Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Andreas Tille]

Hi,

Am Mon, Oct 18, 2021 at 02:57:00AM +0530 schrieb Nilesh Patra:
> No worries, I have done so, and pushed my changes to:
> https://salsa.debian.org/science-team/python-pulp
> I really, _really_ need reviews. The very odd thing here is same content in
> postrm and prerm, and no update-alternatives for installing in postinst --
> I admit, I do not understand pulp very well,
> hence would want reviews.

While Steffen has uploaded meanwhile I think we can remove postrm and
prerm in the next revision.
 
Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Steffen Möller]

Hi Nilesh,

On 17.10.21 23:27, Nilesh Patra wrote:

Hi Steffen,

On Mon, 18 Oct 2021 at 01:41, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote:


On 17.10.21 21:39, Nilesh Patra wrote:

Hi Steffen,

On Mon, 18 Oct 2021 at 01:06, Steffen Möller
mailto:steffen_moel...@gmx.de>> wrote:


On 17.10.21 21:19, Nilesh Patra wrote:

Yeah, snakemake has now moved to pulp 2.0. pulp had another
rev-dep on congress which is now removed from archive.
pulp is maintained in openstack, and I sent out an email to
zigo and openstack-list asking to upgrade,

cf:
https://lists.debian.org/debian-openstack/2021/10/msg1.html




I had been there and already got a reply from zigo (June this
year) that we can go ahead with an update since pulp is (no
longer?) used with Open Stack. I never got around to it,
though. I Just paste our exchange below (don't expect anyone
to mind).

Wonderful, thanks for pasting this!
Are you at it? -- If you could do the needful and upload  :)


Sorry for disappointing you but I am afraid I need to concentrate
on something else this week.


No worries, I have done so, and pushed my changes to:
https://salsa.debian.org/science-team/python-pulp

I really, _really_ need reviews. The very odd thing here is same
content in postrm and prerm, and no update-alternatives for installing
in postinst -- I admit, I do not understand pulp very well,
hence would want reviews.

Could you/someone else please, please take a look and upload?
And oh, BTW I added you in the uploaders field since you planned to
takeover this.


Uploaded.

lintian -i preferred the removal in prerm. So, it is a bit redundant
now. I thought this was fine, though. Is anyone continuing the update of
snakemake now?

Best,
Steffen

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Nilesh Patra]

Hi Steffen,

On Mon, 18 Oct 2021 at 01:41, Steffen Möller  wrote:

>
> On 17.10.21 21:39, Nilesh Patra wrote:
>
> Hi Steffen,
>
> On Mon, 18 Oct 2021 at 01:06, Steffen Möller 
> wrote:
>
>>
>> On 17.10.21 21:19, Nilesh Patra wrote:
>>
>> Yeah, snakemake has now moved to pulp 2.0. pulp had another rev-dep on
>> congress which is now removed from archive.
>> pulp is maintained in openstack, and I sent out an email to zigo and
>> openstack-list asking to upgrade,
>>
>> cf: https://lists.debian.org/debian-openstack/2021/10/msg1.html
>>
>> I had been there and already got a reply from zigo (June this year) that
>> we can go ahead with an update since pulp is (no longer?) used with Open
>> Stack. I never got around to it, though. I Just paste our exchange below
>> (don't expect anyone to mind).
>>
> Wonderful, thanks for pasting this!
> Are you at it? -- If you could do the needful and upload  :)
>
> Sorry for disappointing you but I am afraid I need to concentrate on
> something else this week.
>

No worries, I have done so, and pushed my changes to:
https://salsa.debian.org/science-team/python-pulp
I really, _really_ need reviews. The very odd thing here is same content in
postrm and prerm, and no update-alternatives for installing in postinst --
I admit, I do not understand pulp very well,
hence would want reviews.

Could you/someone else please, please take a look and upload?
And oh, BTW I added you in the uploaders field since you planned to
takeover this.

Thanks!!!
Nilesh

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Steffen Möller]

On 17.10.21 21:39, Nilesh Patra wrote:

Hi Steffen,

On Mon, 18 Oct 2021 at 01:06, Steffen Möller mailto:steffen_moel...@gmx.de>> wrote:


On 17.10.21 21:19, Nilesh Patra wrote:

Yeah, snakemake has now moved to pulp 2.0. pulp had another
rev-dep on congress which is now removed from archive.
pulp is maintained in openstack, and I sent out an email to zigo
and openstack-list asking to upgrade,

cf:
https://lists.debian.org/debian-openstack/2021/10/msg1.html



I had been there and already got a reply from zigo (June this
year) that we can go ahead with an update since pulp is (no
longer?) used with Open Stack. I never got around to it, though. I
Just paste our exchange below (don't expect anyone to mind).

Wonderful, thanks for pasting this!
Are you at it? -- If you could do the needful and upload  :)


Sorry for disappointing you but I am afraid I need to concentrate on
something else this week.

Best,
Steffen

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Nilesh Patra]

Hi Steffen,

On Mon, 18 Oct 2021 at 01:06, Steffen Möller  wrote:

>
> On 17.10.21 21:19, Nilesh Patra wrote:
>
> Yeah, snakemake has now moved to pulp 2.0. pulp had another rev-dep on
> congress which is now removed from archive.
> pulp is maintained in openstack, and I sent out an email to zigo and
> openstack-list asking to upgrade,
>
> cf: https://lists.debian.org/debian-openstack/2021/10/msg1.html
>
> I had been there and already got a reply from zigo (June this year) that
> we can go ahead with an update since pulp is (no longer?) used with Open
> Stack. I never got around to it, though. I Just paste our exchange below
> (don't expect anyone to mind).
>
Wonderful, thanks for pasting this!
Are you at it? -- If you could do the needful and upload  :)

Nilesh

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Steffen Möller]

On 17.10.21 21:19, Nilesh Patra wrote:

On 10/18/21 12:13 AM, Rebecca N. Palmer wrote:

On 15/10/2021 14:46, Andreas Tille wrote:

Hi Rebecca

and whoever might care.  As usual snakemake is troublesome to upgrade.
I have injected the latest version into Git but there are lots of
failed tests.  It would be great if someone could care about this.

I hadn't tried to upgrade snakemake because python-pulp is too old
(#963041).


Yeah, snakemake has now moved to pulp 2.0. pulp had another rev-dep on
congress which is now removed from archive.
pulp is maintained in openstack, and I sent out an email to zigo and
openstack-list asking to upgrade,

cf: https://lists.debian.org/debian-openstack/2021/10/msg1.html


I had been there and already got a reply from zigo (June this year) that
we can go ahead with an update since pulp is (no longer?) used with Open
Stack. I never got around to it, though. I Just paste our exchange below
(don't expect anyone to mind).

On 6/8/21 1:40 PM, Steffen Möller wrote:


Hi Thomas,

Am 07.06.2021 um 09:05 schrieb Thomas Goirand:

On 6/5/21 7:52 PM, Steffen Möller wrote:

Hello,

pulp is outdated. Would you mind updating it or having me update it?
There is no immediate reason for me to update that version, the error I
was looking for that made me check the version but then turned out to be
elsewhere.

Since I do not run OpenStack myself, I cannot test the effect of such a
version bump and would hence prefer the OpenStack team to address this
or to guide me towards it.

Cheers,
Steffen


Hi,

I don't think anything from OpenStack uses python-pulp, so feel free to
take over the package if you care for it.

Cheers,

Thomas Goirand

Ah, nice. That makes it easy. I had a first attempt last week and found
the branch structure of your current repository to be incompatible with
git-buildpackage (under my hands) and hence with tools like
routine-update. For Debian Med (and increasingly Debian Science)
routine-update is helping a lot, the automation also eases team
maintenance. Hence, if you do not mind, I would leave everything intact
for the OpenStack repository, copy'n'paste into a new repository that
Debian Science an.

Best,
Steffen


Hi,

FYI, the only thing you got to do is have this in your ~/.gbp.conf:

[DEFAULT]
builder = sbuild --source-only-changes
cleaner = /bin/true
ignore-branch = True
pristine-tar = False
no-create-orig = True
[buildpackage]
export-dir = ../build-area/

The important bit is the ignore-branch and pristine-tar. IMO, these
options should be by default in gbp, otherwise one has to maintain it in
all of the repositories, and for a large amount of packages, that's too
much (useless) work...

Cheers,

Thomas Goirand (zigo)




The test failures look like this isn't the only problem, [...]


ACK.
Thanks a lot for your work!


Yip! Many thanks also from my side.

Steffen

Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Nilesh Patra]

On 10/18/21 12:13 AM, Rebecca N. Palmer wrote:

On 15/10/2021 14:46, Andreas Tille wrote:

Hi Rebecca

and whoever might care.  As usual snakemake is troublesome to upgrade.
I have injected the latest version into Git but there are lots of
failed tests.  It would be great if someone could care about this.

I hadn't tried to upgrade snakemake because python-pulp is too old (#963041).


Yeah, snakemake has now moved to pulp 2.0. pulp had another rev-dep on congress 
which is now removed from archive.
pulp is maintained in openstack, and I sent out an email to zigo and 
openstack-list asking to upgrade,

cf: https://lists.debian.org/debian-openstack/2021/10/msg1.html


The test failures look like this isn't the only problem, [...]


ACK.
Thanks a lot for your work!

Nilesh




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Re: Lagging behind several versions for snakemake - lots of failed tests in latest version

[Rebecca N. Palmer]

On 15/10/2021 14:46, Andreas Tille wrote:

Hi Rebecca

and whoever might care.  As usual snakemake is troublesome to upgrade.
I have injected the latest version into Git but there are lots of
failed tests.  It would be great if someone could care about this.

Kind regards

   Andreas.



I hadn't tried to upgrade snakemake because python-pulp is too old 
(#963041).


The test failures look like this isn't the only problem, but it is the 
one I'm not allowed to fix myself.

Re: Why is isal limited to just three archs?

[Nilesh Patra]

Hi Thomas,

On 10/16/21 4:07 PM, Graham Inggs wrote:

Hi,

Did you look into the source package? isal is written in assembly
language...

I see at least an erasure_code/ppc64le directory.

I did a quick test build in Ubuntu and the package built and passed
its tests on armhf, ppc64el and riscv64, failing only because of
missing symbols.  Perhaps the reduced libisal2.symbols.arm64 can be
used for other architectures as well?


After Graham's tests, would it be possible to extend the arch list?
I could help test it across more archs if you would like -- porter boxes to 
rescue :)

Nilesh




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Re: RFH: Getting fastp building on more archs

[Andrius Merkys]

Hi Nilesh,

On 2021-10-16 11:44, Nilesh Patra wrote:
> Hi Andrius, the reason is quoted below (reply from zigo on -python)
> 
>> Hi,
>>
>> Did you look into the source package? isal is written in assembly
>> language... 

On the same thread Graham reported success in building isal on armhf,
ppc64el and riscv64. This gives some hope for fastp as well.

Best,
Andrius