GNU bug report logs - #39904
Update of python-anndata

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Roel Janssen <roel <at> roelserve.com>
To: guix-patches <at> gnu.org
Subject: Update of python-anndata
Date: Wed, 04 Mar 2020 11:25:33 +0100

[Message part 1 (text/plain, inline)]

Dear Guix,

I'd like to update our package for python-anndata.  For this I needed to add a
few more packages that are used in the test suite of python-anndata.

I attached the patches.  Note that for python-zarr I disabled the tests because
the majority of the tests need external packages.  We could add all dependencies
to make the test suite work, but that requires a significant amount of work (for
example, the Azure SDK for Python is one of the external dependencies).

Is it OK to move forward with the disabled test suite for python-zarr?

Thanks!

Kind regards,
Roel Janssen

[0004-gnu-Update-python-anndata-to-0.7.1.patch (text/x-patch, attachment)]

[0003-gnu-Add-python-zarr.patch (text/x-patch, attachment)]

[0002-gnu-Add-python-asciitree.patch (text/x-patch, attachment)]

[0001-gnu-Add-python-numcodecs.patch (text/x-patch, attachment)]

Message #10 received at 39904-close <at> debbugs.gnu.org (full text, mbox):

From: Roel Janssen <roel <at> roelserve.com>
To: 39904-close <at> debbugs.gnu.org
Subject: Re: bug#39904: Acknowledgement (Update of python-anndata)
Date: Fri, 06 Mar 2020 10:44:05 +0100

On Wed, 2020-03-04 at 15:01 +0000, GNU bug Tracking System wrote:
> Thank you for filing a new bug report with debbugs.gnu.org.
> 
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So, Ricardo has pushed similar patches in the meantime. Closing this
one.

Kind regards,
Roel Janssen

Message #13 received at 39904 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Roel Janssen <roel <at> roelserve.com>
Cc: 39904 <at> debbugs.gnu.org
Subject: Re: [bug#39904] Update of python-anndata
Date: Fri, 06 Mar 2020 23:00:55 +0100

Hi Roel,

> I'd like to update our package for python-anndata.  For this I needed to add a
> few more packages that are used in the test suite of python-anndata.

I’m sorry I missed this patch series.  I noticed that scanpy failed to
build, so I worked on upgrading it together with anndata.  I must have
started the work right before your patches came in.

> I attached the patches.  Note that for python-zarr I disabled the tests because
> the majority of the tests need external packages.  We could add all dependencies
> to make the test suite work, but that requires a significant amount of work (for
> example, the Azure SDK for Python is one of the external dependencies).

These tests that use external services (such as Azure Storage Blob,
Redis, etc) can be disabled with environment variables, which is what I
did in my version of the package definition.

--
Ricardo

Message #16 received at 39904 <at> debbugs.gnu.org (full text, mbox):

From: Roel Janssen <roel <at> roelserve.com>
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: 39904 <at> debbugs.gnu.org
Subject: Re: [bug#39904] Update of python-anndata
Date: Sat, 07 Mar 2020 09:50:19 +0100

On Fri, 2020-03-06 at 23:00 +0100, Ricardo Wurmus wrote:
> Hi Roel,
> 
> > I'd like to update our package for python-anndata.  For this I
> > needed to add a
> > few more packages that are used in the test suite of python-
> > anndata.
> 
> I’m sorry I missed this patch series.  I noticed that scanpy failed
> to
> build, so I worked on upgrading it together with anndata.  I must
> have
> started the work right before your patches came in.
> 
> > I attached the patches.  Note that for python-zarr I disabled the
> > tests because
> > the majority of the tests need external packages.  We could add all
> > dependencies
> > to make the test suite work, but that requires a significant amount
> > of work (for
> > example, the Azure SDK for Python is one of the external
> > dependencies).
> 
> These tests that use external services (such as Azure Storage Blob,
> Redis, etc) can be disabled with environment variables, which is what
> I
> did in my version of the package definition.

Thanks.

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