Re: Please upgrade ncbi-blast+ and ncbi-entrez-direct to latest versions

[Andreas Tille]

On Tue, Jan 26, 2021 at 08:26:05AM -0500, Aaron M. Ucko wrote:
> 
> I'm already working on ncbi-entrez-direct, and should be able to take
> care of ncbi-blast+ as well.

Thanks a lot!
 
   Andreas. 

-- 
http://fam-tille.de

Re: Please upgrade ncbi-blast+ and ncbi-entrez-direct to latest versions

[Aaron M. Ucko]

Andreas Tille  writes:

> our outdated table[1] that there are updates for ncbi-blast+ and
> ncbi-entrez-direct avialable.  Will you be able to update these right in
> time for the freeze?

Hi, Andreas.

I'm already working on ncbi-entrez-direct, and should be able to take
care of ncbi-blast+ as well.

Thanks for checking, and for pointing out the new ncbi-blast+ release,
which I had previously missed.

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu

Re: Any volunteer to evaluate/fix Python3.9 issues in python-cogent?

[Andreas Tille]

Hi Michael,

On Tue, Jan 26, 2021 at 12:30:58PM +0100, Michael Crusoe wrote:
> > FYI: python-cogent requires numba, numba (which is a just-in-time compiler
> > for Python) got removed from testing for not supporting Python 3.9 yet.
> >
> > They finally backported a patch for numba, but the numba armhf tests are
> > failing https://qa.debian.org/excuses.php?package=numba They tried to
> > work around that with the last upload
> > https://tracker.debian.org/news/1222710/accepted-numba-0520-2-source-into-unstable/
> > but that didn't work yet.

I wonder whether we really need any software related to numerical computing
on armhf - but that's another issue.

> > Python-cogent also depends on jupyter-sphinx and that package is also in a
> > tough place: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=950598

Hmmm.

> and the 'ipywidgets.embed' issue remains with the latest release of
> jupyter-sphinx (I just tested locally)
> 
> ModuleNotFoundError: No module named 'ipywidgets.embed'

Ahhh, OK, I see python-cogent is not even in testing so while it would
be great to have there is no point in excluding it from there.

Thanks a lot for your analysis (and for sure any helping hand to fix
the predependencies is welcome).

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Any volunteer to evaluate/fix Python3.9 issues in python-cogent?

[Michael Crusoe]

On Tue, 26 Jan 2021 at 12:27, Michael Crusoe 
wrote:

> FYI: python-cogent requires numba, numba (which is a just-in-time compiler
> for Python) got removed from testing for not supporting Python 3.9 yet.
>
> They finally backported a patch for numba, but the numba armhf tests are
> failing https://qa.debian.org/excuses.php?package=numba They tried to
> work around that with the last upload
> https://tracker.debian.org/news/1222710/accepted-numba-0520-2-source-into-unstable/
> but that didn't work yet.
>
> Python-cogent also depends on jupyter-sphinx and that package is also in a
> tough place: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=950598
>

and the 'ipywidgets.embed' issue remains with the latest release of
jupyter-sphinx (I just tested locally)

ModuleNotFoundError: No module named 'ipywidgets.embed'

Re: Any volunteer to evaluate/fix Python3.9 issues in python-cogent?

[Michael Crusoe]

FYI: python-cogent requires numba, numba (which is a just-in-time compiler
for Python) got removed from testing for not supporting Python 3.9 yet.

They finally backported a patch for numba, but the numba armhf tests are
failing https://qa.debian.org/excuses.php?package=numba They tried to work
around that with the last upload
https://tracker.debian.org/news/1222710/accepted-numba-0520-2-source-into-unstable/
but that didn't work yet.

Python-cogent also depends on jupyter-sphinx and that package is also in a
tough place: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=950598

On Tue, 26 Jan 2021 at 12:03, Andreas Tille  wrote:

> Hi,
>
> python-cogent is not yet explicitly supporting Python3.9 and the
> packaging was excluding Python3.9 installation.  I removed this
> exclusion[1] since it makes cogent useless in Bullseye.  However, there
> are not really unexpected issues in the test suite.  Any volunteer to at
> least check the amount of work to port to Python3.9 and provide some
> patch for upstream?
>
> Kind regards
>
>  Andreas.
>
> [1]
> https://salsa.debian.org/med-team/python-cogent/-/commit/d0322de57301d93607fb72543894a5873bec372e
>
> --
> http://fam-tille.de
>
>

-- 
Michael R. Crusoe
Co-founder & Lead,
Common Workflow Language project 
https://orcid.org/-0002-2961-9670
m...@commonwl.org

Any volunteer to evaluate/fix Python3.9 issues in python-cogent?

[Andreas Tille]

Hi,

python-cogent is not yet explicitly supporting Python3.9 and the
packaging was excluding Python3.9 installation.  I removed this
exclusion[1] since it makes cogent useless in Bullseye.  However, there
are not really unexpected issues in the test suite.  Any volunteer to at
least check the amount of work to port to Python3.9 and provide some
patch for upstream?

Kind regards

 Andreas.

[1] 
https://salsa.debian.org/med-team/python-cogent/-/commit/d0322de57301d93607fb72543894a5873bec372e

-- 
http://fam-tille.de

Please upgrade ncbi-blast+ and ncbi-entrez-direct to latest versions

[Andreas Tille]

Hi Aaron,

we are approaching the Bullseye freeze and it would be great if we could
update our important packages to the latest versions.  I've noticed in
our outdated table[1] that there are updates for ncbi-blast+ and
ncbi-entrez-direct avialable.  Will you be able to update these right in
time for the freeze?

Kind regards

Andreas.

https://salsa.debian.org/med-team/community/helper-scripts/-/blob/master/outdated_med-packages.txt#L26

-- 
http://fam-tille.de