Set pandoc-defaults/jats.yaml

Author: dhimmel

build/build.sh

@@ -82,17 +82,11 @@ if [ "${BUILD_DOCX:-}" = "true" ]; then
     --defaults="$PANDOC_DEFAULTS_DIR/docx.yaml"
 fi
 
-echo "Exporting JATS XML manuscript"
+echo >&2 "Exporting JATS XML manuscript"
+if [ "${BUILD_JATS:-}" != "false" ]; then
 pandoc --verbose \
---from=markdown \
---to=jats \
---filter=pandoc-fignos \
---filter=pandoc-eqnos \
---filter=pandoc-tablenos \
---bibliography=$BIBLIOGRAPHY_PATH \
---csl=$CSL_PATH \
---metadata link-citations=true \
---output=output/manuscript.xml \
-$INPUT_PATH
+    --defaults="$PANDOC_DEFAULTS_DIR/common.yaml" \
+    --defaults="$PANDOC_DEFAULTS_DIR/jats.yaml"
+fi
 
 echo >&2 "Build complete"

build/pandoc-defaults/jats.yaml

@@ -0,0 +1,8 @@
+# Pandoc --defaults for JATS XML output.
+# Load on top of common defaults.
+to: jats
+output-file: output/manuscript.xml
+reference-doc: build/themes/default.docx
+resource-path:
+ - '.'
+ - content