Started by user Thorsten Vitt
Running as SYSTEM
Building remotely on Rechenknecht in workspace /mnt/data/jenkins/workspace/pydelta-next
The recommended git tool is: NONE
using credential Github
 > /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 https://github.com/cophi-wue/pydelta # timeout=10
Fetching upstream changes from https://github.com/cophi-wue/pydelta
 > /usr/bin/git --version # timeout=10
 > git --version # 'git version 2.11.0'
using GIT_ASKPASS to set credentials 
 > /usr/bin/git fetch --tags --progress -- https://github.com/cophi-wue/pydelta +refs/heads/*:refs/remotes/origin/* # timeout=10
 > /usr/bin/git rev-parse refs/remotes/origin/next^{commit} # timeout=10
Checking out Revision 4f21ac5a68495e172f8cdf7a6d95cb30facc653a (refs/remotes/origin/next)
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f 4f21ac5a68495e172f8cdf7a6d95cb30facc653a # timeout=10
Commit message: "added pytest-cov to dev dependencies"
 > /usr/bin/git rev-list --no-walk 4f21ac5a68495e172f8cdf7a6d95cb30facc653a # timeout=10
[Checks API] No suitable checks publisher found.
No emails were triggered.
$ bash -c "[ -d \$HOME/.pyenv ]"
$ bash -c "cd /mnt/data/jenkins/workspace/pydelta-next && env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.8.6 \$HOME/.pyenv/bin/pyenv local 2>/dev/null || true"
$ bash -c "mkdir \$HOME/.pyenv.lock"
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.8.6 \$HOME/.pyenv/bin/pyenv versions --bare"
Updating pyenv...
$ bash -c "cd \$HOME/.pyenv && git checkout master && git pull"
Already on 'master'
Your branch is up-to-date with 'origin/master'.
Already up-to-date.
Updated pyenv.
Installing 3.8.6...
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.8.6 \$HOME/.pyenv/bin/pyenv install 3.8.6"
Downloading Python-3.8.6.tar.xz...
-> https://www.python.org/ftp/python/3.8.6/Python-3.8.6.tar.xz
Installing Python-3.8.6...
Installed Python-3.8.6 to /mnt/data/jenkins/.pyenv/versions/3.8.6

Installed 3.8.6.
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.8.6 \$HOME/.pyenv/bin/pyenv rehash"
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.8.6 \$HOME/.pyenv/bin/pyenv exec pip list"
Installing tox...
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.8.6 \$HOME/.pyenv/bin/pyenv exec pip install tox"
Collecting tox
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Collecting toml>=0.9.4
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Collecting pyparsing>=2.0.2
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Installing collected packages: toml, filelock, appdirs, distlib, six, virtualenv, py, pluggy, pyparsing, packaging, tox
Successfully installed appdirs-1.4.4 distlib-0.3.1 filelock-3.0.12 packaging-20.4 pluggy-0.13.1 py-1.9.0 pyparsing-2.4.7 six-1.15.0 toml-0.10.1 tox-3.20.1 virtualenv-20.0.34
WARNING: You are using pip version 20.2.1; however, version 20.2.3 is available.
You should consider upgrading via the '/mnt/data/jenkins/.pyenv/versions/3.8.6/bin/python3.8 -m pip install --upgrade pip' command.
Installed tox.
$ bash -c "env PYENV_ROOT\=\$HOME/.pyenv PYENV_VERSION\=3.8.6 \$HOME/.pyenv/bin/pyenv rehash"
$ bash -c "rm -rf \$HOME/.pyenv.lock"
[pydelta-next] $ /bin/sh -xe /tmp/shiningpanda6730850285320424054.sh
+ pip install -r requirements.txt
Obtaining file:///mnt/data/jenkins/workspace/pydelta-next (from -r requirements.txt (line 1))
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Requirement already satisfied: packaging in /mnt/data/jenkins/.pyenv/versions/3.8.6/lib/python3.8/site-packages (from pytest->-r requirements.txt (line 8)) (20.4)
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Using legacy 'setup.py install' for tornado, since package 'wheel' is not installed.
Using legacy 'setup.py install' for pandocfilters, since package 'wheel' is not installed.
Using legacy 'setup.py install' for pyrsistent, since package 'wheel' is not installed.
Installing collected packages: Cython, attrs, iniconfig, pytest, coverage, pytest-cov, pytz, babel, sphinxcontrib-jsmath, sphinxcontrib-applehelp, idna, certifi, urllib3, chardet, requests, sphinxcontrib-qthelp, snowballstemmer, sphinxcontrib-serializinghtml, docutils, alabaster, sphinxcontrib-devhelp, MarkupSafe, Jinja2, sphinxcontrib-htmlhelp, Pygments, imagesize, Sphinx, tornado, ipython-genutils, traitlets, parso, jedi, ptyprocess, pexpect, pickleshare, decorator, backcall, wcwidth, prompt-toolkit, ipython, python-dateutil, jupyter-core, pyzmq, jupyter-client, ipykernel, pandocfilters, pyrsistent, jsonschema, nbformat, nest-asyncio, async-generator, nbclient, mistune, entrypoints, jupyterlab-pygments, testpath, defusedxml, webencodings, bleach, nbconvert, nbsphinx, numpy, scipy, pillow, cycler, kiwisolver, matplotlib, pandas, threadpoolctl, joblib, scikit-learn, regex, delta
    Running setup.py install for tornado: started
    Running setup.py install for tornado: finished with status 'done'
    Running setup.py install for pandocfilters: started
    Running setup.py install for pandocfilters: finished with status 'done'
    Running setup.py install for pyrsistent: started
    Running setup.py install for pyrsistent: finished with status 'done'
  Running setup.py develop for delta
Successfully installed Cython-0.29.21 Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 Sphinx-3.2.1 alabaster-0.7.12 async-generator-1.10 attrs-20.2.0 babel-2.8.0 backcall-0.2.0 bleach-3.2.1 certifi-2020.6.20 chardet-3.0.4 coverage-5.3 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 delta docutils-0.16 entrypoints-0.3 idna-2.10 imagesize-1.2.0 iniconfig-1.0.1 ipykernel-5.3.4 ipython-7.18.1 ipython-genutils-0.2.0 jedi-0.17.2 joblib-0.17.0 jsonschema-3.2.0 jupyter-client-6.1.7 jupyter-core-4.6.3 jupyterlab-pygments-0.1.2 kiwisolver-1.2.0 matplotlib-3.3.2 mistune-0.8.4 nbclient-0.5.0 nbconvert-6.0.7 nbformat-5.0.7 nbsphinx-0.7.1 nest-asyncio-1.4.1 numpy-1.19.2 pandas-1.1.3 pandocfilters-1.4.2 parso-0.7.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-7.2.0 prompt-toolkit-3.0.8 ptyprocess-0.6.0 pyrsistent-0.17.3 pytest-6.1.1 pytest-cov-2.10.1 python-dateutil-2.8.1 pytz-2020.1 pyzmq-19.0.2 regex-2020.10.11 requests-2.24.0 scikit-learn-0.23.2 scipy-1.5.2 snowballstemmer-2.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 testpath-0.4.4 threadpoolctl-2.1.0 tornado-6.0.4 traitlets-5.0.4 urllib3-1.25.10 wcwidth-0.2.5 webencodings-0.5.1
WARNING: You are using pip version 20.2.1; however, version 20.2.3 is available.
You should consider upgrading via the '/mnt/data/jenkins/.pyenv/versions/3.8.6/bin/python3.8 -m pip install --upgrade pip' command.
+ ./setup.py build_sphinx
running build_sphinx
Running Sphinx v3.2.1
WARNING: html_static_path entry '_static' does not exist
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 9 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
preparing documents... done
writing output... [ 11%] CustomizingPipeline
writing output... [ 22%] GettingStarted
writing output... [ 33%] README
writing output... [ 44%] README-branch
writing output... [ 55%] concept
writing output... [ 66%] delta
writing output... [ 77%] index
writing output... [ 88%] modules
writing output... [100%] refactoring-notes

/mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:346: WARNING: 'any' reference target not found: the :math:`n
/mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:616: WARNING: undefined label: /delta.rst#cluster.clustering (if the link has no caption the label must precede a section header)
/mnt/data/jenkins/workspace/pydelta-next/docs/GettingStarted.ipynb:803: WARNING: undefined label: /delta.rst#cluster.flatclustering (if the link has no caption the label must precede a section header)
/mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:31: WARNING: 'any' reference target not found: sort
/mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:32: WARNING: 'any' reference target not found: reparse_column
/mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:33: WARNING: 'any' reference target not found: relativize
/mnt/data/jenkins/workspace/pydelta-next/docs/concept.rst:36: WARNING: 'any' reference target not found: normalize
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator:1: WARNING: 'any' reference target not found: subdir
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.postprocess_tokens:4: WARNING: 'any' reference target not found: lower_case
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.count_tokens:1: WARNING: 'any' reference target not found: lines
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.FeatureGenerator.process_file:3: WARNING: 'any' reference target not found: filename
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus:9: WARNING: 'any' reference target not found: subdir
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus:9: WARNING: 'any' reference target not found: subdir
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.new_data:1: WARNING: 'any' reference target not found: DataFrame
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.get_mfw_table:11: WARNING: 'any' reference target not found: mfwords
/mnt/data/jenkins/workspace/pydelta-next/delta/corpus.py:docstring of delta.corpus.Corpus.top_n:6: WARNING: 'any' reference target not found: mfwords
/mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.DeltaFunction:16: WARNING: 'any' reference target not found: f
/mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.PreprocessingDeltaFunction:7: WARNING: 'any' reference target not found: f
/mnt/data/jenkins/workspace/pydelta-next/delta/deltas.py:docstring of delta.deltas.MetricDeltaFunction:18: WARNING: 'any' reference target not found: fix_symmetry
generating indices...  genindex py-modindexdone
highlighting module code... [ 20%] delta.cluster
highlighting module code... [ 40%] delta.corpus
highlighting module code... [ 60%] delta.deltas
highlighting module code... [ 80%] delta.graphics
highlighting module code... [100%] delta.util

writing additional pages...  searchdone
copying images... [ 33%] ../build/sphinx/doctrees/nbsphinx/CustomizingPipeline_11_0.png
copying images... [ 66%] ../build/sphinx/doctrees/nbsphinx/CustomizingPipeline_22_0.png
copying images... [100%] ../build/sphinx/doctrees/nbsphinx/GettingStarted_22_0.png

copying static files... ... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 20 warnings.

The HTML pages are in build/sphinx/html.
+ pytest --cov=delta --cov-report=xml:coverage.xml
============================= test session starts ==============================
platform linux -- Python 3.8.6, pytest-6.1.1, py-1.9.0, pluggy-0.13.1
rootdir: /mnt/data/jenkins/workspace/pydelta-next, configfile: setup.cfg
plugins: cov-2.10.1
collected 22 items

delta/util.py ...                                                        [ 13%]
test/corpus_test.py ..........                                           [ 59%]
test/deltas_test.py ......                                               [ 86%]
test/test_issue6.py ...                                                  [100%]

=============================== warnings summary ===============================
delta/__init__.py:35
  /mnt/data/jenkins/workspace/pydelta-next/delta/__init__.py:35: UserWarning: KMedoidsClustering not available
    warn("KMedoidsClustering not available")

../../.pyenv/versions/3.8.6/lib/python3.8/site-packages/_pytest/config/__init__.py:1230
  /mnt/data/jenkins/.pyenv/versions/3.8.6/lib/python3.8/site-packages/_pytest/config/__init__.py:1230: PytestConfigWarning: Unknown config option: nb_diff_ignore
  
    self._warn_or_fail_if_strict("Unknown config option: {}\n".format(key))

test/corpus_test.py::test_table_describer
  /mnt/data/jenkins/.pyenv/versions/3.8.6/lib/python3.8/site-packages/pandas/io/parsers.py:452: ParserWarning: Conflicting values for 'delimiter': '	' was provided, but the dialect specifies ','. Using the dialect-specified value.
    parser = TextFileReader(fp_or_buf, **kwds)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
--- generated xml file: /mnt/data/jenkins/workspace/pydelta-next/pytest.xml ----

----------- coverage: platform linux, python 3.8.6-final-0 -----------
Coverage XML written to file coverage.xml

======================== 22 passed, 3 warnings in 5.26s ========================
[htmlpublisher] Archiving HTML reports...
[htmlpublisher] Archiving at PROJECT level /mnt/data/jenkins/workspace/pydelta-next/build/sphinx/html to /mnt/data/jenkins/jobs/pydelta-next/htmlreports/Documentation
Recording test results
[Cobertura] Publishing Cobertura coverage report...

[Cobertura] Publishing Cobertura coverage results...

[Cobertura] Cobertura coverage report found.

[Set GitHub commit status (universal)] SUCCESS on repos [GHRepository@211411ac[nodeId=MDEwOlJlcG9zaXRvcnk4NDYzMzk3MQ==,description=an experimental implementation of Burrow's delta in Python 3,homepage=http://dev.digital-humanities.de/ci/job/pydelta-next/Documentation/index.html,name=pydelta,fork=true,archived=false,size=2994,milestones={},language=Jupyter Notebook,commits={},isTemplate=<null>,url=https://api.github.com/repos/cophi-wue/pydelta,id=84633971,nodeId=<null>,createdAt=2017-03-11T08:03:36Z,updatedAt=2020-10-12T14:34:53Z]] (sha:4f21ac5) with context:pydelta-next
Setting commit status on GitHub for https://github.com/cophi-wue/pydelta/commit/4f21ac5a68495e172f8cdf7a6d95cb30facc653a
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
[Checks API] No suitable checks publisher found.
Notifying upstream projects of job completion
No emails were triggered.
Finished: SUCCESS