Hi Andreas,
Andreas Tille, on 2020-12-06 17:07:14 +0100:
> Permissions granted (can not do much more out of a train with bad
> connectivity)
Thanks for the permission, especially in the poor networking
conditions. I received the acknowledgement of dak, and now
python-biopython is uploaded.
Hav
Permissions granted (can not do much more out of a train with bad connectivity)
On Sun, Dec 06, 2020 at 04:17:05PM +0100, Étienne Mollier wrote:
> Hi Steffen,
>
> Steffen Möller, on 2020-12-06 15:10:52 +0100:
> > The only thing I suggest to add (to help backporting) is to add a
> > version depend
Hi Steffen,
Steffen Möller, on 2020-12-06 15:10:52 +0100:
> The only thing I suggest to add (to help backporting) is to add a
> version dependency on dssp (> 4) to help backporting since the versions
> are diverse across our releases
> (https://packages.debian.org/search?keywords=dssp&searchon=nam
Heya,
The only thing I suggest to add (to help backporting) is to add a
version dependency on dssp (> 4) to help backporting since the versions
are diverse across our releases
(https://packages.debian.org/search?keywords=dssp&searchon=names&exact=1&suite=all§ion=all).
Best,
Steffen
On 06.12.20
Good morning,
I patched python-biopython to correct #976542, which is caused
by the change of default output format in mkdssp 4.0.0, updated
last month. Changes are available on Salsa:
https://salsa.debian.org/med-team/python-biopython
I also triggered discussions with upstream to get a
Hi Steffen,
Steffen Möller, on 2020-10-17 19:54:17 +0200:
> uploaded - thank you for this, had given up on it once :)
You're welcome, thanks for the upload. :)
Cheers,
--
Étienne Mollier
Old rsa/3072: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d
New rsa/4096: 8f91 b227 c7d6 f2b1 948c 8
uploaded - thank you for this, had given up on it once :)
On 17.10.20 14:25, Étienne Mollier wrote:
> Hello,
>
> I prepared an update of python-biopython 1.78+dfsg-3, to address
> #972381 mainly, but it also includes pending removal of some
> makeblastdb overrides. The package is available on Sal
Hello,
I prepared an update of python-biopython 1.78+dfsg-3, to address
#972381 mainly, but it also includes pending removal of some
makeblastdb overrides. The package is available on Salsa for
review and upload:
https://salsa.debian.org/med-team/python-biopython/
The changelog is:
*
Étienne Mollier writes:
> Many, many thanks for your swift update.
No problem.
> I'm reverting most of
> my changes to python-biopython 1.78+dfsg-3 packaging to make
> sure no overrides risk interferring with your tuning during the
> build or autopkgtest, and bump the requirements to ncbi-blast
Hi Aaron,
Aaron M. Ucko, on 2020-10-05 08:57:43 -0400:
> u...@debian.org (Aaron M. Ucko) writes:
>
> > issue a give-back request for python-biopython on mipsel once a suitable
> > new BLAST+ build is available there.
>
> Update: The new BLAST+ build showed up overnight (from my time zone,
> anyw
u...@debian.org (Aaron M. Ucko) writes:
> issue a give-back request for python-biopython on mipsel once a suitable
> new BLAST+ build is available there.
Update: The new BLAST+ build showed up overnight (from my time zone,
anyway) as expected, and python-biopython's mipsel status changed from
"Fa
Étienne Mollier writes:
>
> https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=mipsel&ver=1.78%2Bdfsg-2&stamp=1601713196&raw=0
Thanks for the report! I don't have access to any buildd servers, but I
was able to reproduce makeblastdb failures with current defaults on the
Hi Andreas,
Andreas Tille, on 2020-10-03 10:06:59 +0200:
> uploaded. Thanks a lot for caring for the migration of this
> important package
Thank you as well for the upload. Alas the build log still
looks like the run chokes on makeblastdb memory commit issues.
:(
==
Hi Étienne,
uploaded. Thanks a lot for caring for the migration of this
important package
Andreas.
On Sat, Oct 03, 2020 at 12:08:42AM +0200, Étienne Mollier wrote:
> Hi All,
>
> I think these changes to python-biopython stalled on my machine
> for long enough. The release 1.78+dfsg-2 re
Hi All,
I think these changes to python-biopython stalled on my machine
for long enough. The release 1.78+dfsg-2 reverts the works
around makeblastdb issues on various architectures, and bumps
version requirement to ncbi-blast+ >= 2.10.1-2 instead. This
should allow Biopython to get its missing
Hi Andreas,
Andreas Tille, on 2020-09-14 13:51:18 +0200:
> Hi Étienne,
>
> thanks a lot for your work on this. My suggestions for changes are so
> unimportant that I do not want to rebuild just to fix these.
You're welcome, thank you for your insights and the upload!
> Please add some DEP3 des
Hi Étienne,
thanks a lot for your work on this. My suggestions for changes are so
unimportant that I do not want to rebuild just to fix these.
On Sun, Sep 13, 2020 at 07:17:03PM +0200, Étienne Mollier wrote:
> I have the following lintian warning, which I am not sure what
> to do with. I believ
Greetings,
I pulled Biopython 1.78 into Salsa, and tried to make sure the
continuous integration pipeline went to green. The package
seems to be in almost good condition to reach Sid to me. As
always, I am not against a rereading, I wouldn't be surprised to
learn I missed points while proceeding
Hi Étienne,
On Wed, Jun 17, 2020 at 09:20:37AM +0200, Étienne Mollier wrote:
> > I've just uploaded (today the build went smoothly).
>
> Thank you for the review and upload. :)
You are more than welcome. :-)
> > Thanks a lot for your investigation
>
> You're welcome. Next in my to do list i
Hi Andreas,
Andreas Tille, on 2020-06-17 08:05:57 +0200:
> On Tue, Jun 16, 2020 at 10:41:28PM +0200, Étienne Mollier wrote:
> > I pushed a little change in the d/control file of the package
> > python-biopython in version 1.77+dfsg-2. This was the suggested
> > way to address the bug #962944:
> >
Hi Étienne,
On Tue, Jun 16, 2020 at 10:41:28PM +0200, Étienne Mollier wrote:
> I pushed a little change in the d/control file of the package
> python-biopython in version 1.77+dfsg-2. This was the suggested
> way to address the bug #962944:
>
> https://bugs.debian.org/cgi-bin/bugreport.cgi
Howdy,
I pushed a little change in the d/control file of the package
python-biopython in version 1.77+dfsg-2. This was the suggested
way to address the bug #962944:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962944
I couldn't reproduce any particular problem with the few last
rou
Étienne Mollier, on 2020-06-16 18:51:52 +0200:
> I'm on it. I'm a bit unsure of the maximum possible, but having
> left my machine compute rosetta jobs for more than 80
> consecutive days, all I can say is that the limit is well over
> the million.
It is pid_max according to Linux documentation,
Hi Andrius,
mer...@debian.org, on 2020-06-16 19:46:00 +0300:
> Hi Étienne,
>
> On 2020-06-16 19:41, Étienne Mollier wrote:
> > As a side note, I remarked that t_coffee dislikes it when its
> > PID is greater than 26:
> >
> > $ t_coffee -version
> > PROGRAM: T-COFFEE Version_13.41.0.28
Hi Étienne,
On 2020-06-16 19:41, Étienne Mollier wrote:
> As a side note, I remarked that t_coffee dislikes it when its
> PID is greater than 26:
>
> $ t_coffee -version
> PROGRAM: T-COFFEE Version_13.41.0.28bdc39 (2019-11-30 10:21:53 -
> Revision 5d5a1c1 - Build 465)
>
>
Greetings,
mer...@debian.org, on 2020-06-15 14:48:07 +0300:
> On 2020-06-12 20:40, Steffen Möller wrote:
> > I found this
> >
> > Bio.PDB.mmtf docstring test ... skipped, missing Python dependency
> > Bio.PDB.mmtf.DefaultParser docstring test ... skipped, missing Python
> > dependency
> > Bio.PDB
On 2020-06-12 20:40, Steffen Möller wrote:
> I found this
>
> Bio.PDB.mmtf docstring test ... skipped, missing Python dependency
> Bio.PDB.mmtf.DefaultParser docstring test ... skipped, missing Python
> dependency
> Bio.PDB.mmtf.mmtfio docstring test ... skipped, missing Python dependency
>
> to s
On 2020-06-12 20:40, Steffen Möller wrote:
> to suggest packaging https://github.com/rcsb/mmtf-python - sigh. Any
> takers? Would be quite a fit for next week's hackathon, I presume.
FYI, python3-mmtf has just been mentioned as required by Debichem team.
A RFP bug has just been opened [1]. I am mi
Hello,
I need to thank you for this update. I had not looked at BioPython for a
lnnggg time. Pretty impressive how it all developed.
I found this
Bio.PDB.mmtf docstring test ... skipped, missing Python dependency
Bio.PDB.mmtf.DefaultParser docstring test ... skipped, missing Python
depen
On 12.06.20 18:39, Étienne Mollier wrote:
Hi Steffen,
Steffen Möller, on 2020-06-12 18:31:57 +0200:
I am at it - do you mind me adding you to the list of maintainers?
I suppose you meant the Uploaders field ? Sure, if it helps.
;) it helped in the past - also @Pranav and @Nilesh, you have
Hi Steffen,
Steffen Möller, on 2020-06-12 18:31:57 +0200:
> I am at it - do you mind me adding you to the list of maintainers?
I suppose you meant the Uploaders field ? Sure, if it helps.
Kind Regards,
--
Étienne Mollier
Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d
Help fi
I am at it - do you mind me adding you to the list of maintainers?
Best,
Steffen
On 11.06.20 23:54, Étienne Mollier wrote:
Greetings,
While working on #960756[1] affecting src:python-biopython[2] on
32bit architecture CPUs, uscan caught a newer version of the
library. So I took the liberty o
Greetings,
While working on #960756[1] affecting src:python-biopython[2] on
32bit architecture CPUs, uscan caught a newer version of the
library. So I took the liberty of upgrading the package at the
same time to version 1.77.
[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960756
[2] http
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