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.

Publications from timeline grants

Use publications_from_timeline_grants.py to refresh _publications/ from the grant IDs listed in _data/timeline.yml.

What it does:

• reads RP###### grant IDs from the funding timeline
• queries PubMed using the grants/funding field
• writes publication markdown files directly into _publications/
• deduplicates against existing publication files by PMID and title
• tags generated files with metadata so they can be safely refreshed later

Recommended workflow:

python .\markdown_generator\publications_from_timeline_grants.py --dry-run
python .\markdown_generator\publications_from_timeline_grants.py --clean

Notes:

• --dry-run shows how many publications would be written without changing files.
• --clean removes stale files previously generated by this script if they no longer match PubMed results.
• PubMed grant metadata is incomplete for some papers, so this will improve the publications section automatically but will not catch every Google Scholar result.