Re: RFS ete

2020-07-04 Thread Andreas Tille
Hi,

On Sat, Jul 04, 2020 at 10:48:13PM +0800, zhao feng wrote:
> > The package at
> >
> >  https://salsa.debian.org/med-team/python-ete3
> >
> > builds but is also not finished yet.  I do not remember what had stopped
> > me from finalising and uploading.  Please checkout and moreover if you
> > talk next time about "ete packaging repositor" provide a link. :-)
> 
> Thanks for your information. I have not noticed the existing RFP and
> have issued an ITP
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963732.
> Should I close the ITP I issued ? I wonder how to turn the RFP into ITP.

I do not really mind.  May be merging both bugs is the technical correct
way to go.

> I have created a personal repository at
> https://salsa.debian.org/zhaofeng-shu33-guest/ete/ and the ci passes
> https://salsa.debian.org/zhaofeng-shu33-guest/ete/-/pipelines/152628.
> The package has been uploaded to https://mentors.debian.net/package/ete.

As I said I do not require sponsees to upload to mentors.  The rationale
is that I sometimes want to change things quickly and directly - thus I
always sponsor from salsa repository.

> I am intending to merge these works into
> https://salsa.debian.org/med-team/python-ete3.

Yes, please do so.
 
> Some technical aspect of merging these two repos:
> I have found that med-team/python-ete3 repo uses some patches to deal
> with the offline testing problems. I think there is a more elegant way
> to handle this obstacle.

As I tried to express: Feel free to take over your solution.  There is
no point in sticking to not so good solutions just because they were
invented once.

> To summarize the way: using pytest instead of unittest.
> For more detail, see
> https://lists.debian.org/debian-python/2020/06/msg00035.html.
> So I am planning to override med-team/python-ete3 testing rule by
> using the one of zhaofeng-shu33-guest/ete/.

Yep.  Please go for it! :-)

> For other parts, I think it is not difficult to merge.

Sounds good.

Kind regards

   Andreas.

-- 
http://fam-tille.de



Re: RFS ete

2020-07-04 Thread zhao feng
> The package at
>
>  https://salsa.debian.org/med-team/python-ete3
>
> builds but is also not finished yet.  I do not remember what had stopped
> me from finalising and uploading.  Please checkout and moreover if you
> talk next time about "ete packaging repositor" provide a link. :-)

Thanks for your information. I have not noticed the existing RFP and
have issued an ITP
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=963732.
Should I close the ITP I issued ? I wonder how to turn the RFP into ITP.

I have created a personal repository at
https://salsa.debian.org/zhaofeng-shu33-guest/ete/ and the ci passes
https://salsa.debian.org/zhaofeng-shu33-guest/ete/-/pipelines/152628.
The package has been uploaded to https://mentors.debian.net/package/ete.
I am intending to merge these works into
https://salsa.debian.org/med-team/python-ete3.

Some technical aspect of merging these two repos:
I have found that med-team/python-ete3 repo uses some patches to deal
with the offline testing problems. I think there is a more elegant way
to handle this obstacle.
To summarize the way: using pytest instead of unittest.
For more detail, see
https://lists.debian.org/debian-python/2020/06/msg00035.html.
So I am planning to override med-team/python-ete3 testing rule by
using the one of zhaofeng-shu33-guest/ete/.
For other parts, I think it is not difficult to merge.

Yours
zhaofeng-shu33


On Sat, Jul 4, 2020 at 1:17 AM Andreas Tille  wrote:
>
> On Fri, Jul 03, 2020 at 05:10:32PM +0300, mer...@debian.org wrote:
> > On 2020-07-03 13:50, zhao feng wrote:
> > > Thanks for your help. I can build the package on buster and bullyseye.
> > > Which distribution do you use? I find the version of softwares like
> > > python is quite new.
> >
> > The package fails to build on clean sid chroot. Most likely some Python
> > dependencies are missing from debian/control.
>
> The package at
>
>https://salsa.debian.org/med-team/python-ete3
>
> builds but is also not finished yet.  I do not remember what had stopped
> me from finalising and uploading.  Please checkout and moreover if you
> talk next time about "ete packaging repositor" provide a link. :-)
>
> > By the way, packaging of 'ete3' seems to be ongoing in Debian Med team
> > as well (adding Andreas in CC):
> > https://salsa.debian.org/med-team/python-ete3. I suggest getting in
> > touch with them to keep duplicate efforts minimal.
>
> Definitely.  Thanks for spotting.
>
> Kind regards
>
>  Andreas.
>
> --
> http://fam-tille.de



Re: Debian Science BoF, Debconf20

2020-07-04 Thread Andreas Tille
Hi Anton,

On Fri, Jul 03, 2020 at 09:44:40PM +0200, Anton Gladky wrote:
> I am going to submit a proposal for a BoF (birds of feather) for a
> DebConf20, where Debian Science Team members and other people can meet
> and discuss topics, connected to the Debian Science and similar.
> 
> If somebody wants to join as a co-author, feel free to drop me an email.
> Deadline is 5th of July.

Feel free to add me as co-author.
 
> Also I have prepared here a page [1], where everybody can add a topic to
> discuss (please do not forget to add your name/nick).
> 
> [1] https://pad.systemli.org/p/mvSA33-2dCXhpZz9DChG
 
Nice.

Looking forward to see you "at DebConf" ;-)

 Andreas.

-- 
http://fam-tille.de



Re: RFS ete

2020-07-04 Thread Andreas Tille
On Sat, Jul 04, 2020 at 06:44:29PM +0800, zhao feng wrote:
> 
> > By the way, packaging of 'ete3' seems to be ongoing in Debian Med team
> > as well (adding Andreas in CC):
> > https://salsa.debian.org/med-team/python-ete3. I suggest getting in
> > touch with them to keep duplicate efforts minimal.
> If no further problem exists, I will consider merging the efforts of
> https://salsa.debian.org/med-team/python-ete3 with my repo in the next
> step.

Great.  Just let me know if you might face any trouble.

Kind regards

  Andreas.

-- 
http://fam-tille.de



Re: RFS ete

2020-07-04 Thread zhao feng
> The package fails to build on clean sid chroot. Most likely some Python
> dependencies are missing from debian/control.

I have reproduced the problem both in gitlab ci
(https://salsa.debian.org/zhaofeng-shu33-guest/ete/-/jobs/844865) and
my local docker env (debian:sid).
After verbosing pytest, I find the `render` command crashes the Python
interpreter. This may due to non-gui docker, which is not reproducible
in gui-vm or normal desktop environment.

```
ete3/test/test_api.py::Test_Coretype_Tree::test_treeid PASSED

 [ 95%]
ete3/test/test_api.py::Test_Coretype_Tree::test_ultrametric PASSED

 [ 97%]
ete3/test/test_api.py::Test_Coretype_Treeview::test_renderer Aborted
(core dumped)
```

> I see you have named the repository 'ete3'. This means you want to name
> the source package 'ete3' as well, or was this unintentional?

I create the repository name by mistake.

> The copyright entry for 'SQLite-Levenshtein' seems still missing from
> debian/copyright. Could you please add it?
This part is in public domain, claimed by the author. I am confused
how to write proper paragraph in `debian/copyright`
(https://salsa.debian.org/zhaofeng-shu33-guest/ete/-/blob/master/debian/copyright#L18).

> By the way, packaging of 'ete3' seems to be ongoing in Debian Med team
> as well (adding Andreas in CC):
> https://salsa.debian.org/med-team/python-ete3. I suggest getting in
> touch with them to keep duplicate efforts minimal.
If no further problem exists, I will consider merging the efforts of
https://salsa.debian.org/med-team/python-ete3 with my repo in the next
step.

Yours
zhaofeng-shu33

On Fri, Jul 3, 2020 at 10:10 PM  wrote:
>
> On 2020-07-03 13:50, zhao feng wrote:
> > Thanks for your help. I can build the package on buster and bullyseye.
> > Which distribution do you use? I find the version of softwares like
> > python is quite new.
>
> The package fails to build on clean sid chroot. Most likely some Python
> dependencies are missing from debian/control.
>
> > The upstream uses `ete` as the name of repository but they call the
> > Python package `ete3`. In their paper, they explain the number 3 is
> > the version and in their roadmap they plan to release `ete4`.
> > (https://github.com/etetoolkit/ete/wiki/ROADMAP). I think using a
> > version independent name like `ete` for source package and
> > `python3-ete` for library is convenient. How to do think about it?
>
> I agree that the source package could stay named 'ete'. However, after
> reading the Debian Python naming conventions [1] I became even more
> convinced to name the package 'python3-ete3'.
>
> [1]
> https://www.debian.org/doc/packaging-manuals/python-policy/module_packages.html#package_names
>
> > 2-5 has been fixed now.
>
> The copyright entry for 'SQLite-Levenshtein' seems still missing from
> debian/copyright. Could you please add it?
>
> > I have created a directory in
> > https://salsa.debian.org/science-team/ete3 but I do not have
> > privileges to create a branch. Can you help on it?
>
> I see you have named the repository 'ete3'. This means you want to name
> the source package 'ete3' as well, or was this unintentional?
>
> By the way, packaging of 'ete3' seems to be ongoing in Debian Med team
> as well (adding Andreas in CC):
> https://salsa.debian.org/med-team/python-ete3. I suggest getting in
> touch with them to keep duplicate efforts minimal.
>
> Best wishes,
> Andrius
>