superphy / prairiedog

next-gen pangenome graphs for predictive genomics
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ImportError: No module named '_lzma' #119

Closed kevinkle closed 4 years ago

kevinkle commented 4 years ago

Started cropping up today for no apparent reason

platform linux -- Python 3.5.6, pytest-4.6.3, py-1.8.0, pluggy-0.12.0 -- /root/repo/.tox/py35/bin/python
cachedir: .tox/py35/.pytest_cache
rootdir: /root/repo, inifile: setup.cfg
plugins: cov-2.7.1
collecting ... collecting 30 items / 1 errors / 29 selected                                   2019-07-19 15:33:31 435521b27de6 prairiedog[1978] INFO Initializing LemonGraph object with backing file outputs/pangenome.lemongraph
collected 41 items / 2 errors / 39 selected                                    

==================================== ERRORS ====================================
___________________ ERROR collecting tests/test_graph_ref.py ___________________
ImportError while importing test module '/root/repo/tests/test_graph_ref.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
tests/test_graph_ref.py:1: in <module>
    import pandas as pd
.tox/py35/lib/python3.5/site-packages/pandas/__init__.py:55: in <module>
    from pandas.core.api import (
.tox/py35/lib/python3.5/site-packages/pandas/core/api.py:24: in <module>
    from pandas.core.groupby import Grouper, NamedAgg
.tox/py35/lib/python3.5/site-packages/pandas/core/groupby/__init__.py:1: in <module>
    from pandas.core.groupby.generic import (  # noqa: F401
.tox/py35/lib/python3.5/site-packages/pandas/core/groupby/generic.py:44: in <module>
    from pandas.core.frame import DataFrame
.tox/py35/lib/python3.5/site-packages/pandas/core/frame.py:88: in <module>
    from pandas.core.generic import NDFrame, _shared_docs
.tox/py35/lib/python3.5/site-packages/pandas/core/generic.py:71: in <module>
    from pandas.io.formats.format import DataFrameFormatter, format_percentiles
.tox/py35/lib/python3.5/site-packages/pandas/io/formats/format.py:47: in <module>
    from pandas.io.common import _expand_user, _stringify_path
.tox/py35/lib/python3.5/site-packages/pandas/io/common.py:9: in <module>
    import lzma
/.pyenv/versions/3.5.6/lib/python3.5/lzma.py:26: in <module>
    from _lzma import *
E   ImportError: No module named '_lzma'
_________________ ERROR collecting tests/test_subgraph_ref.py __________________
tests/test_subgraph_ref.py:5: in <module>
    from prairiedog.subgraph_ref import SubgraphRef
prairiedog/subgraph_ref.py:8: in <module>
    from prairiedog.graph_ref import GraphRef
prairiedog/graph_ref.py:6: in <module>
    import pandas as pd
.tox/py35/lib/python3.5/site-packages/pandas/__init__.py:55: in <module>
    from pandas.core.api import (
.tox/py35/lib/python3.5/site-packages/pandas/core/api.py:24: in <module>
    from pandas.core.groupby import Grouper, NamedAgg
.tox/py35/lib/python3.5/site-packages/pandas/core/groupby/__init__.py:1: in <module>
    from pandas.core.groupby.generic import (  # noqa: F401
.tox/py35/lib/python3.5/site-packages/pandas/core/groupby/generic.py:41: in <module>
    import pandas.core.algorithms as algorithms
E   AttributeError: module 'pandas' has no attribute 'core'

----------- coverage: platform linux, python 3.5.6-final-0 -----------
Coverage HTML written to dir htmlcov
Coverage XML written to file coverage.xml

!!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!!
=========================== 2 error in 1.16 seconds ============================
ERROR: InvocationError for command /root/repo/.tox/py35/bin/pytest -v -s --basetemp=/root/repo/.tox/py35/tmp --cov=prairiedog --cov-report=xml --cov-report=html (exited with code 2)
py36 cannot reuse: no previous config /root/repo/.tox/py36/.tox-config1
py36 create: /root/repo/.tox/py36
kevinkle commented 4 years ago

Was an issue with latest version of pandas. Setting pandas<=0.24.2 fixed it