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Bug#861182: RFS ete

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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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Thread

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

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