Sync 134 new citations into references.bib (trigger wiki sync)#21
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… fix Ran discovery/approve.py against pipeline/approved/ to fold the 158 newly approved YAMLs from the trusted-bib bulk import (PR #20) into references.bib. 134 entries added; 36 already present (Guo MiniLFOV, Zhao MiniXL, and other previously-approved papers); 1 skipped (yan_2018_implementing — no DOI in the YAML). references.bib: 14 -> 172 entries. Also: - Fetched missing BibTeX from CrossRef for the 49 OpenAlex-ingested YAMLs whose bibtex_raw was still None after PR #20 merged. - discovery/fulltext.py: normalize month names to lowercase 3-letter abbreviations on fetch (CrossRef emits both full names like "month=July" and the non-standard "month=Sept", either of which bibtexparser's common_strings table doesn't recognize — caused UndefinedString on the first approve run). - Patched 48 already-fetched .bib + .yaml files for the same normalization. Merging this PR pushes references.bib past the sync workflow's path filter (**.bib), which will trigger the sync-to-wiki Action and create the new Publication pages on miniscope.org. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The 1 entry skipped by approve.py earlier ("no BibTeX data") is
Helena Z. H. Yan's Wellesley College senior thesis from 2018, which
the institutional repository never assigned a DOI to. OpenAlex and
CrossRef both confirm no DOI exists for this work.
Hand-crafted a @mastersthesis BibTeX entry from the trusted-bib
metadata + the Wellesley repository URL:
https://repository.wellesley.edu/thesiscollection/574
Author list reduced to Helena Yan (the candidate). The trusted bib
listed Wilson, Newman, Wasserman, and Wiest as co-authors, but those
are the thesis committee, not authors — corrected.
Classification per the trusted bib's tags (Thesis, DAQ, Miniscope V3):
paper_type = Methods
project = Miniscope V3, Miniscope DAQ
keywords = Calcium Imaging, Optogenetics, Place Cells, Hippocampus,
Open-Source
bibtex_source = "trusted_bib_manual" to distinguish from "crossref" in
the audit trail.
references.bib: 172 -> 173 entries.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Citations Summary
Added (159)
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What
Ran `discovery/approve.py` against `pipeline/approved/` to fold the 158 newly approved YAMLs from PR #20 into `references.bib`.
Result: `references.bib` 14 → 172 entries.
Why this is a separate PR
After PR #20 merged, the wiki sync workflow didn't run because its path filter (`.bib`, `scripts/`, `config.json`) didn't match the YAML/vocab changes in that PR. Merging this PR pushes `references.bib` past that path filter and triggers `sync-to-wiki.yml`.
Drive-by fix to `discovery/fulltext.py`
CrossRef occasionally emits BibTeX with month names that `bibtexparser`'s `common_strings` table doesn't recognize:
Either triggers an `UndefinedString` exception during parsing in `approve.py`. Normalized them to standard lowercase 3-letter abbreviations on fetch:
```python
_MONTH_VARIANTS = {
"January": "jan", ..., "December": "dec",
"Sept": "sep", # non-standard CrossRef abbreviation
}
for variant, abbr in _MONTH_VARIANTS.items():
bibtex = re.sub(rf"(month\s*=\s*){variant}\b", rf"\g<1>{abbr}", bibtex, flags=re.IGNORECASE)
```
48 already-fetched `.bib` + `.yaml` files were retroactively patched with the same normalization so the existing data stays consistent.
On merge
The path filter (`**.bib` matched by `references.bib`) triggers `sync-to-wiki.yml`, which will:
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