fix old parameters for pandoc2 in pandoc3

Author: piero-g

fulltext-markdown.sh

@@ -9,6 +9,14 @@
 # Author: Piero Grandesso
 # https://github.com/piero-g/markdown-workflow
 #
+# Todo:
+# rework as a complete loop
+# add media-extract
+# add several fixes via sed, like:
+# - remove mark `\[([^\]]*)\]\{\.mark\}`
+# - fix `\...` and `\"`
+#
+
 
 #####
 # 0. events log and other checks
@@ -109,7 +117,7 @@ printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")] Starting conversion of manuscripts
 		if [ "${manuscript}" != "${manuscript%.${EXT1}}" ]; then
 			printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")]   ${manuscript}: trying to convert it in Markdown..." >> "$workingDir/$eventslog"
 			# actual conversion with Pandoc
-			if pandoc --wrap=none --atx-headers -o "$tempdir/${manuscript%.${EXT1}}.md" "$manuscript" ; then
+			if pandoc --wrap=none --markdown-headings=atx -o "$tempdir/${manuscript%.${EXT1}}.md" "$manuscript" ; then
 				printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")]   ... ${manuscript} was converted!" >> "$workingDir/$eventslog"
 				# archive the processed manuscript
 				mv "$manuscript" "$workingDir/archive/original-version/${manuscript%.${EXT1}}-$(date +"%Y-%m-%dT%H-%M-%S").${EXT1}"
@@ -122,7 +130,7 @@ printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")] Starting conversion of manuscripts
 		elif [ "${manuscript}" != "${manuscript%.${EXT2}}" ]; then
 			printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")]   ${manuscript}: trying to convert it in Markdown..." >> "$workingDir/$eventslog"
 			# actual conversion with Pandoc
-			if pandoc --wrap=none --atx-headers -o "$tempdir/${manuscript%.${EXT2}}.md" "$manuscript" ; then
+			if pandoc --wrap=none --markdown-headings=atx -o "$tempdir/${manuscript%.${EXT2}}.md" "$manuscript" ; then
 				printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")]   ... ${manuscript} was converted!" >> "$workingDir/$eventslog"
 				# archive the processed manuscript
 				mv "$manuscript" "$workingDir/archive/original-version/${manuscript%.${EXT2}}-$(date +"%Y-%m-%dT%H-%M-%S").${EXT2}"
@@ -135,7 +143,7 @@ printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")] Starting conversion of manuscripts
 		elif [ "${manuscript}" != "${manuscript%.${EXT3}}" ]; then
 			printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")]   ${manuscript}: trying to convert it in Markdown..." >> "$workingDir/$eventslog"
 			# actual conversion with Pandoc
-			if pandoc --wrap=none --atx-headers -o "$tempdir/${manuscript%.${EXT3}}.md" "$manuscript" ; then
+			if pandoc --wrap=none --markdown-headings=atx -o "$tempdir/${manuscript%.${EXT3}}.md" "$manuscript" ; then
 				printf '%b\n' "[$(date +"%Y-%m-%d %H:%M:%S")]   ... ${manuscript} was converted!" >> "$workingDir/$eventslog"
 				# archive the processed manuscript
 				mv "$manuscript" "$workingDir/archive/original-version/${manuscript%.${EXT3}}-$(date +"%Y-%m-%dT%H-%M-%S").${EXT3}"

markdown-galleys.sh

@@ -141,25 +141,25 @@ mkdir -p "$workingDir/archive/layout-versions/$today"
 
 # conversion functions
 converttohtml() {
-	# HTML conversion with Pandoc  --self-contained
-	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --filter=pandoc-citeproc --email-obfuscation=references --section-divs --self-contained --template="$workingDir/z-lib/article.html5" --write=html5 --default-image-extension=.low.jpg -o "$workingDir/2-publication/${manuscript%.md}.html"
+	# HTML conversion with Pandoc  --embed-resources --standalone
+	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --citeproc --email-obfuscation=references --section-divs --embed-resources --standalone --template="$workingDir/z-lib/article.html5" --write=html5 --default-image-extension=.low.jpg -o "$workingDir/2-publication/${manuscript%.md}.html"
 }
 converttopdf() {
 	# PDF conversion with Pandoc # -N --toc
-	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --filter=pandoc-citeproc --template="$workingDir/z-lib/article.latex" --pdf-engine=xelatex --default-image-extension=.jpg -s -o "$workingDir/2-publication/${manuscript%.md}.pdf"
+	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --citeproc --template="$workingDir/z-lib/article.latex" --pdf-engine=xelatex --default-image-extension=.jpg -s -o "$workingDir/2-publication/${manuscript%.md}.pdf"
 	# LaTeX
-	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --filter=pandoc-citeproc --template="$workingDir/z-lib/article.latex" --pdf-engine=xelatex --default-image-extension=.jpg -s -o "$workingDir/2-publication/${manuscript%.md}.tex"
+	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --citeproc --template="$workingDir/z-lib/article.latex" --pdf-engine=xelatex --default-image-extension=.jpg -s -o "$workingDir/2-publication/${manuscript%.md}.tex"
 }
 converttoxml() {
 	# JATS XML
-	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --filter=pandoc-citeproc --template="$workingDir/z-lib/article.jats" --write=jats --wrap=none --default-image-extension=.jpg -s -o "$workingDir/2-publication/${manuscript%.md}.jats.xml"
+	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --citeproc --template="$workingDir/z-lib/article.jats" --write=jats --wrap=none --default-image-extension=.jpg -s -o "$workingDir/2-publication/${manuscript%.md}.jats.xml"
 	# TEI XML
-	#pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" --toc ${sectionNum} --filter=pandoc-citeproc --template="$workingDir/z-lib/article.tei" --write=tei -s -o "$workingDir/2-publication/${manuscript%.md}.tei.xml"
+	#pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" --toc ${sectionNum} --citeproc --template="$workingDir/z-lib/article.tei" --write=tei -s -o "$workingDir/2-publication/${manuscript%.md}.tei.xml"
 }
 # this is just a test
 converttoword() {
 	# DOCX format # --reference-doc="$workingDir/z-lib/article.docx"
-	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --filter=pandoc-citeproc  -w docx+styles  -s -o "$workingDir/2-publication/${manuscript%.md}.docx"
+	pandoc "$workingDir/z-lib/journal.yaml" "$workingDir/z-lib/issue.yaml" "${manuscript}" ${sectionNum} --toc --citeproc  -w docx+styles  -s -o "$workingDir/2-publication/${manuscript%.md}.docx"
 }
 # generic function that calls the specific conversions
 converttoformats() {