Bug#861182: RFS ete
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
Bug#861182: RFS ete
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
Bug#861182: RFS ete
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
Bug#861182: RFS ete
> 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
Bug#861182: RFS ete
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
Bug#861182: RFS ete
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
