infrastructure-reference

Reference Module

Bibliographic-reference workflows for the template's two-layer architecture. Output is byte-compatible with the existing projects/templates/template_code_project/manuscript/references.bib format and round-trips through the parser without semantic loss.

citation — BibTeX read/write/convert

from infrastructure.reference.citation import (
    BibEntry, BibDatabase,
    parse_bibfile, parse_bibtex, BibParseError,
    render_entry, render_database, render_entries, write_bibfile,
    paper_to_bibentry, generate_citation_key,
    escape_latex, unescape_latex,
)

Read & validate an existing .bib

db = parse_bibfile("projects/templates/template_code_project/manuscript/references.bib")
print(len(db), "entries")
boyd = db.find("boyd2004convex")
assert boyd.entry_type == "article"
assert boyd.get("author") == "Boyd, Stephen and Vandenberghe, Lieven"

Build entries programmatically

from collections import OrderedDict
entry = BibEntry(
    entry_type="article",
    citation_key="smith2024example",
    fields=OrderedDict([
        ("title", "An Example Paper"),
        ("author", "Smith, Alice and Jones, Bob"),
        ("journal", "Cambridge UP"),
        ("year", "2024"),
        ("pages", "1-10"),  # auto-normalised to "1--10"
        ("doi", "10.1234/example"),
    ]),
)
print(render_entry(entry))

Output (matches the exemplar exactly):

@article{smith2024example,
  title={An Example Paper},
  author={Smith, Alice and Jones, Bob},
  journal={Cambridge UP},
  year={2024},
  pages={1--10},
  doi={10.1234/example}
}

Convert a literature search result to BibTeX

from infrastructure.search.literature import LiteratureClient, SearchQuery, ArxivBackend
from infrastructure.reference.citation import paper_to_bibentry, render_database
from infrastructure.reference.citation.models import BibDatabase

result = LiteratureClient([ArxivBackend()]).search(SearchQuery(text="adam optimizer"))
db = BibDatabase()
for paper in result.papers:
    db.add(paper_to_bibentry(paper))
write_bibfile("output/references.bib", db)