An open source scientific article created using the showyourwork workflow.
Fork this repo to easily use Julia in showyourwork. The following modifications were made to the default template
(You can also see this from the Git diff)
- Defined
src/scripts/paths.jl, replacingsrc/scripts/paths.py(just a convenience file which defines paths when youinclude()it). - Created a
Project.tomlto define Julia dependencies. - Created two example scripts in
src/scripts/:data.jl, to create a dataset and save it tomydata.csv, andplot.jl, to plot the dataset and save it tomyplot.png.
- Created three Snakemake rules:
julia_manifestcreatesManifest.tomlfrom theProject.toml.datacallsdata.jl, and depends onManifest.toml.plotcallsplot.jl, and depends onmydata.csvandManifest.toml.
- Configured
showyourwork.ymlto map.jltojulia.
The Snakefile also defines the JULIA_PROJECT as ".".
These three Julia jobs are dependencies of the final rule, which compiles the LaTeX document using tectonic.
The generated PDF and arXiv tarball will contain myplot.png.
For example, the rule plot:
rule plot:
input:
"Manifest.toml",
data="src/data/mydata.csv",
output: "src/tex/figures/myplot.png"
script: "src/scripts/plot.jl"This Julia script is then able to reference the variable snakemake:
using Gadfly
using Cairo
using CSV
using DataFrames
input_fname = snakemake.input["data"]
output_fname = snakemake.output[1]
data = open(input_fname, "r") do io
CSV.read(io, DataFrame)
end
# Plot x vs y:
p = plot(data, x=:x, y=:y, Geom.line)
# Save:
draw(PNG(output_fname, 10cm, 7.5cm), p)In ms.tex, we can define the corresponding figure as:
\begin{figure}[h!]
\centering
\includegraphics[width=0.5\textwidth]{figures/myplot.png}
\caption{A figure.}
\label{fig:fig1}
\script{../scripts/plot.jl}
\end{figure}Which will add a hyperlink to the script used to generate the figure: