[Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

Mon Apr 2 16:32:42 CEST 2018

Hi,

Thank you for all the work in this transition Andrzej, Lori, Valerie,
Nitesh and Hervé!

I have a few questions about the new system.

1) I already had a github repo (that I manually kept in sync with the
subversion one) for the recountWorkflow. Should I just follow the
instructions at
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/?
I guess that I'll need to do this too
http://bioconductor.org/developers/how-to/git/abandon-changes/#force-bioconductor--to-github-

2) Is repo/vignettes/.html_output still needed?

3) Related to (2), the .html_output file used to ignore the `output`
line in the vignette YAML. I got an email from Lori saying that
output: BiocWorkflowTools::f1000_article is not working for
recountWorfkflow for now (no html vignette). My guess is that the
`output` line now matters, and in my case, that would build a pdf file
which is ignored due to
https://github.com/LieberInstitute/recountWorkflow/blob/master/.Rbuildignore#L12
in my .Rbuildignore.

4) Related to the last 2. What setup do you recommend so I can
maintain a single git repo that produces the files needed for
uploading them to F1000research? Before this transition, I had to
maintain 3 repos: the subversion one for Bioc, my git copy (well,
main), and another one with the files setup for F1000. At some point
in the past, Andrzej recommended that I use "output:
BiocWorkflowTools::f1000_article" to try to have all the files in 1
place. I imagine that I would still need some ifelse() statements for
sentences like the one I have at
https://github.com/LieberInstitute/recountWorkflow/blob/master/vignettes/recount-workflow.Rmd#session-information
I think that this question could be generalized and documented in the
Bioc website.

5) Is there anything else I should be aware of so I can reproduce any
errors? In the past, the Bioc workflow system would trigger a build
immediately after a new push, and due to the custom way workflows were
built (like .html_output), I relied on these builds to check if my
changes had worked or not: specially early on where I had issues with
figures, links to figures and figure captions.

Best,
Leo

On Mon, Apr 2, 2018 at 7:42 AM, Shepherd, Lori
<Lori.Shepherd at roswellpark.org> wrote:
>
> For now the page at
>
> https://www.bioconductor.org/help/workflows/
>
> will remain and be updated accordingly however there is discussion about having this page be removed or redirected.
>
>
> In the next few days I hope to have the new landing pages up and running and will make an announcement when they are live. The new changes involve having a link to the workflows on the biocViews page, that will directly link to a workflow package landing page (like the software, annotation, and experiment package do).
>
>
> Until the release your changes will be visible in devel which will transition over to the new release just as done for software packages -
>
> The workflow are built monday, wednesday, and friday and the new landing pages will reflect when the package is propagated like the other types of packages.
> http://bioconductor.org/checkResults/3.7/workflows-LATEST/
>
>
> 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 at r-project.org> on behalf of Aaron Lun <alun at wehi.edu.au>
> Sent: Sunday, April 1, 2018 2:17:09 PM
> To: Herv� Pag�s; bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)
>
> Thanks everybody, this is much appreciated.
>
> On that note, will the compiled workflows shown at:
>
> https://www.bioconductor.org/help/workflows/
>
> ... be updated to reflect changes in the git repositories for the
> workflows?
>
> Or will the workflow page just directly link to the landing page for
> each package? This would be very convenient, not least because it will
> avoid me having to make pull requests to the bioconductor.org
> repository every time I want to change my workflow blurb.
>
> I'm in the process of fixing and updating my various workflows, and I'm
> wondering when/how my changes will be visible to users.
>
> Cheers,
>
> Aaron
>
> On Fri, 2018-03-30 at 13:10 -0700, Herv� Pag�s wrote:
> > To the authors/maintainers of the workflows:
> >
> >
> > Following the svn-to-git migration of the software and data
> > experiment
> > packages last summer, we've completed the migration of the workflow
> > packages.
> >
> > The canonical location for the workflow source code now is
> > git.bioconductor.org
> >
> > Please use your git client to access/maintain your workflow the same
> > way you would do it for a software or data-experiment package.
> >
> > We've also migrated the workflows to our in-house build system.
> > Starting with Bioc 3.7, the build report for the devel versions of
> > the workflows can be found here:
> >
> >    https://bioconductor.org/checkResults/devel/workflows-LATEST/
> >
> > We run these builds every other day (Mondays, Wednesdays, Fridays).
> > Because of limited build resources, we now run the data-experiment
> > builds on Sundays, Tuesdays, and Thursdays only (instead of daily).
> >
> > The links to the package landing pages are not working yet. This
> > will be addressed in the next few days.
> >
> > Please address any error you see on the report for the workflow
> > you maintain.
> >
> > Note that, from now on, we're also following the same version scheme
> > for these packages as for the software and data-experiment packages.
> > That is, we're using an even y (in x.y.z) in release and an odd y in
> > devel. We'll take care of bumping y at release time (like we do for
> > software and data-experiment packages).
> >
> > After the next Bioconductor release (scheduled for May 1), we'll
> > start
> > building the release versions of the workflows in addition to the
> > devel versions. The build report for the release versions will be
> > here:
> >
> >    https://bioconductor.org/checkResults/release/workflows-LATEST/
> >
> > Finally, please note that with the latest version of BiocInstaller
> > (1.29.5), workflow packages can be installed with biocLite(), like
> > any other Bioconductor package. We'll deprecate the old mechanism
> > (workflowInstall()) at some point in the future.
> >
> > Thanks to Andrzej, Lori, Nitesh, and Valerie for working on this
> > migration.
> >
> > Let us know if you have any question about this.
> >
> > H.
> >
> >
>
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