Add data-raw/regenerate_bib.R helper for vignettes/references.bib

CLAUDE.md

@@ -118,6 +118,8 @@ Two regional reporting vignettes in `vignettes/`:
 
 Both share the same structure (Area of Interest → Trends → Snowpack → Spatial Pattern → Per-Ecoregion → WSGs Across Ecoregions → Interpretation). Heavy data is precomputed by `data-raw/<vignette>_vignette_data.R` into `inst/vignette-data/<vignette>.{rds,tif}` so pkgdown CI doesn't re-fetch from S3 on every render. ASWS QA cross-checks are in `data-raw/qa_snow_validation*.R` — run locally only, results land in `planning/archive/<issue>/`.
 
+**Bibliography regen.** After adding or removing `[@key]` markers in either vignette, regenerate `vignettes/references.bib` from Zotero/BBT by running `Rscript data-raw/regenerate_bib.R`. Pulls source records via rbbt → BBT, writes the union of keys across both vignettes. Requires Zotero running with BBT enabled (BBT 9.x for Zotero 8/9). CI does not run this — the bib is committed and pkgdown reads the static file.
+
 The two-vignette template is the foundation for additional regional reporting appendices (cf #47) — port directly to a `fish_passage_<region>_<year>` reporting context.
 
 ## Data Directories (gitignored)

data-raw/regenerate_bib.R

@@ -0,0 +1,66 @@
+#!/usr/bin/env Rscript
+#
+# data-raw/regenerate_bib.R
+#
+# Regenerate vignettes/references.bib from the union of [@key] markers
+# used in the regional vignettes (kootenay-lake.Rmd, peace-fwcp.Rmd).
+# Pulls source records from Zotero via Better BibTeX (rbbt → BBT).
+#
+# Run after adding/removing [@key] markers in either vignette:
+#   Rscript data-raw/regenerate_bib.R
+#
+# Prerequisites:
+#   - Zotero desktop running with BBT plugin enabled
+#       BBT 9.x for Zotero 8/9; BBT 8.x for Zotero 7
+#       (if BBT shows "disabled by Zotero" in the plugin manager,
+#       reinstall the matching version per soul#43)
+#   - All [@key] markers in either vignette must resolve to items
+#     in the NewGraphEnvironment Zotero library
+#
+# CI does not run this script — vignettes/references.bib is committed
+# and pkgdown reads the static file. Re-run + commit whenever cites
+# change. Keys not used in the vignettes are dropped automatically.
+
+vignettes <- c(
+  here::here("vignettes", "kootenay-lake.Rmd"),
+  here::here("vignettes", "peace-fwcp.Rmd")
+)
+out_path <- here::here("vignettes", "references.bib")
+
+# --- Detect citation keys per vignette ---
+keys_per_rmd <- lapply(vignettes, function(rmd) {
+  rbbt::bbt_detect_citations(paste(readLines(rmd), collapse = "\n"))
+})
+names(keys_per_rmd) <- basename(vignettes)
+
+for (rmd in names(keys_per_rmd)) {
+  message("  ", rmd, ": ", length(keys_per_rmd[[rmd]]), " keys")
+}
+
+# Note any keys that appear in only one vignette (informational —
+# the union still gets written, no manual reconciliation needed)
+all_keys <- sort(unique(unlist(keys_per_rmd)))
+for (rmd in names(keys_per_rmd)) {
+  rmd_only <- setdiff(keys_per_rmd[[rmd]], unlist(keys_per_rmd[setdiff(names(keys_per_rmd), rmd)]))
+  if (length(rmd_only) > 0) {
+    message("  Note: ", length(rmd_only), " key(s) appear only in ",
+            rmd, ": ", paste(rmd_only, collapse = ", "))
+  }
+}
+
+message("\nUnion: ", length(all_keys), " unique keys across ",
+        length(vignettes), " vignettes")
+
+# --- Fetch bib entries for the full union via BBT ---
+bib_text <- rbbt::bbt_bib(all_keys, .action = rbbt::bbt_return)
+
+writeLines(bib_text, out_path)
+
+n_entries <- length(grep("^@", readLines(out_path)))
+message("Wrote ", n_entries, " entries to ", out_path)
+
+if (n_entries != length(all_keys)) {
+  warning("Entry count (", n_entries, ") differs from detected key ",
+          "count (", length(all_keys), "). Check that BBT is reachable ",
+          "and all keys exist in Zotero.")
+}

vignettes/kootenay-lake.Rmd

@@ -11,6 +11,19 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+<!--
+After adding or removing pandoc citation markers in this vignette
+(or in peace-fwcp.Rmd), regenerate vignettes/references.bib by
+running:
+
+  Rscript data-raw/regenerate_bib.R
+
+Pulls source records from Zotero via Better BibTeX (rbbt -> BBT).
+Requires Zotero running with the BBT plugin enabled. CI does not
+run this script — the bib is committed and pkgdown reads it.
+-->
+
+
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,

vignettes/peace-fwcp.Rmd

@@ -11,6 +11,19 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
+<!--
+After adding or removing pandoc citation markers in this vignette
+(or in kootenay-lake.Rmd), regenerate vignettes/references.bib by
+running:
+
+  Rscript data-raw/regenerate_bib.R
+
+Pulls source records from Zotero via Better BibTeX (rbbt -> BBT).
+Requires Zotero running with the BBT plugin enabled. CI does not
+run this script — the bib is committed and pkgdown reads it.
+-->
+
+
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,

vignettes/references.bib

@@ -293,3 +293,4 @@ @article{yue_wang2002Applicabilityprewhitening
   keywords = {cd-issue-53,snowpack-departure-methodology},
   file = {/Users/airvine/Zotero/storage/VSW8UA44/Applicability_of_Prewhitening_to_Eliminate_the_Inf.pdf}
 }
+