README.md

markdown-paper

Scientific paper in markdown using LaTeX. See the pdf-directory for examples.

• markdown-talk - template for a beamer-based presentations
• markdown-letter - template for a letters
• markdown-notes - template for a notes

The source of this document is written in markdown (file paper.md) and translated to latex using pandoc and customized templates located in the templates folder. References are stored in references.bib in bibtex format.

The Makefile.template file details how the translation works.

There is a convenience script build.py that creates a Makefile from Makefile.template that is consistent with the desired template as specified in the template field in the markdown-header. All supported templates are listed in conf.py. Which template to use is specified in the header of the .md-file using the template: field. If the template is not changed, build.py does not need to be rerun but simply calling make will suffice. It is also possible to specify the desired template on the command-line using the -t <template name> option. See python build.py -h for details. Note, however, that not all variables are implemented for all templates.

If you are on linux, simply calling make in the parent directory will compile the report to a pdf-format if all dependencies are installed.

Preview of templates

Supported templates

This is a list of all supported templates along with a list of all variables defined for each template. It is generated using tools/templatevar.py and may or may not be outdated.

elife

• abstract
• acknowledgements
• additionalinformation
• affiliation.name
• affiliation.number
• author.email
• author.footnote
• author.name
• author.orcid
• bibliography
• body
• contribution
• data
• funding
• shorttitle
• title

elsevier

• abstract
• acknowledgements
• additionalinformation
• affiliation
• affiliation.name
• affiliation.number
• author-meta
• author.address
• author.email
• author.footnote
• author.name
• bibliography
• body
• citecolor
• contribution
• journal: journal name (str)
• keyword
• linkcolor
• title
• title-meta
• toc-depth
• urlcolor

scientific_reports

• abstract
• acknowledgements
• additionalinformation
• affiliation.name
• affiliation.number
• author.email
• author.footnote
• author.name
• bibliography
• body
• contribution
• keyword
• title

springer

• abstract
• acknowledgements
• additionalinformation
• author.email
• author.footnote
• author.institute
• author.name
• bibliography
• body
• documentclass_options
• journal
• keyword
• svjourstyle
• title
• toc-depth

wiley

• abbreviation
• abstract
• acknowledgements
• additionalinformation
• affiliation.name
• affiliation.number
• author
• author.email
• author.footnote
• author.institute
• author.name
• bibliography
• body
• contribution
• funding
• journalsection
• keyword
• papertype
• title

Installation

first you need LateX

brew install --cask mactex-no-gui

then add export PATH=$PATH:/Library/TeX/texbin to your .*rc and source it

with conda

conda create --name testenv pandoc pandocfilters
conda activate testenv
pip install pandoc-fignos

linux

sudo apt-get install pandoc pandoc-citeproc
pip install pandoc-fignos

Usage

1. Clone this repository

   git clone
   

2. Write paper in paper.md, refs in references.bib

3. compile with python build.py paper.md

usage: build.py [-h] [-t TEMPLATE] [-b] mdfile

positional arguments:
  mdfile

optional arguments:
  -h, --help            show this help message and exit
  -t TEMPLATE, --template TEMPLATE
                        template to use for translation
  -b, --build-makefile-only
                        build Makefile only or also run latex?

NOTE: paper.md contains example code for tables, figures, equations, references and so on.

Dependencies

• pandoc
• pandoc-fignos
• pandoc-citeproc
• a latex-distribution (e.g., texlive) including bibtex

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Matthias Mittner [email protected]