Jupyter notebook markdown generator

These .ipynb files are Jupyter notebook files that convert a TSV containing structured data about talks (talks.tsv) or presentations (presentations.tsv) into individual markdown files that will be properly formatted for the academicpages template. The notebooks contain a lot of documentation about the process. The .py files are pure python that do the same things if they are executed in a terminal, they just don’t have pretty documentation.

Updating publications from open metadata

The site uses pubs.bib as the source for generated publication pages. To fetch candidate publications from ORCID, OpenAlex, OpenReview, and DOI metadata providers, run this from the repository root:

python scripts/update_publications_bib.py

By default, the updater reads the ORCID iD from _config.yml, scans the OpenReview profile ~Claudia_Soares1 for accepted public venue records, writes a generated metadata snapshot to generated_pubs.bib, and appends only missing records to pubs.bib. Existing hand-curated BibTeX entries are preserved to avoid large formatting-only diffs.

Preprints such as arXiv, CoRR, bioRxiv, medRxiv, SSRN, and generic preprint records are not added as standalone publications. When a preprint has the same title as a published record, the preprint URL is kept as a preprinturl link on the published record. Abstracts are copied to the generated publication page when they are available from BibTeX, OpenAlex, or OpenReview metadata.

Then regenerate the publication pages:

cd markdown_generator
python pubsFromBib.py

The GitHub Actions workflow in .github/workflows/update-publications.yml runs the same process weekly and opens a pull request when generated files change.