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

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Merged
rdhyee merged 1 commit into from
Dec 11, 2025
Merged

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

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9 changes: 5 additions & 4 deletions scripts/generate_vocab_docs.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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

#
Expand All @@ -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/"
Expand All @@ -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/"
Expand All @@ -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."