[Debian-med-packaging] Bug#878498: snakemake FTBFS with Python 3.6 as default

[Kevin Murray]

Hi All

On 08:18 10/12/17, Andreas Tille wrote:
> Ping, could you please throw at least any ENOTIME error.  We should get
> at least *any* working snakemake out.  If I get no response from you
> I'll upload the old version with fixed build system and leave the work
> to get the new version out to somebody else who might have some fun
> later. ;-)

Many apologies, I'm writing my PhD thesis at the moment and everything else has been dropped for the last (and next) 6 months. So it's largely an ENOTIME from me, sorry.

That said...

> On Fri, Dec 08, 2017 at 09:18:42AM +0100, Andreas Tille wrote:
> > Hi,
> > 
> > On Thu, Dec 07, 2017 at 10:49:57AM +0500, Andrey Rahmatullin wrote:
> > > > I've upgraded snakemake in Git to latest upstream but its featuring the
> > > > same issue.  I'm pretty sure you Python people know a simple answer for
> > > > this issue.
> > > Did you see this part?
> > > 
> > > > > The problem is the the following line in debian/rules:
> > > > > 
> > > > >   export PATH:=$(CURDIR)/.pybuild/pythonX.Y_3.5/build/bin:$(PATH)

Ah yes, this is because snakemake expects to have pip installed itself before testing, which requires this hack.

<snip>

> > The problem is that when trying to build this I get a lot of errors in
> > the build time tests.  Is there any volunteer to have a look?

I've gone thru a laptop change since last building Debian packages, so don't have a dev environment set up. If you send me the logs / link to them if they've gone thru the CI infrastructure, I'll take a quick look for anything obvious.

Cheers,
K

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Kevin Murray