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Started by GitHub push by ThoraHagen
Building remotely on build3 (digibib) 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 b3714747ccf8cde3e96a5efca4b6918aa1fe1863 (refs/remotes/origin/testing)
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f b3714747ccf8cde3e96a5efca4b6918aa1fe1863
Commit message: "updated paths in cmd command"
 > /usr/bin/git rev-list --no-walk fa8b872c7b9d265332c411fa666db2371d256e62 # 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/shiningpanda4861151470286543940.sh
+ pip install -U pip
Requirement already up-to-date: pip in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages (18.1)
+ 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 nbsmoke (from -r requirements-dev.txt (line 6))
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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-ku_n97xg/nbsphinx
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Collecting pandas>=0.19.2 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
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Collecting regex>=2017.01.14 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
Collecting gensim>=0.13.2 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
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Collecting lxml>=3.6.4 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
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Collecting matplotlib>=1.5.3 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
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Collecting bokeh>=0.12.6 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/13/a8/6027d0d25f7056fe3c3c1ddcf917e6e2bb981186fd809171906e631b6c08/bokeh-1.0.0.tar.gz (16.1MB)
Collecting metadata_toolbox (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
Collecting cophi_toolbox>=0.1.1.dev0 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
Collecting attrs>=17.4.0 (from pytest->-r requirements-dev.txt (line 4))
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Collecting pluggy>=0.7 (from pytest->-r requirements-dev.txt (line 4))
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Requirement already satisfied, skipping upgrade: setuptools in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages (from pytest->-r requirements-dev.txt (line 4)) (40.4.3)
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))
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Collecting atomicwrites>=1.0 (from pytest->-r requirements-dev.txt (line 4))
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Collecting coverage>=4.4 (from pytest-cov->-r requirements-dev.txt (line 5))
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Collecting nbconvert (from nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/b5/bb/94c493051d60e5b9c0f7f9a368b324201818c1b1c4cae85d1e49a41846c7/nbconvert-5.4.0-py2.py3-none-any.whl
Collecting ipykernel (from nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/d8/b0/f0be5c5ab335196f5cce96e5b889a4fcf5bfe462eb0acc05cd7e2caf65eb/ipykernel-5.1.0-py3-none-any.whl
Collecting pyflakes (from nbsmoke->-r requirements-dev.txt (line 6))
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Collecting requests (from nbsmoke->-r requirements-dev.txt (line 6))
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Collecting nbformat (from nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl
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Collecting ipython-genutils (from nbformat->nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting jsonschema!=2.5.0,>=2.4 (from nbformat->nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/77/de/47e35a97b2b05c2fadbec67d44cfcdcd09b8086951b331d82de90d2912da/jsonschema-2.6.0-py2.py3-none-any.whl
Collecting pyzmq>=13 (from jupyter-client->nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/48/93/59592cb294761aaa40589b544eaa5175446d687ff95beeeb666de60f3274/pyzmq-17.1.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting prompt-toolkit<2.1.0,>=2.0.0 (from jupyter-console->jupyter->-r requirements-dev.txt (line 9))
  Using cached https://files.pythonhosted.org/packages/06/6f/03f10d2206e34a81934b10fb43975a29028e0fe2ae330f9f000bbc0780b7/prompt_toolkit-2.0.6-py3-none-any.whl
Collecting prometheus-client (from notebook->jupyter->-r requirements-dev.txt (line 9))
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 widgetsnbextension~=3.4.0 (from ipywidgets->jupyter->-r requirements-dev.txt (line 9))
  Using cached https://files.pythonhosted.org/packages/8a/81/35789a3952afb48238289171728072d26d6e76649ddc8b3588657a2d78c1/widgetsnbextension-3.4.2-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 bz2file (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
Collecting boto3 (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/79/3a/83343781a55da594eebe96294721e263a2bdb2d4a9f803b4e728483ad8ef/boto3-1.9.31-py2.py3-none-any.whl (128kB)
Collecting boto>=2.32 (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
  Using cached https://files.pythonhosted.org/packages/23/10/c0b78c27298029e4454a472a1919bde20cb182dab1662cec7f2ca1dcc523/boto-2.49.0-py2.py3-none-any.whl
Collecting webencodings (from 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 jedi>=0.10 (from ipython>=5.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/7a/1a/9bd24a185873b998611c2d8d4fb15cd5e8a879ead36355df7ee53e9111bf/jedi-0.13.1-py2.py3-none-any.whl
Collecting backcall (from ipython>=5.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Collecting pexpect; sys_platform != "win32" (from ipython>=5.0.0->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 pickleshare (from ipython>=5.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting simplegeneric>0.8 (from ipython>=5.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
Collecting wcwidth (from prompt-toolkit<2.1.0,>=2.0.0->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/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl
Collecting botocore<1.13.0,>=1.12.31 (from boto3->smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/5f/f0/2bb0dd2ec4f8f4d8eec3ad35532270844ec139ff3f570f335ef849592617/botocore-1.12.31-py2.py3-none-any.whl (4.7MB)
Collecting jmespath<1.0.0,>=0.7.1 (from boto3->smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.2.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 s3transfer<0.2.0,>=0.1.10 (from boto3->smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==1.0.2.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 parso>=0.3.0 (from jedi>=0.10->ipython>=5.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/09/51/9c48a46334be50c13d25a3afe55fa05c445699304c5ad32619de953a2305/parso-0.3.1-py2.py3-none-any.whl
Building wheels for collected packages: nbsphinx, bokeh
  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-wngbcznu/wheels/a3/7b/ff/b71160a2e088926eb13abcf8e0cde94c0aa8400c67d3df57f5
  Running setup.py bdist_wheel for bokeh: started
  Running setup.py bdist_wheel for bokeh: finished with status 'done'
  Stored in directory: /mnt/data/jenkins/.cache/pip/wheels/27/1c/93/5a0696b0c304b3cd53dbcd7fdd0dd55f107e0c389aa59d4ae1
Successfully built nbsphinx bokeh
nbsphinx 0.3.5 has requirement nbconvert!=5.4, but you'll have nbconvert 5.4.0 which is incompatible.
Installing collected packages: attrs, pluggy, six, more-itertools, py, atomicwrites, pytest, coverage, pytest-cov, testpath, webencodings, bleach, defusedxml, pandocfilters, ipython-genutils, decorator, traitlets, jsonschema, jupyter-core, nbformat, MarkupSafe, Jinja2, mistune, entrypoints, Pygments, nbconvert, tornado, pyzmq, python-dateutil, jupyter-client, parso, jedi, backcall, ptyprocess, pexpect, pickleshare, simplegeneric, wcwidth, prompt-toolkit, ipython, ipykernel, pyflakes, certifi, idna, urllib3, chardet, requests, beautifulsoup4, nbsmoke, jupyter-console, prometheus-client, Send2Trash, terminado, notebook, widgetsnbextension, ipywidgets, qtconsole, jupyter, imagesize, alabaster, pytz, babel, docutils, pyparsing, packaging, snowballstemmer, sphinxcontrib-websupport, sphinx, nbsphinx, commonmark, recommonmark, numpy, pandas, regex, scipy, bz2file, jmespath, botocore, s3transfer, boto3, boto, smart-open, gensim, pbr, lda, lxml, kiwisolver, cycler, matplotlib, PyYAML, pillow, bokeh, parse, metadata-toolbox, cophi-toolbox, dariah-topics
  Running setup.py develop for dariah-topics
Successfully installed Jinja2-2.10 MarkupSafe-1.0 PyYAML-3.13 Pygments-2.2.0 Send2Trash-1.5.0 alabaster-0.7.12 atomicwrites-1.2.1 attrs-18.2.0 babel-2.6.0 backcall-0.1.0 beautifulsoup4-4.6.3 bleach-3.0.2 bokeh-1.0.0 boto-2.49.0 boto3-1.9.31 botocore-1.12.31 bz2file-0.98 certifi-2018.10.15 chardet-3.0.4 commonmark-0.5.4 cophi-toolbox-0.1.1.dev0 coverage-4.5.1 cycler-0.10.0 dariah-topics decorator-4.3.0 defusedxml-0.5.0 docutils-0.14 entrypoints-0.2.3 gensim-3.6.0 idna-2.7 imagesize-1.1.0 ipykernel-5.1.0 ipython-7.0.1 ipython-genutils-0.2.0 ipywidgets-7.4.2 jedi-0.13.1 jmespath-0.9.3 jsonschema-2.6.0 jupyter-1.0.0 jupyter-client-5.2.3 jupyter-console-6.0.0 jupyter-core-4.4.0 kiwisolver-1.0.1 lda-1.1.0 lxml-4.2.5 matplotlib-3.0.0 metadata-toolbox-0.1.0.dev0 mistune-0.8.4 more-itertools-4.3.0 nbconvert-5.4.0 nbformat-4.4.0 nbsmoke-0.2.7 nbsphinx-0.3.5 notebook-5.7.0 numpy-1.15.3 packaging-18.0 pandas-0.23.4 pandocfilters-1.4.2 parse-1.9.0 parso-0.3.1 pbr-3.1.1 pexpect-4.6.0 pickleshare-0.7.5 pillow-5.3.0 pluggy-0.8.0 prometheus-client-0.4.2 prompt-toolkit-2.0.6 ptyprocess-0.6.0 py-1.7.0 pyflakes-2.0.0 pyparsing-2.2.2 pytest-3.9.2 pytest-cov-2.6.0 python-dateutil-2.7.3 pytz-2018.6 pyzmq-17.1.2 qtconsole-4.4.2 recommonmark-0.4.0 regex-2018.8.29 requests-2.20.0 s3transfer-0.1.13 scipy-1.1.0 simplegeneric-0.8.1 six-1.11.0 smart-open-1.7.1 snowballstemmer-1.2.1 sphinx-1.8.1 sphinxcontrib-websupport-1.1.0 terminado-0.8.1 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 urllib3-1.24 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.4.2
+ ./setup.py sdist bdist_wheel
running sdist
running egg_info
writing dariah_topics.egg-info/PKG-INFO
writing dependency_links to dariah_topics.egg-info/dependency_links.txt
writing requirements to dariah_topics.egg-info/requires.txt
writing top-level names to dariah_topics.egg-info/top_level.txt
reading manifest file 'dariah_topics.egg-info/SOURCES.txt'
writing manifest file 'dariah_topics.egg-info/SOURCES.txt'
running check
creating dariah_topics-1.0.2.dev0
creating dariah_topics-1.0.2.dev0/dariah_topics
creating dariah_topics-1.0.2.dev0/dariah_topics.egg-info
creating dariah_topics-1.0.2.dev0/test
copying files to dariah_topics-1.0.2.dev0...
copying README.md -> dariah_topics-1.0.2.dev0
copying setup.cfg -> dariah_topics-1.0.2.dev0
copying setup.py -> dariah_topics-1.0.2.dev0
copying dariah_topics/__init__.py -> dariah_topics-1.0.2.dev0/dariah_topics
copying dariah_topics/evaluation.py -> dariah_topics-1.0.2.dev0/dariah_topics
copying dariah_topics/modeling.py -> dariah_topics-1.0.2.dev0/dariah_topics
copying dariah_topics/postprocessing.py -> dariah_topics-1.0.2.dev0/dariah_topics
copying dariah_topics/preprocessing.py -> dariah_topics-1.0.2.dev0/dariah_topics
copying dariah_topics/utils.py -> dariah_topics-1.0.2.dev0/dariah_topics
copying dariah_topics/visualization.py -> dariah_topics-1.0.2.dev0/dariah_topics
copying dariah_topics.egg-info/PKG-INFO -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/SOURCES.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/dependency_links.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/requires.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info
copying dariah_topics.egg-info/top_level.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info
copying test/test_fuzzy_segmenting.py -> dariah_topics-1.0.2.dev0/test
Writing dariah_topics-1.0.2.dev0/setup.cfg
Creating tar archive
removing 'dariah_topics-1.0.2.dev0' (and everything under it)
running bdist_wheel
running build
running build_py
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/postprocessing.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/visualization.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/__init__.py -> 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/evaluation.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-1.0.2.dev0-py3.6.egg-info
running install_scripts
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
creating build/bdist.linux-x86_64/wheel/dariah_topics-1.0.2.dev0.dist-info/WHEEL
creating 'dist/dariah_topics-1.0.2.dev0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' 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-1.0.2.dev0.dist-info/LICENSE'
adding 'dariah_topics-1.0.2.dev0.dist-info/METADATA'
adding 'dariah_topics-1.0.2.dev0.dist-info/WHEEL'
adding 'dariah_topics-1.0.2.dev0.dist-info/top_level.txt'
adding 'dariah_topics-1.0.2.dev0.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/setuptools/dist.py:398: UserWarning: Normalizing '1.0.2.dev' to '1.0.2.dev0'
  normalized_version,
+ pytest --nbsmoke-run
============================= test session starts ==============================
platform linux -- Python 3.6.6, pytest-3.9.2, py-1.7.0, pluggy-0.8.0
rootdir: /mnt/data/jenkins/workspace/DARIAH-Topics, inifile: setup.cfg
plugins: cov-2.6.0, nbsmoke-0.2.7
collected 58 items

dariah_topics/postprocessing.py ...........                              [ 18%]
dariah_topics/preprocessing.py ...........................               [ 65%]
dariah_topics/utils.py ......                                            [ 75%]
notebooks/IntroducingGensim.ipynb F                                      [ 77%]
notebooks/IntroducingLda.ipynb F                                         [ 79%]
notebooks/IntroducingLda_DKProWrapper.ipynb F                            [ 81%]
notebooks/IntroducingMallet.ipynb F                                      [ 82%]
notebooks/Visualizations.ipynb F                                         [ 84%]
test/test_fuzzy_segmenting.py .........                                  [100%]

=================================== FAILURES ===================================
_______________________________________  _______________________________________

self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
PlotDocument...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6ad8e35d08>
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/python3.6/site-packages/_pytest/runner.py:206: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>       lambda: ihook(item=item, **kwds),
        when=when,
        treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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.spec and self.spec.argnames:
            notincall = (
                set(self.spec.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.get_hookimpls(), kwargs)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/manager.py:67: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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") if hook.spec else False,
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:208: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pluggy.callers._Result object at 0x7f6b1b9a4828>

    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/python3.6/site-packages/pluggy/callers.py:80: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:187: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/_pytest/runner.py:116: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/nbsmoke/__init__.py:274: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6b17efdc18>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 1}
resources = {}, km = None

    def preprocess(self, nb, resources, km=None):
        """
        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``.
        km: KernelManager (optional)
            Optional kernel manager. If none is provided, a kernel manager will
            be created.
    
        Returns
        -------
        nb : NotebookNode
            The executed notebook.
        resources : dictionary
            Additional resources used in the conversion process.
        """
    
        with self.setup_preprocessor(nb, resources, km=km):
            self.log.info("Executing notebook with kernel: %s" % self.kernel_name)
>           nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6b17efdc18>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, '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/python3.6/site-packages/nbconvert/preprocessors/base.py:69: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6b17efdc18>
cell = {'cell_type': 'code', 'execution_count': 22, 'metadata': {'scrolled': False}, 'outputs': [{'output_type': 'error', 'en...sualization.PlotDocumentTopics(document_topics)\nshow(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)'}
resources = {}, cell_index = 51

    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' or not cell.source.strip():
            return cell, resources
    
        reply, outputs = self.run_cell(cell, cell_index)
        cell.outputs = outputs
    
        cell_allows_errors = (self.allow_errors or "raises-exception"
                              in cell.metadata.get("tags", []))
    
        if self.force_raise_errors or not cell_allows_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                   PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics)
E                   show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)
E                   ------------------
E                   
E                   ---------------------------------------------------------------------------
E                   AttributeError                            Traceback (most recent call last)
E                   <ipython-input-22-3c545f10dd80> in <module>
E                         1 PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics)
E                   ----> 2 show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)
E                   
E                   ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)
E                       283                      tools=tools, toolbar_location=toolbar_location,
E                       284                      sizing_mode=sizing_mode,
E                   --> 285                      logo=None)
E                       286         fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E                       287                  fill_color={'field': 'Distributions', 'transform': mapper},
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in figure(**kwargs)
E                      1021 
E                      1022 def figure(**kwargs):
E                   -> 1023     return Figure(**kwargs)
E                      1024 figure.__doc__ = Figure.__doc__
E                      1025 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw)
E                       187             kw['title'] = Title(text=title)
E                       188 
E                   --> 189         super(Figure, self).__init__(*arg, **kw)
E                       190 
E                       191         self.x_range = _get_range(opts.x_range)
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py in __init__(self, **kwargs)
E                       259         self._document = None
E                       260         self._temp_document = None
E                   --> 261         super(Model, self).__init__(**kwargs)
E                       262         default_theme.apply_to_model(self)
E                       263 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __init__(self, **properties)
E                       252 
E                       253         for name, value in properties.items():
E                   --> 254             setattr(self, name, value)
E                       255 
E                       256     def __setattr__(self, name, value):
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value)
E                       287 
E                       288             raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E                   --> 289                 (name, self.__class__.__name__, text, nice_join(matches)))
E                       290 
E                       291     def __str__(self):
E                   
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError
_______________________________________  _______________________________________

self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
PlotDocument...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6ad8e35c80>
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/python3.6/site-packages/_pytest/runner.py:206: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>       lambda: ihook(item=item, **kwds),
        when=when,
        treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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.spec and self.spec.argnames:
            notincall = (
                set(self.spec.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.get_hookimpls(), kwargs)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/manager.py:67: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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") if hook.spec else False,
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:208: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pluggy.callers._Result object at 0x7f6af1a22da0>

    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/python3.6/site-packages/pluggy/callers.py:80: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:187: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/_pytest/runner.py:116: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/nbsmoke/__init__.py:274: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af17c93c8>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 1}
resources = {}, km = None

    def preprocess(self, nb, resources, km=None):
        """
        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``.
        km: KernelManager (optional)
            Optional kernel manager. If none is provided, a kernel manager will
            be created.
    
        Returns
        -------
        nb : NotebookNode
            The executed notebook.
        resources : dictionary
            Additional resources used in the conversion process.
        """
    
        with self.setup_preprocessor(nb, resources, km=km):
            self.log.info("Executing notebook with kernel: %s" % self.kernel_name)
>           nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af17c93c8>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, '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/python3.6/site-packages/nbconvert/preprocessors/base.py:69: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af17c93c8>
cell = {'cell_type': 'code', 'execution_count': 23, 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeE...sualization.PlotDocumentTopics(document_topics)\nshow(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)'}
resources = {}, cell_index = 56

    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' or not cell.source.strip():
            return cell, resources
    
        reply, outputs = self.run_cell(cell, cell_index)
        cell.outputs = outputs
    
        cell_allows_errors = (self.allow_errors or "raises-exception"
                              in cell.metadata.get("tags", []))
    
        if self.force_raise_errors or not cell_allows_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                   PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics)
E                   show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)
E                   ------------------
E                   
E                   ---------------------------------------------------------------------------
E                   AttributeError                            Traceback (most recent call last)
E                   <ipython-input-23-3c545f10dd80> in <module>
E                         1 PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics)
E                   ----> 2 show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)
E                   
E                   ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)
E                       283                      tools=tools, toolbar_location=toolbar_location,
E                       284                      sizing_mode=sizing_mode,
E                   --> 285                      logo=None)
E                       286         fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E                       287                  fill_color={'field': 'Distributions', 'transform': mapper},
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in figure(**kwargs)
E                      1021 
E                      1022 def figure(**kwargs):
E                   -> 1023     return Figure(**kwargs)
E                      1024 figure.__doc__ = Figure.__doc__
E                      1025 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw)
E                       187             kw['title'] = Title(text=title)
E                       188 
E                   --> 189         super(Figure, self).__init__(*arg, **kw)
E                       190 
E                       191         self.x_range = _get_range(opts.x_range)
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py in __init__(self, **kwargs)
E                       259         self._document = None
E                       260         self._temp_document = None
E                   --> 261         super(Model, self).__init__(**kwargs)
E                       262         default_theme.apply_to_model(self)
E                       263 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __init__(self, **properties)
E                       252 
E                       253         for name, value in properties.items():
E                   --> 254             setattr(self, name, value)
E                       255 
E                       256     def __setattr__(self, name, value):
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value)
E                       287 
E                       288             raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E                   --> 289                 (name, self.__class__.__name__, text, nice_join(matches)))
E                       290 
E                       291     def __str__(self):
E                   
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError
_______________________________________  _______________________________________

self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
meta = pd.co...0m:

ValueError: No objects to concatenate
ValueError: No objects to concatenate
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6af197f268>
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/python3.6/site-packages/_pytest/runner.py:206: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>       lambda: ihook(item=item, **kwds),
        when=when,
        treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <_HookCaller 'pytest_runtest_call'>, args = ()
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.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.spec and self.spec.argnames:
            notincall = (
                set(self.spec.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.get_hookimpls(), kwargs)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.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/python3.6/site-packages/pluggy/manager.py:67: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'>}

    self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
        methods,
        kwargs,
>       firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.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/python3.6/site-packages/pluggy/callers.py:208: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pluggy.callers._Result object at 0x7f6b1418c828>

    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/python3.6/site-packages/pluggy/callers.py:80: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.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/python3.6/site-packages/pluggy/callers.py:187: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.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/python3.6/site-packages/_pytest/runner.py:116: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.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/python3.6/site-packages/nbsmoke/__init__.py:274: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af196e550>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, 'nbformat_minor': 1}
resources = {}, km = None

    def preprocess(self, nb, resources, km=None):
        """
        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``.
        km: KernelManager (optional)
            Optional kernel manager. If none is provided, a kernel manager will
            be created.
    
        Returns
        -------
        nb : NotebookNode
            The executed notebook.
        resources : dictionary
            Additional resources used in the conversion process.
        """
    
        with self.setup_preprocessor(nb, resources, km=km):
            self.log.info("Executing notebook with kernel: %s" % self.kernel_name)
>           nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af196e550>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, '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/python3.6/site-packages/nbconvert/preprocessors/base.py:69: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af196e550>
cell = {'cell_type': 'code', 'execution_count': 7, 'metadata': {'collapsed': False, 'scrolled': True}, 'outputs': [{'output_t...ath_to_corpus.glob('*.csv')])\nmeta[:5] # by adding '[:5]' to the variable, only the first 5 elements will be printed"}
resources = {}, cell_index = 19

    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' or not cell.source.strip():
            return cell, resources
    
        reply, outputs = self.run_cell(cell, cell_index)
        cell.outputs = outputs
    
        cell_allows_errors = (self.allow_errors or "raises-exception"
                              in cell.metadata.get("tags", []))
    
        if self.force_raise_errors or not cell_allows_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                   meta = pd.concat([metadata.fname2metadata(str(path), pattern=pattern) for path in path_to_corpus.glob('*.csv')])
E                   meta[:5] # by adding '[:5]' to the variable, only the first 5 elements will be printed
E                   ------------------
E                   
E                   ---------------------------------------------------------------------------
E                   ValueError                                Traceback (most recent call last)
E                   <ipython-input-7-30c5c181683a> in <module>
E                   ----> 1 meta = pd.concat([metadata.fname2metadata(str(path), pattern=pattern) for path in path_to_corpus.glob('*.csv')])
E                         2 meta[:5] # by adding '[:5]' to the variable, only the first 5 elements will be printed
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pandas/core/reshape/concat.py in concat(objs, axis, join, join_axes, ignore_index, keys, levels, names, verify_integrity, sort, copy)
E                       223                        keys=keys, levels=levels, names=names,
E                       224                        verify_integrity=verify_integrity,
E                   --> 225                        copy=copy, sort=sort)
E                       226     return op.get_result()
E                       227 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pandas/core/reshape/concat.py in __init__(self, objs, axis, join, join_axes, keys, levels, names, ignore_index, verify_integrity, copy, sort)
E                       257 
E                       258         if len(objs) == 0:
E                   --> 259             raise ValueError('No objects to concatenate')
E                       260 
E                       261         if keys is None:
E                   
E                   ValueError: No objects to concatenate
E                   ValueError: No objects to concatenate

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError
_______________________________________  _______________________________________

self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
PlotDocument...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6af1846e18>
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/python3.6/site-packages/_pytest/runner.py:206: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>       lambda: ihook(item=item, **kwds),
        when=when,
        treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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.spec and self.spec.argnames:
            notincall = (
                set(self.spec.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.get_hookimpls(), kwargs)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/manager.py:67: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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") if hook.spec else False,
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:208: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pluggy.callers._Result object at 0x7f6af1886e48>

    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/python3.6/site-packages/pluggy/callers.py:80: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:187: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/_pytest/runner.py:116: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/nbsmoke/__init__.py:274: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af18864e0>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, 'nbformat_minor': 1}
resources = {}, km = None

    def preprocess(self, nb, resources, km=None):
        """
        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``.
        km: KernelManager (optional)
            Optional kernel manager. If none is provided, a kernel manager will
            be created.
    
        Returns
        -------
        nb : NotebookNode
            The executed notebook.
        resources : dictionary
            Additional resources used in the conversion process.
        """
    
        with self.setup_preprocessor(nb, resources, km=km):
            self.log.info("Executing notebook with kernel: %s" % self.kernel_name)
>           nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af18864e0>
nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, '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/python3.6/site-packages/nbconvert/preprocessors/base.py:69: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af18864e0>
cell = {'cell_type': 'code', 'execution_count': 25, 'metadata': {'collapsed': True}, 'outputs': [{'output_type': 'error', 'en...sualization.PlotDocumentTopics(document_topics)\nshow(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)'}
resources = {}, cell_index = 60

    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' or not cell.source.strip():
            return cell, resources
    
        reply, outputs = self.run_cell(cell, cell_index)
        cell.outputs = outputs
    
        cell_allows_errors = (self.allow_errors or "raises-exception"
                              in cell.metadata.get("tags", []))
    
        if self.force_raise_errors or not cell_allows_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                   PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics)
E                   show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)
E                   ------------------
E                   
E                   ---------------------------------------------------------------------------
E                   AttributeError                            Traceback (most recent call last)
E                   <ipython-input-25-3c545f10dd80> in <module>
E                         1 PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics)
E                   ----> 2 show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)
E                   
E                   ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)
E                       283                      tools=tools, toolbar_location=toolbar_location,
E                       284                      sizing_mode=sizing_mode,
E                   --> 285                      logo=None)
E                       286         fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E                       287                  fill_color={'field': 'Distributions', 'transform': mapper},
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in figure(**kwargs)
E                      1021 
E                      1022 def figure(**kwargs):
E                   -> 1023     return Figure(**kwargs)
E                      1024 figure.__doc__ = Figure.__doc__
E                      1025 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw)
E                       187             kw['title'] = Title(text=title)
E                       188 
E                   --> 189         super(Figure, self).__init__(*arg, **kw)
E                       190 
E                       191         self.x_range = _get_range(opts.x_range)
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py in __init__(self, **kwargs)
E                       259         self._document = None
E                       260         self._temp_document = None
E                   --> 261         super(Model, self).__init__(**kwargs)
E                       262         default_theme.apply_to_model(self)
E                       263 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __init__(self, **properties)
E                       252 
E                       253         for name, value in properties.items():
E                   --> 254             setattr(self, name, value)
E                       255 
E                       256     def __setattr__(self, name, value):
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value)
E                       287 
E                       288             raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E                   --> 289                 (name, self.__class__.__name__, text, nice_join(matches)))
E                       290 
E                       291     def __str__(self):
E                   
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError
_______________________________________  _______________________________________

self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
interactive_...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6af18d7ea0>
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/python3.6/site-packages/_pytest/runner.py:206: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

>       lambda: ihook(item=item, **kwds),
        when=when,
        treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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.spec and self.spec.argnames:
            notincall = (
                set(self.spec.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.get_hookimpls(), kwargs)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/manager.py:67: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook = <_HookCaller 'pytest_runtest_call'>
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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") if hook.spec else False,
    )

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:208: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <pluggy.callers._Result object at 0x7f6af195a518>

    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/python3.6/site-packages/pluggy/callers.py:80: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>]
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/python3.6/site-packages/pluggy/callers.py:187: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/_pytest/runner.py:116: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

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/python3.6/site-packages/nbsmoke/__init__.py:274: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af195ac18>
nb = {'cells': [{'cell_type': 'code', 'execution_count': 1, 'metadata': {}, 'outputs': [], 'source': 'from cophi_toolbox im...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 2}
resources = {}, km = None

    def preprocess(self, nb, resources, km=None):
        """
        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``.
        km: KernelManager (optional)
            Optional kernel manager. If none is provided, a kernel manager will
            be created.
    
        Returns
        -------
        nb : NotebookNode
            The executed notebook.
        resources : dictionary
            Additional resources used in the conversion process.
        """
    
        with self.setup_preprocessor(nb, resources, km=km):
            self.log.info("Executing notebook with kernel: %s" % self.kernel_name)
>           nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af195ac18>
nb = {'cells': [{'cell_type': 'code', 'execution_count': 1, 'metadata': {}, 'outputs': [], 'source': 'from cophi_toolbox im...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, '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/python3.6/site-packages/nbconvert/preprocessors/base.py:69: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af195ac18>
cell = {'cell_type': 'code', 'execution_count': 21, 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeE...                                                     colorbar=False)\nshow(interactive_heatmap, notebook_handle=True)'}
resources = {}, cell_index = 26

    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' or not cell.source.strip():
            return cell, resources
    
        reply, outputs = self.run_cell(cell, cell_index)
        cell.outputs = outputs
    
        cell_allows_errors = (self.allow_errors or "raises-exception"
                              in cell.metadata.get("tags", []))
    
        if self.force_raise_errors or not cell_allows_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                   interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=800,
E                                                                                height=550,
E                                                                                colorbar=False)
E                   show(interactive_heatmap, notebook_handle=True)
E                   ------------------
E                   
E                   ---------------------------------------------------------------------------
E                   AttributeError                            Traceback (most recent call last)
E                   <ipython-input-21-0ec82b4d408d> in <module>
E                         1 interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=800,
E                         2                                                              height=550,
E                   ----> 3                                                              colorbar=False)
E                         4 show(interactive_heatmap, notebook_handle=True)
E                   
E                   ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)
E                       283                      tools=tools, toolbar_location=toolbar_location,
E                       284                      sizing_mode=sizing_mode,
E                   --> 285                      logo=None)
E                       286         fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E                       287                  fill_color={'field': 'Distributions', 'transform': mapper},
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in figure(**kwargs)
E                      1021 
E                      1022 def figure(**kwargs):
E                   -> 1023     return Figure(**kwargs)
E                      1024 figure.__doc__ = Figure.__doc__
E                      1025 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw)
E                       187             kw['title'] = Title(text=title)
E                       188 
E                   --> 189         super(Figure, self).__init__(*arg, **kw)
E                       190 
E                       191         self.x_range = _get_range(opts.x_range)
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py in __init__(self, **kwargs)
E                       259         self._document = None
E                       260         self._temp_document = None
E                   --> 261         super(Model, self).__init__(**kwargs)
E                       262         default_theme.apply_to_model(self)
E                       263 
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __init__(self, **properties)
E                       252 
E                       253         for name, value in properties.items():
E                   --> 254             setattr(self, name, value)
E                       255 
E                       256     def __setattr__(self, name, value):
E                   
E                   ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value)
E                       287 
E                       288             raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E                   --> 289                 (name, self.__class__.__name__, text, nice_join(matches)))
E                       290 
E                       291     def __str__(self):
E                   
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale
E                   AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale

../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError
--- generated xml file: /mnt/data/jenkins/workspace/DARIAH-Topics/tests.xml ----

----------- coverage: platform linux, python 3.6.6-final-0 -----------
Coverage HTML written to dir htmlcov
Coverage XML written to file coverage.xml

=============================== warnings summary ===============================
/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/scipy/sparse/sparsetools.py:21: DeprecationWarning: `scipy.sparse.sparsetools` is deprecated!
scipy.sparse.sparsetools is a private module for scipy.sparse, and should not be used.
  _deprecated()

/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead.
  score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc)
/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead.
  score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc)

/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead.
  score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc)
/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead.
  score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc)

/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.
  """

/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.
  """

/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/cophi_toolbox/preprocessing.py:625: 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]))

/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/cophi_toolbox/preprocessing.py:625: 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]))

/mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/jupyter_client/manager.py:72: DeprecationWarning: KernelManager._kernel_name_changed is deprecated in traitlets 4.1: use @observe and @unobserve instead.
  def _kernel_name_changed(self, name, old, new):
source:409: DeprecationWarning: invalid escape sequence \.

source:409: DeprecationWarning: invalid escape sequence \.

source:409: DeprecationWarning: invalid escape sequence \.

source:409: DeprecationWarning: invalid escape sequence \.

source:409: DeprecationWarning: invalid escape sequence \.

-- Docs: https://docs.pytest.org/en/latest/warnings.html
============== 5 failed, 53 passed, 15 warnings in 120.85 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@50ab1296[description=A Python library for topic modeling.,homepage=https://dariah-de.github.io/Topics,name=Topics,fork=true,size=42293,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=[Thu, 25 Oct 2018 10:41:23 GMT], ETag=[W/"3b8962e9f2c24ae0e50646a4b1003161"], Last-Modified=[Thu, 04 Oct 2018 17:51:13 GMT], OkHttp-Received-Millis=[1540464083940], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1540464083693], 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=[91EF:4347:40AAE2B:90CC6F4:5BD19DD3], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4987], X-RateLimit-Reset=[1540466257], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/DARIAH-DE/Topics,id=69341969]] (sha:b371474) with context:DARIAH-Topics
Setting commit status on GitHub for https://github.com/DARIAH-DE/Topics/commit/b3714747ccf8cde3e96a5efca4b6918aa1fe1863
[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] 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