[Bioc-devel] Best practice on commit

Hervé Pagès hpages at fredhutch.org
Thu Mar 15 16:26:40 CET 2018


Just to clarify, all software packages are built and checked every
night, independently of whether their version got bumped or not.
The version bump only allows the modified package to propagate
to the public repo and become available via biocLite(), possibly
replacing the previous version of the package (if one is already

The package landing page on the website should reflect what's in
the public repo for a given BioC version at any time (the landing
pages can lag behind by about 20 min which is the time it takes
to regenerate all the package landing pages after the daily package


On 03/15/2018 07:15 AM, Tyler Smith wrote:
> On Sun, Mar 11, 2018, at 4:10 AM, Egon Willighagen wrote:
>> But previously I learned that when you push
>> something to the repository, you should bump the question, so currently I
>> do this for every change I made, leaving a ridiculous number of minor
>> release and really short NEWS entries...
> I wondered about this, particularly for the NEWS entries. What I have been doing is bumping the version number for each commit - to make sure that the checks on the server get run - but collapsing multiple version bullets into a single NEWS item. i.e., my NEWS looks like:
> ++++
> Changes in version 1.5.6 (2018-03-08)
> -------------------------------------
> User Visible Changes:
>      * BUG FIX: the G2 peak of the B sample was not getting incorporated
>        into model construction, which caused model fitting to fail on
>        samples with histograms skewed towards the left.
>      * Updated DebrisModel documentation.
> Internal Changes:
>      * Fixed broken test.
> Changes in version 1.5.3 (2018-01-17)
> -------------------------------------
> ++++
> I think that will be more convenient for users, who won't care that the bug fix, updated documentation, and fixed test were actually three different commits. If they do want that level of detail, that information is available directly from the repository. And from my perspective, I definitely wanted to bump the version for at least the test fix and the bug fix, to make sure that the server-side tests were run.
> Best,
> Tyler
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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