Populate references.bib via valency-mcp

Populate references.bib via valency-mcp

Drive the valency-mcp server to find and fetch bibtex entries for a list of topics or arxiv IDs, then merge them into references.bib in the current paper repo.

User input in $ARGUMENTS: a free-form list of topics, arxiv IDs, or author names with optional flags. Examples:

• /paper:refs CosmoPower emulators Tinker mass function FFTLog Hamilton
• /paper:refs 2106.03846 1712.00788 0803.2706
• /paper:refs --author="Spurio Mancini" --start-date=2020-01-01

Steps

1. Read the current references.bib to see what's already there; you'll merge by cite key, never duplicate.

2. For each topic / ID:

   • If it looks like an arxiv ID (\d{4}\.\d{4,5} or [a-z\-]+/\d{7}) → get_paper_by_id.
   • Otherwise → search_by_title (with limit=3, include_abstract=false) and pick the top hit. If unsure, ask the user.
   • For author searches → search_by_author.

3. Batch fetch bibtex via export_papers_bibtex(paper_ids=[...]) — much faster than one-at-a-time calls.

4. Rename cite keys to short, memorable forms before merging (FirstAuthorYearKeyword, e.g. SpurioMancini2022, Tinker2008, ACTDR62025). The valency tool returns keys like spurioMancini2022cosmopoweremulating... which are correct but ugly.

5. Fix common bibtex issues before merging:

   • @article entries without journal= → convert to @misc with eprint = ..., archivePrefix = {arXiv}, primaryClass = {...}, OR add the journal field if you know it.
   • UTF-8 accents → LaTeX form ({\\'e} etc.).
   • URLs with <i> or <sub> HTML tags from CrossRef → strip them.

6. Hand-write entries for sources not on arxiv:

   • JMLR papers (e.g.\ NUTS, Hoffman-Gelman 2014).
   • Software releases (\\misc with howpublished = {\\url{...}}).
   • IAU symposia, conference proceedings, observatory tech notes.
   • PhD theses.

7. Append to references.bib under a sensible section header (e.g. % ---- Halo model ----, % ---- Surveys ----, % ---- JAX / SBI ----). Group thematically, not chronologically.

8. Rebuild to verify (latexmk -pdf paper.tex); report any remaining Citation .* undefined warnings.

Pitfalls

• Generic title searches return junk: "Hamilton FFTLog" might return the wrong Hamilton paper. Always show the user the top hit
  • abstract before committing if you're not 100% sure.
• Wrong CrossRef metadata: \\textit{i} and <sub> HTML tags occasionally leak through. Scan references.bib after writing.
• Cite-key collisions: never have two @article{Smith2020, ...} entries with the same key — bibtex silently uses the first.
• Group editor with care: if the user runs /paper:refs repeatedly and we keep adding to references.bib, deduplicate by key.