Hi Leo, thank you, good point! As suggested, once I make the transition I will post a note on the BiocStyle version number implementing it.
Best, Andrzej On Mon, Aug 7, 2017 at 8:32 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
