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Compatibility issue with latest intervalltree and test suite issues #8

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tillea opened this issue Jan 28, 2019 · 1 comment
Open

Compatibility issue with latest intervalltree and test suite issues #8

tillea opened this issue Jan 28, 2019 · 1 comment

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@tillea
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tillea commented Jan 28, 2019

Hi,
thanks to the Debian Maintainer of intervaltree who submitted a patch we were able to adapt intervalltree-bio to the new interface of intervaltree. Unfortunately the test suite of intervaltree-bio is somehow inspecting also the quilt patch dir we are using in Debian for patches and is stumbling upon a file in the hidden directory .pc:

==================================== ERRORS ====================================
 ERROR collecting .pc/offline-test-data.patch/tests/genomeintervaltree_test.py _
import file mismatch:
imported module "genomeintervaltree_test" has this __file__ attribute:
  /tmp/autopkgtest-lxc.eq47c7wz/downtmp/build.ctx/src/.pc/0001-Replace-all-.search-calls-with-.overlap-in-tests-and.patch/tests/genomeintervaltree_test.py
which is not the same as the test file we want to collect:
  /tmp/autopkgtest-lxc.eq47c7wz/downtmp/build.ctx/src/.pc/offline-test-data.patch/tests/genomeintervaltree_test.py
HINT: remove __pycache__ / .pyc files and/or use a unique basename for your test file modules
=============================== warnings summary ===============================
/usr/lib/python3/dist-packages/sortedcontainers/sortedlist.py:20
  /usr/lib/python3/dist-packages/sortedcontainers/sortedlist.py:20: DeprecationWarning: Using or importing the ABCs from "collections" instead of from "collections.abc" is deprecated, and in 3.8 it will    stop working
    from collections import Sequence, MutableSequence
  /usr/lib/python3/dist-packages/sortedcontainers/sortedlist.py:20: DeprecationWarning: Using or importing the ABCs from "collections" instead of from "collections.abc" is deprecated, and in 3.8 it will    stop working
    from collections import Sequence, MutableSequence

/usr/lib/python3/dist-packages/sortedcontainers/sortedset.py:16
  /usr/lib/python3/dist-packages/sortedcontainers/sortedset.py:16: DeprecationWarning: Using or importing the ABCs from "collections" instead of from "collections.abc" is deprecated, and in 3.8 it will     stop working
    from collections import MutableSet, Sequence, Set
  /usr/lib/python3/dist-packages/sortedcontainers/sortedset.py:16: DeprecationWarning: Using or importing the ABCs from "collections" instead of from "collections.abc" is deprecated, and in 3.8 it will     stop working
    from collections import MutableSet, Sequence, Set

/usr/lib/python3/dist-packages/sortedcontainers/sorteddict.py:21
  /usr/lib/python3/dist-packages/sortedcontainers/sorteddict.py:21: DeprecationWarning: Using or importing the ABCs from "collections" instead of from "collections.abc" is deprecated, and in 3.8 it will    stop working
    from collections import ItemsView, KeysView, ValuesView, Sequence
  /usr/lib/python3/dist-packages/sortedcontainers/sorteddict.py:21: DeprecationWarning: Using or importing the ABCs from "collections" instead of from "collections.abc" is deprecated, and in 3.8 it will    stop working
    from collections import ItemsView, KeysView, ValuesView, Sequence
  /usr/lib/python3/dist-packages/sortedcontainers/sorteddict.py:21: DeprecationWarning: Using or importing the ABCs from "collections" instead of from "collections.abc" is deprecated, and in 3.8 it will    stop working
    from collections import ItemsView, KeysView, ValuesView, Sequence

-- Docs: https://docs.pytest.org/en/latest/warnings.html
!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!
===================== 7 warnings, 1 error in 0.13 seconds ======================

I have no idea why the test is checking the dir .pc nor how to fix this.
Kind regards, Andreas.
@osallou
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osallou commented Mar 9, 2019

looks like more a pytest issue looking at all _test.py files.
autopkgtest should ignore this path

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@osallou @tillea