WikiPathways News

A newsletter project for WikiPathways, modeled on the CDK News newsletter (see this Wikipedia page). WikiPathways News is published as one volume per year, several issues per volume. One issue is assembled from a title page, an editorial, and one or more articles, all typeset with a shared house style defined in WPnews.sty. Issues are grouped into volumes; a volume typically has at least two issues.

All content of WikiPathways News is written by people. Originality is more important than volume. Articles will get DOIs via Zenodo and are submitted using a well-defined LaTeX or Markdown template.

Editorial policy

The WikiPathways News accepts original articles describing work involving WikiPathways. Summaries of new research articles is allowed, as well is descriptions of use cases, hackathon reports, etc. Work that has a potential to be published as journal article is discouraged. Articles are written in English. Work will be copy-edited but not peer reviewed. Software and data should be properly cited. Only CC-BY-licensed material is published.

Editorial team

• Martina Kutmon
• Egon Willighagen

Project layout

This repository holds many issues over time: vol1/issue1/, vol1/issue2/, vol2/issue1/, and so on, each an independent, standalone-buildable newsletter. Everything an issue needs that doesn't change between issues - the house style, the logo, the pandoc pipeline for Markdown-authored articles - lives once at the repository root and is shared by every issue.

WPnews.sty          House style: title page, two-column article layout,
                     \address/\email/\orcidlink/ROR/affiliation macros, etc.
WPicon.png           WikiPathways icon (CC BY-SA 4.0, Alex Pico), used on
                     the title page.
resources/           Shared pandoc template and Lua filters used by
                      Markdown-authored articles (see TECHNOLOGY.md).
Makefile              Builds every issue found under vol*/issue*/.

template/              Starting point for a new issue - copy this to start
                        vol<N>/issue<M>/ (see "Starting a new issue" below).
                        Not itself a real issue, and not built by the root
                        Makefile.

vol1/issue1/            An issue. Its content is currently placeholder
                         lipsum (https://ctan.org/pkg/lipsum) text.
vol1/issue2/, ...        More issues, added the same way over time.

Inside every issue folder (template/, and every vol<N>/issue<M>/):

newsletter.tex        Top-level document for this issue: title page +
                       \input of each article + back-page colophon.
Makefile               Builds this issue (see "Building" below).

editorial/              The issue's editorial (LaTeX).
article1/                A LaTeX-authored article.
article2/                A Markdown-authored article (converted via
                          pandoc), with a citation and reference list.
article3/                A Markdown-authored article with no citations, to
                          demonstrate a references section is optional.

Each of editorial/, article1/, article2/, article3/ is buildable standalone (producing its own wrapper.pdf) and is also pulled into the merged newsletter.pdf for that issue.

Building

Build every issue in the repository:

make            # -> vol1/issue1/newsletter.pdf, vol1/issue2/newsletter.pdf, ...
make clean      # remove build artifacts from every issue
make distclean  # clean every issue's top-level folder and every article subfolder

Build a single issue:

cd vol1/issue1 && make            # -> vol1/issue1/newsletter.pdf
cd vol1/issue1 && make update     # rebuild newsletter.pdf only (assumes articles built)
cd vol1/issue1 && make clean
cd vol1/issue1 && make distclean  # also clean every article subfolder

To work on a single article without rebuilding the whole issue:

cd vol1/issue1/article1 && make      # -> vol1/issue1/article1/wrapper.pdf
cd vol1/issue1/article2 && make      # -> vol1/issue1/article2/wrapper.pdf

Requires a TeX Live installation (lualatex, biblatex, biber) and, for Markdown-authored articles, pandoc (tested with pandoc 3.1).

Starting a new issue

cp -r template vol1/issue2   # or vol2/issue1, etc.

Then, in the new folder's newsletter.tex, fill in \volume{}, \volnumber{} and \date{} (marked VOLUME/ISSUE/MONTH YEAR in the template - these are independent of the vol<N>/issue<M> folder name, which is just this repository's own bookkeeping), replace the placeholder editorial/articles with real content (or delete an articleN/ folder and its \input line in newsletter.tex if the issue has fewer articles), and it's ready to build like any other issue - cd vol1/issue2 && make.

The copied folder's paths already point at the shared root files two levels up (../../WPnews.sty, ../../../resources/, etc.) - this only works correctly once the folder is at vol<N>/issue<M>/ (two levels below the repository root), which is why template/ itself cannot be built in place; see TECHNOLOGY.md.

Writing an article

There are two ways to author an article for an issue. Both end up as an art.tex fragment that gets \input into a wrapper.tex (for standalone builds) and into that issue's newsletter.tex (for the merged issue), inside WPnews.sty's article environment.

1. Directly in LaTeX (see article1/, editorial/)

Write art.tex using the macros WPnews.sty provides:

\title{Article Title}
\subtitle{One or two sentences describing the article.}
\author{by Jane Doe\orcidlink{0000-0003-4567-8901}}

\maketitle

\section*{Introduction}
... article text ...

\address{Jane Doe\orcidlink{0000-0003-4567-8901}\\
Some University, Some Country\\
\email{jane.doe@example.org}}

\printbibliography   % optional, needs \addbibresource{art.bib} in
                      % wrapper.tex's preamble and a matching art.bib

Add a wrapper.tex and Makefile copied from article1/ in the same issue (drop the \addbibresource/\printbibliography lines if the article has no citations, as in editorial/), then add the new folder to that issue's Makefile's separateArts/distclean targets, add \addbibresource{<folder>/art.bib} to that issue's newsletter.tex's preamble if it has one, and \input the article from newsletter.tex.

2. In Markdown, converted with pandoc (see article2/)

Write art.md with a YAML header carrying the title, subtitle, authors (with optional orcid and an affiliation index), an affiliations list (with optional ror identifiers), and an optional doi:

---
title: Article Title
doi: 10.xxxx/xxxxx
authors:
  - name: Jane Doe
    email: jane.doe@example.org
    orcid: 0000-0003-4567-8901
    affiliation: 1
affiliations:
  - name: Some University, Some Country
    index: 1
    ror: 00hx57361
---

# Introduction

Article text, with pandoc-style citations, e.g. [@usesMethodIn:LoremVis2026]
(a CiTO-annotated citation key — see TECHNOLOGY.md), resolved against a
matching `art.bib`.

That article's Makefile runs pandoc with the shared template and filters in resources/ (at the repository root) to turn art.md into an art.tex fragment in the same house style as hand-written articles — including resolved ORCID/ROR badges — and native \cite{}/\printbibliography calls that render through the same biblatex setup as LaTeX-authored articles (see TECHNOLOGY.md). Copy article2/ (in the same issue) as a starting point for a new Markdown article (note that a bib entry's citation key must be unique across every article within that issue, since all of an issue's articles' .bib files are loaded together in its newsletter.tex - keys can be reused across different issues, which never share a compilation), and wire it into that issue's Makefile/newsletter.tex the same way as above.

See TECHNOLOGY.md for how both pipelines work under the hood, and CONTRIBUTING.md for the tools used to develop and test this project.