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 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 regex>=2017.01.14 (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)
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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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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)
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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 [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-22-3c545f10dd80>[0m in [0;36m<module>[0;34m[0m
E [1;32m 1[0m [0mPlotDocumentTopics[0m [0;34m=[0m [0mvisualization[0m[0;34m.[0m[0mPlotDocumentTopics[0m[0;34m([0m[0mdocument_topics[0m[0;34m)[0m[0;34m[0m[0m
E [0;32m----> 2[0;31m [0mshow[0m[0;34m([0m[0mPlotDocumentTopics[0m[0;34m.[0m[0minteractive_heatmap[0m[0;34m([0m[0;34m)[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m
E [0m
E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(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)[0m
E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m
E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m
E [0;32m--> 285[0;31m logo=None)
E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m
E [1;32m 1021[0m [0;34m[0m[0m
E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m
E [1;32m 1025[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m
E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 188[0m [0;34m[0m[0m
E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 190[0m [0;34m[0m[0m
E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m
E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 263[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m
E [1;32m 252[0m [0;34m[0m[0m
E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 255[0m [0;34m[0m[0m
E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m
E [1;32m 287[0m [0;34m[0m[0m
E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches)))
E [0m[1;32m 290[0m [0;34m[0m[0m
E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: 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 [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-23-3c545f10dd80>[0m in [0;36m<module>[0;34m[0m
E [1;32m 1[0m [0mPlotDocumentTopics[0m [0;34m=[0m [0mvisualization[0m[0;34m.[0m[0mPlotDocumentTopics[0m[0;34m([0m[0mdocument_topics[0m[0;34m)[0m[0;34m[0m[0m
E [0;32m----> 2[0;31m [0mshow[0m[0;34m([0m[0mPlotDocumentTopics[0m[0;34m.[0m[0minteractive_heatmap[0m[0;34m([0m[0;34m)[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m
E [0m
E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(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)[0m
E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m
E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m
E [0;32m--> 285[0;31m logo=None)
E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m
E [1;32m 1021[0m [0;34m[0m[0m
E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m
E [1;32m 1025[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m
E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 188[0m [0;34m[0m[0m
E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 190[0m [0;34m[0m[0m
E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m
E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 263[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m
E [1;32m 252[0m [0;34m[0m[0m
E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 255[0m [0;34m[0m[0m
E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m
E [1;32m 287[0m [0;34m[0m[0m
E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches)))
E [0m[1;32m 290[0m [0;34m[0m[0m
E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: 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[0;34m:[0m[0;34m[0m[0m
[0;31mValueError[0m: 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 [0;31m---------------------------------------------------------------------------[0m
E [0;31mValueError[0m Traceback (most recent call last)
E [0;32m<ipython-input-7-30c5c181683a>[0m in [0;36m<module>[0;34m[0m
E [0;32m----> 1[0;31m [0mmeta[0m [0;34m=[0m [0mpd[0m[0;34m.[0m[0mconcat[0m[0;34m([0m[0;34m[[0m[0mmetadata[0m[0;34m.[0m[0mfname2metadata[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mpath[0m[0;34m)[0m[0;34m,[0m [0mpattern[0m[0;34m=[0m[0mpattern[0m[0;34m)[0m [0;32mfor[0m [0mpath[0m [0;32min[0m [0mpath_to_corpus[0m[0;34m.[0m[0mglob[0m[0;34m([0m[0;34m'*.csv'[0m[0;34m)[0m[0;34m][0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 2[0m [0mmeta[0m[0;34m[[0m[0;34m:[0m[0;36m5[0m[0;34m][0m [0;31m# by adding '[:5]' to the variable, only the first 5 elements will be printed[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pandas/core/reshape/concat.py[0m in [0;36mconcat[0;34m(objs, axis, join, join_axes, ignore_index, keys, levels, names, verify_integrity, sort, copy)[0m
E [1;32m 223[0m [0mkeys[0m[0;34m=[0m[0mkeys[0m[0;34m,[0m [0mlevels[0m[0;34m=[0m[0mlevels[0m[0;34m,[0m [0mnames[0m[0;34m=[0m[0mnames[0m[0;34m,[0m[0;34m[0m[0m
E [1;32m 224[0m [0mverify_integrity[0m[0;34m=[0m[0mverify_integrity[0m[0;34m,[0m[0;34m[0m[0m
E [0;32m--> 225[0;31m copy=copy, sort=sort)
E [0m[1;32m 226[0m [0;32mreturn[0m [0mop[0m[0;34m.[0m[0mget_result[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 227[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pandas/core/reshape/concat.py[0m in [0;36m__init__[0;34m(self, objs, axis, join, join_axes, keys, levels, names, ignore_index, verify_integrity, copy, sort)[0m
E [1;32m 257[0m [0;34m[0m[0m
E [1;32m 258[0m [0;32mif[0m [0mlen[0m[0;34m([0m[0mobjs[0m[0;34m)[0m [0;34m==[0m [0;36m0[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m--> 259[0;31m [0;32mraise[0m [0mValueError[0m[0;34m([0m[0;34m'No objects to concatenate'[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 260[0m [0;34m[0m[0m
E [1;32m 261[0m [0;32mif[0m [0mkeys[0m [0;32mis[0m [0;32mNone[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;31mValueError[0m: 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 [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-25-3c545f10dd80>[0m in [0;36m<module>[0;34m[0m
E [1;32m 1[0m [0mPlotDocumentTopics[0m [0;34m=[0m [0mvisualization[0m[0;34m.[0m[0mPlotDocumentTopics[0m[0;34m([0m[0mdocument_topics[0m[0;34m)[0m[0;34m[0m[0m
E [0;32m----> 2[0;31m [0mshow[0m[0;34m([0m[0mPlotDocumentTopics[0m[0;34m.[0m[0minteractive_heatmap[0m[0;34m([0m[0;34m)[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m
E [0m
E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(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)[0m
E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m
E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m
E [0;32m--> 285[0;31m logo=None)
E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m
E [1;32m 1021[0m [0;34m[0m[0m
E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m
E [1;32m 1025[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m
E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 188[0m [0;34m[0m[0m
E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 190[0m [0;34m[0m[0m
E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m
E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 263[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m
E [1;32m 252[0m [0;34m[0m[0m
E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 255[0m [0;34m[0m[0m
E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m
E [1;32m 287[0m [0;34m[0m[0m
E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches)))
E [0m[1;32m 290[0m [0;34m[0m[0m
E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: 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 [0;31m---------------------------------------------------------------------------[0m
E [0;31mAttributeError[0m Traceback (most recent call last)
E [0;32m<ipython-input-21-0ec82b4d408d>[0m in [0;36m<module>[0;34m[0m
E [1;32m 1[0m interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=800,
E [1;32m 2[0m [0mheight[0m[0;34m=[0m[0;36m550[0m[0;34m,[0m[0;34m[0m[0m
E [0;32m----> 3[0;31m colorbar=False)
E [0m[1;32m 4[0m [0mshow[0m[0;34m([0m[0minteractive_heatmap[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m
E
E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(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)[0m
E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m
E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m
E [0;32m--> 285[0;31m logo=None)
E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1,
E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m
E [1;32m 1021[0m [0;34m[0m[0m
E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m
E [1;32m 1025[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m
E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 188[0m [0;34m[0m[0m
E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 190[0m [0;34m[0m[0m
E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m
E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m
E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m
E [1;32m 263[0m [0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m
E [1;32m 252[0m [0;34m[0m[0m
E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m
E [0m[1;32m 255[0m [0;34m[0m[0m
E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m
E [1;32m 287[0m [0;34m[0m[0m
E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" %
E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches)))
E [0m[1;32m 290[0m [0;34m[0m[0m
E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m
E
E [0;31mAttributeError[0m: 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