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paper

Article draft for "Global access to botanical resources: assessing the digital availability of types and specimens and open access literature"

This article repository is part of the OA-WCVP github organisation. Its sibling repositories (ipni-oa, ipni-oa-map-charts, wcvp-gbif-processing etc) are responsible for data access, analysis and visualisation; this repository integrates their archived analytical runs into the paper output.

Article structure

A separate markdown file holds the text for each of the sections in the article:

  • Summary
  • Keywords
  • Societal Impact Statement
  • Introduction
  • Materials and Methods
  • Results
  • Discussion
  • Acknowledgements
  • Author Contribution
  • Data Availability Statement
  • Conflict of Interest Statement
  • References

The document compilation process (described below) concatenates these together to form a single output.

How to use this repository

Editorial changes

Edits to the markdown source for the article can be made in github, or by cloning the repository and editing locally (allows for offline working).

Adding an author

Authors (and their affiliations) are defined in YAML in the preamble document fragment.

Document compilation

Automated compilation

A github action compiles the output document when a tag is applied to the repository. PDF and Word (.docx) versions of the article are made available as build artifacts.

Local document compilation

Pre-requisites

The article text is formatted in Markdown and is compiled to an output format (PDF, word etc) using pandoc. Execution of the compilation process is managed with the build tool make. Ensure that make, pandoc and lualatex are installed and available from your PATH, ie that you can execute the following in a shell:

  • make -v
  • pandoc -v
  • lualatex -v

Note: if you are compiling the article on Ubuntu, the pandoc version which is in the standard repository is not compatible with the lua filters that are used in this repository. Please install a more up-to-date version through the pandoc repository. The compilation is tested using Ubuntu 20.04 and pandoc version 2.19.1.

How to run the compilation

The article can be compiled into several formats, ie pdf, docx and html.

  • PDF format: make build/article.pdf or shorthand make pdf
  • docx format: make build/article.docx or shorthand make docx
  • HTML format: make build/article.html or shorthand make html
  • All formats: make all
Cleaning up downloaded and processed files
  • make clean
  • make sterilise

Useful links

Contact information

Nicky Nicolson, RBG Kew ([email protected])