Debian Science BoF, Debconf20

2020-07-03 Thread Anton Gladky
Dear members of Debian Science Team,

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.

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

Best regards

Anton




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Re: RFS ete

2020-07-03 Thread Andreas Tille
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: RFS ete

2020-07-03 Thread Andreas Tille
Hi,

On Tue, Jun 30, 2020 at 12:01:59PM +0300, mer...@debian.org wrote:
> On 2020-06-30 11:56, zhao feng wrote:
> > To access further information about this package, please visit the
> > following URL:
> > 
> >   https://mentors.debian.net/package/ete

I'd love to sponsor any package that is relevant for Debian Med but my
personal policy is to sponsor only from **salsa.debian.org** .  BTW,
there is an ITP for ete (#861182) which was turned into an RFP.  You
should at least claim ownership for this bug and turn it into ITP again.
 
Since the package is clearly in the scope of Debian Med I would like
you to become a member of Debian Med team and maintain the package in
the existing repository[1].

So my suggestion is the following:

   1. I've added zhaofeng to the Debian Med team (guessing its you)
   2. You push all your changes to that repository - feel free to
  be "rude" and change what you consider necessary to change,
  make you also the "Uploader"
   3. You ping me once you consider ready via the mailing list
debian-...@lists.debian.org
   4. I'll welcome you in the Debian Med team and upload the
  package (if Andrius will not beat me in this ;-) )

Does this sound like a good plan to you?

@Andrius: Thanks for keeping me in CC - I would have missed this
otherwise.

Kind regards

  Andreas.


[1] https://salsa.debian.org/med-team/python-ete3

-- 
http://fam-tille.de



Re: RFS ete

2020-07-03 Thread merkys
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



Re: RFS ete

2020-07-03 Thread zhao feng
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.
> 1. I am under the impression that the Python package should be named
> 'ete3', not 'ete'. After installing the .deb package Python command
> 'import ete3' fails.
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?

The import error has been fixed.

2-5 has been fixed now.
> 6. Please consider maintaining this package under the umbrella of Debian
> Python or Science teams. To do so, join the appropriate team, move the
> packaging repository to their namespace, and adjust Maintainer and
> Uploaders fields in debian/control.
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?

Yours
zhaofeng-shu33

On Fri, Jul 3, 2020 at 1:17 PM  wrote:
>
> Hello,
>
> On 2020-07-02 17:23, zhao feng wrote:
> > ok, the warning has been fixed by 3.1.1-3
>
> Thanks for fixing lintian issues. I have cloned your repository, tried
> to build it, and ran into the following problem:
>
>dh_auto_test -O--buildsystem=pybuild
> pybuild --test -i python{version} -p 3.8
> I: pybuild base:217: cd
> /home/andrius/debian-packages/ete/.pybuild/cpython3_3.8_ete/build;
> python3.8 -m pytest -k "not test_ncbiquery and not test_skbio and not
> test_ncbi_compare and not test_get_topology and not
> test_01tree_annotation and not test_00_update_database"
> ete3/test/test_api.py
> = test session starts
> ==
> platform linux -- Python 3.8.4rc1, pytest-4.6.11, py-1.8.1, pluggy-0.13.0
> rootdir: /home/andrius/debian-packages/ete
> plugins: timeout-1.3.3, cov-2.8.1
> collected 51 items / 6 deselected / 45 selected
>
> ete3/test/test_api.py Aborted
> E: pybuild pybuild:352: test: plugin distutils failed with: exit
> code=134: cd
> /home/andrius/debian-packages/ete/.pybuild/cpython3_3.8_ete/build;
> python3.8 -m pytest -k "not test_ncbiquery and not test_skbio and not
> test_ncbi_compare and not test_get_topology and not
> test_01tree_annotation and not test_00_update_database"
> ete3/test/test_api.py
> dh_auto_test: error: pybuild --test -i python{version} -p 3.8 returned
> exit code 13
> make: *** [debian/rules:9: build] Error 25
> dpkg-buildpackage: error: debian/rules build subprocess returned exit
> status 2
> debuild: fatal error at line 1182:
> dpkg-buildpackage -us -uc -ui -i -I failed
> gbp:error: 'debuild -i -I -uc -us' failed: it exited with 29
>
> Do you know what might be the reason?
>
> A few more issues to address to address:
>
> 1. I am under the impression that the Python package should be named
> 'ete3', not 'ete'. After installing the .deb package Python command
> 'import ete3' fails.
>
> 2. Directory 'SQLite-Levenshtein' (SQLite extension for Levenshtein
> algorithm) should not be present in the .deb package, at least not in
> its current form. However, it could be packaged separately in the future.
>
> 3. If 'SQLite-Levenshtein' remains in the source, it should be mentioned
> in debian/copyright.
>
> 4. The copyright for ETE is GPL-3+.
>
> 5. Please consider licensing debian/ directory under the same license
> too to avoid possible license incompatibilities.
>
> 6. Please consider maintaining this package under the umbrella of Debian
> Python or Science teams. To do so, join the appropriate team, move the
> packaging repository to their namespace, and adjust Maintainer and
> Uploaders fields in debian/control.
>
> Thanks for your efforts to package ete.
>
> Best wishes,
> Andrius
>