Fix vocab generation: use vocab CLI instead of vocab2md.py (isamplesorg#48)

PR isamplesorg#46 switched from `vocab markdown` to `python vocab2md.py`, but
vocab2md.py requires rdflib which isn't in requirements.txt.

The workflow already installs vocab_tools via pipx, which provides
the `vocab` CLI. This reverts to using that CLI.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

Author: rdhyee

scripts/generate_vocab_docs.sh

@@ -2,6 +2,7 @@
 #
 # Regenerates the vocabulary markdown files from the GH sources
 #
+# Uses 'vocab' CLI from vocab_tools (installed via pipx in workflow)
 #
 
 # get the core sample type vocabularies
@@ -15,7 +16,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.qmd"
     echo "Generating ${fname}..."
-    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 #
@@ -33,7 +34,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.md"
     echo "Generating ${fname}..."
-    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/"
@@ -43,7 +44,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.md"
     echo "Generating ${fname}..."
-    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/"
@@ -53,7 +54,7 @@ mkdir -p "${DEST_FOLDER}"
 for src in ${SOURCES[@]}; do
     fname="${src%%.*}.md"
     echo "Generating ${fname}..."
-    python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
+    vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
 done
 
 echo "Done."