[Reference] fix image embedding in DOCX output

build/build.sh

@@ -52,6 +52,8 @@ then
     --to=docx \
     --filter pandoc-fignos \
     --filter pandoc-tablenos \
+    --filter pandoc-img-glob \
+    --filter build/pandoc-svg.py \
     --bibliography=$BIBLIOGRAPHY_PATH \
     --metadata link-citations=true \
     --csl=$CSL_PATH \

build/environment.yml

@@ -17,6 +17,9 @@ dependencies:
     - git+https://github.com/greenelab/manubot@b0da17625e1f12091159f15a329391b85c205565
     - pandoc-eqnos==0.16
     - pandoc-fignos==0.20
+    - pandoc-img-glob==0.1.3
+    - pandocfilters==1.4.1
+    - panflute==1.10.5
     - pandoc-tablenos==0.16
     - pybase62==0.3.2
     - pysha3==1.0.2

build/pandoc-svg.py

@@ -0,0 +1,65 @@
+#! /usr/bin/env python
+"""
+Pandoc filter to convert svg files to pdf as suggested at:
+https://github.com/jgm/pandoc/issues/265#issuecomment-27317316
+"""
+
+__author__ = "Jerome Robert"
+
+import mimetypes
+import subprocess
+import os
+import sys
+import re
+import urllib
+from pandocfilters import toJSONFilter, Para, Image
+
+fmt_to_option = {
+    "docx": ("--export-pdf", "pdf")
+}
+
+
+build_dir = os.getcwd()
+img_dir = "content/images/"
+
+
+def svg_to_any(key, value, fmt, meta):
+    if key == 'Image':
+        if len(value) == 2:
+            # before pandoc 1.16
+            alt, [src, title] = value
+            attrs = None
+        else:
+            attrs, alt, [src, title] = value
+        mimet, _ = mimetypes.guess_type(src)
+        option = fmt_to_option.get(fmt)
+        if mimet == 'image/svg+xml' and option:
+            web_image = re.compile('^http[s]?://')
+            if web_image.match(src):
+                base_name = os.path.basename(src)
+                base_name, _ = os.path.splitext(base_name)
+                eps_name = os.path.join(build_dir, img_dir, base_name + "." + option[1])
+                file_name = src
+            else:
+                base_name, _ = os.path.splitext(src)
+                eps_name = os.path.join(build_dir, base_name + "." + option[1])
+                file_name = os.path.join(build_dir, src)
+            try:
+                mtime = os.path.getmtime(eps_name)
+            except OSError:
+                mtime = -1
+            try:
+                 src_mtime = os.path.getmtime(src)
+            except FileNotFoundError:
+                src_mtime = -1
+            if mtime < src_mtime or web_image.match(src):
+                cmd_line = ['inkscape', option[0], eps_name, file_name]
+                sys.stderr.write("Running %s\n" % " ".join(cmd_line))
+                subprocess.call(cmd_line, stdout=sys.stderr.fileno())
+            if attrs:
+                return Image(attrs, alt, [eps_name, title])
+            else:
+                return Image(alt, [eps_name, title])
+
+if __name__ == "__main__":
+    toJSONFilter(svg_to_any)

content/00.front-matter.md

@@ -11,15 +11,15 @@ on {{date}}.
 {% for author in authors %}
 + **{{author.name}}**<br>
   {%- if author.orcid is defined %}
-    ![ORCID icon](images/orcid.svg){height="13px"}
+    ![ORCID icon](images/orcid.svg){height="13px" width="13px"}
     [{{author.orcid}}](https://orcid.org/{{author.orcid}})
   {%- endif %}
   {%- if author.github is defined %}
-    · ![GitHub icon](images/github.svg){height="13px"}
+    · ![GitHub icon](images/github.svg){height="13px" width="13px"}
     [{{author.github}}](https://github.com/{{author.github}})
   {%- endif %}
   {%- if author.twitter is defined %}
-    · ![Twitter icon](images/twitter.svg){height="13px"}
+    · ![Twitter icon](images/twitter.svg){height="13px" width="13px"}
     [{{author.twitter}}](https://twitter.com/{{author.twitter}})
   {%- endif %}<br>
   <small>