Hi Andrzej, Could you let us know when you make the change which BiocStyle version implemented the change? That way we can update our description files.
In the meantime, I switched my vignettes to use BiocStyle::html_document2 although I need to use figure captions and references to take advantage of all the things html_document2 has to offer. Best, Leo On Mon, Aug 7, 2017 at 8:05 AM, Andrzej Oleś <andrzej.o...@gmail.com> wrote: > 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]( > http://bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/PureCN.pdf) > (PDF from Rnw source), or [A-vsn.html]( > http://bioconductor.org/packages/devel/bioc/vignettes/vsn/inst/doc/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]( > http://bioconductor.org/developers/how-to/deprecation/). 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]( > https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/LatexStyle2.pdf) > (for .Rnw vignettes) or [Authoring R Markdown Vignettes]( > https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html) > (for .Rmd vignettes). Any remaining issues should be reported as a [GitHub > issue](https://github.com/Bioconductor/BiocStyle/issues). As an interim > solution you can still use the previous format function renamed > to `*_old` in order to build your package. > > > Kind regards, > Andrzej Oleś > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
