Re: RFS ete

2020-07-05 Thread Andreas Tille
Hi,

On Sun, Jul 05, 2020 at 06:13:36PM +0800, zhao feng wrote:
> I have merged the work into https://salsa.debian.org/med-team/python-ete3

Thanks a lot for the merge.  I was running routine-update to modernise
packaging on it and added you to Uploaders (I guess Alba is lacking
time for that package so its better to have your ID here as well).

Unfortunately the build time test is running into a failure:


dh_auto_test
I: pybuild base:217: cd 
/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/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 and not test_renderer" 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: /build/python-ete3-3.1.1+dfsg
collected 0 items / 1 errors

 ERRORS 
___ ERROR collecting .pybuild/cpython3_3.8_ete3/build/ete3/test/test_api.py 
ImportError while importing test module 
'/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/build/ete3/test/test_api.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
ete3/test/test_api.py:17: in 
from .test_treeview.test_all_treeview import *
ete3/test/test_treeview/test_all_treeview.py:10: in 
from ... import Tree, TreeStyle, NodeStyle, PhyloTree, faces, random_color
E   ImportError: cannot import name 'TreeStyle' from 'ete3' 
(/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/build/ete3/__init__.py)
--- Captured stdout 
/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/build/bin/
=== warnings summary ===
ete3/coretype/tree.py:363
  
/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/build/ete3/coretype/tree.py:363:
 DeprecationWarning: invalid escape sequence \-
"""

ete3/coretype/tree.py:434
  
/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/build/ete3/coretype/tree.py:434:
 DeprecationWarning: invalid escape sequence \-
"""Prunes the topology of a node to conserve only the selected list of leaf
...
ete3/phylomedb/phylomeDB3.py:757
  
/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/build/ete3/phylomedb/phylomeDB3.py:757:
 DeprecationWarning: invalid escape sequence \w
QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"

ete3/phylomedb/phylomeDB3.py:758
  
/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/build/ete3/phylomedb/phylomeDB3.py:758:
 DeprecationWarning: invalid escape sequence \w
QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"

-- Docs: https://docs.pytest.org/en/latest/warnings.html
!!! Interrupted: 1 errors during collection 
= 41 warnings, 1 error in 0.93 seconds =
E: pybuild pybuild:352: test: plugin distutils failed with: exit code=2: cd 
/build/python-ete3-3.1.1+dfsg/.pybuild/cpython3_3.8_ete3/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 and not test_renderer" ete3/test/test_api.py
dh_auto_test: error: pybuild --test -i python{version} -p 3.8 returned exit 
code 13


I also thin checking the DeprecationWarnings might be worth investigating.

Regarding the tests your way in d/rules looks better now.  However, what
is the motivation to exclude skbio?

Finally I'm wondering whether the binary package should be rather
Architecture: all .

Kind regards and thanks so far for your work on this

 Andreas.

-- 
http://fam-tille.de



Re: RFS ete

2020-07-05 Thread zhao feng
I have merged the work into https://salsa.debian.org/med-team/python-ete3
Detail can also be checked from https://mentors.debian.net/package/python-ete3

On Sat, Jul 4, 2020 at 11:19 PM Andreas Tille  wrote:
>
> 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 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: 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
>



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
>



Re: RFS ete

2020-07-02 Thread merkys
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



Re: RFS ete

2020-07-02 Thread zhao feng
ok, the warning has been fixed by 3.1.1-3

On Thu, Jul 2, 2020 at 5:31 PM  wrote:
>
> Hi,
>
> I have tried building the package from the packaging repository on
> salsa, however, 'upstream' and 'pristine-tar' branches are missing
> there. Could you please push them with 'salsa push' or 'git push --all
> && git push --tags'?
>
> On 2020-07-02 11:03, zhao feng wrote:
> > feng@debian:~/ete$ lintian python3-ete_3.1.1-1.1_all.deb
> > W: python3-ete: binary-without-manpage usr/bin/ete3
> > W: python3-ete: copyright-has-url-from-dh_make-boilerplate
> > W: python3-ete: description-synopsis-starts-with-article
> > W: python3-ete: executable-not-elf-or-script
> > usr/lib/python3/dist-packages/ete3/test/test_circle_label.py
> > W: python3-ete: executable-not-elf-or-script
> > usr/lib/python3/dist-packages/ete3/test/test_treeview/barchart_and_piechart_faces.py
> > W: python3-ete: executable-not-elf-or-script
> > usr/lib/python3/dist-packages/ete3/test/test_treeview/bubble_map.py
> > W: python3-ete: executable-not-elf-or-script ... use
> > --no-tag-display-limit to see all (or pipe to a file/program)
> > W: python3-ete: file-in-unusual-dir usr/ete3/tools/ete_build.cfg
> > W: python3-ete: non-standard-dir-in-usr usr/ete3/
> > W: python3-ete: package-contains-vcs-control-file
> > usr/lib/python3/dist-packages/ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore
> > feng@debian:~/ete$ lintian --version
> > Lintian v2.80.0
>
> These lintian warnings too should be fixed. Most of them are rather easy
> to fix.
>
> Best wishes,
> Andrius
>



Re: RFS ete

2020-07-02 Thread merkys
Hi,

I have tried building the package from the packaging repository on
salsa, however, 'upstream' and 'pristine-tar' branches are missing
there. Could you please push them with 'salsa push' or 'git push --all
&& git push --tags'?

On 2020-07-02 11:03, zhao feng wrote:
> feng@debian:~/ete$ lintian python3-ete_3.1.1-1.1_all.deb
> W: python3-ete: binary-without-manpage usr/bin/ete3
> W: python3-ete: copyright-has-url-from-dh_make-boilerplate
> W: python3-ete: description-synopsis-starts-with-article
> W: python3-ete: executable-not-elf-or-script
> usr/lib/python3/dist-packages/ete3/test/test_circle_label.py
> W: python3-ete: executable-not-elf-or-script
> usr/lib/python3/dist-packages/ete3/test/test_treeview/barchart_and_piechart_faces.py
> W: python3-ete: executable-not-elf-or-script
> usr/lib/python3/dist-packages/ete3/test/test_treeview/bubble_map.py
> W: python3-ete: executable-not-elf-or-script ... use
> --no-tag-display-limit to see all (or pipe to a file/program)
> W: python3-ete: file-in-unusual-dir usr/ete3/tools/ete_build.cfg
> W: python3-ete: non-standard-dir-in-usr usr/ete3/
> W: python3-ete: package-contains-vcs-control-file
> usr/lib/python3/dist-packages/ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore
> feng@debian:~/ete$ lintian --version
> Lintian v2.80.0

These lintian warnings too should be fixed. Most of them are rather easy
to fix.

Best wishes,
Andrius



Re: RFS ete

2020-07-02 Thread zhao feng
I have tried to reproduce the lintian error on my virtual machine but
I can't. I do not know what's happening with the report from
mentors.debian.net.

feng@debian:~/ete$ lintian python3-ete_3.1.1-1.1_all.deb
W: python3-ete: binary-without-manpage usr/bin/ete3
W: python3-ete: copyright-has-url-from-dh_make-boilerplate
W: python3-ete: description-synopsis-starts-with-article
W: python3-ete: executable-not-elf-or-script
usr/lib/python3/dist-packages/ete3/test/test_circle_label.py
W: python3-ete: executable-not-elf-or-script
usr/lib/python3/dist-packages/ete3/test/test_treeview/barchart_and_piechart_faces.py
W: python3-ete: executable-not-elf-or-script
usr/lib/python3/dist-packages/ete3/test/test_treeview/bubble_map.py
W: python3-ete: executable-not-elf-or-script ... use
--no-tag-display-limit to see all (or pipe to a file/program)
W: python3-ete: file-in-unusual-dir usr/ete3/tools/ete_build.cfg
W: python3-ete: non-standard-dir-in-usr usr/ete3/
W: python3-ete: package-contains-vcs-control-file
usr/lib/python3/dist-packages/ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore
feng@debian:~/ete$ lintian --version
Lintian v2.80.0

On Tue, Jun 30, 2020 at 5:02 PM  wrote:
>
> Hello,
>
> 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
>
> mentors.debian.net report lintian errors for this package. These have to
> be addressed prior to sponsoring.
>
> Best wishes,
> Andrius
>



Re: RFS ete

2020-06-30 Thread merkys
Hello,

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

mentors.debian.net report lintian errors for this package. These have to
be addressed prior to sponsoring.

Best wishes,
Andrius