[Bioc-devel] "extra" unit tests

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Fri Oct 27 16:59:39 CEST 2017


I find it really, really hard to write classic unit testing for analytical
/ methods functions.  Unit testing works well and goes a long way for the
part of our stack which is infrastructure and basic classes.  I am
concerned about to what extent our analytic stack actually gets tested
well, even within a package. I am doing some in my packages, but it was
hard and takes execution time.

I agree with Martin that we don't just want to increase the limit on build
time. Most likely that will just mean people spend less time on making
things fast for release. And by "people" I am counting myself.

Best,
Kasper

On Fri, Oct 27, 2017 at 9:49 AM, Sean Davis <seandavi at gmail.com> wrote:

> We do similar testing (mostly upstream of package building) for GEOmetadb
> and SRAdb. I have been thinking of this problem as "integration testing"
> rather than "unit testing".
>
> https://stackoverflow.com/questions/5357601/whats-the-
> difference-between-unit-tests-and-integration-tests
>
> The build system as it exists is great for unit testing, but not so much
> for integration tests. Workflow-based "testing" might fall under the
> integration testing definition. The unit testing frameworks in R (testthat,
> for example) can be applied to integration testing, but I think it is worth
> keeping the two types of testing somewhat separate for the reasons pointed
> out in the stackoverflow discussion.
>
> Sean
>
>
> On Thu, Oct 26, 2017 at 11:41 PM, Levi Waldron <
> lwaldron.research at gmail.com>
> wrote:
>
> > The specific cases I had in mind were curatedMetagenomicData and
> > curatedTCGAData - thinking that the entire databases should be downloaded
> > and syntax-checked at some point, because there could be problems either
> > with the remote data files or how the convenience downloading functions
> > process them. But they're big downloads, so it's slow and hundreds of GB
> > download.
> >
> > Regular http size and timestamp tests would be lightweight and good
> (sounds
> > doable if I don't exactly how yet). But still, in curatedTCGAData
> > especially, the post-download processing is complicated: converting
> tables
> > to SummarizedExperiment and RaggedExperiment, mapping the columns in each
> > omics data type to the clinical & pathological data, and assembling a
> > MultiAssayExperiment containing any combination of omics types for one or
> > more cancer types, and adding metadata (sorry for the shameless plug for
> > the forthcoming curatedTCGAData...). But anyways I'm not sure how to know
> > the objects will be assembled correctly without testing them in normal
> use
> > situations.
> >
> > For non wastefulness, it's actually something where a workflow-type check
> > would make sense - only run if a size, timestamp, or downloader/assembler
> > file is changed, not documentation or some other change unrelated to the
> > download & assembly.
> >
> >
> >
> > On Thu, Oct 26, 2017 at 5:11 AM, Martin Morgan <
> > martin.morgan at roswellpark.org> wrote:
> >
> > > There is currently some capacity in the build system to support
> > 'extended'
> > > builds.
> > >
> > > One possibility would be to provide facilities for packages to 'opt in'
> > to
> > > a distinct 'extended' build, with a (weekly?) build report. One could
> > also
> > > just increase the timeouts of the current builds.
> > >
> > > I think there is considerable value to imposing relatively severe time
> > and
> > > space limitations on packages. A lot of R code is very poorly written,
> > and
> > > the limits force the developer to confront that; admittedly a common
> > > response is not to write better R code. The unit test concept is really
> > > about highly focused tests on modular software; my own 'long' tests
> have
> > in
> > > retrospect often been misguided attempts to throw the kitchen sink at
> > code
> > > and hope that it covers things, rather than to decompose complicated
> > > functions into testable units that can then be assembled with some
> degree
> > > of confidence. Some of the most challenging code to test involves web
> > > services; probably the approach is not to perform numerous queries but
> to
> > > verify that that the service is responsive and providing a version that
> > > your package supports, with non-web queries validating conformance to
> the
> > > version. Often build times are dominated by vignettes analyzing 'real'
> > > data; these are probably more suited to ExperimentData packages where
> > there
> > > are already more liberal space and time limits, and where the extended
> > > computation time does not undermine the pedagogical value of easily
> > > reproduced vignette code.
> > >
> > > I wonder how many people would opt in to an extended build. That
> wasn't,
> > > for instance, what Levi asked about at the start of the thread.
> > >
> > > Martin
> > >
> > >
> > > On 10/25/2017 01:05 PM, Vincent Carey wrote:
> > >
> > >> What about some more hardware to improve throughput?  I think
> > complicating
> > >> the test
> > >> driving software is less desirable -- although perhaps it is just a
> day
> > of
> > >> week check somewhere.
> > >> I can imagine that it fails on wednesday but then passes on thursday
> and
> > >> developer ignores the event...
> > >> The failure has to become sticky.  I vote for more hardware and a
> > uniform
> > >> and stringent testing protocol.
> > >>
> > >> If there is no grant money for hardware maybe we have to look for more
> > >> commercial sponsorship.  This
> > >> part of the project should not be pinching pennies.
> > >>
> > >>
> > >> On Wed, Oct 25, 2017 at 12:56 PM, Kasper Daniel Hansen <
> > >> kasperdanielhansen at gmail.com> wrote:
> > >>
> > >> I think we need to think about this in the long term. Can we add
> support
> > >>> for these major tests in the build system, perhaps not every day, but
> > >>> every
> > >>> week or month?  The alternative, that it is up to the developer, is
> not
> > >>> great I think.  We should still advocate for people writing quicker
> > >>> tests,
> > >>> but there are some things which just take time.  The advantage of the
> > >>> build
> > >>> system is that it gets tested on the official 3 platforms, with
> > official
> > >>> setup.
> > >>>
> > >>> Best,
> > >>> Kasper
> > >>>
> > >>>
> > >>>
> > >>> On Wed, Oct 25, 2017 at 11:27 AM, Michael Lawrence <
> > >>> lawrence.michael at gene.com> wrote:
> > >>>
> > >>> Looks like BiocCodeTools should start checking whether people are
> using
> > >>>> that and at least make a NOTE of it.
> > >>>>
> > >>>> On Tue, Oct 24, 2017 at 8:17 PM, Peter Hickey <
> peter.hickey at gmail.com
> > >
> > >>>> wrote:
> > >>>>
> > >>>> A partial answer if you are using the 'testthat' framework: you can
> > use
> > >>>>> `testthat::skip_on_bioc()` to specify that a test should be skipped
> > if
> > >>>>>
> > >>>> it
> > >>>
> > >>>> is running on the BioC build machines. The test will otherwise be
> run
> > >>>>> (e.g., during local development). There are some other
> > >>>>>
> > >>>> `testthat::skip*()`
> > >>>>
> > >>>>> functions that may also be useful.
> > >>>>> Cheers,
> > >>>>> Pete
> > >>>>>
> > >>>>> On Wed, 25 Oct 2017 at 12:47 Levi Waldron <
> > lwaldron.research at gmail.com
> > >>>>>
> > >>>>
> > >>>> wrote:
> > >>>>>
> > >>>>> Any thoughts about how to implement optional or "extra" unit tests,
> > >>>>>>
> > >>>>> that
> > >>>>
> > >>>>> are too resource intensive to be part of the Bioconductor daily
> > >>>>>>
> > >>>>> builds,
> > >>>
> > >>>> but
> > >>>>>
> > >>>>>> that should be run once in a while, say with major updates?
> > >>>>>>
> > >>>>>>          [[alternative HTML version deleted]]
> > >>>>>>
> > >>>>>> _______________________________________________
> > >>>>>> Bioc-devel at r-project.org mailing list
> > >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>>>>
> > >>>>>>
> > >>>>>          [[alternative HTML version deleted]]
> > >>>>>
> > >>>>> _______________________________________________
> > >>>>> Bioc-devel at r-project.org mailing list
> > >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>>>
> > >>>>>
> > >>>>          [[alternative HTML version deleted]]
> > >>>>
> > >>>> _______________________________________________
> > >>>> Bioc-devel at r-project.org mailing list
> > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>>
> > >>>>
> > >>>          [[alternative HTML version deleted]]
> > >>>
> > >>> _______________________________________________
> > >>> Bioc-devel at r-project.org mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>
> > >>>
> > >>         [[alternative HTML version deleted]]
> > >>
> > >> _______________________________________________
> > >> Bioc-devel at r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >>
> > >
> > > This email message may contain legally privileged
> and/or...{{dropped:2}}
> > >
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> >
> >
> >
> > --
> > Levi Waldron
> > http://www.waldronlab.org
> > Assistant Professor of Biostatistics     CUNY School of Public Health
> > US: +1 646-364-9616                                           Skype:
> > levi.waldron
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> --
> Sean Davis, MD, PhD
> Center for Cancer Research
> National Cancer Institute
> National Institutes of Health
> Bethesda, MD 20892
> https://seandavi.github.io/
> https://twitter.com/seandavis12
>
>         [[alternative HTML version deleted]]
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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