Published manuscript can be found here:
Gulcay, Ezgi, Paul Iacomi, Youngsang Ko, Jong-San Chang, Guillaume Rioland, Sabine Devautour-Vinot, and Guillaume Maurin. ‘Breaking the Upper Bound of Siloxane Uptake: Metal–Organic Frameworks as an Adsorbent Platform’. Journal of Materials Chemistry A, 2021, 10.1039.D1TA02275J. https://doi.org/10.1039/D1TA02275J.
- The main manuscript/SI file, written in Latex
- A host of other formats:
- PDF, compiling Latex for final manuscripts
- DOCX, for sharing with collaborators
- HTML, for online publishing on a static website
The Latex manuscript can also be stripped and simplified for a 1-file submission to a journal accepting this format. Check out the PDF manuscript and its SI.
- latexmk - for pdf compilation
- python3.6+ - for running consolidations scripts
- git-latexdiff - for pdf diffs
- pandoc - for conversion to html/docx/odt/md
- inkscape - converting any svgs to png/pdf
This project relies on the following folder organisation:
├─ Makefile # makefile for building
├─ manuscript.tex # manuscript file (!do not add content here)
├─ manuscript-si.tex # SI manuscript file (!do not add content here)
├─ manuscript-pd.tex # special pandoc manuscript file (!do not add content here)
│
├───docs # main manuscript .tex files (!content goes here)
│ └───SI # manuscript SI .tex files (!SI content goes here)
├───figs # manuscript figures
├───refs # bibtex references
├───scripts # general scripts live here
│ └───pandoc-scholar # custom fork of `pandoc-scholar`
└───templates # latex/doc templates
├───acs # ACS Latex template
├───els # Elsevier Latex template
├───pandoc # pandoc templates
├───pi # personal latex template
└───rsc # RSC Latex template
Following make commands are available:
make build
: will use latexmk to compile the manuscript and SI
make svg2fig
: will use inkscape to convert svg to png+pdf
make tex2md
: convert tex manuscript to markdown for a pandoc
make diff
: convert tex manuscript to markdown for a pandoc
make submit-condense
: condense the manuscript into one single file/folder for journal submission
make submit-zip
: zip all needed files from previous step
make submit-clean
: delete all files from condensing command
A clean and modern paper template, which would not look out of place in a contemporary academic journal. The template class itself is a submodule which can be found in another repo
Template options include:
- One or two column display with the
twocolumn
switch. - Include a table of contents "highlight" image, with the
toc
switch. - Academic affiliation in a footnote (standard) or below the
authors in the title, with the
affiltop
switch. - Line numbering for revisions with the
lineno
switch. - Format change for communication or review-type articles
with the
commun
andreview
switches. - An option to generate a Supplemental Information PDF, by creating a separate
file and using the
SI
class switch. The figures and tables in the SI can then be referenced in the main manuscript. Warning: you should compile the SI first!
The default template can be switched to other templates for common journals
(such as RSC, Elsevier and ACS). In the manuscript.tex
file, the \style{}
command controls this.
A single file exists for storing all metadata ./templates/metadata
. Once
declared here, they will be used in all individual templates.
Python scripts are provided to merge all latex files in a single file and then archive it alongside data, figures and references, often the choice for most journals. The scripts are not foolproof, but should work for most cases. Three scripts are provided with the following roles:
condense
will join all files in a single TEX file, remove any non-essential code, then create a directory./processed/
with the only the basic files needed to compile the PDF.zip
will create an archive with the basic project files in the./processed/
directory. No PDF files will be included!clean
will delete all the output of the above scripts.
PDFs which show differences between current and previous manuscript state can be
generated using
git-latexdiff, which is a
layer of abstraction around git
and latexdiff
. For example:
git latexdiff master HEAD --main manuscript.tex --pdf-viewer sumatrapdf --latexmk