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Updates to BiocStyle formatting

Dear Bioconductor Developers,

We would like that in the next release most of the vignettes which use BiocStyle benefit from the updated formatting introduced over the last year. For this, all BiocStyle format functions will be switched to the new style. This transition will happen on Friday, August 18.

BiocStyle 2.0

The new style was developed in collaboration with a professional graphics designer with the aim to address some of the shortcomings of the original implementation (e.g., inconsistent formatting both within the document and across output formats; non-distinctive structuring elements, for example running head and figure captions). Additionally, we introduced new features, including:

  • Common formatting regardless of input (Rnw/Rmd) and output format (PDF/HTML)
  • Consistent layout providing a clear separation between content and structuring elements emphasized by horizontal alignment
  • Standardized way of specifying author affiliations
  • Cross references in R Markdown based on the bookdown syntax
  • Support for recent additions to R Markdown (floating TOC, code folding, ...)
  • Footnotes typeset as margin notes

The updated style is invoked through BiocStyle::latex2, BiocStyle::pdf_document2 and BiocStyle::html_document2 functions. Feel free to have a look at some live examples, for example, at PureCN.pdf (PDF from Rnw source), or A-vsn.html (HTML from Rmd source).

Switch to the new style

To streamline the process, the transition will happen automatically by replacing the previous format functions by the new ones as follows. Functions whose name ends with "2": BiocStyle::latex2, BiocStyle::pdf_document2 and BiocStyle::html_document2 will be renamed by stripping the trailing "2" such that they replace their old counterparts, e.g. BiocStyle::latex. At the same time, the latter ones will be archived by appending _old to their names so that, for example, BiocStyle:latex will become BiocStyle::latex_old. Function names with the trailing "2" will be kept until the release as aliases. Both these and the "old" functions will be marked as deprecated, and made defunct after the release following the Function Deprecation Guidelines. The following list summarizes the changes.

BiocStyle::latex          -> BiocStyle::latex_old
BiocStyle::latex2         -> BiocStyle::latex

BiocStyle::pdf_document   -> BiocStyle::pdf_document_old
BiocStyle::pdf_document2  -> BiocStyle::pdf_document

BiocStyle::html_document  -> BiocStyle::html_document_old
BiocStyle::html_document2 -> BiocStyle::html_document

How does this affect me?

Scenario 1: Already using the new style (latex2, pdf_document2 or html_document2)

Congratulations, thank you for test driving the new style! Once these functions get deprecated, please rename your BiocStyle format function calls by removing the trailing "2".

Scenario 2: Currently using the original style (latex, pdf_document or html_document)

Typically, no special action will be needed. We worked hard to provide as much backwards compatibility as possible, so your vignette should compile with the new style right out of the box. However, some vignettes might require some small tweaks to build after the update. This affects mostly PDF output because of the more complex LaTeX macro definitions and the additional dependencies of the new style. Should you experience any problems, please first make sure that the source of your vignette meets the guidelines described in Bioconductor LaTeX Style 2.0 (for .Rnw vignettes) or Authoring R Markdown Vignettes (for .Rmd vignettes). Any remaining issues should be reported as a GitHub issue. As an interim solution you can still use the previous format function renamed to *_old in order to build your package.