diff --git a/build/build.sh b/build/build.sh
index e40ff643..950956f7 100644
--- a/build/build.sh
+++ b/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 \
diff --git a/build/environment.yml b/build/environment.yml
index 354fa1b1..bf4553d9 100644
--- a/build/environment.yml
+++ b/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
diff --git a/build/pandoc-svg.py b/build/pandoc-svg.py
new file mode 100644
index 00000000..7b4594fd
--- /dev/null
+++ b/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)
diff --git a/content/00.front-matter.md b/content/00.front-matter.md
index be8a2b8b..428c5138 100644
--- a/content/00.front-matter.md
+++ b/content/00.front-matter.md
@@ -11,15 +11,15 @@ on {{date}}.
{% for author in authors %}
+ **{{author.name}}**
{%- if author.orcid is defined %}
- {height="13px"}
+ {height="13px" width="13px"}
[{{author.orcid}}](https://orcid.org/{{author.orcid}})
{%- endif %}
{%- if author.github is defined %}
- · {height="13px"}
+ · {height="13px" width="13px"}
[{{author.github}}](https://github.com/{{author.github}})
{%- endif %}
{%- if author.twitter is defined %}
- · {height="13px"}
+ · {height="13px" width="13px"}
[{{author.twitter}}](https://twitter.com/{{author.twitter}})
{%- endif %}
diff --git a/references/pandoc-reference.docx b/references/pandoc-reference.docx
index a2a657a9..1c4f68cc 100644
Binary files a/references/pandoc-reference.docx and b/references/pandoc-reference.docx differ