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Started by GitHub push by ThoraHagen Building remotely on build3 (digibib) in workspace /mnt/data/jenkins/workspace/DARIAH-Topics > /usr/bin/git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > /usr/bin/git config remote.origin.url git://github.com/DARIAH-DE/Topics # timeout=10 Fetching upstream changes from git://github.com/DARIAH-DE/Topics > /usr/bin/git --version # timeout=10 using GIT_ASKPASS to set credentials > /usr/bin/git fetch --tags --progress git://github.com/DARIAH-DE/Topics +refs/heads/*:refs/remotes/origin/* > /usr/bin/git rev-parse refs/remotes/origin/testing^{commit} # timeout=10 > /usr/bin/git rev-parse refs/remotes/origin/origin/testing^{commit} # timeout=10 Checking out Revision b3714747ccf8cde3e96a5efca4b6918aa1fe1863 (refs/remotes/origin/testing) > /usr/bin/git config core.sparsecheckout # timeout=10 > /usr/bin/git checkout -f b3714747ccf8cde3e96a5efca4b6918aa1fe1863 Commit message: "updated paths in cmd command" > /usr/bin/git rev-list --no-walk fa8b872c7b9d265332c411fa666db2371d256e62 # timeout=10 [DARIAH-Topics] $ /usr/bin/python3 /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenv.py /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9 Using base prefix '/usr' New python executable in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/bin/python3 Also creating executable in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/bin/python Installing setuptools, pip, wheel...done. [DARIAH-Topics] $ /bin/sh -xe /tmp/shiningpanda4861151470286543940.sh + pip install -U pip Requirement already up-to-date: pip in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages (18.1) + pip install -U -r requirements-dev.txt Obtaining file:///mnt/data/jenkins/workspace/DARIAH-Topics (from -r requirements.txt (line 1)) Collecting pytest (from -r requirements-dev.txt (line 4)) Using cached https://files.pythonhosted.org/packages/80/2a/2995cbec008f624e1dd8ddc5350535a5d2f33c10b82c06037298e6c52bee/pytest-3.9.2-py2.py3-none-any.whl 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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Collecting numpy>=1.3 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Using cached https://files.pythonhosted.org/packages/16/21/2e88568c134cc3c8d22af290865e2abbd86efa58a1358ffcb19b6c74f9a3/numpy-1.15.3-cp36-cp36m-manylinux1_x86_64.whl Collecting lxml>=3.6.4 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Using cached https://files.pythonhosted.org/packages/03/a4/9eea8035fc7c7670e5eab97f34ff2ef0ddd78a491bf96df5accedb0e63f5/lxml-4.2.5-cp36-cp36m-manylinux1_x86_64.whl Collecting matplotlib>=1.5.3 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Using cached https://files.pythonhosted.org/packages/ed/89/dd823436a5f8d5ca9304b51b554863bfd366ca84708d5812f5ee87c923bc/matplotlib-3.0.0-cp36-cp36m-manylinux1_x86_64.whl Collecting bokeh>=0.12.6 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Downloading https://files.pythonhosted.org/packages/13/a8/6027d0d25f7056fe3c3c1ddcf917e6e2bb981186fd809171906e631b6c08/bokeh-1.0.0.tar.gz (16.1MB) Collecting metadata_toolbox (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Collecting cophi_toolbox>=0.1.1.dev0 (from dariah-topics==1.0.2.dev0->-r requirements.txt (line 1)) Collecting attrs>=17.4.0 (from pytest->-r requirements-dev.txt (line 4)) Using cached https://files.pythonhosted.org/packages/3a/e1/5f9023cc983f1a628a8c2fd051ad19e76ff7b142a0faf329336f9a62a514/attrs-18.2.0-py2.py3-none-any.whl 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 Requirement already satisfied, skipping upgrade: setuptools in /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages (from pytest->-r requirements-dev.txt (line 4)) (40.4.3) Collecting more-itertools>=4.0.0 (from pytest->-r requirements-dev.txt (line 4)) Using cached 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https://files.pythonhosted.org/packages/02/ee/b6e02dc6529e82b75bb06823ff7d005b141037cb1416b10c6f00fc419dca/Pygments-2.2.0-py2.py3-none-any.whl Collecting imagesize (from sphinx->-r requirements-dev.txt (line 10)) Using cached https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl Collecting Jinja2>=2.3 (from sphinx->-r requirements-dev.txt (line 10)) Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl Collecting alabaster<0.8,>=0.7 (from sphinx->-r requirements-dev.txt (line 10)) Using cached https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx->-r requirements-dev.txt (line 10)) Using cached 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https://files.pythonhosted.org/packages/62/94/5430ebaa83f91cc7a9f687ff5238e26164a779cca2ef9903232268b0a318/Pillow-5.3.0-cp36-cp36m-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 testpath (from nbconvert->nbsmoke->-r requirements-dev.txt (line 6)) Using cached https://files.pythonhosted.org/packages/be/a4/162f9ebb6489421fe46dcca2ae420369edfee4b563c668d93cb4605d12ba/testpath-0.4.2-py2.py3-none-any.whl Collecting bleach (from nbconvert->nbsmoke->-r requirements-dev.txt (line 6)) Using cached https://files.pythonhosted.org/packages/d4/0d/4696373c3b714f6022d668fbab619690a42050dbeacede6d10ed97fbd3e2/bleach-3.0.2-py2.py3-none-any.whl Collecting defusedxml (from nbconvert->nbsmoke->-r requirements-dev.txt (line 6)) Using cached 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https://files.pythonhosted.org/packages/d7/14/2a0004d487464d120c9fb85313a75cd3d71a7506955be458eebfe19a6b1d/s3transfer-0.1.13-py2.py3-none-any.whl Collecting parso>=0.3.0 (from jedi>=0.10->ipython>=5.0.0->ipykernel->nbsmoke->-r requirements-dev.txt (line 6)) Using cached https://files.pythonhosted.org/packages/09/51/9c48a46334be50c13d25a3afe55fa05c445699304c5ad32619de953a2305/parso-0.3.1-py2.py3-none-any.whl Building wheels for collected packages: nbsphinx, bokeh Running setup.py bdist_wheel for nbsphinx: started Running setup.py bdist_wheel for nbsphinx: finished with status 'done' Stored in directory: /tmp/pip-ephem-wheel-cache-wngbcznu/wheels/a3/7b/ff/b71160a2e088926eb13abcf8e0cde94c0aa8400c67d3df57f5 Running setup.py bdist_wheel for bokeh: started Running setup.py bdist_wheel for bokeh: finished with status 'done' Stored in directory: /mnt/data/jenkins/.cache/pip/wheels/27/1c/93/5a0696b0c304b3cd53dbcd7fdd0dd55f107e0c389aa59d4ae1 Successfully built nbsphinx bokeh nbsphinx 0.3.5 has requirement nbconvert!=5.4, but you'll have nbconvert 5.4.0 which is incompatible. Installing collected packages: attrs, pluggy, six, more-itertools, py, atomicwrites, pytest, coverage, pytest-cov, testpath, webencodings, bleach, defusedxml, pandocfilters, ipython-genutils, decorator, traitlets, jsonschema, jupyter-core, nbformat, MarkupSafe, Jinja2, mistune, entrypoints, Pygments, nbconvert, tornado, pyzmq, python-dateutil, jupyter-client, parso, jedi, backcall, ptyprocess, pexpect, pickleshare, simplegeneric, wcwidth, prompt-toolkit, ipython, ipykernel, pyflakes, certifi, idna, urllib3, chardet, requests, beautifulsoup4, nbsmoke, jupyter-console, prometheus-client, Send2Trash, terminado, notebook, widgetsnbextension, ipywidgets, qtconsole, jupyter, imagesize, alabaster, pytz, babel, docutils, pyparsing, packaging, snowballstemmer, sphinxcontrib-websupport, sphinx, nbsphinx, commonmark, recommonmark, numpy, pandas, regex, scipy, bz2file, jmespath, botocore, s3transfer, boto3, boto, smart-open, gensim, pbr, lda, lxml, kiwisolver, cycler, matplotlib, PyYAML, pillow, bokeh, parse, metadata-toolbox, cophi-toolbox, dariah-topics Running setup.py develop for dariah-topics Successfully installed Jinja2-2.10 MarkupSafe-1.0 PyYAML-3.13 Pygments-2.2.0 Send2Trash-1.5.0 alabaster-0.7.12 atomicwrites-1.2.1 attrs-18.2.0 babel-2.6.0 backcall-0.1.0 beautifulsoup4-4.6.3 bleach-3.0.2 bokeh-1.0.0 boto-2.49.0 boto3-1.9.31 botocore-1.12.31 bz2file-0.98 certifi-2018.10.15 chardet-3.0.4 commonmark-0.5.4 cophi-toolbox-0.1.1.dev0 coverage-4.5.1 cycler-0.10.0 dariah-topics decorator-4.3.0 defusedxml-0.5.0 docutils-0.14 entrypoints-0.2.3 gensim-3.6.0 idna-2.7 imagesize-1.1.0 ipykernel-5.1.0 ipython-7.0.1 ipython-genutils-0.2.0 ipywidgets-7.4.2 jedi-0.13.1 jmespath-0.9.3 jsonschema-2.6.0 jupyter-1.0.0 jupyter-client-5.2.3 jupyter-console-6.0.0 jupyter-core-4.4.0 kiwisolver-1.0.1 lda-1.1.0 lxml-4.2.5 matplotlib-3.0.0 metadata-toolbox-0.1.0.dev0 mistune-0.8.4 more-itertools-4.3.0 nbconvert-5.4.0 nbformat-4.4.0 nbsmoke-0.2.7 nbsphinx-0.3.5 notebook-5.7.0 numpy-1.15.3 packaging-18.0 pandas-0.23.4 pandocfilters-1.4.2 parse-1.9.0 parso-0.3.1 pbr-3.1.1 pexpect-4.6.0 pickleshare-0.7.5 pillow-5.3.0 pluggy-0.8.0 prometheus-client-0.4.2 prompt-toolkit-2.0.6 ptyprocess-0.6.0 py-1.7.0 pyflakes-2.0.0 pyparsing-2.2.2 pytest-3.9.2 pytest-cov-2.6.0 python-dateutil-2.7.3 pytz-2018.6 pyzmq-17.1.2 qtconsole-4.4.2 recommonmark-0.4.0 regex-2018.8.29 requests-2.20.0 s3transfer-0.1.13 scipy-1.1.0 simplegeneric-0.8.1 six-1.11.0 smart-open-1.7.1 snowballstemmer-1.2.1 sphinx-1.8.1 sphinxcontrib-websupport-1.1.0 terminado-0.8.1 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 urllib3-1.24 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.4.2 + ./setup.py sdist bdist_wheel running sdist running egg_info writing dariah_topics.egg-info/PKG-INFO writing dependency_links to dariah_topics.egg-info/dependency_links.txt writing requirements to dariah_topics.egg-info/requires.txt writing top-level names to dariah_topics.egg-info/top_level.txt reading manifest file 'dariah_topics.egg-info/SOURCES.txt' writing manifest file 'dariah_topics.egg-info/SOURCES.txt' running check creating dariah_topics-1.0.2.dev0 creating dariah_topics-1.0.2.dev0/dariah_topics creating dariah_topics-1.0.2.dev0/dariah_topics.egg-info creating dariah_topics-1.0.2.dev0/test copying files to dariah_topics-1.0.2.dev0... copying README.md -> dariah_topics-1.0.2.dev0 copying setup.cfg -> dariah_topics-1.0.2.dev0 copying setup.py -> dariah_topics-1.0.2.dev0 copying dariah_topics/__init__.py -> dariah_topics-1.0.2.dev0/dariah_topics copying dariah_topics/evaluation.py -> dariah_topics-1.0.2.dev0/dariah_topics copying dariah_topics/modeling.py -> dariah_topics-1.0.2.dev0/dariah_topics copying dariah_topics/postprocessing.py -> dariah_topics-1.0.2.dev0/dariah_topics copying dariah_topics/preprocessing.py -> dariah_topics-1.0.2.dev0/dariah_topics copying dariah_topics/utils.py -> dariah_topics-1.0.2.dev0/dariah_topics copying dariah_topics/visualization.py -> dariah_topics-1.0.2.dev0/dariah_topics copying dariah_topics.egg-info/PKG-INFO -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info copying dariah_topics.egg-info/SOURCES.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info copying dariah_topics.egg-info/dependency_links.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info copying dariah_topics.egg-info/requires.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info copying dariah_topics.egg-info/top_level.txt -> dariah_topics-1.0.2.dev0/dariah_topics.egg-info copying test/test_fuzzy_segmenting.py -> dariah_topics-1.0.2.dev0/test Writing dariah_topics-1.0.2.dev0/setup.cfg Creating tar archive removing 'dariah_topics-1.0.2.dev0' (and everything under it) running bdist_wheel running build running build_py installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/postprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/preprocessing.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/visualization.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/utils.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/__init__.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/modeling.py -> build/bdist.linux-x86_64/wheel/dariah_topics copying build/lib/dariah_topics/evaluation.py -> build/bdist.linux-x86_64/wheel/dariah_topics running install_egg_info Copying dariah_topics.egg-info to build/bdist.linux-x86_64/wheel/dariah_topics-1.0.2.dev0-py3.6.egg-info running install_scripts adding license file "LICENSE" (matched pattern "LICEN[CS]E*") creating build/bdist.linux-x86_64/wheel/dariah_topics-1.0.2.dev0.dist-info/WHEEL creating 'dist/dariah_topics-1.0.2.dev0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'dariah_topics/__init__.py' adding 'dariah_topics/evaluation.py' adding 'dariah_topics/modeling.py' adding 'dariah_topics/postprocessing.py' adding 'dariah_topics/preprocessing.py' adding 'dariah_topics/utils.py' adding 'dariah_topics/visualization.py' adding 'dariah_topics-1.0.2.dev0.dist-info/LICENSE' adding 'dariah_topics-1.0.2.dev0.dist-info/METADATA' adding 'dariah_topics-1.0.2.dev0.dist-info/WHEEL' adding 'dariah_topics-1.0.2.dev0.dist-info/top_level.txt' adding 'dariah_topics-1.0.2.dev0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/setuptools/dist.py:398: UserWarning: Normalizing '1.0.2.dev' to '1.0.2.dev0' normalized_version, + pytest --nbsmoke-run ============================= test session starts ============================== platform linux -- Python 3.6.6, pytest-3.9.2, py-1.7.0, pluggy-0.8.0 rootdir: /mnt/data/jenkins/workspace/DARIAH-Topics, inifile: setup.cfg plugins: cov-2.6.0, nbsmoke-0.2.7 collected 58 items dariah_topics/postprocessing.py ........... [ 18%] dariah_topics/preprocessing.py ........................... [ 65%] dariah_topics/utils.py ...... [ 75%] notebooks/IntroducingGensim.ipynb F [ 77%] notebooks/IntroducingLda.ipynb F [ 79%] notebooks/IntroducingLda_DKProWrapper.ipynb F [ 81%] notebooks/IntroducingMallet.ipynb F [ 82%] notebooks/Visualizations.ipynb F [ 84%] test/test_fuzzy_segmenting.py ......... [100%] =================================== FAILURES =================================== _______________________________________ _______________________________________ self = <CallInfo when='call' exception: An error occurred while executing the following cell: ------------------ PlotDocument...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale > func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6ad8e35d08> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:206: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>} notincall = set() def __call__(self, *args, **kwargs): if args: raise TypeError("hook calling supports only keyword arguments") assert not self.is_historic() if self.spec and self.spec.argnames: notincall = ( set(self.spec.argnames) - set(["__multicall__"]) - set(kwargs.keys()) ) if notincall: warnings.warn( "Argument(s) {} which are declared in the hookspec " "can not be found in this hook call".format(tuple(notincall)), stacklevel=2, ) > return self._hookexec(self, self.get_hookimpls(), kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30> hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>} def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>} self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall( methods, kwargs, > firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pluggy.callers._Result object at 0x7f6b1b9a4828> def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'> def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:116: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingGensim.ipynb'> def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6b17efdc18> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {}, km = None def preprocess(self, nb, resources, km=None): """ Preprocess notebook executing each code cell. The input argument `nb` is modified in-place. Parameters ---------- nb : NotebookNode Notebook being executed. resources : dictionary Additional resources used in the conversion process. For example, passing ``{'metadata': {'path': run_path}}`` sets the execution path to ``run_path``. km: KernelManager (optional) Optional kernel manager. If none is provided, a kernel manager will be created. Returns ------- nb : NotebookNode The executed notebook. resources : dictionary Additional resources used in the conversion process. """ with self.setup_preprocessor(nb, resources, km=km): self.log.info("Executing notebook with kernel: %s" % self.kernel_name) > nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6b17efdc18> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6b17efdc18> cell = {'cell_type': 'code', 'execution_count': 22, 'metadata': {'scrolled': False}, 'outputs': [{'output_type': 'error', 'en...sualization.PlotDocumentTopics(document_topics)\nshow(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)'} resources = {}, cell_index = 51 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E ------------------ E E [0;31m---------------------------------------------------------------------------[0m E [0;31mAttributeError[0m Traceback (most recent call last) E [0;32m<ipython-input-22-3c545f10dd80>[0m in [0;36m<module>[0;34m[0m E [1;32m 1[0m [0mPlotDocumentTopics[0m [0;34m=[0m [0mvisualization[0m[0;34m.[0m[0mPlotDocumentTopics[0m[0;34m([0m[0mdocument_topics[0m[0;34m)[0m[0;34m[0m[0m E [0;32m----> 2[0;31m [0mshow[0m[0;34m([0m[0mPlotDocumentTopics[0m[0;34m.[0m[0minteractive_heatmap[0m[0;34m([0m[0;34m)[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m E [0m E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)[0m E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m E [0;32m--> 285[0;31m logo=None) E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m E [1;32m 1021[0m [0;34m[0m[0m E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m E [1;32m 1025[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 188[0m [0;34m[0m[0m E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 190[0m [0;34m[0m[0m E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 263[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m E [1;32m 252[0m [0;34m[0m[0m E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 255[0m [0;34m[0m[0m E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m E [1;32m 287[0m [0;34m[0m[0m E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches))) E [0m[1;32m 290[0m [0;34m[0m[0m E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;31mAttributeError[0m: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = <CallInfo when='call' exception: An error occurred while executing the following cell: ------------------ PlotDocument...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale > func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6ad8e35c80> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:206: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>} notincall = set() def __call__(self, *args, **kwargs): if args: raise TypeError("hook calling supports only keyword arguments") assert not self.is_historic() if self.spec and self.spec.argnames: notincall = ( set(self.spec.argnames) - set(["__multicall__"]) - set(kwargs.keys()) ) if notincall: warnings.warn( "Argument(s) {} which are declared in the hookspec " "can not be found in this hook call".format(tuple(notincall)), stacklevel=2, ) > return self._hookexec(self, self.get_hookimpls(), kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30> hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>} def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>} self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall( methods, kwargs, > firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pluggy.callers._Result object at 0x7f6af1a22da0> def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'> def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:116: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda.ipynb'> def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af17c93c8> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {}, km = None def preprocess(self, nb, resources, km=None): """ Preprocess notebook executing each code cell. The input argument `nb` is modified in-place. Parameters ---------- nb : NotebookNode Notebook being executed. resources : dictionary Additional resources used in the conversion process. For example, passing ``{'metadata': {'path': run_path}}`` sets the execution path to ``run_path``. km: KernelManager (optional) Optional kernel manager. If none is provided, a kernel manager will be created. Returns ------- nb : NotebookNode The executed notebook. resources : dictionary Additional resources used in the conversion process. """ with self.setup_preprocessor(nb, resources, km=km): self.log.info("Executing notebook with kernel: %s" % self.kernel_name) > nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af17c93c8> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af17c93c8> cell = {'cell_type': 'code', 'execution_count': 23, 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeE...sualization.PlotDocumentTopics(document_topics)\nshow(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)'} resources = {}, cell_index = 56 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E ------------------ E E [0;31m---------------------------------------------------------------------------[0m E [0;31mAttributeError[0m Traceback (most recent call last) E [0;32m<ipython-input-23-3c545f10dd80>[0m in [0;36m<module>[0;34m[0m E [1;32m 1[0m [0mPlotDocumentTopics[0m [0;34m=[0m [0mvisualization[0m[0;34m.[0m[0mPlotDocumentTopics[0m[0;34m([0m[0mdocument_topics[0m[0;34m)[0m[0;34m[0m[0m E [0;32m----> 2[0;31m [0mshow[0m[0;34m([0m[0mPlotDocumentTopics[0m[0;34m.[0m[0minteractive_heatmap[0m[0;34m([0m[0;34m)[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m E [0m E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)[0m E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m E [0;32m--> 285[0;31m logo=None) E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m E [1;32m 1021[0m [0;34m[0m[0m E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m E [1;32m 1025[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 188[0m [0;34m[0m[0m E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 190[0m [0;34m[0m[0m E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 263[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m E [1;32m 252[0m [0;34m[0m[0m E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 255[0m [0;34m[0m[0m E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m E [1;32m 287[0m [0;34m[0m[0m E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches))) E [0m[1;32m 290[0m [0;34m[0m[0m E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;31mAttributeError[0m: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = <CallInfo when='call' exception: An error occurred while executing the following cell: ------------------ meta = pd.co...0m[0;34m:[0m[0;34m[0m[0m [0;31mValueError[0m: No objects to concatenate ValueError: No objects to concatenate > func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6af197f268> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:206: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'>} notincall = set() def __call__(self, *args, **kwargs): if args: raise TypeError("hook calling supports only keyword arguments") assert not self.is_historic() if self.spec and self.spec.argnames: notincall = ( set(self.spec.argnames) - set(["__multicall__"]) - set(kwargs.keys()) ) if notincall: warnings.warn( "Argument(s) {} which are declared in the hookspec " "can not be found in this hook call".format(tuple(notincall)), stacklevel=2, ) > return self._hookexec(self, self.get_hookimpls(), kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30> hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'>} def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'>} self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall( methods, kwargs, > firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pluggy.callers._Result object at 0x7f6b1418c828> def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'> def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:116: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingLda_DKProWrapper.ipynb'> def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af196e550> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {}, km = None def preprocess(self, nb, resources, km=None): """ Preprocess notebook executing each code cell. The input argument `nb` is modified in-place. Parameters ---------- nb : NotebookNode Notebook being executed. resources : dictionary Additional resources used in the conversion process. For example, passing ``{'metadata': {'path': run_path}}`` sets the execution path to ``run_path``. km: KernelManager (optional) Optional kernel manager. If none is provided, a kernel manager will be created. Returns ------- nb : NotebookNode The executed notebook. resources : dictionary Additional resources used in the conversion process. """ with self.setup_preprocessor(nb, resources, km=km): self.log.info("Executing notebook with kernel: %s" % self.kernel_name) > nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af196e550> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af196e550> cell = {'cell_type': 'code', 'execution_count': 7, 'metadata': {'collapsed': False, 'scrolled': True}, 'outputs': [{'output_t...ath_to_corpus.glob('*.csv')])\nmeta[:5] # by adding '[:5]' to the variable, only the first 5 elements will be printed"} resources = {}, cell_index = 19 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E meta = pd.concat([metadata.fname2metadata(str(path), pattern=pattern) for path in path_to_corpus.glob('*.csv')]) E meta[:5] # by adding '[:5]' to the variable, only the first 5 elements will be printed E ------------------ E E [0;31m---------------------------------------------------------------------------[0m E [0;31mValueError[0m Traceback (most recent call last) E [0;32m<ipython-input-7-30c5c181683a>[0m in [0;36m<module>[0;34m[0m E [0;32m----> 1[0;31m [0mmeta[0m [0;34m=[0m [0mpd[0m[0;34m.[0m[0mconcat[0m[0;34m([0m[0;34m[[0m[0mmetadata[0m[0;34m.[0m[0mfname2metadata[0m[0;34m([0m[0mstr[0m[0;34m([0m[0mpath[0m[0;34m)[0m[0;34m,[0m [0mpattern[0m[0;34m=[0m[0mpattern[0m[0;34m)[0m [0;32mfor[0m [0mpath[0m [0;32min[0m [0mpath_to_corpus[0m[0;34m.[0m[0mglob[0m[0;34m([0m[0;34m'*.csv'[0m[0;34m)[0m[0;34m][0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 2[0m [0mmeta[0m[0;34m[[0m[0;34m:[0m[0;36m5[0m[0;34m][0m [0;31m# by adding '[:5]' to the variable, only the first 5 elements will be printed[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pandas/core/reshape/concat.py[0m in [0;36mconcat[0;34m(objs, axis, join, join_axes, ignore_index, keys, levels, names, verify_integrity, sort, copy)[0m E [1;32m 223[0m [0mkeys[0m[0;34m=[0m[0mkeys[0m[0;34m,[0m [0mlevels[0m[0;34m=[0m[0mlevels[0m[0;34m,[0m [0mnames[0m[0;34m=[0m[0mnames[0m[0;34m,[0m[0;34m[0m[0m E [1;32m 224[0m [0mverify_integrity[0m[0;34m=[0m[0mverify_integrity[0m[0;34m,[0m[0;34m[0m[0m E [0;32m--> 225[0;31m copy=copy, sort=sort) E [0m[1;32m 226[0m [0;32mreturn[0m [0mop[0m[0;34m.[0m[0mget_result[0m[0;34m([0m[0;34m)[0m[0;34m[0m[0m E [1;32m 227[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pandas/core/reshape/concat.py[0m in [0;36m__init__[0;34m(self, objs, axis, join, join_axes, keys, levels, names, ignore_index, verify_integrity, copy, sort)[0m E [1;32m 257[0m [0;34m[0m[0m E [1;32m 258[0m [0;32mif[0m [0mlen[0m[0;34m([0m[0mobjs[0m[0;34m)[0m [0;34m==[0m [0;36m0[0m[0;34m:[0m[0;34m[0m[0m E [0;32m--> 259[0;31m [0;32mraise[0m [0mValueError[0m[0;34m([0m[0;34m'No objects to concatenate'[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 260[0m [0;34m[0m[0m E [1;32m 261[0m [0;32mif[0m [0mkeys[0m [0;32mis[0m [0;32mNone[0m[0;34m:[0m[0;34m[0m[0m E E [0;31mValueError[0m: No objects to concatenate E ValueError: No objects to concatenate ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = <CallInfo when='call' exception: An error occurred while executing the following cell: ------------------ PlotDocument...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale > func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6af1846e18> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:206: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>} notincall = set() def __call__(self, *args, **kwargs): if args: raise TypeError("hook calling supports only keyword arguments") assert not self.is_historic() if self.spec and self.spec.argnames: notincall = ( set(self.spec.argnames) - set(["__multicall__"]) - set(kwargs.keys()) ) if notincall: warnings.warn( "Argument(s) {} which are declared in the hookspec " "can not be found in this hook call".format(tuple(notincall)), stacklevel=2, ) > return self._hookexec(self, self.get_hookimpls(), kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30> hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>} def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>} self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall( methods, kwargs, > firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pluggy.callers._Result object at 0x7f6af1886e48> def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'> def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:116: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/IntroducingMallet.ipynb'> def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af18864e0> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {}, km = None def preprocess(self, nb, resources, km=None): """ Preprocess notebook executing each code cell. The input argument `nb` is modified in-place. Parameters ---------- nb : NotebookNode Notebook being executed. resources : dictionary Additional resources used in the conversion process. For example, passing ``{'metadata': {'path': run_path}}`` sets the execution path to ``run_path``. km: KernelManager (optional) Optional kernel manager. If none is provided, a kernel manager will be created. Returns ------- nb : NotebookNode The executed notebook. resources : dictionary Additional resources used in the conversion process. """ with self.setup_preprocessor(nb, resources, km=km): self.log.info("Executing notebook with kernel: %s" % self.kernel_name) > nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af18864e0> nb = {'cells': [{'cell_type': 'markdown', 'metadata': {}, 'source': "# Topics – Easy Topic Modeling in Python\n\nThe text m...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.5.1'}}, 'nbformat': 4, 'nbformat_minor': 1} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af18864e0> cell = {'cell_type': 'code', 'execution_count': 25, 'metadata': {'collapsed': True}, 'outputs': [{'output_type': 'error', 'en...sualization.PlotDocumentTopics(document_topics)\nshow(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True)'} resources = {}, cell_index = 60 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E PlotDocumentTopics = visualization.PlotDocumentTopics(document_topics) E show(PlotDocumentTopics.interactive_heatmap(), notebook_handle=True) E ------------------ E E [0;31m---------------------------------------------------------------------------[0m E [0;31mAttributeError[0m Traceback (most recent call last) E [0;32m<ipython-input-25-3c545f10dd80>[0m in [0;36m<module>[0;34m[0m E [1;32m 1[0m [0mPlotDocumentTopics[0m [0;34m=[0m [0mvisualization[0m[0;34m.[0m[0mPlotDocumentTopics[0m[0;34m([0m[0mdocument_topics[0m[0;34m)[0m[0;34m[0m[0m E [0;32m----> 2[0;31m [0mshow[0m[0;34m([0m[0mPlotDocumentTopics[0m[0;34m.[0m[0minteractive_heatmap[0m[0;34m([0m[0;34m)[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m E [0m E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)[0m E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m E [0;32m--> 285[0;31m logo=None) E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m E [1;32m 1021[0m [0;34m[0m[0m E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m E [1;32m 1025[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 188[0m [0;34m[0m[0m E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 190[0m [0;34m[0m[0m E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 263[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m E [1;32m 252[0m [0;34m[0m[0m E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 255[0m [0;34m[0m[0m E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m E [1;32m 287[0m [0;34m[0m[0m E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches))) E [0m[1;32m 290[0m [0;34m[0m[0m E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;31mAttributeError[0m: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError _______________________________________ _______________________________________ self = <CallInfo when='call' exception: An error occurred while executing the following cell: ------------------ interactive_...e, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale > func = <function call_runtest_hook.<locals>.<lambda> at 0x7f6af18d7ea0> when = 'call', treat_keyboard_interrupt_as_exception = False def __init__(self, func, when, treat_keyboard_interrupt_as_exception=False): #: context of invocation: one of "setup", "call", #: "teardown", "memocollect" self.when = when self.start = time() try: > self.result = func() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:206: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > lambda: ihook(item=item, **kwds), when=when, treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"), ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:188: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_HookCaller 'pytest_runtest_call'>, args = () kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>} notincall = set() def __call__(self, *args, **kwargs): if args: raise TypeError("hook calling supports only keyword arguments") assert not self.is_historic() if self.spec and self.spec.argnames: notincall = ( set(self.spec.argnames) - set(["__multicall__"]) - set(kwargs.keys()) ) if notincall: warnings.warn( "Argument(s) {} which are declared in the hookspec " "can not be found in this hook call".format(tuple(notincall)), stacklevel=2, ) > return self._hookexec(self, self.get_hookimpls(), kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/hooks.py:284: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <_pytest.config.PytestPluginManager object at 0x7f6b1bd0cd30> hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>} def _hookexec(self, hook, methods, kwargs): # called from all hookcaller instances. # enable_tracing will set its own wrapping function at self._inner_hookexec > return self._inner_hookexec(hook, methods, kwargs) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:67: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook = <_HookCaller 'pytest_runtest_call'> methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>} self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall( methods, kwargs, > firstresult=hook.spec.opts.get("firstresult") if hook.spec else False, ) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/manager.py:61: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: res = hook_impl.function(*args) if res is not None: results.append(res) if firstresult: # halt further impl calls break except BaseException: excinfo = sys.exc_info() finally: if firstresult: # first result hooks return a single value outcome = _Result(results[0] if results else None, excinfo) else: outcome = _Result(results, excinfo) # run all wrapper post-yield blocks for gen in reversed(teardowns): try: gen.send(outcome) _raise_wrapfail(gen, "has second yield") except StopIteration: pass > return outcome.get_result() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <pluggy.callers._Result object at 0x7f6af195a518> def get_result(self): """Get the result(s) for this hook call. If the hook was marked as a ``firstresult`` only a single value will be returned otherwise a list of results. """ __tracebackhide__ = True if self._excinfo is None: return self._result else: ex = self._excinfo if _py3: > raise ex[1].with_traceback(ex[2]) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:80: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/mnt/data/jenkins/shiningpanda/jobs/62c67c92/vi...6b170ee828>>, <HookImpl plugin_name='logging-plugin', plugin=<_pytest.logging.LoggingPlugin object at 0x7f6b17084c50>>] caller_kwargs = {'item': <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'>} firstresult = False def _multicall(hook_impls, caller_kwargs, firstresult=False): """Execute a call into multiple python functions/methods and return the result(s). ``caller_kwargs`` comes from _HookCaller.__call__(). """ __tracebackhide__ = True results = [] excinfo = None try: # run impl and wrapper setup functions in a loop teardowns = [] try: for hook_impl in reversed(hook_impls): try: args = [caller_kwargs[argname] for argname in hook_impl.argnames] except KeyError: for argname in hook_impl.argnames: if argname not in caller_kwargs: raise HookCallError( "hook call must provide argument %r" % (argname,) ) if hook_impl.hookwrapper: try: gen = hook_impl.function(*args) next(gen) # first yield teardowns.append(gen) except StopIteration: _raise_wrapfail(gen, "did not yield") else: > res = hook_impl.function(*args) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/pluggy/callers.py:187: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ item = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'> def pytest_runtest_call(item): _update_current_test_var(item, "call") sys.last_type, sys.last_value, sys.last_traceback = (None, None, None) try: > item.runtest() ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/_pytest/runner.py:116: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <RunNb '/mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb'> def runtest(self): self._skip() with io.open(self.name,encoding='utf8') as nb: notebook = nbformat.read(nb, as_version=4) # TODO: which kernel? run in pytest's or use new one (make it option) _timeout = self.parent.parent.config.getini('nbsmoke_cell_timeout') kwargs = dict(timeout=int(_timeout) if _timeout!='' else 300, allow_errors=False, # or sys.version_info[1] ? kernel_name='python') ep = ExecutePreprocessor(**kwargs) with cwd(os.path.dirname(self.name)): # jupyter notebook always does this, right? > ep.preprocess(notebook,{}) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbsmoke/__init__.py:274: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af195ac18> nb = {'cells': [{'cell_type': 'code', 'execution_count': 1, 'metadata': {}, 'outputs': [], 'source': 'from cophi_toolbox im...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 2} resources = {}, km = None def preprocess(self, nb, resources, km=None): """ Preprocess notebook executing each code cell. The input argument `nb` is modified in-place. Parameters ---------- nb : NotebookNode Notebook being executed. resources : dictionary Additional resources used in the conversion process. For example, passing ``{'metadata': {'path': run_path}}`` sets the execution path to ``run_path``. km: KernelManager (optional) Optional kernel manager. If none is provided, a kernel manager will be created. Returns ------- nb : NotebookNode The executed notebook. resources : dictionary Additional resources used in the conversion process. """ with self.setup_preprocessor(nb, resources, km=km): self.log.info("Executing notebook with kernel: %s" % self.kernel_name) > nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:361: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af195ac18> nb = {'cells': [{'cell_type': 'code', 'execution_count': 1, 'metadata': {}, 'outputs': [], 'source': 'from cophi_toolbox im...'nbconvert_exporter': 'python', 'pygments_lexer': 'ipython3', 'version': '3.6.5'}}, 'nbformat': 4, 'nbformat_minor': 2} resources = {} def preprocess(self, nb, resources): """ Preprocessing to apply on each notebook. Must return modified nb, resources. If you wish to apply your preprocessing to each cell, you might want to override preprocess_cell method instead. Parameters ---------- nb : NotebookNode Notebook being converted resources : dictionary Additional resources used in the conversion process. Allows preprocessors to pass variables into the Jinja engine. """ for index, cell in enumerate(nb.cells): > nb.cells[index], resources = self.preprocess_cell(cell, resources, index) ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/base.py:69: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f6af195ac18> cell = {'cell_type': 'code', 'execution_count': 21, 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeE... colorbar=False)\nshow(interactive_heatmap, notebook_handle=True)'} resources = {}, cell_index = 26 def preprocess_cell(self, cell, resources, cell_index): """ Executes a single code cell. See base.py for details. To execute all cells see :meth:`preprocess`. """ if cell.cell_type != 'code' or not cell.source.strip(): return cell, resources reply, outputs = self.run_cell(cell, cell_index) cell.outputs = outputs cell_allows_errors = (self.allow_errors or "raises-exception" in cell.metadata.get("tags", [])) if self.force_raise_errors or not cell_allows_errors: for out in outputs: if out.output_type == 'error': > raise CellExecutionError.from_cell_and_msg(cell, out) E nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: E ------------------ E interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=800, E height=550, E colorbar=False) E show(interactive_heatmap, notebook_handle=True) E ------------------ E E [0;31m---------------------------------------------------------------------------[0m E [0;31mAttributeError[0m Traceback (most recent call last) E [0;32m<ipython-input-21-0ec82b4d408d>[0m in [0;36m<module>[0;34m[0m E [1;32m 1[0m interactive_heatmap = PlotDocumentTopics.interactive_heatmap(width=800, E [1;32m 2[0m [0mheight[0m[0;34m=[0m[0;36m550[0m[0;34m,[0m[0;34m[0m[0m E [0;32m----> 3[0;31m colorbar=False) E [0m[1;32m 4[0m [0mshow[0m[0;34m([0m[0minteractive_heatmap[0m[0;34m,[0m [0mnotebook_handle[0m[0;34m=[0m[0;32mTrue[0m[0;34m)[0m[0;34m[0m[0m E E [0;32m~/workspace/DARIAH-Topics/dariah_topics/visualization.py[0m in [0;36minteractive_heatmap[0;34m(self, palette, reverse_palette, tools, width, height, x_axis_location, toolbar_location, sizing_mode, line_color, grid_line_color, axis_line_color, major_tick_line_color, major_label_text_font_size, major_label_standoff, major_label_orientation, colorbar)[0m E [1;32m 283[0m [0mtools[0m[0;34m=[0m[0mtools[0m[0;34m,[0m [0mtoolbar_location[0m[0;34m=[0m[0mtoolbar_location[0m[0;34m,[0m[0;34m[0m[0m E [1;32m 284[0m [0msizing_mode[0m[0;34m=[0m[0msizing_mode[0m[0;34m,[0m[0;34m[0m[0m E [0;32m--> 285[0;31m logo=None) E [0m[1;32m 286[0m fig.rect(x='Documents', y='Topics', source=source, width=1, height=1, E [1;32m 287[0m [0mfill_color[0m[0;34m=[0m[0;34m{[0m[0;34m'field'[0m[0;34m:[0m [0;34m'Distributions'[0m[0;34m,[0m [0;34m'transform'[0m[0;34m:[0m [0mmapper[0m[0;34m}[0m[0;34m,[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36mfigure[0;34m(**kwargs)[0m E [1;32m 1021[0m [0;34m[0m[0m E [1;32m 1022[0m [0;32mdef[0m [0mfigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m-> 1023[0;31m [0;32mreturn[0m [0mFigure[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 1024[0m [0mfigure[0m[0;34m.[0m[0m__doc__[0m [0;34m=[0m [0mFigure[0m[0;34m.[0m[0m__doc__[0m[0;34m[0m[0m E [1;32m 1025[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/plotting/figure.py[0m in [0;36m__init__[0;34m(self, *arg, **kw)[0m E [1;32m 187[0m [0mkw[0m[0;34m[[0m[0;34m'title'[0m[0;34m][0m [0;34m=[0m [0mTitle[0m[0;34m([0m[0mtext[0m[0;34m=[0m[0mtitle[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 188[0m [0;34m[0m[0m E [0;32m--> 189[0;31m [0msuper[0m[0;34m([0m[0mFigure[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m*[0m[0marg[0m[0;34m,[0m [0;34m**[0m[0mkw[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 190[0m [0;34m[0m[0m E [1;32m 191[0m [0mself[0m[0;34m.[0m[0mx_range[0m [0;34m=[0m [0m_get_range[0m[0;34m([0m[0mopts[0m[0;34m.[0m[0mx_range[0m[0;34m)[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/model.py[0m in [0;36m__init__[0;34m(self, **kwargs)[0m E [1;32m 259[0m [0mself[0m[0;34m.[0m[0m_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [1;32m 260[0m [0mself[0m[0;34m.[0m[0m_temp_document[0m [0;34m=[0m [0;32mNone[0m[0;34m[0m[0m E [0;32m--> 261[0;31m [0msuper[0m[0;34m([0m[0mModel[0m[0;34m,[0m [0mself[0m[0;34m)[0m[0;34m.[0m[0m__init__[0m[0;34m([0m[0;34m**[0m[0mkwargs[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 262[0m [0mdefault_theme[0m[0;34m.[0m[0mapply_to_model[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m[0m[0m E [1;32m 263[0m [0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__init__[0;34m(self, **properties)[0m E [1;32m 252[0m [0;34m[0m[0m E [1;32m 253[0m [0;32mfor[0m [0mname[0m[0;34m,[0m [0mvalue[0m [0;32min[0m [0mproperties[0m[0;34m.[0m[0mitems[0m[0;34m([0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E [0;32m--> 254[0;31m [0msetattr[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m[0m[0m E [0m[1;32m 255[0m [0;34m[0m[0m E [1;32m 256[0m [0;32mdef[0m [0m__setattr__[0m[0;34m([0m[0mself[0m[0;34m,[0m [0mname[0m[0;34m,[0m [0mvalue[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;32m~/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/bokeh/core/has_props.py[0m in [0;36m__setattr__[0;34m(self, name, value)[0m E [1;32m 287[0m [0;34m[0m[0m E [1;32m 288[0m raise AttributeError("unexpected attribute '%s' to %s, %s attributes are %s" % E [0;32m--> 289[0;31m (name, self.__class__.__name__, text, nice_join(matches))) E [0m[1;32m 290[0m [0;34m[0m[0m E [1;32m 291[0m [0;32mdef[0m [0m__str__[0m[0;34m([0m[0mself[0m[0;34m)[0m[0;34m:[0m[0;34m[0m[0m E E [0;31mAttributeError[0m: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale E AttributeError: unexpected attribute 'logo' to Figure, possible attributes are above, aspect_scale, background_fill_alpha, background_fill_color, below, border_fill_alpha, border_fill_color, css_classes, disabled, extra_x_ranges, extra_y_ranges, h_symmetry, height, hidpi, inner_height, inner_width, js_event_callbacks, js_property_callbacks, layout_height, layout_width, left, lod_factor, lod_interval, lod_threshold, lod_timeout, match_aspect, min_border, min_border_bottom, min_border_left, min_border_right, min_border_top, name, outline_line_alpha, outline_line_cap, outline_line_color, outline_line_dash, outline_line_dash_offset, outline_line_join, outline_line_width, output_backend, plot_height, plot_width, renderers, right, sizing_mode, subscribed_events, tags, title, title_location, toolbar, toolbar_location, toolbar_sticky, v_symmetry, width, x_range, x_scale, y_range or y_scale ../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/nbconvert/preprocessors/execute.py:385: CellExecutionError --- generated xml file: /mnt/data/jenkins/workspace/DARIAH-Topics/tests.xml ---- ----------- coverage: platform linux, python 3.6.6-final-0 ----------- Coverage HTML written to dir htmlcov Coverage XML written to file coverage.xml =============================== warnings summary =============================== /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/scipy/sparse/sparsetools.py:21: DeprecationWarning: `scipy.sparse.sparsetools` is deprecated! scipy.sparse.sparsetools is a private module for scipy.sparse, and should not be used. _deprecated() /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead. score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc) /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead. score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc) /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead. score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc) /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/gensim/models/ldamodel.py:1077: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.from_iter(generator)) or the python sum builtin instead. score += np.sum(cnt * logsumexp(Elogthetad + Elogbeta[:, int(id)]) for id, cnt in doc) /mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py:1: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. """ /mnt/data/jenkins/workspace/DARIAH-Topics/dariah_topics/postprocessing.py:1: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. """ /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/cophi_toolbox/preprocessing.py:625: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id])) /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/cophi_toolbox/preprocessing.py:625: FutureWarning: set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead document_term_matrix.set_value((document_id, type_id), 0, int(bag_of_words[document_id][type_id])) /mnt/data/jenkins/shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.6/site-packages/jupyter_client/manager.py:72: DeprecationWarning: KernelManager._kernel_name_changed is deprecated in traitlets 4.1: use @observe and @unobserve instead. def _kernel_name_changed(self, name, old, new): source:409: DeprecationWarning: invalid escape sequence \. source:409: DeprecationWarning: invalid escape sequence \. source:409: DeprecationWarning: invalid escape sequence \. source:409: DeprecationWarning: invalid escape sequence \. source:409: DeprecationWarning: invalid escape sequence \. -- Docs: https://docs.pytest.org/en/latest/warnings.html ============== 5 failed, 53 passed, 15 warnings in 120.85 seconds ============== Build step 'Virtualenv Builder' marked build as failure Recording test results [Cobertura] Publishing Cobertura coverage report... [Cobertura] Publishing Cobertura coverage results... [Cobertura] Cobertura coverage report found. [Set GitHub commit status (universal)] ERROR on repos [GHRepository@50ab1296[description=A Python library for topic modeling.,homepage=https://dariah-de.github.io/Topics,name=Topics,fork=true,size=42293,milestones={},language=Python,commits={},responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/json; charset=utf-8], Date=[Thu, 25 Oct 2018 10:41:23 GMT], ETag=[W/"3b8962e9f2c24ae0e50646a4b1003161"], Last-Modified=[Thu, 04 Oct 2018 17:51:13 GMT], OkHttp-Received-Millis=[1540464083940], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1540464083693], Referrer-Policy=[origin-when-cross-origin, strict-origin-when-cross-origin], Server=[GitHub.com], Status=[200 OK], Strict-Transport-Security=[max-age=31536000; includeSubdomains; preload], Transfer-Encoding=[chunked], Vary=[Accept, Authorization, Cookie, X-GitHub-OTP], X-Accepted-OAuth-Scopes=[repo], X-Content-Type-Options=[nosniff], X-Frame-Options=[deny], X-GitHub-Media-Type=[github.v3; format=json], X-GitHub-Request-Id=[91EF:4347:40AAE2B:90CC6F4:5BD19DD3], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4987], X-RateLimit-Reset=[1540466257], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/DARIAH-DE/Topics,id=69341969]] (sha:b371474) with context:DARIAH-Topics Setting commit status on GitHub for https://github.com/DARIAH-DE/Topics/commit/b3714747ccf8cde3e96a5efca4b6918aa1fe1863 [BFA] Scanning build for known causes... [BFA] No failure causes found [BFA] Done. 0s Started calculate disk usage of build Finished Calculation of disk usage of build in 0 seconds Started calculate disk usage of workspace Finished Calculation of disk usage of workspace in 0 seconds Notifying upstream projects of job completion [ci-game] evaluating rule: Build result [ci-game] evaluating rule: Increased number of passed tests [ci-game] evaluating rule: Decreased number of passed tests [ci-game] evaluating rule: Increased number of failed tests [ci-game] evaluating rule: Decreased number of failed tests [ci-game] evaluating rule: Increased number of skipped tests [ci-game] evaluating rule: Decreased number of skipped tests [ci-game] evaluating rule: Open HIGH priority tasks [ci-game] evaluating rule: Open NORMAL priority tasks [ci-game] evaluating rule: Open LOW priority tasks [ci-game] evaluating rule: Changed number of compiler warnings Finished: FAILURE