This repository helps you write your academic grant, paper, biosketch, or CV in
markdown
format. It provides templates, style files, and helper scripts that
are useful for building media output as PDF from markdown
files. This
repository bring us closer to the goal of authoring scientific documents in
markdown to completely separate content from
style.
Here are some examples of the output that you can produce with mediabuilder:
- Manuscript: Render the .md manuscript source into a PDF
- NIH biosketch: Render the .md biosketch source into a PDF
- NIH-formatted basic grant: Render the .md grant source into a PDF
-
Install software prerequisites:
- Install pandoc to convert markdown to PDF.
- Install inkscape to convert SVG to PDF.
- Install libreoffice (optional) for some recipes that read
xls
ordocx
files. - Install ghostscript (optional) if you need to merge PDFs (should be standard on linux).
-
Clone and configure
mediabuilder
:- Clone nsheff/mediabuilder (this repository, cloned with
--recursive
to get the nsheff/pandoc-wrapfig submodule) - Configure
mediabuilder
. The examples use an environment variable$CODEBASE
, to where you will store this repo:
export CODEBASE=`pwd`/ git clone git@github.com:nsheff/mediabuilder.git --recursive
- Clone nsheff/mediabuilder (this repository, cloned with
-
Assemble your BibTeX database (optional).
If you want to produce a media type that includes citations, you will also need a
bibtex
file with your references. My favorite BibTeX management software is JabRef, because it is free, actively developed, and uses BibTeX as its native file format. The default makefile (mediabuilder.make) will use an${BIBTEXDB}
environment variable to look for yourbibtex
database. You can set it like this:export BIBTEXDB=path/to/db.bib
-
Produce your content in markdown format.
There are working examples of different media types in the examples folder. There you can find a grant, manuscript, and CV (pending). For each example there is a basic
Makefile
, which provides examples of recipes for building different media types. For example, this will render the example manuscript:cd examples/manuscript make manuscript
This will render the
.md
manuscript source into a PDF
With these items, just follow some of the recipes below to use the mediabuilder assets to help build your output.
I've also produced docker containers for pandoc
, inkscape
, libreoffice
that make this easier if you use docker:
docker pull nsheff/pandocker
docker pull nsheff/inkscape-docker
docker pull nsheff/libre
This repository contains:
- tex_templates - a collection of tex templates for, e.g. NIH grants.
- tex_utilities - some bonus tex software to do things like add page numbers to an existing PDF
- bin - Small scripted utilities to build figures, extract bibliographies, suppress page numbers, merge PDFs, select versions of grant source files, etc. Documented in /bin/README.md.
- csl - Contains some citation styles, which are derived from the citationstyles project repository, or from Zotero collection (https://github.com/citation-style-language/styles); it's the set of styles I use frequently, with some possible additions or adjustments for particular things I need. You can use any style from that repository or define your own
- docx_templates - Word document templates for different grant agencies. To be used in YAML RMarkdown header as
output:
word_document:
reference_docx: styles.doc/NSF_grant_style.docx
Running libreoffice
on the command-line like this will silently fail if you
already have libreoffice
running. If you use a containerized version, you can
get around that issue. Use my libre
docker container so you can run it while the real one is open.
budget:
echo "Make sure libreoffice isn't already open"
libreoffice --headless --invisible --convert-to pdf \
--outdir output \
src/budget_worksheet.xlsx
To set page printing limits in libreoffice calc:
- go to View > Page Break
- now select the area to print
- choose: Format > Print Ranges > Define
pdf:
soffice --convert-to pdf output/toc.docx \
--outdir output
merge:
$(mbin)/mergepdf output/merged.pdf \
output/title_page.pdf \
output/research_proposal.pdf \
output/assembly_plan.pdf
To add page numbers:
- put the PDF document into the
tex_utilities/addpages.tex
file. - Run:
pdflatex addpages.tex
- Page numbers are added at addpages.pdf!
You can refer to figures by label instead of by number, which makes reordering figures within documents easy. It also makes it possible to move figures from one document to another without renumbering.
![\label{abstract}Fig. \ref{abstract}: Example figure](fig/example_figure.png)
Refer to figures with \ref{label}
.
By default, pandoc will include your references cited just right at the end of the document. That works for some grants, but others want a separate reference document. To accomodate this, we need to do 2 things: 1) make a bibliography-only file; 2) suppress the bibliography in the main file.
- make a bibliography-only file
I wrote a script that does this: bin/getrefs
You can run getrefs on your markdown files, and pipe the results pandoc:
getrefs document.md | pandoc ...
However, this will also include any commented references, which is probably
not what you want. So, there's a more complicated recipe in the
mediabuilder.make Makefile called refs
that will do this for you. It looks like this:
# Requires pandoc 2 with --strip-comments implemented
refs_nocomment:
pandoc --strip-comments -t markdown `$(mbin)/ver src/specific_aims` \
`$(mbin)/ver src/significance_innovation` \
`$(mbin)/ver src/aim1` `$(mbin)/ver src/aim2` `$(mbin)/ver src/aim3` | \
$(mbin)/getrefs | \
pandoc -o output/references.pdf $(PANDOC_FLAGS)
- Suppress the bibliography in the main
.md
files.
One way to do this is to use a csl
file that doesn't have a style for a
bibliography. I don't like that, though, because it requires mucking around with
style files, and you may want to produce a document with the bibliography some
time. The better alternative is this: In the file itself, put in a yaml header:
---
suppress-bibliography: True
---
Or, I also wrote a little helper script that will do this for you on-the-fly: bin/nobib. Use it like getrefs:
$(mbin)/nobib file.md | \
pandoc \
-o output/approach.pdf \
That will suppress the bibliography in the output. Done!