Claude/repo website spec review uv7lac

.github/ISSUE_TEMPLATE/suggest-bibliography.yml

@@ -46,22 +46,20 @@ body:
       label: Relevant method tags
       multiple: true
       options:
+        # extraction
         - silica-column
         - magnetic-bead
         - phenol-chloroform
         - ctab
-        - chelex
-        - tagmentation
-        - ligation
+        - commercial-kit
+        - diy-approach
+        # library
         - single-stranded
-        - pcr-free
-        - hybridization-capture
+        - double-stranded
+        # sequencing
         - genome-skimming
         - shotgun-wgs
         - target-capture
-        - metabarcoding
-        - rad-seq
-        - sanger
     validations:
       required: false
   - type: input

.github/ISSUE_TEMPLATE/suggest-method.yml

@@ -58,14 +58,10 @@ body:
       label: Preservation type*
       multiple: true
       options:
-        - dry-pinned
-        - study-skin
-        - herbarium-pressed
+        - dry
         - fluid-ethanol
         - fluid-formalin
         - frozen
-        - dried-tissue
-        - bone-subfossil
         - "Other (describe in detail box)"
     validations:
       required: true
@@ -79,7 +75,8 @@ body:
         - magnetic-bead
         - phenol-chloroform
         - ctab
-        - chelex
+        - commercial-kit
+        - diy-approach
         - "Other (describe in detail box)"
     validations:
       required: true
@@ -89,11 +86,10 @@ body:
       label: Library prep method*
       multiple: true
       options:
-        - tagmentation
-        - ligation
         - single-stranded
-        - pcr-free
-        - hybridization-capture
+        - double-stranded
+        - commercial-kit
+        - diy-approach
         - "Other (describe in detail box)"
     validations:
       required: true
@@ -106,9 +102,6 @@ body:
         - genome-skimming
         - shotgun-wgs
         - target-capture
-        - metabarcoding
-        - rad-seq
-        - sanger
         - "Other (describe in detail box)"
     validations:
       required: true

CONTRIBUTING.md

@@ -67,10 +67,12 @@ truth. CI (`scripts/validate_entries.rb`) fails the build if an entry uses a
 value that isn't listed there, which keeps filtering consistent and stops typos
 fragmenting the taxonomy.
 
-**Need a new tag value?** Add it to `_data/tags.yml` in the same PR. If that
-value is also offered as a dropdown in an issue form, add it to the matching
-list in `.github/ISSUE_TEMPLATE/*.yml` too — the forms can't read `tags.yml`
-automatically. The maintainer curates this vocabulary.
+**Need a new tag value?** Add it to `_data/tags.yml` in the same PR, and add it
+to the matching dropdown in `.github/ISSUE_TEMPLATE/*.yml` too — the forms can't
+read `tags.yml` automatically. CI enforces this: `scripts/validate_entries.rb`
+fails if a form dropdown and the vocabulary drift apart in either direction (a
+stale option, or a vocab value the form doesn't offer). The maintainer curates
+this vocabulary.
 
 ## Local preview
 

scripts/validate_entries.rb

@@ -1,16 +1,19 @@
 #!/usr/bin/env ruby
 # frozen_string_literal: true
 #
-# Validates every method and bibliography entry against the controlled
-# vocabulary in _data/tags.yml and a small required-field schema.
-# Exits non-zero (failing CI) if any entry is invalid. Run:
+# Validates (1) every method and bibliography entry against the controlled
+# vocabulary in _data/tags.yml and a small required-field schema, and (2) that
+# the GitHub Issue Form dropdowns stay in sync with that vocabulary (the forms
+# can't read _data/tags.yml, so this guards against drift).
+# Exits non-zero (failing CI) if anything is invalid. Run:
 #   ruby scripts/validate_entries.rb
 
 require "yaml"
 require "date"
 
 ROOT = File.expand_path("..", __dir__)
 TAGS = YAML.safe_load_file(File.join(ROOT, "_data", "tags.yml"))
+FACETS = YAML.safe_load_file(File.join(ROOT, "_data", "facets.yml"))
 
 errors = []
 
@@ -96,9 +99,55 @@ def as_array(v)
   end
 end
 
+# --- issue-form vocabulary sync -------------------------------------------
+# Each form dropdown must offer exactly the vocabulary it maps to: no stale
+# values (offered but no longer in tags.yml) and no missing values (in the
+# vocab but not offered). The "Other (describe…)" escape hatch is exempt.
+def facet_vocab(facet)
+  facet["grouped"] ? TAGS[facet["key"]].values.flatten : (TAGS[facet["key"]] || [])
+end
+
+def check_form(rel, expected, errors)
+  path = File.join(ROOT, rel)
+  unless File.exist?(path)
+    errors << "#{rel}: file not found"
+    return
+  end
+  form = YAML.safe_load_file(path)
+  dropdowns = (form["body"] || []).each_with_object({}) do |b, h|
+    h[b["id"]] = b if b.is_a?(Hash) && b["type"] == "dropdown"
+  end
+
+  expected.each do |id, vocab|
+    field = dropdowns[id]
+    unless field
+      errors << "#{rel}: expected dropdown `#{id}` is missing"
+      next
+    end
+    offered = Array(field.dig("attributes", "options")).reject { |o| o.to_s.start_with?("Other") }
+
+    dupes = offered.select { |o| offered.count(o) > 1 }.uniq
+    dupes.each { |v| errors << "#{rel}: `#{id}` lists \"#{v}\" more than once" }
+
+    (offered - vocab).each { |v| errors << "#{rel}: `#{id}` offers \"#{v}\" which is not in _data/tags.yml" }
+    (vocab - offered).each { |v| errors << "#{rel}: `#{id}` is missing vocab value \"#{v}\" (add it or the form drifts from tags.yml)" }
+  end
+end
+
+# Method form: one dropdown per method-applicable facet, plus outcome.
+method_expected = {}
+FACETS.select { |f| f["methods"] }.each { |f| method_expected[f["key"]] = facet_vocab(f) }
+method_expected["outcome"] = TAGS["outcome"] || []
+check_form(".github/ISSUE_TEMPLATE/suggest-method.yml", method_expected, errors)
+
+# Bibliography form: a single `tags` dropdown = union of bibliography-applicable
+# facet vocabularies (deduped).
+bib_tag_vocab = FACETS.select { |f| f["bibliography"] }.flat_map { |f| facet_vocab(f) }.uniq
+check_form(".github/ISSUE_TEMPLATE/suggest-bibliography.yml", { "tags" => bib_tag_vocab }, errors)
+
 # --- report ----------------------------------------------------------------
 if errors.empty?
-  puts "✓ All entries valid."
+  puts "✓ All entries and issue forms valid."
   exit 0
 else
   warn "✗ #{errors.length} validation error(s):"