Console Output
Started by GitHub push by severinsimmler
Building remotely on build3 (digibib) in workspace /mnt/data/jenkins/workspace/DARIAH-Topics
> git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
> git config remote.origin.url https://github.com/DARIAH-DE/Topics # timeout=10
Fetching upstream changes from https://github.com/DARIAH-DE/Topics
> git --version # timeout=10
using GIT_ASKPASS to set credentials
> git fetch --tags --progress https://github.com/DARIAH-DE/Topics +refs/heads/*:refs/remotes/origin/*
> git rev-parse refs/remotes/origin/testing^{commit} # timeout=10
> git rev-parse refs/remotes/origin/origin/testing^{commit} # timeout=10
Checking out Revision c3c24d1bd1dfaacb849753308063479f4e485422 (refs/remotes/origin/testing)
Commit message: "Create postprocessing.py"
> git config core.sparsecheckout # timeout=10
> git checkout -f c3c24d1bd1dfaacb849753308063479f4e485422
> git rev-list 1dfa7d433fae7fc8e6b1d8945385eff25482c7dc # 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/shiningpanda525964995238463916.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
+ pip install -U -r requirements-dev.txt
Obtaining file:///mnt/data/jenkins/workspace/DARIAH-Topics (from -r requirements.txt (line 1))
Collecting nose (from -r requirements-dev.txt (line 2))
Using cached nose-1.3.7-py3-none-any.whl
Collecting nosexcover (from -r requirements-dev.txt (line 3))
Using cached nosexcover-1.0.11-py2.py3-none-any.whl
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Using cached jupyter-1.0.0-py2.py3-none-any.whl
Collecting sphinx (from -r requirements-dev.txt (line 5))
Using cached Sphinx-1.6.4-py2.py3-none-any.whl
Collecting nbsphinx (from -r requirements-dev.txt (line 6))
Using cached nbsphinx-0.2.14-py2.py3-none-any.whl
Collecting recommonmark (from -r requirements-dev.txt (line 7))
Using cached recommonmark-0.4.0-py2.py3-none-any.whl
Collecting pandas>=0.19.2 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached pandas-0.20.3-cp35-cp35m-manylinux1_x86_64.whl
Collecting regex>=2017.01.14 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Collecting gensim>=0.13.2 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
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Using cached lda-1.0.5-cp35-cp35m-manylinux1_x86_64.whl
Collecting numpy>=1.3 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached numpy-1.13.3-cp35-cp35m-manylinux1_x86_64.whl
Collecting lxml>=3.6.4 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached lxml-4.0.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting flask>=0.11.1 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached Flask-0.12.2-py2.py3-none-any.whl
Collecting matplotlib>=1.5.3 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached matplotlib-2.0.2-cp35-cp35m-manylinux1_x86_64.whl
Collecting bokeh>=0.12.6 (from dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Collecting coverage>=3.4 (from nosexcover->-r requirements-dev.txt (line 3))
Using cached coverage-4.4.1-cp35-cp35m-manylinux1_x86_64.whl
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Collecting Pygments>=2.0 (from sphinx->-r requirements-dev.txt (line 5))
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Collecting sphinxcontrib-websupport (from sphinx->-r requirements-dev.txt (line 5))
Using cached sphinxcontrib_websupport-1.0.1-py2.py3-none-any.whl
Collecting Jinja2>=2.3 (from sphinx->-r requirements-dev.txt (line 5))
Using cached Jinja2-2.9.6-py2.py3-none-any.whl
Collecting snowballstemmer>=1.1 (from sphinx->-r requirements-dev.txt (line 5))
Using cached snowballstemmer-1.2.1-py2.py3-none-any.whl
Collecting alabaster<0.8,>=0.7 (from sphinx->-r requirements-dev.txt (line 5))
Using cached alabaster-0.7.10-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx->-r requirements-dev.txt (line 5))
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Collecting six>=1.5 (from sphinx->-r requirements-dev.txt (line 5))
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Collecting docutils>=0.11 (from sphinx->-r requirements-dev.txt (line 5))
Using cached docutils-0.14-py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx->-r requirements-dev.txt (line 5))
Using cached Babel-2.5.1-py2.py3-none-any.whl
Requirement already up-to-date: setuptools in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages (from sphinx->-r requirements-dev.txt (line 5))
Collecting traitlets (from nbsphinx->-r requirements-dev.txt (line 6))
Using cached traitlets-4.3.2-py2.py3-none-any.whl
Collecting nbformat (from nbsphinx->-r requirements-dev.txt (line 6))
Using cached nbformat-4.4.0-py2.py3-none-any.whl
Collecting commonmark<=0.5.4 (from recommonmark->-r requirements-dev.txt (line 7))
Collecting pytz>=2011k (from pandas>=0.19.2->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached pytz-2017.2-py2.py3-none-any.whl
Collecting python-dateutil>=2 (from pandas>=0.19.2->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached python_dateutil-2.6.1-py2.py3-none-any.whl
Collecting scipy>=0.18.1 (from gensim>=0.13.2->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached scipy-0.19.1-cp35-cp35m-manylinux1_x86_64.whl
Collecting smart-open>=1.2.1 (from gensim>=0.13.2->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Collecting pbr>=0.6 (from lda>=1.0.5->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached pbr-3.1.1-py2.py3-none-any.whl
Collecting Werkzeug>=0.7 (from flask>=0.11.1->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached Werkzeug-0.12.2-py2.py3-none-any.whl
Collecting itsdangerous>=0.21 (from flask>=0.11.1->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Collecting click>=2.0 (from flask>=0.11.1->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached click-6.7-py2.py3-none-any.whl
Collecting pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib>=1.5.3->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached pyparsing-2.2.0-py2.py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib>=1.5.3->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached cycler-0.10.0-py2.py3-none-any.whl
Collecting PyYAML>=3.10 (from bokeh>=0.12.6->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Collecting tornado>=4.3 (from bokeh>=0.12.6->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Collecting ipython>=4.0.0 (from ipykernel->jupyter->-r requirements-dev.txt (line 4))
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Using cached jupyter_client-5.1.0-py2.py3-none-any.whl
Collecting widgetsnbextension~=3.0.0 (from ipywidgets->jupyter->-r requirements-dev.txt (line 4))
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Collecting prompt-toolkit<2.0.0,>=1.0.0 (from jupyter-console->jupyter->-r requirements-dev.txt (line 4))
Using cached prompt_toolkit-1.0.15-py3-none-any.whl
Collecting terminado>=0.3.3; sys_platform != "win32" (from notebook->jupyter->-r requirements-dev.txt (line 4))
Collecting bleach (from nbconvert->jupyter->-r requirements-dev.txt (line 4))
Using cached bleach-2.1.1-py2.py3-none-any.whl
Collecting testpath (from nbconvert->jupyter->-r requirements-dev.txt (line 4))
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Collecting mistune>=0.7.4 (from nbconvert->jupyter->-r requirements-dev.txt (line 4))
Using cached mistune-0.7.4-py2.py3-none-any.whl
Collecting entrypoints>=0.2.2 (from nbconvert->jupyter->-r requirements-dev.txt (line 4))
Using cached entrypoints-0.2.3-py2.py3-none-any.whl
Collecting pandocfilters>=1.4.1 (from nbconvert->jupyter->-r requirements-dev.txt (line 4))
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx->-r requirements-dev.txt (line 5))
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx->-r requirements-dev.txt (line 5))
Using cached chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.7,>=2.5 (from requests>=2.0.0->sphinx->-r requirements-dev.txt (line 5))
Using cached idna-2.6-py2.py3-none-any.whl
Collecting urllib3<1.23,>=1.21.1 (from requests>=2.0.0->sphinx->-r requirements-dev.txt (line 5))
Using cached urllib3-1.22-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx->-r requirements-dev.txt (line 5))
Using cached certifi-2017.7.27.1-py2.py3-none-any.whl
Collecting decorator (from traitlets->nbsphinx->-r requirements-dev.txt (line 6))
Using cached decorator-4.1.2-py2.py3-none-any.whl
Collecting jsonschema!=2.5.0,>=2.4 (from nbformat->nbsphinx->-r requirements-dev.txt (line 6))
Using cached jsonschema-2.6.0-py2.py3-none-any.whl
Collecting bz2file (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Collecting boto>=2.32 (from smart-open>=1.2.1->gensim>=0.13.2->dariah-topics==0.3.0.dev1->-r requirements.txt (line 1))
Using cached boto-2.48.0-py2.py3-none-any.whl
Collecting pexpect; sys_platform != "win32" (from ipython>=4.0.0->ipykernel->jupyter->-r requirements-dev.txt (line 4))
Using cached pexpect-4.2.1-py2.py3-none-any.whl
Collecting pickleshare (from ipython>=4.0.0->ipykernel->jupyter->-r requirements-dev.txt (line 4))
Using cached pickleshare-0.7.4-py2.py3-none-any.whl
Collecting jedi>=0.10 (from ipython>=4.0.0->ipykernel->jupyter->-r requirements-dev.txt (line 4))
Using cached jedi-0.11.0-py2.py3-none-any.whl
Collecting simplegeneric>0.8 (from ipython>=4.0.0->ipykernel->jupyter->-r requirements-dev.txt (line 4))
Collecting pyzmq>=13 (from jupyter-client->ipykernel->jupyter->-r requirements-dev.txt (line 4))
Using cached pyzmq-16.0.2-cp35-cp35m-manylinux1_x86_64.whl
Collecting wcwidth (from prompt-toolkit<2.0.0,>=1.0.0->jupyter-console->jupyter->-r requirements-dev.txt (line 4))
Using cached wcwidth-0.1.7-py2.py3-none-any.whl
Collecting ptyprocess (from terminado>=0.3.3; sys_platform != "win32"->notebook->jupyter->-r requirements-dev.txt (line 4))
Using cached ptyprocess-0.5.2-py2.py3-none-any.whl
Collecting html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre (from bleach->nbconvert->jupyter->-r requirements-dev.txt (line 4))
Using cached html5lib-1.0b10-py2.py3-none-any.whl
Collecting parso==0.1.0 (from jedi>=0.10->ipython>=4.0.0->ipykernel->jupyter->-r requirements-dev.txt (line 4))
Using cached parso-0.1.0-py2.py3-none-any.whl
Collecting webencodings (from html5lib!=1.0b1,!=1.0b2,!=1.0b3,!=1.0b4,!=1.0b5,!=1.0b6,!=1.0b7,!=1.0b8,>=0.99999999pre->bleach->nbconvert->jupyter->-r requirements-dev.txt (line 4))
Using cached webencodings-0.5.1-py2.py3-none-any.whl
Installing collected packages: nose, coverage, nosexcover, tornado, ptyprocess, pexpect, ipython-genutils, decorator, six, traitlets, pickleshare, parso, jedi, wcwidth, prompt-toolkit, Pygments, simplegeneric, ipython, pyzmq, python-dateutil, jupyter-core, jupyter-client, ipykernel, jsonschema, nbformat, MarkupSafe, Jinja2, terminado, webencodings, html5lib, bleach, testpath, mistune, entrypoints, pandocfilters, nbconvert, notebook, widgetsnbextension, ipywidgets, qtconsole, jupyter-console, jupyter, imagesize, sphinxcontrib-websupport, snowballstemmer, alabaster, chardet, idna, urllib3, certifi, requests, docutils, pytz, babel, sphinx, nbsphinx, commonmark, recommonmark, numpy, pandas, regex, scipy, bz2file, boto, smart-open, gensim, pbr, lda, lxml, Werkzeug, itsdangerous, click, flask, pyparsing, cycler, matplotlib, PyYAML, bokeh, dariah-topics
Running setup.py develop for dariah-topics
Successfully installed Jinja2-2.9.6 MarkupSafe-1.0 PyYAML-3.12 Pygments-2.2.0 Werkzeug-0.12.2 alabaster-0.7.10 babel-2.5.1 bleach-2.1.1 bokeh-0.12.9 boto-2.48.0 bz2file-0.98 certifi-2017.7.27.1 chardet-3.0.4 click-6.7 commonmark-0.5.4 coverage-4.4.1 cycler-0.10.0 dariah-topics decorator-4.1.2 docutils-0.14 entrypoints-0.2.3 flask-0.12.2 gensim-3.0.0 html5lib-1.0b10 idna-2.6 imagesize-0.7.1 ipykernel-4.6.1 ipython-6.2.1 ipython-genutils-0.2.0 ipywidgets-7.0.1 itsdangerous-0.24 jedi-0.11.0 jsonschema-2.6.0 jupyter-1.0.0 jupyter-client-5.1.0 jupyter-console-5.2.0 jupyter-core-4.3.0 lda-1.0.5 lxml-4.0.0 matplotlib-2.0.2 mistune-0.7.4 nbconvert-5.3.1 nbformat-4.4.0 nbsphinx-0.2.14 nose-1.3.7 nosexcover-1.0.11 notebook-5.1.0 numpy-1.13.3 pandas-0.20.3 pandocfilters-1.4.2 parso-0.1.0 pbr-3.1.1 pexpect-4.2.1 pickleshare-0.7.4 prompt-toolkit-1.0.15 ptyprocess-0.5.2 pyparsing-2.2.0 python-dateutil-2.6.1 pytz-2017.2 pyzmq-16.0.2 qtconsole-4.3.1 recommonmark-0.4.0 regex-2017.9.23 requests-2.18.4 scipy-0.19.1 simplegeneric-0.8.1 six-1.11.0 smart-open-1.5.3 snowballstemmer-1.2.1 sphinx-1.6.4 sphinxcontrib-websupport-1.0.1 terminado-0.6 testpath-0.3.1 tornado-4.5.2 traitlets-4.3.2 urllib3-1.22 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.0.3
+ ./setup.py sdist bdist_wheel
running sdist
running egg_info
writing top-level names to dariah_topics.egg-info/top_level.txt
writing requirements to dariah_topics.egg-info/requires.txt
writing dependency_links to dariah_topics.egg-info/dependency_links.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
warning: check: missing required meta-data: url
creating dariah_topics-0.3.0.dev1
creating dariah_topics-0.3.0.dev1/dariah_topics
creating dariah_topics-0.3.0.dev1/dariah_topics.egg-info
creating dariah_topics-0.3.0.dev1/test
copying files to dariah_topics-0.3.0.dev1...
copying README.md -> dariah_topics-0.3.0.dev1
copying setup.cfg -> dariah_topics-0.3.0.dev1
copying setup.py -> dariah_topics-0.3.0.dev1
copying dariah_topics/__init__.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics/doclist.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics/evaluation.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics/mallet.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics/meta.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics/postprocessing.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics/preprocessing.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics/visualization.py -> dariah_topics-0.3.0.dev1/dariah_topics
copying dariah_topics.egg-info/PKG-INFO -> dariah_topics-0.3.0.dev1/dariah_topics.egg-info
copying dariah_topics.egg-info/SOURCES.txt -> dariah_topics-0.3.0.dev1/dariah_topics.egg-info
copying dariah_topics.egg-info/dependency_links.txt -> dariah_topics-0.3.0.dev1/dariah_topics.egg-info
copying dariah_topics.egg-info/requires.txt -> dariah_topics-0.3.0.dev1/dariah_topics.egg-info
copying dariah_topics.egg-info/top_level.txt -> dariah_topics-0.3.0.dev1/dariah_topics.egg-info
copying test/test_fuzzy_segmenting.py -> dariah_topics-0.3.0.dev1/test
Writing dariah_topics-0.3.0.dev1/setup.cfg
Creating tar archive
removing 'dariah_topics-0.3.0.dev1' (and everything under it)
running bdist_wheel
running build
running build_py
copying dariah_topics/postprocessing.py -> build/lib/dariah_topics
copying dariah_topics/preprocessing.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/wheel
creating build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/postprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/preprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/visualization.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/testing.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/doclist.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/model_creation.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/meta.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/mallet.py -> build/bdist.linux-x86_64/wheel/dariah_topics
copying build/lib/dariah_topics/evaluation.py -> build/bdist.linux-x86_64/wheel/dariah_topics
running install_egg_info
Copying dariah_topics.egg-info to build/bdist.linux-x86_64/wheel/dariah_topics-0.3.0.dev1-py3.5.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/dariah_topics-0.3.0.dev1.dist-info/WHEEL
creating '/mnt/data/jenkins/workspace/DARIAH-Topics/dist/dariah_topics-0.3.0.dev1-py3-none-any.whl' and adding '.' to it
adding 'dariah_topics/__init__.py'
adding 'dariah_topics/doclist.py'
adding 'dariah_topics/evaluation.py'
adding 'dariah_topics/mallet.py'
adding 'dariah_topics/meta.py'
adding 'dariah_topics/model_creation.py'
adding 'dariah_topics/postprocessing.py'
adding 'dariah_topics/preprocessing.py'
adding 'dariah_topics/testing.py'
adding 'dariah_topics/visualization.py'
adding 'dariah_topics-0.3.0.dev1.dist-info/DESCRIPTION.rst'
adding 'dariah_topics-0.3.0.dev1.dist-info/metadata.json'
adding 'dariah_topics-0.3.0.dev1.dist-info/top_level.txt'
adding 'dariah_topics-0.3.0.dev1.dist-info/WHEEL'
adding 'dariah_topics-0.3.0.dev1.dist-info/METADATA'
adding 'dariah_topics-0.3.0.dev1.dist-info/RECORD'
+ ./setup.py build_sphinx -a
running build_sphinx
Running Sphinx v1.6.4
loading pickled environment... done
[autosummary] generating autosummary for: CONTRIBUTING.md, Introducing_MALLET.ipynb, Introducing_gensim.ipynb, Introducing_lda.ipynb, README.md, demonstrator/README.md, docs/gen/dariah_topics.doclist.rst, docs/gen/dariah_topics.evaluation.rst, docs/gen/dariah_topics.mallet.rst, docs/gen/dariah_topics.meta.rst, docs/gen/dariah_topics.preprocessing.rst, docs/gen/dariah_topics.rst, docs/gen/dariah_topics.visualization.rst, docs/gen/modules.rst, index.rst, presentation_topic_over_time.ipynb
WordCloud functions not available, they require the wordcloud module
building [mo]: all of 0 po files
building [html]: all source files
updating environment: 0 added, 2 changed, 0 removed
reading sources... [ 50%] docs/gen/dariah_topics.preprocessing
reading sources... [100%] docs/gen/dariah_topics.visualization
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_doc_term_matrix:9: WARNING: Definition list ends without a blank line; unexpected unindent.
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:16: WARNING: Unexpected indentation.
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.filter_pos_tags:8: WARNING: Unexpected indentation.
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.read_from_csv:11: WARNING: Unexpected indentation.
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: Unknown target name: "bag-of-words".
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.filter_pos_tags:4: WARNING: Unknown target name: "dariah-dkpro-wrapper".
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.read_from_csv:4: WARNING: Unknown target name: "dariah-dkpro-wrapper".
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.save_sparse_bow:4: WARNING: Unknown target name: ".mm file".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /mnt/data/jenkins/workspace/DARIAH-Topics/presentation_topic_over_time.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 6%] CONTRIBUTING
writing output... [ 12%] Introducing_MALLET
writing output... [ 18%] Introducing_gensim
writing output... [ 25%] Introducing_lda
writing output... [ 31%] README
writing output... [ 37%] demonstrator/README
writing output... [ 43%] docs/gen/dariah_topics
writing output... [ 50%] docs/gen/dariah_topics.doclist
writing output... [ 56%] docs/gen/dariah_topics.evaluation
writing output... [ 62%] docs/gen/dariah_topics.mallet
writing output... [ 68%] docs/gen/dariah_topics.meta
writing output... [ 75%] docs/gen/dariah_topics.preprocessing
writing output... [ 81%] docs/gen/dariah_topics.visualization
writing output... [ 87%] docs/gen/modules
writing output... [ 93%] index
writing output... [100%] presentation_topic_over_time
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/doclist.py:docstring of dariah_topics.doclist.BaseDocList.full_path:: WARNING: 'any' reference target not found: Path
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/doclist.py:docstring of dariah_topics.doclist.BaseDocList.full_path:10: WARNING: 'any' reference target not found: Path()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/doclist.py:docstring of dariah_topics.doclist.BaseDocList.get_docs:6: WARNING: 'any' reference target not found: _get_item(self, index)
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/doclist.py:docstring of dariah_topics.doclist.PathDocList.full_path:: WARNING: 'any' reference target not found: Path
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/doclist.py:docstring of dariah_topics.doclist.PathDocList.full_path:10: WARNING: 'any' reference target not found: Path()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/doclist.py:docstring of dariah_topics.doclist.PathDocList.with_segment_files:5: WARNING: 'any' reference target not found: strings.Formatter
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_binary:: WARNING: 'any' reference target not found: stoplist
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_binary:: WARNING: 'any' reference target not found: replacements_files
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_binary:: WARNING: 'any' reference target not found: gram_sizes=1,2
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_model:: WARNING: 'any' reference target not found: output_model
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_model:: WARNING: 'any' reference target not found: output_state
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_model:: WARNING: 'any' reference target not found: output_model
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_model:: WARNING: 'any' reference target not found: output_state
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_model:: WARNING: 'any' reference target not found: output_topic_docs
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_model:: WARNING: 'any' reference target not found: output_doc_topics
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/mallet.py:docstring of dariah_topics.mallet.create_mallet_model:: WARNING: 'any' reference target not found: num_iterations = 0
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.AbstractCorpus.flatten_segments:3: WARNING: 'any' reference target not found: documents
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.AbstractCorpus.flatten_segments:7: WARNING: more than one target found for 'any' cross-reference 'segments': could be :py:meth: or :py:meth:
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.AbstractCorpus.flatten_segments:7: WARNING: 'any' reference target not found: segments=True
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.TableCorpus.flatten_segments:3: WARNING: 'any' reference target not found: documents
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.TableCorpus.flatten_segments:7: WARNING: more than one target found for 'any' cross-reference 'segments': could be :py:meth: or :py:meth:
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.TableCorpus.flatten_segments:7: WARNING: 'any' reference target not found: segments=True
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.fn2metadata:: WARNING: 'any' reference target not found: (?<name>pattern)
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.fn2metadata:: WARNING: 'any' reference target not found: _
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.fn2metadata:: WARNING: 'any' reference target not found: author
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/meta.py:docstring of dariah_topics.meta.fn2metadata:: WARNING: 'any' reference target not found: title
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_doc_term_matrix:4: WARNING: 'any' reference target not found: _wordcounts()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: _create_large_counter()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: _create_sparse_index()`
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: get_labels()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: doc_labels
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: doc_tokens
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: type_dictionary
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: doc_ids
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: type_dictionary
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.create_sparse_bow:4: WARNING: 'any' reference target not found: doc_dictionary
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.find_hapax:4: WARNING: 'any' reference target not found: create_sparse_matrix()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.find_stopwords:4: WARNING: 'any' reference target not found: create_sparse_matrix()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.make_doc2bow_list:4: WARNING: 'any' reference target not found: get_document_topics()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.read_from_csv:4: WARNING: 'any' reference target not found: create_document_list()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.read_from_tei:4: WARNING: 'any' reference target not found: create_document_list()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.read_from_txt:4: WARNING: 'any' reference target not found: create_document_list()
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.segment:1: WARNING: 'any' reference target not found: segment_size
/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/preprocessing.py:docstring of dariah_topics.preprocessing.tokenize:4: WARNING: 'any' reference target not found: lower
generating indices... genindex py-modindex
highlighting module code... [ 16%] dariah_topics.doclist
highlighting module code... [ 33%] dariah_topics.visualization
highlighting module code... [ 50%] dariah_topics.evaluation
highlighting module code... [ 66%] dariah_topics.meta
highlighting module code... [ 83%] dariah_topics.preprocessing
highlighting module code... [100%] dariah_topics.mallet
writing additional pages... search
copying images... [ 12%] build/sphinx/doctrees/nbsphinx/Introducing_lda_72_0.png
copying images... [ 25%] build/sphinx/doctrees/nbsphinx/Introducing_lda_71_1.png
copying images... [ 37%] build/sphinx/doctrees/nbsphinx/presentation_topic_over_time_18_2.png
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copying images... [ 87%] build/sphinx/doctrees/nbsphinx/presentation_topic_over_time_20_0.png
copying images... [100%] build/sphinx/doctrees/nbsphinx/Introducing_gensim_88_1.png
copying static files... /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/sphinx/application.py:445: RemovedInSphinx17Warning: app.status_iterator() is now deprecated. Use sphinx.util.status_iterator() instead.
RemovedInSphinx17Warning)
WARNING: html_static_path entry '/mnt/data/jenkins/workspace/DARIAH-Topics/docs/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 54 warnings.
+ nosetests --cover-html
FFFFFFFFFFFF.......................
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 254, in _
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 272, in dariah_topics.postprocessing._
Failed example:
sparse_bow = create_sparse_bow(doc_labels, doc_tokens, type_dictionary, doc_dictionary)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._[4]>", line 1, in <module>
sparse_bow = create_sparse_bow(doc_labels, doc_tokens, type_dictionary, doc_dictionary)
NameError: name 'create_sparse_bow' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 279, in dariah_topics.postprocessing._
Failed example:
make_doc2bow_list(sparse_bow)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._[11]>", line 1, in <module>
make_doc2bow_list(sparse_bow)
NameError: name 'make_doc2bow_list' is not defined
-------------------- >> begin captured logging << --------------------
gensim.models.doc2vec: DEBUG: Fast version of gensim.models.doc2vec is being used
summa.preprocessing.cleaner: INFO: 'pattern' package not found; tag filters are not available for English
gensim.corpora.dictionary: INFO: adding document #0 to Dictionary(0 unique tokens: [])
gensim.corpora.dictionary: INFO: built Dictionary(4 unique tokens: ['test', 'corpus', 'testing', 'for']) from 2 documents (total 4 corpus positions)
gensim.models.ldamodel: INFO: using symmetric alpha at 1.0
gensim.models.ldamodel: INFO: using symmetric eta at 0.25
gensim.models.ldamodel: INFO: using serial LDA version on this node
gensim.models.ldamodel: INFO: running online (single-pass) LDA training, 1 topics, 1 passes over the supplied corpus of 2 documents, updating model once every 2 documents, evaluating perplexity every 2 documents, iterating 1x with a convergence threshold of 0.001000
gensim.models.ldamodel: WARNING: too few updates, training might not converge; consider increasing the number of passes or iterations to improve accuracy
gensim.models.ldamodel: DEBUG: bound: at document #0
gensim.models.ldamodel: INFO: -1.689 per-word bound, 3.2 perplexity estimate based on a held-out corpus of 2 documents with 4 words
gensim.models.ldamodel: INFO: PROGRESS: pass 0, at document #2/2
gensim.models.ldamodel: DEBUG: performing inference on a chunk of 2 documents
gensim.models.ldamodel: DEBUG: 0/2 documents converged within 1 iterations
gensim.models.ldamodel: DEBUG: updating topics
gensim.models.ldamodel: INFO: topic #0 (1.000): 0.250*"test" + 0.250*"corpus" + 0.250*"for" + 0.250*"testing"
gensim.models.ldamodel: INFO: topic diff=0.241321, rho=1.000000
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._save_matrix_market
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._save_matrix_market
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 107, in _save_matrix_market
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 132, in dariah_topics.postprocessing._save_matrix_market
Failed example:
document_term_matrix = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels, large_corpus=True)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._save_matrix_market[5]>", line 1, in <module>
document_term_matrix = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels, large_corpus=True)
AttributeError: module 'dariah_topics.preprocessing' has no attribute 'create_document_term_matrix'
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 133, in dariah_topics.postprocessing._save_matrix_market
Failed example:
_save_matrix_market(document_term_matrix, path)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._save_matrix_market[6]>", line 1, in <module>
_save_matrix_market(document_term_matrix, path)
NameError: name 'document_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 134, in dariah_topics.postprocessing._save_matrix_market
Failed example:
with open(os.path.join(path, 'document_term_matrix.mm'), 'r', encoding='utf-8') as file:
print(file.read()) #doctest: +NORMALIZE_WHITESPACE
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._save_matrix_market[7]>", line 1, in <module>
with open(os.path.join(path, 'document_term_matrix.mm'), 'r', encoding='utf-8') as file:
FileNotFoundError: [Errno 2] No such file or directory: 'tmp/document_term_matrix.mm'
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._show_gensim_doc_topics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._show_gensim_doc_topics
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 506, in _show_gensim_doc_topics
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 531, in dariah_topics.postprocessing._show_gensim_doc_topics
Failed example:
doc_topic = visualization.create_doc_topic(corpus, model, doc_labels)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_gensim_doc_topics[7]>", line 1, in <module>
doc_topic = visualization.create_doc_topic(corpus, model, doc_labels)
NameError: name 'visualization' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 532, in dariah_topics.postprocessing._show_gensim_doc_topics
Failed example:
len(doc_topic.T) == 2
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_gensim_doc_topics[8]>", line 1, in <module>
len(doc_topic.T) == 2
NameError: name 'doc_topic' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 533, in dariah_topics.postprocessing._show_gensim_doc_topics
Failed example:
True
Expected nothing
Got:
True
-------------------- >> begin captured logging << --------------------
gensim.corpora.mmcorpus: INFO: storing corpus in Matrix Market format to /tmp/corpus.mm
gensim.matutils: INFO: saving sparse matrix to /tmp/corpus.mm
gensim.matutils: INFO: PROGRESS: saving document #0
gensim.matutils: INFO: saved 2x2 matrix, density=25.000% (1/4)
gensim.matutils: DEBUG: closing /tmp/corpus.mm
gensim.matutils: DEBUG: closing /tmp/corpus.mm
gensim.corpora.indexedcorpus: INFO: saving MmCorpus index to /tmp/corpus.mm.index
gensim.corpora.indexedcorpus: INFO: loaded corpus index from /tmp/corpus.mm.index
gensim.matutils: INFO: initializing corpus reader from /tmp/corpus.mm
gensim.matutils: INFO: accepted corpus with 2 documents, 2 features, 1 non-zero entries
gensim.models.ldamodel: INFO: using symmetric alpha at 1.0
gensim.models.ldamodel: INFO: using symmetric eta at 0.5
gensim.models.ldamodel: INFO: using serial LDA version on this node
gensim.models.ldamodel: INFO: running online (single-pass) LDA training, 1 topics, 1 passes over the supplied corpus of 2 documents, updating model once every 2 documents, evaluating perplexity every 2 documents, iterating 50x with a convergence threshold of 0.001000
gensim.models.ldamodel: WARNING: too few updates, training might not converge; consider increasing the number of passes or iterations to improve accuracy
gensim.models.ldamodel: DEBUG: bound: at document #0
gensim.models.ldamodel: INFO: -1.127 per-word bound, 2.2 perplexity estimate based on a held-out corpus of 2 documents with 0 words
gensim.models.ldamodel: INFO: PROGRESS: pass 0, at document #2/2
gensim.models.ldamodel: DEBUG: performing inference on a chunk of 2 documents
gensim.models.ldamodel: DEBUG: 2/2 documents converged within 50 iterations
gensim.models.ldamodel: DEBUG: updating topics
gensim.models.ldamodel: INFO: topic #0 (1.000): 0.600*"corpus" + 0.400*"test"
gensim.models.ldamodel: INFO: topic diff=0.419180, rho=1.000000
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._show_gensim_topics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._show_gensim_topics
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 329, in _show_gensim_topics
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 352, in dariah_topics.postprocessing._show_gensim_topics
Failed example:
isinstance(gensim2dataframe(model, 4), pd.DataFrame)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_gensim_topics[6]>", line 1, in <module>
isinstance(gensim2dataframe(model, 4), pd.DataFrame)
NameError: name 'gensim2dataframe' is not defined
-------------------- >> begin captured logging << --------------------
gensim.corpora.dictionary: INFO: adding document #0 to Dictionary(0 unique tokens: [])
gensim.corpora.dictionary: INFO: built Dictionary(4 unique tokens: ['test', 'corpus', 'testing', 'for']) from 2 documents (total 4 corpus positions)
gensim.models.ldamodel: INFO: using symmetric alpha at 1.0
gensim.models.ldamodel: INFO: using symmetric eta at 0.25
gensim.models.ldamodel: INFO: using serial LDA version on this node
gensim.models.ldamodel: INFO: running online (single-pass) LDA training, 1 topics, 1 passes over the supplied corpus of 2 documents, updating model once every 2 documents, evaluating perplexity every 2 documents, iterating 1x with a convergence threshold of 0.001000
gensim.models.ldamodel: WARNING: too few updates, training might not converge; consider increasing the number of passes or iterations to improve accuracy
gensim.models.ldamodel: DEBUG: bound: at document #0
gensim.models.ldamodel: INFO: -1.686 per-word bound, 3.2 perplexity estimate based on a held-out corpus of 2 documents with 4 words
gensim.models.ldamodel: INFO: PROGRESS: pass 0, at document #2/2
gensim.models.ldamodel: DEBUG: performing inference on a chunk of 2 documents
gensim.models.ldamodel: DEBUG: 0/2 documents converged within 1 iterations
gensim.models.ldamodel: DEBUG: updating topics
gensim.models.ldamodel: INFO: topic #0 (1.000): 0.250*"test" + 0.250*"corpus" + 0.250*"for" + 0.250*"testing"
gensim.models.ldamodel: INFO: topic diff=0.252138, rho=1.000000
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._show_lda_doc_topics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._show_lda_doc_topics
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 402, in _show_lda_doc_topics
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 423, in dariah_topics.postprocessing._show_lda_doc_topics
Failed example:
doc_term_matrix = create_doc_term_matrix(corpus, ['doc1', 'doc2'])
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_doc_topics[2]>", line 1, in <module>
doc_term_matrix = create_doc_term_matrix(corpus, ['doc1', 'doc2'])
NameError: name 'create_doc_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 424, in dariah_topics.postprocessing._show_lda_doc_topics
Failed example:
vocab = doc_term_matrix.columns
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_doc_topics[3]>", line 1, in <module>
vocab = doc_term_matrix.columns
NameError: name 'doc_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 426, in dariah_topics.postprocessing._show_lda_doc_topics
Failed example:
model.fit(doc_term_matrix.as_matrix().astype(int))
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_doc_topics[5]>", line 1, in <module>
model.fit(doc_term_matrix.as_matrix().astype(int))
NameError: name 'doc_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 427, in dariah_topics.postprocessing._show_lda_doc_topics
Failed example:
topics = lda2dataframe(model, vocab)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_doc_topics[6]>", line 1, in <module>
topics = lda2dataframe(model, vocab)
NameError: name 'lda2dataframe' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 428, in dariah_topics.postprocessing._show_lda_doc_topics
Failed example:
doc_topic = lda_doc_topic(model, vocab, ['doc1', 'doc2'])
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_doc_topics[7]>", line 1, in <module>
doc_topic = lda_doc_topic(model, vocab, ['doc1', 'doc2'])
NameError: name 'lda_doc_topic' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 429, in dariah_topics.postprocessing._show_lda_doc_topics
Failed example:
len(doc_topic.T) == 2
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_doc_topics[8]>", line 1, in <module>
len(doc_topic.T) == 2
NameError: name 'doc_topic' is not defined
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._show_lda_topics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._show_lda_topics
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 290, in _show_lda_topics
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 310, in dariah_topics.postprocessing._show_lda_topics
Failed example:
doc_term_matrix = create_doc_term_matrix(corpus, ['doc1', 'doc2'])
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_topics[2]>", line 1, in <module>
doc_term_matrix = create_doc_term_matrix(corpus, ['doc1', 'doc2'])
NameError: name 'create_doc_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 311, in dariah_topics.postprocessing._show_lda_topics
Failed example:
vocab = doc_term_matrix.columns
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_topics[3]>", line 1, in <module>
vocab = doc_term_matrix.columns
NameError: name 'doc_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 313, in dariah_topics.postprocessing._show_lda_topics
Failed example:
model.fit(doc_term_matrix.as_matrix().astype(int))
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_topics[5]>", line 1, in <module>
model.fit(doc_term_matrix.as_matrix().astype(int))
NameError: name 'doc_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 314, in dariah_topics.postprocessing._show_lda_topics
Failed example:
df = lda2dataframe(model, vocab, num_keys=1)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_topics[6]>", line 1, in <module>
df = lda2dataframe(model, vocab, num_keys=1)
NameError: name 'lda2dataframe' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 315, in dariah_topics.postprocessing._show_lda_topics
Failed example:
len(df) == 1
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_lda_topics[7]>", line 1, in <module>
len(df) == 1
NameError: name 'df' is not defined
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._show_mallet_doc_topics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._show_mallet_doc_topics
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 452, in _show_mallet_doc_topics
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 463, in dariah_topics.postprocessing._show_mallet_doc_topics
Failed example:
df = show_doc_topic_matrix(outfolder)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_mallet_doc_topics[1]>", line 1, in <module>
df = show_doc_topic_matrix(outfolder)
NameError: name 'show_doc_topic_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 464, in dariah_topics.postprocessing._show_mallet_doc_topics
Failed example:
len(df.T)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_mallet_doc_topics[2]>", line 1, in <module>
len(df.T)
NameError: name 'df' is not defined
======================================================================
FAIL: Doctest: dariah_topics.postprocessing._show_mallet_topics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing._show_mallet_topics
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 363, in _show_mallet_topics
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 377, in dariah_topics.postprocessing._show_mallet_topics
Failed example:
df = show_topics_keys(outfolder, num_topics=10)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_mallet_topics[1]>", line 1, in <module>
df = show_topics_keys(outfolder, num_topics=10)
NameError: name 'show_topics_keys' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 378, in dariah_topics.postprocessing._show_mallet_topics
Failed example:
len(df)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing._show_mallet_topics[2]>", line 1, in <module>
len(df)
NameError: name 'df' is not defined
======================================================================
FAIL: Doctest: dariah_topics.postprocessing.save_document_term_matrix
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing.save_document_term_matrix
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 40, in save_document_term_matrix
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 81, in dariah_topics.postprocessing.save_document_term_matrix
Failed example:
document_term_matrix = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing.save_document_term_matrix[5]>", line 1, in <module>
document_term_matrix = preprocessing.create_document_term_matrix(tokenized_corpus, document_labels)
AttributeError: module 'dariah_topics.preprocessing' has no attribute 'create_document_term_matrix'
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 82, in dariah_topics.postprocessing.save_document_term_matrix
Failed example:
save_document_term_matrix(document_term_matrix, path)
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing.save_document_term_matrix[6]>", line 1, in <module>
save_document_term_matrix(document_term_matrix, path)
NameError: name 'document_term_matrix' is not defined
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 83, in dariah_topics.postprocessing.save_document_term_matrix
Failed example:
preprocessing.read_document_term_matrix(os.path.join(path, 'document_term_matrix.csv')) #doctest +NORMALIZE_WHITESPACE
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing.save_document_term_matrix[7]>", line 1, in <module>
preprocessing.read_document_term_matrix(os.path.join(path, 'document_term_matrix.csv')) #doctest +NORMALIZE_WHITESPACE
AttributeError: module 'dariah_topics.preprocessing' has no attribute 'read_document_term_matrix'
======================================================================
FAIL: Doctest: dariah_topics.postprocessing.save_model
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing.save_model
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 195, in save_model
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 215, in dariah_topics.postprocessing.save_model
Failed example:
with open(os.path.join(path, '*.txt'), 'r', encoding='utf-8') as file:
print(file.read())
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing.save_model[4]>", line 1, in <module>
with open(os.path.join(path, '*.txt'), 'r', encoding='utf-8') as file:
FileNotFoundError: [Errno 2] No such file or directory: 'tmp/*.txt'
-------------------- >> begin captured logging << --------------------
dariah_topics.postprocessing: INFO: Saving tokenized corpus to tmp ...
dariah_topics.postprocessing: INFO: Creating directory tmp ...
dariah_topics.postprocessing: DEBUG: Current file: document_label
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: Doctest: dariah_topics.postprocessing.save_tokenized_corpus
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing.save_tokenized_corpus
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 156, in save_tokenized_corpus
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 179, in dariah_topics.postprocessing.save_tokenized_corpus
Failed example:
with open(os.path.join(path, '*.txt'), 'r', encoding='utf-8') as file:
print(file.read())
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing.save_tokenized_corpus[4]>", line 1, in <module>
with open(os.path.join(path, '*.txt'), 'r', encoding='utf-8') as file:
FileNotFoundError: [Errno 2] No such file or directory: 'tmp/*.txt'
-------------------- >> begin captured logging << --------------------
dariah_topics.postprocessing: INFO: Saving tokenized corpus to tmp ...
dariah_topics.postprocessing: DEBUG: Current file: document_label
--------------------- >> end captured logging << ---------------------
======================================================================
FAIL: Doctest: dariah_topics.postprocessing.show_topics
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 2190, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for dariah_topics.postprocessing.show_topics
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 222, in show_topics
----------------------------------------------------------------------
File "/mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py", line 242, in dariah_topics.postprocessing.show_topics
Failed example:
with open(os.path.join(path, '*.txt'), 'r', encoding='utf-8') as file:
print(file.read())
Exception raised:
Traceback (most recent call last):
File "/usr/lib/python3.5/doctest.py", line 1321, in __run
compileflags, 1), test.globs)
File "<doctest dariah_topics.postprocessing.show_topics[4]>", line 1, in <module>
with open(os.path.join(path, '*.txt'), 'r', encoding='utf-8') as file:
FileNotFoundError: [Errno 2] No such file or directory: 'tmp/*.txt'
-------------------- >> begin captured logging << --------------------
dariah_topics.postprocessing: INFO: Saving tokenized corpus to tmp ...
dariah_topics.postprocessing: DEBUG: Current file: document_label
--------------------- >> end captured logging << ---------------------
Name Stmts Miss Cover
-----------------------------------------------------
dariah_topics/__init__.py 0 0 100%
dariah_topics/doclist.py 93 8 91%
dariah_topics/postprocessing.py 149 116 22%
dariah_topics/preprocessing.py 223 17 92%
dariah_topics/visualization.py 176 93 47%
-----------------------------------------------------
TOTAL 641 234 63%
----------------------------------------------------------------------
Ran 35 tests in 84.312s
FAILED (failures=12)
Build step 'Virtualenv Builder' marked build as failure
Recording test results
[Cobertura] Publishing Cobertura coverage report...
Publishing Cobertura coverage results...
Cobertura coverage report found.
[Set GitHub commit status (universal)] ERROR on repos [GHRepository@2eaade72[description=A python library for topic modeling.,homepage=,name=Topics,license=<null>,fork=true,size=186599,milestones={},language=Jupyter Notebook,commits={},url=https://api.github.com/repos/DARIAH-DE/Topics,id=69341969]] (sha:c3c24d1) with context:DARIAH-Topics
Setting commit status on GitHub for https://github.com/DARIAH-DE/Topics/commit/c3c24d1bd1dfaacb849753308063479f4e485422
[BFA] Scanning build for known causes...
[BFA] No failure causes found
[BFA] Done. 0s
Started calculate disk usage of build
Finished Calculation of disk usage of build in 0 seconds
Started calculate disk usage of workspace
Finished Calculation of disk usage of workspace in 0 seconds
Notifying upstream projects of job completion
[ci-game] evaluating rule: Build result
[ci-game] scored: -10.0
[ci-game] evaluating rule: Increased number of passed tests
[ci-game] evaluating rule: Decreased number of passed tests
[ci-game] evaluating rule: Increased number of failed tests
[ci-game] evaluating rule: Decreased number of failed tests
[ci-game] evaluating rule: Increased number of skipped tests
[ci-game] evaluating rule: Decreased number of skipped tests
[ci-game] evaluating rule: Open HIGH priority tasks
[ci-game] evaluating rule: Open NORMAL priority tasks
[ci-game] evaluating rule: Open LOW priority tasks
[ci-game] evaluating rule: Changed number of compiler warnings
Finished: FAILURE
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