Re: 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/153000
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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