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Bug#861182: RFS ete

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  Bug#861182: RFS ete Andreas Tille <tille@debian.org> - 2020-07-03 19:30 +0200
    Bug#861182: RFS ete zhao feng <zhaofengshu33@gmail.com> - 2020-07-04 17:00 +0200
      Bug#861182: RFS ete Andreas Tille <andreas@an3as.eu> - 2020-07-04 17:30 +0200
        Bug#861182: RFS ete zhao feng <zhaofengshu33@gmail.com> - 2020-07-05 12:20 +0200
          Bug#861182: RFS ete Andreas Tille <andreas@an3as.eu> - 2020-07-05 12:40 +0200
            Bug#861182: Bug#963732: RFS ete zhao feng <zhaofengshu33@gmail.com> - 2020-07-05 14:00 +0200
              Bug#963732: RFS ete Andreas Tille <andreas@an3as.eu> - 2020-07-05 15:40 +0200
                Bug#861182: Bug#963732: RFS ete zhao feng <zhaofengshu33@gmail.com> - 2020-07-06 04:10 +0200
                  Bug#861182: Bug#963732: RFS ete Andreas Tille <andreas@fam-tille.de> - 2020-07-06 08:30 +0200

#1016354 — Bug#861182: RFS ete

On Fri, Jul 03, 2020 at 05:10:32PM +0300, merkys@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

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#1016477

> 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 <tille@debian.org> wrote:
>
> On Fri, Jul 03, 2020 at 05:10:32PM +0300, merkys@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

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#1016483

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

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#1016566

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 <andreas@an3as.eu> 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

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#1016572

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 <module>
    from .test_treeview.test_all_treeview import *
ete3/test/test_treeview/test_all_treeview.py:10: in <module>
    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

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#1016592 — Bug#861182: Bug#963732: RFS ete

Got it, thanks!

I have enabled the pipeline in one fork
https://salsa.debian.org/zhaofeng-shu33-guest/python-ete3/-/pipelines/15300
0
and I think the build error does not exist any more.

> I also thin checking the DeprecationWarnings might be worth investigating.
This may be related with some upstream code problem. Do you think it
is necessary to write patches for test warning?

> Regarding the tests your way in d/rules looks better now.  However, what
> is the motivation to exclude skbio?
I haven't noticed that `python3-skbio` is available in testing. Now it
is added back.

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

On Sun, Jul 5, 2020 at 6:36 PM Andreas Tille <andreas@an3as.eu> wrote:
>
> 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 <module>
>     from .test_treeview.test_all_treeview import *
> ete3/test/test_treeview/test_all_treeview.py:10: in <module>
>     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

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#1016602 — Bug#963732: RFS ete

On Sun, Jul 05, 2020 at 07:49:41PM +0800, zhao feng wrote:
> I have enabled the pipeline in one fork
> https://salsa.debian.org/zhaofeng-shu33-guest/python-ete3/-/pipelines/153000
> and I think the build error does not exist any more.

Yes, I've uploaded now.
 
> > Finally I'm wondering whether the binary package should be rather
> > Architecture: all .
> Done

Uploaded.  Unfortunately I realised to late that the python3-*
dependencies are not resolved automatically.  I've added these manually
in Git and will upload with the source-only upload that is needed after
the package is accepted.

Thanks for your work on this

     Andreas.

PS: Future discussion is better on debian-med@lists.debian.org.
    In case you might have other packages that are interesting for
    bioinformatics please also do this in Debian Med team.

-- 
http://fam-tille.de

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#1016721 — Bug#861182: Bug#963732: RFS ete

Thanks a lot!

> Uploaded.  Unfortunately I realised to late that the python3-*
> dependencies are not resolved automatically.  I've added these manually
> in Git and will upload with the source-only upload that is needed after
> the package is accepted.

To run the unittest we need some more dependencies like `scipy`, `qt`
but they are optional for the runtime of `ete3`.
That is, users can still use some API of `ete3` without `qt`, `skbio `.

On Sun, Jul 5, 2020 at 9:31 PM Andreas Tille <andreas@an3as.eu> wrote:
>
> On Sun, Jul 05, 2020 at 07:49:41PM +0800, zhao feng wrote:
> > I have enabled the pipeline in one fork
> > https://salsa.debian.org/zhaofeng-shu33-guest/python-ete3/-/pipelines/153000
> > and I think the build error does not exist any more.
>
> Yes, I've uploaded now.
>
> > > Finally I'm wondering whether the binary package should be rather
> > > Architecture: all .
> > Done
>
> Uploaded.  Unfortunately I realised to late that the python3-*
> dependencies are not resolved automatically.  I've added these manually
> in Git and will upload with the source-only upload that is needed after
> the package is accepted.
>
> Thanks for your work on this
>
>      Andreas.
>
> PS: Future discussion is better on debian-med@lists.debian.org.
>     In case you might have other packages that are interesting for
>     bioinformatics please also do this in Debian Med team.
>
> --
> http://fam-tille.de

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#1016735 — Bug#861182: Bug#963732: RFS ete

On Mon, Jul 06, 2020 at 10:00:38AM +0800, zhao feng wrote:
> > Uploaded.  Unfortunately I realised to late that the python3-*
> > dependencies are not resolved automatically.  I've added these manually
> > in Git and will upload with the source-only upload that is needed after
> > the package is accepted.
> 
> To run the unittest we need some more dependencies like `scipy`, `qt`
> but they are optional for the runtime of `ete3`.
> That is, users can still use some API of `ete3` without `qt`, `skbio `.

So I turned these into Recommends now.

Kind regards

       Andreas.

-- 
http://fam-tille.de

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