Console Output
Started by GitHub push by SKrywinski
Building remotely on Rechenknecht in workspace /mnt/data/jenkins/workspace/DARIAH-Topics
> /usr/bin/git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
> /usr/bin/git config remote.origin.url git://github.com/DARIAH-DE/Topics # timeout=10
Fetching upstream changes from git://github.com/DARIAH-DE/Topics
> /usr/bin/git --version # timeout=10
using GIT_ASKPASS to set credentials
> /usr/bin/git fetch --tags --progress git://github.com/DARIAH-DE/Topics +refs/heads/*:refs/remotes/origin/*
> /usr/bin/git rev-parse refs/remotes/origin/testing^{commit} # timeout=10
> /usr/bin/git rev-parse refs/remotes/origin/origin/testing^{commit} # timeout=10
Checking out Revision 6951841891e07d6dd5eadeb09c897aa3b405cfdb (refs/remotes/origin/testing)
> /usr/bin/git config core.sparsecheckout # timeout=10
> /usr/bin/git checkout -f 6951841891e07d6dd5eadeb09c897aa3b405cfdb
Commit message: "import preprocessing from cophi_toolbox instead of dariah_topics renames from cophi_toolbox Issues #5, #9, #13"
> /usr/bin/git rev-list --no-walk 694096a9989b2e90dc9bf567b3fe9d941fbe523b # timeout=10
[DARIAH-Topics] $ /usr/bin/python3 /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenv.py /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9
Using base prefix '/usr'
New python executable in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/bin/python3
Also creating executable in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
[DARIAH-Topics] $ /bin/sh -xe /tmp/shiningpanda229209115333750503.sh
+ pip install -U pip
Requirement already up-to-date: pip in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages (10.0.1)
+ pip install -U -r requirements-dev.txt
Obtaining file:///mnt/data/jenkins/workspace/DARIAH-Topics (from -r requirements.txt (line 1))
Collecting pytest (from -r requirements-dev.txt (line 4))
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Collecting pytest-cov (from -r requirements-dev.txt (line 5))
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Collecting nbsphinx from git+https://github.com/spatialaudio/nbsphinx#egg=nbsphinx (from -r requirements-dev.txt (line 11))
Cloning https://github.com/spatialaudio/nbsphinx to /tmp/pip-install-9qz8cps9/nbsphinx
Collecting recommonmark (from -r requirements-dev.txt (line 12))
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Collecting pandas>=0.19.2 (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
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Collecting regex>=2017.01.14 (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Collecting gensim>=0.13.2 (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
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Collecting lxml>=3.6.4 (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
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Collecting matplotlib>=1.5.3 (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
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Collecting bokeh>=0.12.6 (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Collecting metadata_toolbox (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Collecting cophi_toolbox (from dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Collecting py>=1.5.0 (from pytest->-r requirements-dev.txt (line 4))
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Collecting attrs>=17.4.0 (from pytest->-r requirements-dev.txt (line 4))
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Collecting pluggy<0.7,>=0.5 (from pytest->-r requirements-dev.txt (line 4))
Using cached https://files.pythonhosted.org/packages/ba/65/ded3bc40bbf8d887f262f150fbe1ae6637765b5c9534bd55690ed2c0b0f7/pluggy-0.6.0-py3-none-any.whl
Collecting atomicwrites>=1.0 (from pytest->-r requirements-dev.txt (line 4))
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Requirement not upgraded as not directly required: setuptools in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages (from pytest->-r requirements-dev.txt (line 4)) (39.2.0)
Collecting more-itertools>=4.0.0 (from pytest->-r requirements-dev.txt (line 4))
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Collecting six>=1.10.0 (from pytest->-r requirements-dev.txt (line 4))
Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting coverage>=3.7.1 (from pytest-cov->-r requirements-dev.txt (line 5))
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Collecting nbformat (from nbsmoke->-r requirements-dev.txt (line 6))
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Using cached https://files.pythonhosted.org/packages/39/ea/280d6c0d92f8e3ca15fd798bbcc2ea141489f9539de7133d8fe10ea4b049/nbconvert-5.3.1-py2.py3-none-any.whl
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Collecting notebook (from jupyter->-r requirements-dev.txt (line 9))
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Collecting Pygments>=2.0 (from sphinx->-r requirements-dev.txt (line 10))
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Using cached https://files.pythonhosted.org/packages/ff/fa/64acc09fc845a6b2dc0724d6f3f81e829b778ed5e9a7559567b4f19a3f4b/widgetsnbextension-3.2.1-py2.py3-none-any.whl
Collecting prompt-toolkit<2.0.0,>=1.0.0 (from jupyter-console->jupyter->-r requirements-dev.txt (line 9))
Using cached https://files.pythonhosted.org/packages/04/d1/c6616dd03701e7e2073f06d5c3b41b012256e42b72561f16a7bd86dd7b43/prompt_toolkit-1.0.15-py3-none-any.whl
Collecting Send2Trash (from notebook->jupyter->-r requirements-dev.txt (line 9))
Using cached https://files.pythonhosted.org/packages/49/46/c3dc27481d1cc57b9385aff41c474ceb7714f7935b1247194adae45db714/Send2Trash-1.5.0-py3-none-any.whl
Collecting terminado>=0.8.1 (from notebook->jupyter->-r requirements-dev.txt (line 9))
Using cached https://files.pythonhosted.org/packages/2e/20/a26211a24425923d46e1213b376a6ee60dc30bcdf1b0c345e2c3769deb1c/terminado-0.8.1-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx->-r requirements-dev.txt (line 10))
Collecting decorator (from traitlets->nbsphinx->-r requirements-dev.txt (line 11))
Using cached https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting boto>=2.32 (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/bd/b7/a88a67002b1185ed9a8e8a6ef15266728c2361fcb4f1d02ea331e4c7741d/boto-2.48.0-py2.py3-none-any.whl
Collecting boto3 (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/2f/e0/b9e3b23e100e0df42d3646e1d126a0f5e3d738921be142a2f0133ed502a5/boto3-1.7.37-py2.py3-none-any.whl
Collecting bz2file (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Collecting html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre (from bleach->nbconvert->nbsmoke->-r requirements-dev.txt (line 6))
Using cached https://files.pythonhosted.org/packages/a5/62/bbd2be0e7943ec8504b517e62bab011b4946e1258842bc159e5dfde15b96/html5lib-1.0.1-py2.py3-none-any.whl
Collecting pickleshare (from ipython>=4.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Using cached https://files.pythonhosted.org/packages/9f/17/daa142fc9be6b76f26f24eeeb9a138940671490b91cb5587393f297c8317/pickleshare-0.7.4-py2.py3-none-any.whl
Collecting simplegeneric>0.8 (from ipython>=4.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Collecting jedi>=0.10 (from ipython>=4.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Using cached https://files.pythonhosted.org/packages/e7/42/074192a165622e645ed4aeade63e76e56b3496a044569b3c6cae3a918352/jedi-0.12.0-py2.py3-none-any.whl
Collecting backcall (from ipython>=4.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Collecting pexpect; sys_platform != "win32" (from ipython>=4.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Using cached https://files.pythonhosted.org/packages/89/e6/b5a1de8b0cc4e07ca1b305a4fcc3f9806025c1b651ea302646341222f88b/pexpect-4.6.0-py2.py3-none-any.whl
Collecting wcwidth (from prompt-toolkit<2.0.0,>=1.0.0->jupyter-console->jupyter->-r requirements-dev.txt (line 9))
Using cached https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Collecting ptyprocess; os_name != "nt" (from terminado>=0.8.1->notebook->jupyter->-r requirements-dev.txt (line 9))
Using cached https://files.pythonhosted.org/packages/ff/4e/fa4a73ccfefe2b37d7b6898329e7dbcd1ac846ba3a3b26b294a78a3eb997/ptyprocess-0.5.2-py2.py3-none-any.whl
Collecting s3transfer<0.2.0,>=0.1.10 (from boto3->smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/d7/14/2a0004d487464d120c9fb85313a75cd3d71a7506955be458eebfe19a6b1d/s3transfer-0.1.13-py2.py3-none-any.whl
Collecting botocore<1.11.0,>=1.10.37 (from boto3->smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/0b/97/60eba2ca866d346459bfb6f95ff5b2b611d7b1b844d0733acb436d59c893/botocore-1.10.37-py2.py3-none-any.whl
Collecting jmespath<1.0.0,>=0.7.1 (from boto3->smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.0.dev0->-r requirements.txt (line 1))
Using cached https://files.pythonhosted.org/packages/b7/31/05c8d001f7f87f0f07289a5fc0fc3832e9a57f2dbd4d3b0fee70e0d51365/jmespath-0.9.3-py2.py3-none-any.whl
Collecting webencodings (from html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre->bleach->nbconvert->nbsmoke->-r requirements-dev.txt (line 6))
Using cached https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
Collecting parso>=0.2.0 (from jedi>=0.10->ipython>=4.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Using cached https://files.pythonhosted.org/packages/cd/3e/5908f9577dbd1e5df53e64349bfd11e46b726c1e4d8cd676bbe8aa4de316/parso-0.2.1-py2.py3-none-any.whl
Building wheels for collected packages: nbsphinx
Running setup.py bdist_wheel for nbsphinx: started
Running setup.py bdist_wheel for nbsphinx: finished with status 'done'
Stored in directory: /tmp/pip-ephem-wheel-cache-pj6rv26g/wheels/a3/7b/ff/b71160a2e088926eb13abcf8e0cde94c0aa8400c67d3df57f5
Successfully built nbsphinx
Installing collected packages: py, attrs, pluggy, atomicwrites, six, more-itertools, pytest, coverage, pytest-cov, jsonschema, decorator, ipython-genutils, traitlets, jupyter-core, nbformat, pyzmq, tornado, python-dateutil, jupyter-client, mistune, webencodings, html5lib, bleach, Pygments, entrypoints, pandocfilters, MarkupSafe, Jinja2, testpath, nbconvert, urllib3, chardet, certifi, idna, requests, beautifulsoup4, pyflakes, pickleshare, simplegeneric, parso, jedi, backcall, ptyprocess, pexpect, wcwidth, prompt-toolkit, ipython, ipykernel, nbsmoke, Send2Trash, terminado, notebook, widgetsnbextension, ipywidgets, jupyter-console, qtconsole, jupyter, pyparsing, packaging, sphinxcontrib-websupport, docutils, snowballstemmer, alabaster, pytz, babel, imagesize, sphinx, nbsphinx, commonmark, recommonmark, numpy, pandas, regex, scipy, boto, jmespath, botocore, s3transfer, boto3, bz2file, smart-open, gensim, pbr, lda, lxml, cycler, kiwisolver, matplotlib, PyYAML, bokeh, parse, metadata-toolbox, cophi-toolbox, dariah-topics
Running setup.py develop for dariah-topics
Successfully installed Jinja2-2.10 MarkupSafe-1.0 PyYAML-3.12 Pygments-2.2.0 Send2Trash-1.5.0 alabaster-0.7.10 atomicwrites-1.1.5 attrs-18.1.0 babel-2.6.0 backcall-0.1.0 beautifulsoup4-4.6.0 bleach-2.1.3 bokeh-0.12.16 boto-2.48.0 boto3-1.7.37 botocore-1.10.37 bz2file-0.98 certifi-2018.4.16 chardet-3.0.4 commonmark-0.5.4 cophi-toolbox-0.1.0.dev0 coverage-4.5.1 cycler-0.10.0 dariah-topics decorator-4.3.0 docutils-0.14 entrypoints-0.2.3 gensim-3.4.0 html5lib-1.0.1 idna-2.7 imagesize-1.0.0 ipykernel-4.8.2 ipython-6.4.0 ipython-genutils-0.2.0 ipywidgets-7.2.1 jedi-0.12.0 jmespath-0.9.3 jsonschema-2.6.0 jupyter-1.0.0 jupyter-client-5.2.3 jupyter-console-5.2.0 jupyter-core-4.4.0 kiwisolver-1.0.1 lda-1.0.5 lxml-4.2.1 matplotlib-2.2.2 metadata-toolbox-0.1.0.dev0 mistune-0.8.3 more-itertools-4.2.0 nbconvert-5.3.1 nbformat-4.4.0 nbsmoke-0.2.7 nbsphinx-0.3.3 notebook-5.5.0 numpy-1.14.5 packaging-17.1 pandas-0.23.1 pandocfilters-1.4.2 parse-1.8.4 parso-0.2.1 pbr-4.0.4 pexpect-4.6.0 pickleshare-0.7.4 pluggy-0.6.0 prompt-toolkit-1.0.15 ptyprocess-0.5.2 py-1.5.3 pyflakes-2.0.0 pyparsing-2.2.0 pytest-3.6.1 pytest-cov-2.5.1 python-dateutil-2.7.3 pytz-2018.4 pyzmq-17.0.0 qtconsole-4.3.1 recommonmark-0.4.0 regex-2018.6.9 requests-2.19.0 s3transfer-0.1.13 scipy-1.1.0 simplegeneric-0.8.1 six-1.11.0 smart-open-1.5.7 snowballstemmer-1.2.1 sphinx-1.7.5 sphinxcontrib-websupport-1.1.0 terminado-0.8.1 testpath-0.3.1 tornado-5.0.2 traitlets-4.3.2 urllib3-1.23 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.2.1
+ ./setup.py sdist bdist_wheel
running sdist
running egg_info
writing top-level names to dariah_topics.egg-info/top_level.txt
writing dependency_links to dariah_topics.egg-info/dependency_links.txt
writing requirements to dariah_topics.egg-info/requires.txt
writing dariah_topics.egg-info/PKG-INFO
reading manifest file 'dariah_topics.egg-info/SOURCES.txt'
writing manifest file 'dariah_topics.egg-info/SOURCES.txt'
running check
creating dariah_topics-1.0.0.dev0
creating dariah_topics-1.0.0.dev0/dariah_topics
creating dariah_topics-1.0.0.dev0/dariah_topics.egg-info
creating dariah_topics-1.0.0.dev0/test
copying files to dariah_topics-1.0.0.dev0...
copying README.md -> dariah_topics-1.0.0.dev0
copying setup.cfg -> dariah_topics-1.0.0.dev0
copying setup.py -> dariah_topics-1.0.0.dev0
copying dariah_topics/__init__.py -> dariah_topics-1.0.0.dev0/dariah_topics
copying dariah_topics/evaluation.py -> dariah_topics-1.0.0.dev0/dariah_topics
copying dariah_topics/modeling.py -> dariah_topics-1.0.0.dev0/dariah_topics
copying dariah_topics/postprocessing.py -> dariah_topics-1.0.0.dev0/dariah_topics
copying dariah_topics/preprocessing.py -> dariah_topics-1.0.0.dev0/dariah_topics
copying dariah_topics/utils.py -> dariah_topics-1.0.0.dev0/dariah_topics
copying dariah_topics/visualization.py -> dariah_topics-1.0.0.dev0/dariah_topics
copying dariah_topics.egg-info/PKG-INFO -> dariah_topics-1.0.0.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/SOURCES.txt -> dariah_topics-1.0.0.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/dependency_links.txt -> dariah_topics-1.0.0.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/requires.txt -> dariah_topics-1.0.0.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/top_level.txt -> dariah_topics-1.0.0.dev0/dariah_topics.egg-info
copying test/test_fuzzy_segmenting.py -> dariah_topics-1.0.0.dev0/test
Writing dariah_topics-1.0.0.dev0/setup.cfg
Creating tar archive
removing 'dariah_topics-1.0.0.dev0' (and everything under it)
running bdist_wheel
running build
running build_py
copying dariah_topics/preprocessing.py -> build/lib/dariah_topics
copying dariah_topics/postprocessing.py -> build/lib/dariah_topics
copying dariah_topics/__init__.py -> build/lib/dariah_topics
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/modeling.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/preprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/utils.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/postprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/evaluation.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/__init__.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/visualization.py -> build/bdist.linux-x86_64/wheel/dariah_topics
running install_egg_info
Copying dariah_topics.egg-info to build/bdist.linux-x86_64/wheel/dariah_topics-1.0.0.dev0-py3.5.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/dariah_topics-1.0.0.dev0.dist-info/WHEEL
creating '/mnt/data/jenkins/workspace/DARIAH-Topics/dist/dariah_topics-1.0.0.dev0-py3-none-any.whl' and adding '.' to it
adding 'dariah_topics/__init__.py'
adding 'dariah_topics/evaluation.py'
adding 'dariah_topics/modeling.py'
adding 'dariah_topics/postprocessing.py'
adding 'dariah_topics/preprocessing.py'
adding 'dariah_topics/utils.py'
adding 'dariah_topics/visualization.py'
adding 'dariah_topics-1.0.0.dev0.dist-info/top_level.txt'
adding 'dariah_topics-1.0.0.dev0.dist-info/WHEEL'
adding 'dariah_topics-1.0.0.dev0.dist-info/METADATA'
adding 'dariah_topics-1.0.0.dev0.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/setuptools/dist.py:398: UserWarning: Normalizing '1.0.0.dev' to '1.0.0.dev0'
normalized_version,
+ pytest --nbsmoke-run
============================= test session starts ==============================
platform linux -- Python 3.5.3, pytest-3.6.1, py-1.5.3, pluggy-0.6.0
rootdir: /mnt/data/jenkins/workspace/DARIAH-Topics, inifile: setup.cfg
plugins: cov-2.5.1, nbsmoke-0.2.7
collected 57 items
dariah_topics/postprocessing.py ........F.. [ 19%]
dariah_topics/preprocessing.py ........................... [ 66%]
dariah_topics/utils.py ...... [ 77%]
notebooks/IntroducingGensim.ipynb F [ 78%]
notebooks/IntroducingLda.ipynb F [ 80%]
notebooks/IntroducingMallet.ipynb F [ 82%]
notebooks/Visualizations.ipynb F [ 84%]
test/test_fuzzy_segmenting.py ......... [100%]
=================================== FAILURES ===================================
______________ [doctest] dariah_topics.postprocessing.save_model _______________
157
158 Returns:
159 None.
160
161 Example:
162 >>> from lda import LDA
163 >>> from gensim.models import LdaModel
164 >>> from cophi_toolbox import preprocessing
165 >>> save_model(LDA, 'model.pickle')
166 >>> preprocessing.read_model('model.pickle') == LDA
UNEXPECTED EXCEPTION: AttributeError("module 'cophi_toolbox.preprocessing' has no attribute 'read_model'",)
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing.save_model[4]>", line 1, in <module>
AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_model'
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py:166: UnexpectedException
_______________________________________ _______________________________________
self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
corpus = lis...ing' has no attribute 'read_files'
AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f323a2fbea0>
when = 'call', treat_keyboard_interrupt_as_exception = False
def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
self.when = when
self.start = time()
try:
> self.result = func()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds),
when=when,
treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:181:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_call'>, args = ()
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>}
notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.argnames:
notincall = set(self.argnames) - set(['__multicall__']) - set(
kwargs.keys())
if notincall:
warnings.warn(
"Argument(s) {} which are declared in the hookspec "
"can not be found in this hook call"
.format(tuple(notincall)),
stacklevel=2,
)
> return self._hookexec(self, self._nonwrappers + self._wrappers, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:617:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7f3268364390>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>}
def _hookexec(self, hook, methods, kwargs):
# called from all hookcaller instances.
# enable_tracing will set its own wrapping function at self._inner_hookexec
> return self._inner_hookexec(hook, methods, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>}
self._inner_hookexec = lambda hook, methods, kwargs: \
hook.multicall(
methods, kwargs,
> firstresult=hook.spec_opts.get('firstresult'),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:216:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
res = hook_impl.function(*args)
if res is not None:
results.append(res)
if firstresult: # halt further impl calls
break
except BaseException:
excinfo = sys.exc_info()
finally:
if firstresult: # first result hooks return a single value
outcome = _Result(results[0] if results else None, excinfo)
else:
outcome = _Result(results, excinfo)
# run all wrapper post-yield blocks
for gen in reversed(teardowns):
try:
gen.send(outcome)
_raise_wrapfail(gen, "has second yield")
except StopIteration:
pass
> return outcome.get_result()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7f323a2d16d8>
def get_result(self):
"""Get the result(s) for this hook call.
If the hook was marked as a ``firstresult`` only a single value
will be returned otherwise a list of results.
"""
__tracebackhide__ = True
if self._excinfo is None:
return self._result
else:
ex = self._excinfo
if _py3:
> raise ex[1].with_traceback(ex[2])
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:76:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
> res = hook_impl.function(*args)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:180:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>
def pytest_runtest_call(item):
_update_current_test_var(item, "call")
sys.last_type, sys.last_value, sys.last_traceback = (None, None, None)
try:
> item.runtest()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:109:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>
def runtest(self):
self._skip()
with io.open(self.name,encoding='utf8') as nb:
notebook = nbformat.read(nb, as_version=4)
# TODO: which kernel? run in pytest's or use new one (make it option)
_timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout')
kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300,
allow_errors=False,
# or sys.version_info[1] ?
kernel_name='python')
ep = ExecutePreprocessor(**kwargs)
with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right?
> ep.preprocess(notebook,{})
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f32643c30b8>
nb = {'metadata': {'git': {'suppress_outputs': True}, 'kernelspec': {'language': 'python', 'name': 'python3', 'display_name...: None, 'source': 'static_heatmap = PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()'}], 'nbformat_minor': 1}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocess notebook executing each code cell.
The input argument `nb` is modified in-place.
Parameters
----------
nb : NotebookNode
Notebook being executed.
resources : dictionary
Additional resources used in the conversion process. For example,
passing ``{'metadata': {'path': run_path}}`` sets the
execution path to ``run_path``.
Returns
-------
nb : NotebookNode
The executed notebook.
resources : dictionary
Additional resources used in the conversion process.
"""
path = resources.get('metadata', {}).get('path', '')
if path == '':
path = None
# clear display_id map
self._display_id_map = {}
# from jupyter_client.manager import start_new_kernel
def start_new_kernel(startup_timeout=60, kernel_name='python', **kwargs):
km = self.kernel_manager_class(kernel_name=kernel_name)
km.start_kernel(**kwargs)
kc = km.client()
kc.start_channels()
try:
kc.wait_for_ready(timeout=startup_timeout)
except RuntimeError:
kc.stop_channels()
km.shutdown_kernel()
raise
return km, kc
kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python')
if self.kernel_name:
kernel_name = self.kernel_name
self.log.info("Executing notebook with kernel: %s" % kernel_name)
self.km, self.kc = start_new_kernel(
startup_timeout=self.startup_timeout,
kernel_name=kernel_name,
extra_arguments=self.extra_arguments,
cwd=path)
self.kc.allow_stdin = False
self.nb = nb
try:
> nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:262:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f32643c30b8>
nb = {'metadata': {'git': {'suppress_outputs': True}, 'kernelspec': {'language': 'python', 'name': 'python3', 'display_name...: None, 'source': 'static_heatmap = PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()'}], 'nbformat_minor': 1}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocessing to apply on each notebook.
Must return modified nb, resources.
If you wish to apply your preprocessing to each cell, you might want
to override preprocess_cell method instead.
Parameters
----------
nb : NotebookNode
Notebook being converted
resources : dictionary
Additional resources used in the conversion process. Allows
preprocessors to pass variables into the Jinja engine.
"""
for index, cell in enumerate(nb.cells):
> nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f32643c30b8>
cell = {'cell_type': 'code', 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeError', 'evalue': "modul...list(preprocessing.read_files(meta.index))\ncorpus[0][:255] # printing the first 255 characters of the first document'}
resources = {}, cell_index = 17
def preprocess_cell(self, cell, resources, cell_index):
"""
Executes a single code cell. See base.py for details.
To execute all cells see :meth:`preprocess`.
"""
if cell.cell_type != 'code':
return cell, resources
reply, outputs = self.run_cell(cell, cell_index)
cell.outputs = outputs
if not self.allow_errors:
for out in outputs:
if out.output_type == 'error':
> raise CellExecutionError.from_cell_and_msg(cell, out)
E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:
E ------------------
E corpus = list(preprocessing.read_files(meta.index))
E corpus[0][:255] # printing the first 255 characters of the first document
E ------------------
E
E [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-7-1004dfe5ae0a>[0m in [0;36m<module>[0;34m()[0m
E [0;32m----> 1[0;31m [0mcorpus[0m [0;34m=[0m [0mlist[0m[0;34m([0m[0mpreprocessing[0m[0;34m.[0m[0mread_files[0m[0;34m([0m[0mmeta[0m[0;34m.[0m[0mindex[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 2[0m [0mcorpus[0m[0;34m[[0m[0;36m0[0m[0;34m][0m[0;34m[[0m[0;34m:[0m[0;36m255[0m[0;34m][0m [0;31m# printing the first 255 characters of the first document[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
E AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:286: CellExecutionError
_______________________________________ _______________________________________
self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
corpus = lis...ing' has no attribute 'read_files'
AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f323935d268>
when = 'call', treat_keyboard_interrupt_as_exception = False
def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
self.when = when
self.start = time()
try:
> self.result = func()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds),
when=when,
treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:181:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_call'>, args = ()
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>}
notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.argnames:
notincall = set(self.argnames) - set(['__multicall__']) - set(
kwargs.keys())
if notincall:
warnings.warn(
"Argument(s) {} which are declared in the hookspec "
"can not be found in this hook call"
.format(tuple(notincall)),
stacklevel=2,
)
> return self._hookexec(self, self._nonwrappers + self._wrappers, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:617:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7f3268364390>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>}
def _hookexec(self, hook, methods, kwargs):
# called from all hookcaller instances.
# enable_tracing will set its own wrapping function at self._inner_hookexec
> return self._inner_hookexec(hook, methods, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>}
self._inner_hookexec = lambda hook, methods, kwargs: \
hook.multicall(
methods, kwargs,
> firstresult=hook.spec_opts.get('firstresult'),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:216:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
res = hook_impl.function(*args)
if res is not None:
results.append(res)
if firstresult: # halt further impl calls
break
except BaseException:
excinfo = sys.exc_info()
finally:
if firstresult: # first result hooks return a single value
outcome = _Result(results[0] if results else None, excinfo)
else:
outcome = _Result(results, excinfo)
# run all wrapper post-yield blocks
for gen in reversed(teardowns):
try:
gen.send(outcome)
_raise_wrapfail(gen, "has second yield")
except StopIteration:
pass
> return outcome.get_result()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7f323a278b70>
def get_result(self):
"""Get the result(s) for this hook call.
If the hook was marked as a ``firstresult`` only a single value
will be returned otherwise a list of results.
"""
__tracebackhide__ = True
if self._excinfo is None:
return self._result
else:
ex = self._excinfo
if _py3:
> raise ex[1].with_traceback(ex[2])
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:76:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
> res = hook_impl.function(*args)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:180:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>
def pytest_runtest_call(item):
_update_current_test_var(item, "call")
sys.last_type, sys.last_value, sys.last_traceback = (None, None, None)
try:
> item.runtest()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:109:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>
def runtest(self):
self._skip()
with io.open(self.name,encoding='utf8') as nb:
notebook = nbformat.read(nb, as_version=4)
# TODO: which kernel? run in pytest's or use new one (make it option)
_timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout')
kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300,
allow_errors=False,
# or sys.version_info[1] ?
kernel_name='python')
ep = ExecutePreprocessor(**kwargs)
with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right?
> ep.preprocess(notebook,{})
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f32393fe6d8>
nb = {'metadata': {'git': {'suppress_outputs': True}, 'kernelspec': {'language': 'python', 'name': 'python3', 'display_name...: None, 'source': 'static_heatmap = PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()'}], 'nbformat_minor': 1}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocess notebook executing each code cell.
The input argument `nb` is modified in-place.
Parameters
----------
nb : NotebookNode
Notebook being executed.
resources : dictionary
Additional resources used in the conversion process. For example,
passing ``{'metadata': {'path': run_path}}`` sets the
execution path to ``run_path``.
Returns
-------
nb : NotebookNode
The executed notebook.
resources : dictionary
Additional resources used in the conversion process.
"""
path = resources.get('metadata', {}).get('path', '')
if path == '':
path = None
# clear display_id map
self._display_id_map = {}
# from jupyter_client.manager import start_new_kernel
def start_new_kernel(startup_timeout=60, kernel_name='python', **kwargs):
km = self.kernel_manager_class(kernel_name=kernel_name)
km.start_kernel(**kwargs)
kc = km.client()
kc.start_channels()
try:
kc.wait_for_ready(timeout=startup_timeout)
except RuntimeError:
kc.stop_channels()
km.shutdown_kernel()
raise
return km, kc
kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python')
if self.kernel_name:
kernel_name = self.kernel_name
self.log.info("Executing notebook with kernel: %s" % kernel_name)
self.km, self.kc = start_new_kernel(
startup_timeout=self.startup_timeout,
kernel_name=kernel_name,
extra_arguments=self.extra_arguments,
cwd=path)
self.kc.allow_stdin = False
self.nb = nb
try:
> nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:262:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f32393fe6d8>
nb = {'metadata': {'git': {'suppress_outputs': True}, 'kernelspec': {'language': 'python', 'name': 'python3', 'display_name...: None, 'source': 'static_heatmap = PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()'}], 'nbformat_minor': 1}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocessing to apply on each notebook.
Must return modified nb, resources.
If you wish to apply your preprocessing to each cell, you might want
to override preprocess_cell method instead.
Parameters
----------
nb : NotebookNode
Notebook being converted
resources : dictionary
Additional resources used in the conversion process. Allows
preprocessors to pass variables into the Jinja engine.
"""
for index, cell in enumerate(nb.cells):
> nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f32393fe6d8>
cell = {'cell_type': 'code', 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeError', 'evalue': "modul...list(preprocessing.read_files(meta.index))\ncorpus[0][:255] # printing the first 255 characters of the first document'}
resources = {}, cell_index = 18
def preprocess_cell(self, cell, resources, cell_index):
"""
Executes a single code cell. See base.py for details.
To execute all cells see :meth:`preprocess`.
"""
if cell.cell_type != 'code':
return cell, resources
reply, outputs = self.run_cell(cell, cell_index)
cell.outputs = outputs
if not self.allow_errors:
for out in outputs:
if out.output_type == 'error':
> raise CellExecutionError.from_cell_and_msg(cell, out)
E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:
E ------------------
E corpus = list(preprocessing.read_files(meta.index))
E corpus[0][:255] # printing the first 255 characters of the first document
E ------------------
E
E [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-7-1004dfe5ae0a>[0m in [0;36m<module>[0;34m()[0m
E [0;32m----> 1[0;31m [0mcorpus[0m [0;34m=[0m [0mlist[0m[0;34m([0m[0mpreprocessing[0m[0;34m.[0m[0mread_files[0m[0;34m([0m[0mmeta[0m[0;34m.[0m[0mindex[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 2[0m [0mcorpus[0m[0;34m[[0m[0;36m0[0m[0;34m][0m[0;34m[[0m[0;34m:[0m[0;36m255[0m[0;34m][0m [0;31m# printing the first 255 characters of the first document[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
E AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:286: CellExecutionError
_______________________________________ _______________________________________
self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
corpus = lis...ing' has no attribute 'read_files'
AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f323932ba60>
when = 'call', treat_keyboard_interrupt_as_exception = False
def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
self.when = when
self.start = time()
try:
> self.result = func()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds),
when=when,
treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:181:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_call'>, args = ()
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>}
notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.argnames:
notincall = set(self.argnames) - set(['__multicall__']) - set(
kwargs.keys())
if notincall:
warnings.warn(
"Argument(s) {} which are declared in the hookspec "
"can not be found in this hook call"
.format(tuple(notincall)),
stacklevel=2,
)
> return self._hookexec(self, self._nonwrappers + self._wrappers, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:617:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7f3268364390>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>}
def _hookexec(self, hook, methods, kwargs):
# called from all hookcaller instances.
# enable_tracing will set its own wrapping function at self._inner_hookexec
> return self._inner_hookexec(hook, methods, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>}
self._inner_hookexec = lambda hook, methods, kwargs: \
hook.multicall(
methods, kwargs,
> firstresult=hook.spec_opts.get('firstresult'),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:216:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
res = hook_impl.function(*args)
if res is not None:
results.append(res)
if firstresult: # halt further impl calls
break
except BaseException:
excinfo = sys.exc_info()
finally:
if firstresult: # first result hooks return a single value
outcome = _Result(results[0] if results else None, excinfo)
else:
outcome = _Result(results, excinfo)
# run all wrapper post-yield blocks
for gen in reversed(teardowns):
try:
gen.send(outcome)
_raise_wrapfail(gen, "has second yield")
except StopIteration:
pass
> return outcome.get_result()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7f3239231160>
def get_result(self):
"""Get the result(s) for this hook call.
If the hook was marked as a ``firstresult`` only a single value
will be returned otherwise a list of results.
"""
__tracebackhide__ = True
if self._excinfo is None:
return self._result
else:
ex = self._excinfo
if _py3:
> raise ex[1].with_traceback(ex[2])
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:76:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
> res = hook_impl.function(*args)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:180:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>
def pytest_runtest_call(item):
_update_current_test_var(item, "call")
sys.last_type, sys.last_value, sys.last_traceback = (None, None, None)
try:
> item.runtest()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:109:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>
def runtest(self):
self._skip()
with io.open(self.name,encoding='utf8') as nb:
notebook = nbformat.read(nb, as_version=4)
# TODO: which kernel? run in pytest's or use new one (make it option)
_timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout')
kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300,
allow_errors=False,
# or sys.version_info[1] ?
kernel_name='python')
ep = ExecutePreprocessor(**kwargs)
with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right?
> ep.preprocess(notebook,{})
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f3239231518>
nb = {'metadata': {'git': {'suppress_outputs': True}, 'kernelspec': {'language': 'python', 'name': 'python3', 'display_name...: None, 'source': 'static_heatmap = PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()'}], 'nbformat_minor': 1}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocess notebook executing each code cell.
The input argument `nb` is modified in-place.
Parameters
----------
nb : NotebookNode
Notebook being executed.
resources : dictionary
Additional resources used in the conversion process. For example,
passing ``{'metadata': {'path': run_path}}`` sets the
execution path to ``run_path``.
Returns
-------
nb : NotebookNode
The executed notebook.
resources : dictionary
Additional resources used in the conversion process.
"""
path = resources.get('metadata', {}).get('path', '')
if path == '':
path = None
# clear display_id map
self._display_id_map = {}
# from jupyter_client.manager import start_new_kernel
def start_new_kernel(startup_timeout=60, kernel_name='python', **kwargs):
km = self.kernel_manager_class(kernel_name=kernel_name)
km.start_kernel(**kwargs)
kc = km.client()
kc.start_channels()
try:
kc.wait_for_ready(timeout=startup_timeout)
except RuntimeError:
kc.stop_channels()
km.shutdown_kernel()
raise
return km, kc
kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python')
if self.kernel_name:
kernel_name = self.kernel_name
self.log.info("Executing notebook with kernel: %s" % kernel_name)
self.km, self.kc = start_new_kernel(
startup_timeout=self.startup_timeout,
kernel_name=kernel_name,
extra_arguments=self.extra_arguments,
cwd=path)
self.kc.allow_stdin = False
self.nb = nb
try:
> nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:262:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f3239231518>
nb = {'metadata': {'git': {'suppress_outputs': True}, 'kernelspec': {'language': 'python', 'name': 'python3', 'display_name...: None, 'source': 'static_heatmap = PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()'}], 'nbformat_minor': 1}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocessing to apply on each notebook.
Must return modified nb, resources.
If you wish to apply your preprocessing to each cell, you might want
to override preprocess_cell method instead.
Parameters
----------
nb : NotebookNode
Notebook being converted
resources : dictionary
Additional resources used in the conversion process. Allows
preprocessors to pass variables into the Jinja engine.
"""
for index, cell in enumerate(nb.cells):
> nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f3239231518>
cell = {'cell_type': 'code', 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeError', 'evalue': "modul...list(preprocessing.read_files(meta.index))\ncorpus[0][:255] # printing the first 255 characters of the first document'}
resources = {}, cell_index = 18
def preprocess_cell(self, cell, resources, cell_index):
"""
Executes a single code cell. See base.py for details.
To execute all cells see :meth:`preprocess`.
"""
if cell.cell_type != 'code':
return cell, resources
reply, outputs = self.run_cell(cell, cell_index)
cell.outputs = outputs
if not self.allow_errors:
for out in outputs:
if out.output_type == 'error':
> raise CellExecutionError.from_cell_and_msg(cell, out)
E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:
E ------------------
E corpus = list(preprocessing.read_files(meta.index))
E corpus[0][:255] # printing the first 255 characters of the first document
E ------------------
E
E [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-7-1004dfe5ae0a>[0m in [0;36m<module>[0;34m()[0m
E [0;32m----> 1[0;31m [0mcorpus[0m [0;34m=[0m [0mlist[0m[0;34m([0m[0mpreprocessing[0m[0;34m.[0m[0mread_files[0m[0;34m([0m[0mmeta[0m[0;34m.[0m[0mindex[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 2[0m [0mcorpus[0m[0;34m[[0m[0;36m0[0m[0;34m][0m[0;34m[[0m[0;34m:[0m[0;36m255[0m[0;34m][0m [0;31m# printing the first 255 characters of the first document[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
E AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:286: CellExecutionError
_______________________________________ _______________________________________
self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
corpus = lis...ing' has no attribute 'read_files'
AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f323935d378>
when = 'call', treat_keyboard_interrupt_as_exception = False
def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
self.when = when
self.start = time()
try:
> self.result = func()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds),
when=when,
treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:181:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_call'>, args = ()
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>}
notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.argnames:
notincall = set(self.argnames) - set(['__multicall__']) - set(
kwargs.keys())
if notincall:
warnings.warn(
"Argument(s) {} which are declared in the hookspec "
"can not be found in this hook call"
.format(tuple(notincall)),
stacklevel=2,
)
> return self._hookexec(self, self._nonwrappers + self._wrappers, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:617:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7f3268364390>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>}
def _hookexec(self, hook, methods, kwargs):
# called from all hookcaller instances.
# enable_tracing will set its own wrapping function at self._inner_hookexec
> return self._inner_hookexec(hook, methods, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>}
self._inner_hookexec = lambda hook, methods, kwargs: \
hook.multicall(
methods, kwargs,
> firstresult=hook.spec_opts.get('firstresult'),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:216:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
res = hook_impl.function(*args)
if res is not None:
results.append(res)
if firstresult: # halt further impl calls
break
except BaseException:
excinfo = sys.exc_info()
finally:
if firstresult: # first result hooks return a single value
outcome = _Result(results[0] if results else None, excinfo)
else:
outcome = _Result(results, excinfo)
# run all wrapper post-yield blocks
for gen in reversed(teardowns):
try:
gen.send(outcome)
_raise_wrapfail(gen, "has second yield")
except StopIteration:
pass
> return outcome.get_result()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7f323940c898>
def get_result(self):
"""Get the result(s) for this hook call.
If the hook was marked as a ``firstresult`` only a single value
will be returned otherwise a list of results.
"""
__tracebackhide__ = True
if self._excinfo is None:
return self._result
else:
ex = self._excinfo
if _py3:
> raise ex[1].with_traceback(ex[2])
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:76:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>}
firstresult = False
def _multicall(hook_impls, caller_kwargs, firstresult=False):
"""Execute a call into multiple python functions/methods and return the
result(s).
``caller_kwargs`` comes from _HookCaller.__call__().
"""
__tracebackhide__ = True
results = []
excinfo = None
try: # run impl and wrapper setup functions in a loop
teardowns = []
try:
for hook_impl in reversed(hook_impls):
try:
args = [caller_kwargs[argname] for argname in hook_impl.argnames]
except KeyError:
for argname in hook_impl.argnames:
if argname not in caller_kwargs:
raise HookCallError(
"hook call must provide argument %r" % (argname,))
if hook_impl.hookwrapper:
try:
gen = hook_impl.function(*args)
next(gen) # first yield
teardowns.append(gen)
except StopIteration:
_raise_wrapfail(gen, "did not yield")
else:
> res = hook_impl.function(*args)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:180:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>
def pytest_runtest_call(item):
_update_current_test_var(item, "call")
sys.last_type, sys.last_value, sys.last_traceback = (None, None, None)
try:
> item.runtest()
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:109:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>
def runtest(self):
self._skip()
with io.open(self.name,encoding='utf8') as nb:
notebook = nbformat.read(nb, as_version=4)
# TODO: which kernel? run in pytest's or use new one (make it option)
_timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout')
kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300,
allow_errors=False,
# or sys.version_info[1] ?
kernel_name='python')
ep = ExecutePreprocessor(**kwargs)
with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right?
> ep.preprocess(notebook,{})
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f323940cfd0>
nb = {'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}, 'language_info': {'... width=800)\nshow(interactive_barchart_per_document, notebook_handle=True)"}], 'nbformat_minor': 2}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocess notebook executing each code cell.
The input argument `nb` is modified in-place.
Parameters
----------
nb : NotebookNode
Notebook being executed.
resources : dictionary
Additional resources used in the conversion process. For example,
passing ``{'metadata': {'path': run_path}}`` sets the
execution path to ``run_path``.
Returns
-------
nb : NotebookNode
The executed notebook.
resources : dictionary
Additional resources used in the conversion process.
"""
path = resources.get('metadata', {}).get('path', '')
if path == '':
path = None
# clear display_id map
self._display_id_map = {}
# from jupyter_client.manager import start_new_kernel
def start_new_kernel(startup_timeout=60, kernel_name='python', **kwargs):
km = self.kernel_manager_class(kernel_name=kernel_name)
km.start_kernel(**kwargs)
kc = km.client()
kc.start_channels()
try:
kc.wait_for_ready(timeout=startup_timeout)
except RuntimeError:
kc.stop_channels()
km.shutdown_kernel()
raise
return km, kc
kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python')
if self.kernel_name:
kernel_name = self.kernel_name
self.log.info("Executing notebook with kernel: %s" % kernel_name)
self.km, self.kc = start_new_kernel(
startup_timeout=self.startup_timeout,
kernel_name=kernel_name,
extra_arguments=self.extra_arguments,
cwd=path)
self.kc.allow_stdin = False
self.nb = nb
try:
> nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:262:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f323940cfd0>
nb = {'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}, 'language_info': {'... width=800)\nshow(interactive_barchart_per_document, notebook_handle=True)"}], 'nbformat_minor': 2}
resources = {}
def preprocess(self, nb, resources):
"""
Preprocessing to apply on each notebook.
Must return modified nb, resources.
If you wish to apply your preprocessing to each cell, you might want
to override preprocess_cell method instead.
Parameters
----------
nb : NotebookNode
Notebook being converted
resources : dictionary
Additional resources used in the conversion process. Allows
preprocessors to pass variables into the Jinja engine.
"""
for index, cell in enumerate(nb.cells):
> nb.cells[index], resources = self.preprocess_cell(cell, resources, index)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f323940cfd0>
cell = {'cell_type': 'code', 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeError', 'evalue': "modul...list(preprocessing.read_files(meta.index))\ncorpus[0][:255] # printing the first 255 characters of the first document'}
resources = {}, cell_index = 3
def preprocess_cell(self, cell, resources, cell_index):
"""
Executes a single code cell. See base.py for details.
To execute all cells see :meth:`preprocess`.
"""
if cell.cell_type != 'code':
return cell, resources
reply, outputs = self.run_cell(cell, cell_index)
cell.outputs = outputs
if not self.allow_errors:
for out in outputs:
if out.output_type == 'error':
> raise CellExecutionError.from_cell_and_msg(cell, out)
E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell:
E ------------------
E corpus = list(preprocessing.read_files(meta.index))
E corpus[0][:255] # printing the first 255 characters of the first document
E ------------------
E
E [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-4-1004dfe5ae0a>[0m in [0;36m<module>[0;34m()[0m
E [0;32m----> 1[0;31m [0mcorpus[0m [0;34m=[0m [0mlist[0m[0;34m([0m[0mpreprocessing[0m[0;34m.[0m[0mread_files[0m[0;34m([0m[0mmeta[0m[0;34m.[0m[0mindex[0m[0;34m)[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 2[0m [0mcorpus[0m[0;34m[[0m[0;36m0[0m[0;34m][0m[0;34m[[0m[0;34m:[0m[0;36m255[0m[0;34m][0m [0;31m# printing the first 255 characters of the first document[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
E AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:286: CellExecutionError
--- generated xml file: /mnt/data/jenkins/workspace/DARIAH-Topics/tests.xml ----
----------- coverage: platform linux, python 3.5.3-final-0 -----------
Coverage HTML written to dir htmlcov
Coverage XML written to file coverage.xml
=============================== warnings summary ===============================
dariah_topics/postprocessing.py::dariah_topics.postprocessing._show_lda_document_topics
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py:1: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.
"""
dariah_topics/postprocessing.py::dariah_topics.postprocessing._show_lda_topics
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py:1: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.
"""
dariah_topics/postprocessing.py::dariah_topics.postprocessing.doc2bow
/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/cophi_toolbox/preprocessing.py:624: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/postprocessing.py::dariah_topics.postprocessing.save_document_term_matrix
/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/cophi_toolbox/preprocessing.py:624: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing._create_large_corpus_model
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing._hapax_legomena_large_corpus_model
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing._list_mfw_large_corpus_model
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing._remove_features_from_large_corpus_model
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing.create_document_term_matrix
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing.find_hapax_legomena
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing.list_mfw
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
dariah_topics/preprocessing.py::dariah_topics.preprocessing.remove_features
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:732: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead
document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id]))
-- Docs: http://doc.pytest.org/en/latest/warnings.html
============== 5 failed, 52 passed, 12 warnings in 130.57 seconds ==============
Build step 'Virtualenv Builder' marked build as failure
Recording test results
[Cobertura] Publishing Cobertura coverage report...
[Cobertura] Publishing Cobertura coverage results...
[Cobertura] Cobertura coverage report found.
[Set GitHub commit status (universal)] ERROR on repos [GHRepository@51ee05b5[description=A Python library for topic modeling.,homepage=https://dariah-de.github.io/Topics,name=Topics,fork=true,size=42271,milestones={},language=Python,commits={},responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/json; charset=utf-8], Date=[Wed, 13 Jun 2018 15:12:11 GMT], ETag=[W/"31f7150108d94b8dd6a57beccf0e4832"], Last-Modified=[Mon, 04 Jun 2018 10:20:02 GMT], OkHttp-Received-Millis=[1528902731741], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1528902731535], Referrer-Policy=[origin-when-cross-origin, strict-origin-when-cross-origin], Server=[GitHub.com], Status=[200 OK], Strict-Transport-Security=[max-age=31536000; includeSubdomains; preload], Transfer-Encoding=[chunked], Vary=[Accept, Authorization, Cookie, X-GitHub-OTP], X-Accepted-OAuth-Scopes=[repo], X-Content-Type-Options=[nosniff], X-Frame-Options=[deny], X-GitHub-Media-Type=[github.v3; format=json], X-GitHub-Request-Id=[9AA0:0FDE:3720D9:7EFF29:5B21344B], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4997], X-RateLimit-Reset=[1528906075], X-Runtime-rack=[0.108915], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/DARIAH-DE/Topics,id=69341969]] (sha:6951841) with context:DARIAH-Topics
Setting commit status on GitHub for https://github.com/DARIAH-DE/Topics/commit/6951841891e07d6dd5eadeb09c897aa3b405cfdb
[BFA] Scanning build for known causes...
[BFA] No failure causes found
[BFA] Done. 0s
Started calculate disk usage of build
Finished Calculation of disk usage of build in 0 seconds
Started calculate disk usage of workspace
Finished Calculation of disk usage of workspace in 0 seconds
Notifying upstream projects of job completion
[ci-game] evaluating rule: Build result
[ci-game] scored: -10.0
[ci-game] evaluating rule: Increased number of passed tests
[ci-game] evaluating rule: Decreased number of passed tests
[ci-game] evaluating rule: Increased number of failed tests
[ci-game] evaluating rule: Decreased number of failed tests
[ci-game] evaluating rule: Increased number of skipped tests
[ci-game] evaluating rule: Decreased number of skipped tests
[ci-game] evaluating rule: Open HIGH priority tasks
[ci-game] evaluating rule: Open NORMAL priority tasks
[ci-game] evaluating rule: Open LOW priority tasks
[ci-game] evaluating rule: Changed number of compiler warnings
Finished: FAILURE
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