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nipy / nipype

Workflows and interfaces for neuroimaging packages
https://nipype.readthedocs.org/en/latest/
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Test failure when installing from latest Nipype master branch #2189

Closed mick-d closed 7 years ago

mick-d commented 7 years ago

Summary

Nipype testing failed almost immediately after fresh install from latest Nipype master branch

Actual behavior

❯ python -c "import nipype; nipype.test()"
======================================================================================================= test session starts ========================================================================================================
platform linux -- Python 3.5.2, pytest-3.2.2, py-1.4.34, pluggy-0.4.0
rootdir: /home/userx, inifile:
collecting 54 items / 1 errors                                                                                                                                                                                                      
============================================================================================================== ERRORS ==============================================================================================================
_________________________________________________________ ERROR collecting python_envs/sci35pype/lib/python3.5/site-packages/nipype/algorithms/tests/test_auto_ErrorMap.py _________________________________________________________
python_envs/sci35pype/lib/python3.5/site-packages/nipype/algorithms/tests/test_auto_ErrorMap.py:2: in <module>
    from nipype.testing import assert_equal
E   ImportError: cannot import name 'assert_equal'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
=

Expected behavior

TEST: OK

How to replicate the behavior

Script/Workflow details

Cf code above

Platform details:

Please paste the output of: python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"

{'traits_version': '4.6.0', 'nibabel_version': '2.1.0', 'sys_version': '3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:53:06) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]', 'scipy_version': '0.19.1', 'sys_platform': 'linux', 'nipype_version': '1.0.0-dev', 'networkx_version': '1.11', 'numpy_version': '1.13.1', 'sys_executable': '/home/userx/python_envs/sci35pype/bin/python', 'commit_source': 'installation', 'pkg_path': '/home/userx/python_envs/sci35pype/lib/python3.5/site-packages/nipype', 'commit_hash': '20b25da'}
1.0.0-dev

Execution environment

Conda environment

# packages in environment at /home/userx/python_envs/sci35pype:
#
_nb_ext_conf              0.3.0                    py35_0  
anaconda-client           1.5.1                    py35_0  
bzip2                     1.0.6                         3  
cairo                     1.12.18                       6  
click                     6.7                       <pip>
clyent                    1.2.2                    py35_0  
curl                      7.49.1                        1    conda-forge
cycler                    0.10.0                   py35_0  
dbus                      1.10.10                       0  
decorator                 4.1.2                     <pip>
decorator                 4.0.10                   py35_0  
dipy                      0.11.0                    <pip>
entrypoints               0.2.2                    py35_0  
expat                     2.1.0                         0  
fontconfig                2.11.1                        6  
freeglut                  3.0.0                         4    conda-forge
freetype                  2.5.5                         1  
funcsigs                  1.0.2                     <pip>
funcsigs                  0.4                      py35_0  
future                    0.16.0                    <pip>
future                    0.15.2                   py35_0    conda-forge
glib                      2.43.0                        1  
gsl                       1.16                          1    r
gst-plugins-base          1.8.0                         0  
gstreamer                 1.8.0                         0  
h5py                      2.6.0               np111py35_2  
harfbuzz                  0.9.35                        6    r
hdf5                      1.8.17                        7    conda-forge
icu                       54.1                          0  
ipykernel                 4.5.0                    py35_0  
ipython                   5.1.0                    py35_0  
ipython_genutils          0.1.0                    py35_0  
ipywidgets                5.2.2                    py35_0  
jinja2                    2.8                      py35_1  
joblib                    0.11                     py35_0  
jpeg                      9b                            0    conda-forge
jsoncpp                   0.10.6                        1    conda-forge
jsonschema                2.5.1                    py35_0  
jupyter                   1.0.0                    py35_3  
jupyter_client            4.4.0                    py35_0  
jupyter_console           5.0.0                    py35_0  
jupyter_core              4.2.0                    py35_0  
libffi                    3.2.1                         0  
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libiconv                  1.14                          3    conda-forge
libpng                    1.6.22                        0  
libsodium                 1.0.10                        0  
libtiff                   4.0.6                         7    conda-forge
libxcb                    1.12                          1  
libxml2                   2.9.2                         0  
libxslt                   1.1.28                        0  
lxml                      4.0.0                     <pip>
lxml                      3.6.4                    py35_0  
markupsafe                0.23                     py35_2  
matplotlib                1.5.1               np111py35_0  
metakernel                0.14.0                    <pip>
mistune                   0.7.3                    py35_0  
mkl                       11.3.3                        0  
mock                      2.0.0                     <pip>
nb_anacondacloud          1.2.0                    py35_0  
nb_conda                  2.0.0                    py35_0  
nb_conda_kernels          2.0.0                    py35_0  
nbconvert                 4.2.0                    py35_0  
nbformat                  4.1.0                    py35_0  
nbpresent                 3.0.2                    py35_0  
ncurses                   5.9                           8    r
networkx                  1.11                     py35_0  
nibabel                   2.1.0                    py35_0    conda-forge
nibabel                   2.1.0                     <pip>
nilearn                   0.2.5                    py35_1    conda-forge
nipype                    1.0.0.dev0                <pip>
nose                      1.3.7                    py35_1  
notebook                  4.2.3                    py35_0  
numpy                     1.13.1                    <pip>
numpy                     1.11.2                   py35_0  
octave_kernel             0.16.1                    <pip>
openssl                   1.0.2j                        0  
pandas                    0.19.0              np111py35_0  
pango                     1.36.8                        3    r
path.py                   8.2.1                    py35_0  
pbr                       3.1.1                     <pip>
pcre                      8.38                          1    conda-forge
pexpect                   4.0.1                    py35_0  
pickleshare               0.7.4                    py35_0  
pip                       9.0.1                    py35_1  
pixman                    0.32.6                        0    conda-forge
prompt_toolkit            1.0.8                    py35_0  
prov                      1.4.0                    py35_1    conda-forge
prov                      1.5.0                     <pip>
psutil                    5.0.1                    py35_0  
ptyprocess                0.5.1                    py35_0  
py                        1.4.34                    <pip>
pydicom                   0.9.9                    py35_0    conda-forge
pydotplus                 2.0.2                    py35_0    conda-forge
pygments                  2.1.3                    py35_0  
pyparsing                 2.1.4                    py35_0  
pyqt                      4.11.4                   py35_1    conda-forge
pytest                    3.2.2                     <pip>
python                    3.5.2                         0  
python-dateutil           2.6.1                     <pip>
python-dateutil           2.5.3                    py35_0  
pytz                      2016.7                   py35_0  
pyyaml                    3.12                     py35_0  
pyzmq                     16.0.0                   py35_0  
qt                        4.8.7                         3  
qtconsole                 4.2.1                    py35_0    conda-forge
r                         3.3.1                  r3.3.1_0    r
r-assertthat              0.1                    r3.3.1_4    r
r-base                    3.3.1                         1    r
r-base64enc               0.1_3                  r3.3.1_0    r
r-bh                      1.60.0_2               r3.3.1_0    r
r-bitops                  1.0_6                  r3.3.1_2    r
r-boot                    1.3_18                 r3.3.1_0    r
r-cairo                   1.5_9                  r3.3.1_0    r
r-car                     2.1_2                  r3.3.1_0    r
r-caret                   6.0_70                 r3.3.1_0    r
r-catools                 1.17.1                 r3.3.1_2    r
r-chron                   2.3_47                 r3.3.1_0    r
r-class                   7.3_14                 r3.3.1_0    r
r-cluster                 2.0.4                  r3.3.1_0    r
r-codetools               0.2_14                 r3.3.1_0    r
r-colorspace              1.2_6                  r3.3.1_0    r
r-crayon                  1.3.1                  r3.3.1_0    r
r-curl                    0.9.7                  r3.3.1_0    r
r-data.table              1.9.6                  r3.3.1_0    r
r-dbi                     0.4_1                  r3.3.1_0    r
r-dichromat               2.0_0                        1a    r
r-digest                  0.6.9                  r3.3.1_0    r
r-dplyr                   0.4.3                  r3.3.1_0    r
r-essentials              1.4.3                  r3.3.1_0    r
r-evaluate                0.9                    r3.3.1_0    r
r-foreach                 1.4.3                  r3.3.1_0    r
r-foreign                 0.8_66                 r3.3.1_0    r
r-formatr                 1.4                    r3.3.1_0    r
r-ggplot2                 2.1.0                  r3.3.1_0    r
r-gistr                   0.3.6                  r3.3.1_0    r
r-glmnet                  2.0_5                  r3.3.1_0    r
r-gtable                  0.2.0                  r3.3.1_0    r
r-hexbin                  1.27.1                 r3.3.1_0    r
r-highr                   0.6                    r3.3.1_0    r
r-htmltools               0.3.5                  r3.3.1_0    r
r-htmlwidgets             0.6                    r3.3.1_0    r
r-httpuv                  1.3.3                  r3.3.1_0    r
r-httr                    1.2.0                  r3.3.1_0    r
r-irdisplay               0.4.3                  r3.3.1_2    r
r-irkernel                0.7                    r3.3.1_2    r
r-iterators               1.0.8                  r3.3.1_0    r
r-jsonlite                0.9.22                 r3.3.1_0    r
r-kernsmooth              2.23_15                r3.3.1_0    r
r-knitr                   1.13                   r3.3.1_0    r
r-labeling                0.3                    r3.3.1_2    r
r-lattice                 0.20_33                r3.3.1_0    r
r-lazyeval                0.2.0                  r3.3.1_0    r
r-lme4                    1.1_12                 r3.3.1_0    r
r-magrittr                1.5                    r3.3.1_2    r
r-maps                    3.1.0                  r3.3.1_0    r
r-markdown                0.7.7                  r3.3.1_2    r
r-mass                    7.3_45                 r3.3.1_0    r
r-matrix                  1.2_6                  r3.3.1_0    r
r-matrixmodels            0.4_1                  r3.3.1_0    r
r-memoise                 1.0.0                  r3.3.1_0    r
r-mgcv                    1.8_12                 r3.3.1_0    r
r-mime                    0.4                    r3.3.1_0    r
r-minqa                   1.2.4                  r3.3.1_2    r
r-munsell                 0.4.3                  r3.3.1_0    r
r-nlme                    3.1_128                r3.3.1_0    r
r-nloptr                  1.0.4                  r3.3.1_2    r
r-nnet                    7.3_12                 r3.3.1_0    r
r-openssl                 0.9.4                  r3.3.1_0    r
r-pbdzmq                  0.2_3                  r3.3.1_0    r
r-pbkrtest                0.4_6                  r3.3.1_0    r
r-plyr                    1.8.4                  r3.3.1_0    r
r-pryr                    0.1.2                  r3.3.1_0    r
r-quantmod                0.4_5                  r3.3.1_2    r
r-quantreg                5.26                   r3.3.1_0    r
r-r6                      2.1.2                  r3.3.1_0    r
r-randomforest            4.6_12                 r3.3.1_0    r
r-rbokeh                  0.4.2                  r3.3.1_0    r
r-rcolorbrewer            1.1_2                  r3.3.1_3    r
r-rcpp                    0.12.5                 r3.3.1_0    r
r-rcppeigen               0.3.2.8.1              r3.3.1_0    r
r-recommended             3.3.1                  r3.3.1_0    r
r-repr                    0.7                    r3.3.1_0    r
r-reshape2                1.4.1                  r3.3.1_2    r
r-rmarkdown               0.9.6                  r3.3.1_0    r
r-rpart                   4.1_10                 r3.3.1_0    r
r-scales                  0.4.0                  r3.3.1_0    r
r-shiny                   0.13.2                 r3.3.1_0    r
r-sparsem                 1.7                    r3.3.1_0    r
r-spatial                 7.3_11                 r3.3.1_0    r
r-stringi                 1.1.1                  r3.3.1_0    r
r-stringr                 1.0.0                  r3.3.1_0    r
r-survival                2.39_4                 r3.3.1_0    r
r-tibble                  1.0                    r3.3.1_0    r
r-tidyr                   0.5.1                  r3.3.1_0    r
r-ttr                     0.23_1                 r3.3.1_0    r
r-uuid                    0.1_2                  r3.3.1_0    r
r-xtable                  1.8_2                  r3.3.1_0    r
r-xts                     0.9_7                  r3.3.1_2    r
r-yaml                    2.1.13                 r3.3.1_2    r
r-zoo                     1.7_13                 r3.3.1_0    r
rdflib                    4.2.2                     <pip>
readline                  6.2                           2  
requests                  2.11.1                   py35_0  
scikit-learn              0.18                np111py35_0  
scipy                     0.19.1                    <pip>
scipy                     0.18.1              np111py35_0  
seaborn                   0.7.1                    py35_0  
setuptools                27.2.0                   py35_0  
simplegeneric             0.8.1                    py35_1  
simplejson                3.11.1                    <pip>
simplejson                3.10.0                   py35_0  
sip                       4.18                     py35_0  
six                       1.10.0                   py35_0  
six                       1.11.0                    <pip>
sqlite                    3.13.0                        0  
terminado                 0.6                      py35_0  
tk                        8.5.18                        0  
tornado                   4.4.2                    py35_0  
traitlets                 4.3.1                    py35_0  
traits                    4.6.0                    py35_0  
vtk                       7.0.0                    py35_1    conda-forge
wcwidth                   0.1.7                    py35_0  
wheel                     0.29.0                   py35_0  
widgetsnbextension        1.2.6                    py35_0  
xlrd                      1.0.0                    py35_0  
xvfbwrapper               0.2.8                    py35_0    conda-forge
xz                        5.2.2                         0  
yaml                      0.1.6                         0  
zeromq                    4.1.5                         0  
zlib                      1.2.8                         3
djarecka commented 7 years ago

I can't see nipype/algorithms/tests/test_auto_ErrorMap.py in the current master. Are you sure it's not your test?

mick-d commented 7 years ago

Thanks @djarecka for looking into it. Somehow it seems that merging the new master into an old nipype repo did not delete some of the old test files (such as test_auto_ErrorMap.py), which is quite strange. Wiping out this old repository fixed the issue, thanks a lot.