File Structure

citations/
  published.yaml
  preprints.yaml
  theses.yaml
  software.yaml

tools/
  generate_using_xgi.py

docs/
  source/
    using_xgi.rst (Auto-generated)

How to Add or Edit Entries

All content is stored in YAML files under the citations/ directory. Each file corresponds to a section of the page.

1. Published Papers (published.yaml)

Each entry is a dictionary keyed by a unique identifier:

tong_hic3_2025:
  tags:
    - XGI
  authors:
    - Yuyan Tong
    - Renhao Hong
  title: "Hi-C3: a statistical inference-based model..."
  year: 2025
  reference: "Briefings in Bioinformatics, Volume 26, Issue 5, bbaf568"
  links:
    paper: https://doi.org/...
    code: https://github.com/...

Notes:

  • tags should include XGI and/or XGI-DATA
  • authors must be in order
  • reference is free-form (journal, conference, etc.)
  • links is optional but highly recommended

2. Preprints (preprints.yaml)

akcakir_exploring_2024:
  tags:
    - XGI
  authors:
    - Gülşah Akçakır
  title: Exploring the interplay...
  year: 2024
  reference: "arXiv:2407.12728"
  links:
    paper: https://arxiv.org/abs/2407.12728

3. Theses (theses.yaml)

sampson_complex_2025:
  tags:
    - XGI
  authors:
    - Corbit Sampson
  title: "Complex Social Systems..."
  year: 2025
  university: "The University of Colorado at Boulder"
  links:
    thesis: https://...

Note: Use university instead of reference.

4. Software (software.yaml)

hoi:
  url: https://brainets.github.io/hoi/

hypercontagion:
  url: https://hypercontagion.readthedocs.io/en/latest

Generating the .rst Page

After updating any YAML file, regenerate the page:

python tools/generate_using_xgi.py

This will overwrite:

docs/source/using_xgi.rst

Sorting and Formatting Rules

The script automatically:

  • Groups entries by year (descending)
  • Sorts within each year by first author’s last name
  • Numbers entries automatically
  • Formats links and citations for Sphinx

Important Guidelines

  • Do not manually edit using_xgi.rst
  • Always run the generator after making changes
  • Ensure YAML is valid (spacing matters!)
  • Keep keys (e.g., tong_hic3_2025) unique

Workflow Summary

  1. Edit the appropriate YAML file

  2. Save changes

  3. Run:

    python tools/generate_using_xgi.py

  4. Commit both the YAML and generated .rst

Tips

  • Copy an existing entry as a template when adding new ones
  • Keep formatting consistent (quotes for long titles help)
  • Add links to the paper and code whenever possible (DOIs prefered)