infrastructure-reference · diff
git:20260531.112973e to git:20260606.243a3c4
30 added, 1 removed. Audit A to A.
---
name: infrastructure-reference
- description: Bibliographic-reference utilities for research projects. Read, write, and convert BibTeX entries that match the syntax/semantics of projects/templates/template_code_project/manuscript/references.bib (consumed by Pandoc with --natbib during PDF render -- see infrastructure/rendering/_pdf_combined_renderer.py). Currently exposes the `citation` submodule (BibTeX I/O + Paper→BibEntry conversion); designed to host additional reference workflows (e.g. CSL-JSON export, ORCID lookups) without breaking the public API.
+ description: Bibliographic-reference utilities for research projects. Read, write, and convert BibTeX entries that match the syntax/semantics of projects/templates/template_code_project/manuscript/references.bib (consumed by Pandoc with --natbib during PDF render -- see infrastructure/rendering/_pdf_combined_pandoc.py). Exposes the `citation` submodule (BibTeX I/O + Paper→BibEntry conversion) and the `verification` submodule (deterministic reference-existence gate against Crossref/OpenAlex/arXiv with a persistent SQLite cache); designed to host additional reference workflows without breaking the public API.
---
# 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
```python
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`
```python
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
```python
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):
```bibtex
@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
```python
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)
```
### Validate / format from the CLI
```bash
# Round-trip-parse a .bib file.
uv run python -m infrastructure.reference.citation.cli validate \
projects/templates/template_code_project/manuscript/references.bib
# Re-emit a .bib in canonical format (overwrites in place).
uv run python -m infrastructure.reference.citation.cli format path/to/refs.bib
# Convert a JSON file of literature-search Paper records into BibTeX.
uv run python -m infrastructure.reference.citation.cli convert \
output/papers.json output/references.bib
```
+
+ ## `verification` — reference-existence anti-hallucination gate
+
+ Resolves each cited reference against Crossref → OpenAlex (DOI), arXiv (id), or
+ Crossref title search, and classifies it `ok` / `mismatch` / `fabricated` /
+ `unverifiable` / `unchecked` / `anachronism`. Offline-first (consults only the
+ persistent SQLite cache unless `allow_network=True`); reports `unchecked` on an
+ offline cache miss so a skipped check never reads as clean.
+
+ ```python
+ from infrastructure.reference.verification import (
+ ReferenceResolver, ResolutionCache, verify_bibfile, verify_database, verify_entry,
+ VerificationStatus, VerificationReport, ReferenceVerdict, BLOCKING_STATUSES,
+ )
+
+ resolver = ReferenceResolver(cache=ResolutionCache("cache.db"), allow_network=True)
+ report = verify_bibfile("references.bib", resolver, as_of_year=2026)
+ print(report.summary_line())
+ assert not report.has_blocking # no fabricated / mismatch / anachronism
+ ```
+
+ ```bash
+ # Offline (cache-only, CI-safe) vs live resolution; gate on blocking verdicts.
+ uv run python -m infrastructure.reference.verification verify references.bib
+ uv run python -m infrastructure.reference.verification verify references.bib --live --as-of-year 2026 --fail-on-issues
+ uv run python -m infrastructure.reference.verification cache-clear
+ ```
+
+ See [`verification/SKILL.md`](verification/SKILL.md) for the full descriptor.
## Format Guarantees
* **2-space indent** on every field line.
* **Trailing comma** after every field except the last.
* **`pages={N--M}`** (BibTeX em-dash) regardless of input form (`-`, `–`, `—`).
* **Author normalisation** around ` and `.
* **Verbatim fields** (`year`, `volume`, `number`, `month`, `edition`, `isbn`,
`issn`, `doi`, `url`) are emitted without LaTeX escaping.
* **Unicode is preserved** (Pandoc / XeLaTeX handle it natively, matching the
exemplar's convention).
* **`book` / `phdthesis` / `techreport` / `misc`** entries never receive a
spurious `journal=` field even when their source declared a venue.
## Related Modules
* [`infrastructure.search.literature`](../search/literature/SKILL.md) —
discovery side of the literature workflow.
* [`infrastructure.publishing.citations`](../publishing/SKILL.md) — citation
*string* generation (APA / MLA) for human-facing markdown sections.