Started by GitHub push by ThoraHagen Building remotely on Rechenknecht in workspace /mnt/data/jenkins/workspace/DARIAH-Topics Cloning the remote Git repository Cloning repository git://github.com/DARIAH-DE/Topics > /usr/bin/git init /mnt/data/jenkins/workspace/DARIAH-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 config remote.origin.url git://github.com/DARIAH-DE/Topics # timeout=10 > /usr/bin/git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > /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 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 b3714747ccf8cde3e96a5efca4b6918aa1fe1863 # 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/shiningpanda7121193602667143410.sh + pip install -U pip Requirement already up-to-date: pip in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages (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)) Downloading https://files.pythonhosted.org/packages/bb/d5/7601c468ded9a59478dcb39d21e24d58bb375681c64a06fbb629d2bc2ac3/pytest-4.0.0-py2.py3-none-any.whl (217kB) Collecting pytest-cov (from -r requirements-dev.txt (line 5)) Using cached https://files.pythonhosted.org/packages/30/0a/1b009b525526cd3cd9f52f52391b426c5a3597447be811a10bcb1f6b05eb/pytest_cov-2.6.0-py2.py3-none-any.whl Collecting nbsmoke (from -r requirements-dev.txt (line 6)) Using cached 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https://files.pythonhosted.org/packages/54/4c/e387febde4dfffa6bd81d1feff7c3764816c8030561e5676a3f4ac635447/lda-1.1.0-cp35-cp35m-manylinux1_x86_64.whl Collecting numpy>=1.3 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/86/04/bd774106ae0ae1ada68c67efe89f1a16b2aa373cc2db15d974002a9f136d/numpy-1.15.4-cp35-cp35m-manylinux1_x86_64.whl (13.8MB) Collecting lxml>=3.6.4 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Using cached https://files.pythonhosted.org/packages/eb/e2/02d18a1b3021b65409dd860f91cf0d68d79900f172bb3cc93cff21c3c951/lxml-4.2.5-cp35-cp35m-manylinux1_x86_64.whl Collecting matplotlib>=1.5.3 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/ad/4c/0415f15f96864c3a2242b1c74041a806c100c1b21741206c5d87684437c6/matplotlib-3.0.2-cp35-cp35m-manylinux1_x86_64.whl (12.9MB) Collecting bokeh>=0.12.6 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/68/e1/4cb565f6186b31be1917e26372c0fab24683cd6e0faa542321a01460748e/bokeh-1.0.1.tar.gz (16.1MB) Collecting metadata_toolbox (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Collecting cophi_toolbox>=0.1.1.dev0 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Collecting pluggy>=0.7 (from pytest->-r requirements-dev.txt (line 4)) Using cached https://files.pythonhosted.org/packages/1c/e7/017c262070af41fe251401cb0d0e1b7c38f656da634cd0c15604f1f30864/pluggy-0.8.0-py2.py3-none-any.whl Collecting attrs>=17.4.0 (from pytest->-r requirements-dev.txt (line 4)) Using cached https://files.pythonhosted.org/packages/3a/e1/5f9023cc983f1a628a8c2fd051ad19e76ff7b142a0faf329336f9a62a514/attrs-18.2.0-py2.py3-none-any.whl Collecting more-itertools>=4.0.0 (from pytest->-r requirements-dev.txt (line 4)) Using cached 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https://files.pythonhosted.org/packages/94/dd/fe6c4d683b09eb05342bd2816b7779663f71762b4fa9c2d5203d35d17354/jupyter_client-5.2.3-py2.py3-none-any.whl Collecting nbconvert (from nbsmoke->-r requirements-dev.txt (line 6)) Using cached https://files.pythonhosted.org/packages/b5/bb/94c493051d60e5b9c0f7f9a368b324201818c1b1c4cae85d1e49a41846c7/nbconvert-5.4.0-py2.py3-none-any.whl Collecting pyflakes (from nbsmoke->-r requirements-dev.txt (line 6)) Using cached https://files.pythonhosted.org/packages/44/98/af7a72c9a543b1487d92813c648cb9b9adfbc96faef5455d60f4439aa99b/pyflakes-2.0.0-py2.py3-none-any.whl Collecting requests (from nbsmoke->-r requirements-dev.txt (line 6)) Downloading https://files.pythonhosted.org/packages/ff/17/5cbb026005115301a8fb2f9b0e3e8d32313142fe8b617070e7baad20554f/requests-2.20.1-py2.py3-none-any.whl (57kB) Collecting ipykernel (from nbsmoke->-r requirements-dev.txt (line 6)) Using cached https://files.pythonhosted.org/packages/d8/b0/f0be5c5ab335196f5cce96e5b889a4fcf5bfe462eb0acc05cd7e2caf65eb/ipykernel-5.1.0-py3-none-any.whl Collecting beautifulsoup4 (from nbsmoke->-r requirements-dev.txt (line 6)) Using cached https://files.pythonhosted.org/packages/21/0a/47fdf541c97fd9b6a610cb5fd518175308a7cc60569962e776ac52420387/beautifulsoup4-4.6.3-py3-none-any.whl Collecting notebook (from jupyter->-r requirements-dev.txt (line 9)) Downloading https://files.pythonhosted.org/packages/a2/5d/d1907cd32ac00b5ead56f6e61d9794fa60ef105a22ac5da6e7556011580f/notebook-5.7.2-py2.py3-none-any.whl (9.0MB) Collecting qtconsole (from jupyter->-r requirements-dev.txt (line 9)) Downloading https://files.pythonhosted.org/packages/e0/7a/8aefbc0ed078dec7951ac9a06dcd1869243ecd7bcbce26fa47bf5e469a8f/qtconsole-4.4.3-py2.py3-none-any.whl (113kB) Collecting ipywidgets (from jupyter->-r requirements-dev.txt (line 9)) Using cached 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requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl (506kB) Collecting python-dateutil>=2.5.0 (from pandas>=0.19.2->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl (225kB) Collecting scipy>=0.18.1 (from gensim>=0.13.2->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Using cached https://files.pythonhosted.org/packages/cd/32/5196b64476bd41d596a8aba43506e2403e019c90e1a3dfc21d51b83db5a6/scipy-1.1.0-cp35-cp35m-manylinux1_x86_64.whl Collecting smart-open>=1.2.1 (from gensim>=0.13.2->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Collecting pbr<4,>=0.6 (from lda>=1.0.5->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Using cached 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(from bokeh>=0.12.6->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Collecting pillow>=4.0 (from bokeh>=0.12.6->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/bc/cc/b6e47b0075ca4267855d77850af7ea4194d2fc591664f1d70e5151b50637/Pillow-5.3.0-cp35-cp35m-manylinux1_x86_64.whl (2.0MB) Collecting tornado>=4.3 (from bokeh>=0.12.6->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Collecting parse>=1.8.2 (from metadata_toolbox->dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) 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 jupyter-core (from nbformat->nbsmoke->-r requirements-dev.txt (line 6)) Using cached 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cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-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 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 ptyprocess; os_name != "nt" (from terminado>=0.8.1->notebook->jupyter->-r requirements-dev.txt (line 9)) Using cached 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https://files.pythonhosted.org/packages/b7/31/05c8d001f7f87f0f07289a5fc0fc3832e9a57f2dbd4d3b0fee70e0d51365/jmespath-0.9.3-py2.py3-none-any.whl Collecting botocore<1.13.0,>=1.12.50 (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/82/c1/a26012b4dbca2e2ae06d7b24dc6b4378c0b0544d25f3e3f216612db37033/botocore-1.12.50-py2.py3-none-any.whl (4.9MB) 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, regex, 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-gvbsin4o/wheels/a3/7b/ff/b71160a2e088926eb13abcf8e0cde94c0aa8400c67d3df57f5 Running setup.py bdist_wheel for regex: started Running setup.py bdist_wheel for regex: finished with status 'done' Stored in directory: /mnt/data/jenkins/.cache/pip/wheels/56/b8/60/93cb6f51554e529246d89c994c1cba7b64d768ff1680062661 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/04/dc/69/0fe79e7fa6a44f344d5be532011ff43a362ed60060d82589be Successfully built nbsphinx regex bokeh nbsphinx 0.3.5 has requirement nbconvert!=5.4, but you'll have nbconvert 5.4.0 which is incompatible. Installing collected packages: pluggy, attrs, six, more-itertools, pathlib2, atomicwrites, py, pytest, coverage, pytest-cov, jsonschema, decorator, ipython-genutils, traitlets, jupyter-core, nbformat, python-dateutil, pyzmq, tornado, jupyter-client, mistune, MarkupSafe, Jinja2, Pygments, testpath, pandocfilters, defusedxml, entrypoints, webencodings, bleach, nbconvert, pyflakes, idna, certifi, urllib3, chardet, requests, pickleshare, backcall, wcwidth, prompt-toolkit, ptyprocess, pexpect, parso, jedi, ipython, ipykernel, beautifulsoup4, nbsmoke, Send2Trash, prometheus-client, terminado, notebook, qtconsole, widgetsnbextension, ipywidgets, jupyter-console, jupyter, docutils, snowballstemmer, alabaster, pyparsing, packaging, sphinxcontrib-websupport, imagesize, pytz, babel, 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-1.1.0 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-1.0.1 boto-2.49.0 boto3-1.9.50 botocore-1.12.50 bz2file-0.98 certifi-2018.10.15 chardet-3.0.4 commonmark-0.5.4 cophi-toolbox-0.1.1.dev0 coverage-4.5.2 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-7.1.1 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-3.0.2 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-5.7.2 numpy-1.15.4 packaging-18.0 pandas-0.23.4 pandocfilters-1.4.2 parse-1.9.0 parso-0.3.1 pathlib2-2.3.2 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-2.0.7 ptyprocess-0.6.0 py-1.7.0 pyflakes-2.0.0 pyparsing-2.3.0 pytest-4.0.0 pytest-cov-2.6.0 python-dateutil-2.7.5 pytz-2018.7 pyzmq-17.1.2 qtconsole-4.4.3 recommonmark-0.4.0 regex-2018.11.22 requests-2.20.1 s3transfer-0.1.13 scipy-1.1.0 six-1.11.0 smart-open-1.7.1 snowballstemmer-1.2.1 sphinx-1.8.2 sphinxcontrib-websupport-1.1.0 terminado-0.8.1 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 urllib3-1.24.1 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.4.2 + ./setup.py sdist bdist_wheel running sdist running egg_info writing requirements to dariah_topics.egg-info/requires.txt writing dependency_links to dariah_topics.egg-info/dependency_links.txt writing top-level names to dariah_topics.egg-info/top_level.txt writing dariah_topics.egg-info/PKG-INFO reading manifest file 'dariah_topics.egg-info/SOURCES.txt' writing manifest file 'dariah_topics.egg-info/SOURCES.txt' running check creating dariah_topics-1.0.2.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 dist Creating tar archive removing 'dariah_topics-1.0.2.dev0' (and everything under it) running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/dariah_topics copying dariah_topics/modeling.py -> build/lib/dariah_topics copying dariah_topics/preprocessing.py -> build/lib/dariah_topics copying dariah_topics/utils.py -> build/lib/dariah_topics copying dariah_topics/postprocessing.py -> build/lib/dariah_topics copying dariah_topics/evaluation.py -> build/lib/dariah_topics copying dariah_topics/__init__.py -> build/lib/dariah_topics copying dariah_topics/visualization.py -> build/lib/dariah_topics installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/modeling.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/preprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/utils.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/postprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/evaluation.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/__init__.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/visualization.py -> build/bdist.linux-x86_64/wheel/dariah_topics running install_egg_info Copying dariah_topics.egg-info to build/bdist.linux-x86_64/wheel/dariah_topics-1.0.2.dev0-py3.5.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/python3.5/site-packages/setuptools/dist.py:470: UserWarning: Normalizing '1.0.2.dev' to '1.0.2.dev0' normalized_version, + pytest --nbsmoke-run ============================= test session starts ============================== platform linux -- Python 3.5.3, pytest-4.0.0, 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 = func = . at 0x7f904b899bf8> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:211: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:193: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': } 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/python3.5/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f908ec88390> hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } 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/python3.5/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:121: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} 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/python3.5/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cell = {'cell_type': 'code', 'metadata': {'scrolled': False}, 'source': 'PlotDocumentTopics = visualization.PlotDocumentTopic...r, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale"}], 'execution_count': 22} resources = {}, cell_index = 51 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E ------------------ E E --------------------------------------------------------------------------- E AttributeError Traceback (most recent call last) E  in  E  1 PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E ----> 2 show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E  E ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar) E  283 tools=tools, toolbar_location=toolbar_location, E  284 sizing_mode=sizing_mode, E --> 285 logo=None) E  286 fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E  287 fill_color={'field': 'Distributions', 'transform': mapper}, E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in figure(**kwargs) E  1021  E  1022 def figure(**kwargs): E -> 1023 return Figure(**kwargs) E  1024 figure.__doc__ = Figure.__doc__ E  1025  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw) E  187 kw['title'] = Title(text=title) E  188  E --> 189 super(Figure, self).__init__(*arg, **kw) E  190  E  191 self.x_range = _get_range(opts.x_range) E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/model.py in __init__(self, **kwargs) E  259 self._document = None E  260 self._temp_document = None E --> 261 super(Model, self).__init__(**kwargs) E  262 default_theme.apply_to_model(self) E  263  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __init__(self, **properties) E  252  E  253 for name, value in properties.items(): E --> 254 setattr(self, name, value) E  255  E  256 def __setattr__(self, name, value): E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value) E  287  E  288 raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E --> 289 (name, self.__class__.__name__, text, nice_join(matches))) E  290  E  291 def __str__(self): E E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = func = . at 0x7f90622377b8> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:211: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:193: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': } 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/python3.5/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f908ec88390> hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } 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/python3.5/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:121: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} 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/python3.5/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cell = {'cell_type': 'code', 'metadata': {}, 'source': 'PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics...r, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale"}], 'execution_count': 23} resources = {}, cell_index = 56 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E ------------------ E E --------------------------------------------------------------------------- E AttributeError Traceback (most recent call last) E  in  E  1 PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E ----> 2 show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E  E ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar) E  283 tools=tools, toolbar_location=toolbar_location, E  284 sizing_mode=sizing_mode, E --> 285 logo=None) E  286 fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E  287 fill_color={'field': 'Distributions', 'transform': mapper}, E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in figure(**kwargs) E  1021  E  1022 def figure(**kwargs): E -> 1023 return Figure(**kwargs) E  1024 figure.__doc__ = Figure.__doc__ E  1025  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw) E  187 kw['title'] = Title(text=title) E  188  E --> 189 super(Figure, self).__init__(*arg, **kw) E  190  E  191 self.x_range = _get_range(opts.x_range) E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/model.py in __init__(self, **kwargs) E  259 self._document = None E  260 self._temp_document = None E --> 261 super(Model, self).__init__(**kwargs) E  262 default_theme.apply_to_model(self) E  263  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __init__(self, **properties) E  252  E  253 for name, value in properties.items(): E --> 254 setattr(self, name, value) E  255  E  256 def __setattr__(self, name, value): E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value) E  287  E  288 raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E --> 289 (name, self.__class__.__name__, text, nice_join(matches))) E  290  E  291 def __str__(self): E E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = func = . at 0x7f90620f56a8> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:211: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:193: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': } 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/python3.5/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f908ec88390> hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } 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/python3.5/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:121: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} 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/python3.5/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cell = {'cell_type': 'code', 'metadata': {'collapsed': False, 'scrolled': True}, 'source': "meta = pd.concat([metadata.fname2...0m: No objects to concatenate'], 'output_type': 'error', 'evalue': 'No objects to concatenate'}], 'execution_count': 7} resources = {}, cell_index = 19 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E meta = pd.concat([metadata.fname2metadata(str(path), pattern=pattern) for path in path_to_corpus.glob('*.csv')]) E meta[:5] # by adding '[:5]' to the variable, only the first 5 elements will be printed E ------------------ E E --------------------------------------------------------------------------- E ValueError Traceback (most recent call last) E  in  E ----> 1 meta = pd.concat([metadata.fname2metadata(str(path), pattern=pattern) for path in path_to_corpus.glob('*.csv')]) E  2 meta[:5] # by adding '[:5]' to the variable, only the first 5 elements will be printed E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pandas/core/reshape/concat.py in concat(objs, axis, join, join_axes, ignore_index, keys, levels, names, verify_integrity, sort, copy) E  223 keys=keys, levels=levels, names=names, E  224 verify_integrity=verify_integrity, E --> 225 copy=copy, sort=sort) E  226 return op.get_result() E  227  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pandas/core/reshape/concat.py in __init__(self, objs, axis, join, join_axes, keys, levels, names, ignore_index, verify_integrity, copy, sort) E  257  E  258 if len(objs) == 0: E --> 259 raise ValueError('No objects to concatenate') E  260  E  261 if keys is None: E E ValueError: No objects to concatenate E ValueError: No objects to concatenate ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = func = . at 0x7f90620f57b8> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:211: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:193: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': } 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/python3.5/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f908ec88390> hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } 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/python3.5/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:121: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} 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/python3.5/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 1, 'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}...= PlotDocumentTopics.static_heatmap()\nstatic_heatmap.show()', 'outputs': [], 'execution_count': None}], 'nbformat': 4} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cell = {'cell_type': 'code', 'metadata': {'collapsed': True}, 'source': 'PlotDocumentTopics = visualization.PlotDocumentTopic...r, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale"}], 'execution_count': 25} resources = {}, cell_index = 60 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E ------------------ E E --------------------------------------------------------------------------- E AttributeError Traceback (most recent call last) E  in  E  1 PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E ----> 2 show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E  E ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar) E  283 tools=tools, toolbar_location=toolbar_location, E  284 sizing_mode=sizing_mode, E --> 285 logo=None) E  286 fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E  287 fill_color={'field': 'Distributions', 'transform': mapper}, E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in figure(**kwargs) E  1021  E  1022 def figure(**kwargs): E -> 1023 return Figure(**kwargs) E  1024 figure.__doc__ = Figure.__doc__ E  1025  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw) E  187 kw['title'] = Title(text=title) E  188  E --> 189 super(Figure, self).__init__(*arg, **kw) E  190  E  191 self.x_range = _get_range(opts.x_range) E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/model.py in __init__(self, **kwargs) E  259 self._document = None E  260 self._temp_document = None E --> 261 super(Model, self).__init__(**kwargs) E  262 default_theme.apply_to_model(self) E  263  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __init__(self, **properties) E  252  E  253 for name, value in properties.items(): E --> 254 setattr(self, name, value) E  255  E  256 def __setattr__(self, name, value): E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value) E  287  E  288 raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E --> 289 (name, self.__class__.__name__, text, nice_join(matches))) E  290  E  291 def __str__(self): E E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = func = . at 0x7f9062120ae8> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:211: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:193: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': } 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/python3.5/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f908ec88390> hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [>, >] kwargs = {'item': } 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/python3.5/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [>, >] caller_kwargs = {'item': } firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:121: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 2, 'metadata': {'language_info': {'mimetype': 'text/x-python', 'nbconvert_exporter': 'python', 'cod...how(interactive_barchart_per_document, notebook_handle=True)", 'outputs': [], 'execution_count': None}], 'nbformat': 4} 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/python3.5/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = nb = {'nbformat_minor': 2, 'metadata': {'language_info': {'mimetype': 'text/x-python', 'nbconvert_exporter': 'python', 'cod...how(interactive_barchart_per_document, notebook_handle=True)", 'outputs': [], 'execution_count': None}], 'nbformat': 4} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = cell = {'cell_type': 'code', 'metadata': {}, 'source': 'interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=80...r, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale"}], 'execution_count': 21} resources = {}, cell_index = 26 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=800, E height=550, E colorbar=False) E show(interactive_heatmap, notebook_handle=True) E ------------------ E E --------------------------------------------------------------------------- E AttributeError Traceback (most recent call last) E  in  E  1 interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=800, E  2 height=550, E ----> 3 colorbar=False) E  4 show(interactive_heatmap, notebook_handle=True) E E ~/workspace/DARIAH-Topics/dariah_topics/visualization.py in interactive_heatmap(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar) E  283 tools=tools, toolbar_location=toolbar_location, E  284 sizing_mode=sizing_mode, E --> 285 logo=None) E  286 fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E  287 fill_color={'field': 'Distributions', 'transform': mapper}, E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in figure(**kwargs) E  1021  E  1022 def figure(**kwargs): E -> 1023 return Figure(**kwargs) E  1024 figure.__doc__ = Figure.__doc__ E  1025  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/plotting/figure.py in __init__(self, *arg, **kw) E  187 kw['title'] = Title(text=title) E  188  E --> 189 super(Figure, self).__init__(*arg, **kw) E  190  E  191 self.x_range = _get_range(opts.x_range) E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/model.py in __init__(self, **kwargs) E  259 self._document = None E  260 self._temp_document = None E --> 261 super(Model, self).__init__(**kwargs) E  262 default_theme.apply_to_model(self) E  263  E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __init__(self, **properties) E  252  E  253 for name, value in properties.items(): E --> 254 setattr(self, name, value) E  255  E  256 def __setattr__(self, name, value): E E ~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/bokeh/core/has_props.py in __setattr__(self, name, value) E  287  E  288 raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E --> 289 (name, self.__class__.__name__, text, nice_join(matches))) E  290  E  291 def __str__(self): E E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError --- generated xml file: /mnt/data/jenkins/workspace/DARIAH-Topics/tests.xml ---- ----------- coverage: platform linux, python 3.5.3-final-0 ----------- Coverage HTML written to dir htmlcov Coverage XML written to file coverage.xml =============================== warnings summary =============================== /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/scipy/sparse/sparsetools.py:21 /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/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() dariah_topics/postprocessing.py::dariah_topics.postprocessing._show_gensim_document_topics /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/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/python3.5/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) dariah_topics/postprocessing.py::dariah_topics.postprocessing._show_gensim_topics /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/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/python3.5/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) dariah_topics/postprocessing.py::dariah_topics.postprocessing._show_lda_document_topics /mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py:1: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. """ dariah_topics/postprocessing.py::dariah_topics.postprocessing._show_lda_topics /mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py:1: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. """ dariah_topics/postprocessing.py::dariah_topics.postprocessing.doc2bow /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/cophi_toolbox/preprocessing.py: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])) dariah_topics/postprocessing.py::dariah_topics.postprocessing.save_document_term_matrix /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/cophi_toolbox/preprocessing.py: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])) notebooks/IntroducingGensim.ipynb::/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/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): -- Docs: https://docs.pytest.org/en/latest/warnings.html ============== 5 failed, 53 passed, 10 warnings in 163.31 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@6cfcf1a6[description=A Python library for topic modeling.,homepage=https://dariah-de.github.io/Topics,name=Topics,fork=true,size=42294,milestones={},language=Python,commits={},responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/octet-stream], Date=[Thu, 22 Nov 2018 12:20:04 GMT], ETag=["000d500583338110c48ab48d6bffc9e1"], Last-Modified=[Thu, 08 Nov 2018 02:39:54 GMT], OkHttp-Received-Millis=[1542889204987], OkHttp-Response-Source=[CONDITIONAL_CACHE 304], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1542889204665], Referrer-Policy=[origin-when-cross-origin, strict-origin-when-cross-origin], Server=[GitHub.com], Status=[304 Not Modified], 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=[E7AF:061E:94B601:1393D8A:5BF69EF4], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4998], X-RateLimit-Reset=[1542892716], 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