[Bioc-devel] NEWS.md

[Henrik Bengtsson]

Note that in R-devel, we have that
(https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):

* news() gains support for ‘NEWS.md’ files.

That is, news(package = pkg) not only finds NEWS.md (as before) but
also parses it (into sections etc.) analogously to how it parses
NEWS.Rd and NEWS.

Because of this, I'd say a package should use only one of the NEWS,
NEWS.Rd, and NEWS.md files.

Also, I believe CRAN has parsed NEWS.md files for quite a while now
and rendered them as HTML.  I think Bioconductor should do the same
thing (sounds like this is what Lluís argued for), especially with the
new NEWS.md support by news().

/Henrik
On Tue, Sep 25, 2018 at 2:08 PM Laurent Gatto <lg390 using cam.ac.uk> wrote:
>
>
> Dear all,
>
> My experience (and things may have changed since I set this up) is that
> NEWS and NEWS.md serve different purposes despite a very similar
> syntax. The former is used by news() and displayed on the Bioconductor
> page (would NEWS.md be used if NEWS was absent?), while the one with the
> md extension displays nicely (including links) on github and in pkgdown
> sites.
>
> My solution is a Makefile recipe [1] (contributed by Sebastian Gibb)
> that converts NEWS.md into NEWS while updating the syntax and removing
> markdown links (typically to github issues, that are automatically
> expanded from #123 to a full URL via a github hook).
>
> NEWS: #' create plain text NEWS from NEWS.md if available
>         test -f ${PKGDIR}/NEWS.md && sed '/^# .*$$/d; /^## .*$$/{s/^## //g; p; s/./-/g}; /^###\+/{s/./\u&/g}; s/^##\+ //g; 1,2{/^[[:space:]]*$$/d}; s/\[\(#[0-9]\+\)\]([^)]\+)/\1/g' ${PKGDIR}/NEWS.md > ${PKGDIR}/NEWS
>
> (where ${PKGDIR} is the package directory)
>
> Unsure whether this helps or adds further to the confusion.
>
> Best wishes,
>
> Laurent
>
> [1] https://github.com/ComputationalProteomicsUnit/maker
>
>
> On 25 September 2018 13:55, Shepherd, Lori wrote:
>
> > It can be used currently.  If you remove the .md extension but keep the format in should be recognized.  As described in the ?news help page
> >
> >
> >
> >      If 'package' is '"R"' (default), a news db is built with the news
> >      since the 3.0.0 release of R (corresponding to R's top-level
> >      'NEWS' file).  Otherwise, if the given add-on package can be found
> >      in the given libraries, it is attempted to read its news in
> >      structured form from files 'inst/NEWS.Rd', 'NEWS' or 'inst/NEWS'
> >      (in that order).
> >
> >
> >
> > Please also note your news file is formatted incorrectly.  from the ?news
> >
> >
> >      The plain text 'NEWS' files in add-on packages use a variety of
> >      different formats; the default news reader should be capable to
> >      extract individual news entries from a majority of packages from
> >      the standard repositories, which use (slight variations of) the
> >      following format:
> >
> >         • Entries are grouped according to version, with version header
> >           "Changes in version" at the beginning of a line, followed by
> >           a version number, optionally followed by an ISO 8601 format
> >           date, possibly parenthesized.
> >
> >         • Entries may be grouped according to category, with a category
> >           header (different from a version header) starting at the
> >           beginning of a line.
> >
> >         • Entries are written as itemize-type lists, using one of 'o',
> >           '*', '-' or '+' as item tag.  Entries must be indented, and
> >           ideally use a common indentation for the item texts.
> >
> >
> >
> >
> > Please remove the pound sign (# ) from the header entry -  and use "Changes in version"  not "BioCor"
> >
> >
> > so for example:
> >
> >
> >
> > # BioCor 0.99.25
> >
> > * Update Vignette to just output html
> >
> > # BioCor 0.99.24
> >
> > * Submit the package to the Bioconductor project
> >
> > # BioCor 0.99.23
> >
> > * Add the Bioconductor webhook
> >
> >
> > Would become
> >
> >
> > Changes in version 0.99.25
> >
> > * Update Vignette to just output html
> >
> > Changes in version 0.99.24
> >
> > * Submit the package to the Bioconductor project
> >
> > Changes in version 0.99.23
> >
> > * Add the Bioconductor webhook
> >
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Cancer Institute
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Lluís Revilla <lluis.revilla using gmail.com>
> > Sent: Tuesday, September 25, 2018 3:20:39 AM
> > To: bioc-devel
> > Subject: [Bioc-devel] NEWS.md
> >
> > Dear Bioconductor team,
> >
> > I found that the new R version 3.5.1, to be used with the new release of
> > Bioconductor, supports the ‘NEWS.md' files.
> >
> > I updated my package (BioCor) to use `NEWS.md`. However, on the devel
> > landing page of the package stills shows the old file NEWS file. This is
> > consistent with the developer page (
> > https://www.bioconductor.org/developers/package-guidelines/#news).
> >
> > Will this be a requirement or can I keep the NEWS.md file?
> >
> > Many thanks,
> >
> > Lluís
> >
> >         [[alternative HTML version deleted]]
> >
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> >       [[alternative HTML version deleted]]
> >
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>
> --
> Laurent Gatto | @lgatt0
> http://lgatto.github.io/
>
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