Console Output
Started by an SCM change
Building remotely on build3 (digibib) in workspace /mnt/data/jenkins/workspace/cophi_toolbox
> /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/cophi-wue/cophi-toolbox # timeout=10
Fetching upstream changes from git://github.com/cophi-wue/cophi-toolbox
> /usr/bin/git --version # timeout=10
using GIT_ASKPASS to set credentials
> /usr/bin/git fetch --tags --progress git://github.com/cophi-wue/cophi-toolbox +refs/heads/*:refs/remotes/origin/*
Seen branch in repository origin/ddw
Seen branch in repository origin/gh-pages
Seen branch in repository origin/master
Seen branch in repository origin/oop
Seen branch in repository origin/testing
Seen 5 remote branches
> /usr/bin/git show-ref --tags -d # timeout=10
Checking out Revision eba6bd7ce1631c22ee2e56ffbc2c251f1521f858 (origin/testing)
> /usr/bin/git config core.sparsecheckout # timeout=10
> /usr/bin/git checkout -f eba6bd7ce1631c22ee2e56ffbc2c251f1521f858
Commit message: "feat: export api function"
> /usr/bin/git rev-list --no-walk 87ad8c0d1c16f527fc879071b3f82915f36fb8ae # timeout=10
[cophi_toolbox] $ /bin/sh -xe /tmp/jenkins3448607359920418474.sh
+ tox
GLOB sdist-make: /mnt/data/jenkins/workspace/cophi_toolbox/setup.py
py34 create: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/py34
ERROR: InterpreterNotFound: python3.4
py35 inst-nodeps: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/dist/cophi-1.1.0.zip
py35 installed: atomicwrites==1.2.1,attrs==18.2.0,cophi==1.1.0,coverage==4.5.1,lxml==4.2.5,more-itertools==4.3.0,numpy==1.15.3,pandas==0.23.4,pathlib2==2.3.2,pluggy==0.8.0,py==1.7.0,pytest==3.9.3,pytest-cov==2.6.0,python-dateutil==2.7.5,pytz==2018.6,regex==2018.8.29,six==1.11.0
py35 runtests: PYTHONHASHSEED='3605800431'
py35 runtests: commands[0] | pytest
============================= test session starts ==============================
platform linux -- Python 3.5.6, pytest-3.9.3, py-1.7.0, pluggy-0.8.0
rootdir: /mnt/data/jenkins/workspace/cophi_toolbox, inifile: setup.cfg
plugins: cov-2.6.0
collected 91 items
tests/test_api.py ..F [ 3%]
tests/test_complexity.py ...................... [ 27%]
tests/test_model.py .................................................... [ 84%]
......... [ 94%]
tests/test_utils.py ..... [100%]
=================================== FAILURES ===================================
_________________________________ test_export __________________________________
corpus = <cophi.model.Corpus object at 0x7f7ff79ba358>
def test_export(corpus):
output = pathlib.Path("corpus.svmlight")
> cophi.export(corpus.dtm, output, "svmlight")
tests/test_api.py:35:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src/cophi/api.py:98: in export
cophi.model.Corpus.svmlight(corpus, filepath)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'cophi.model.Corpus'>, dtm = <function corpus at 0x7f7ff8949400>
filepath = PosixPath('corpus.svmlight')
@classmethod
def svmlight(cls, dtm, filepath):
"""Export corpus to SVMLight format.
Parameters:
dtm: Document-term matrix.
filepath: Path to output file.
"""
with pathlib.Path(filepath).open("w", encoding="utf-8") as file:
> for title, document in dtm.iterrows():
E AttributeError: 'function' object has no attribute 'iterrows'
src/cophi/model.py:689: AttributeError
--- generated xml file: /mnt/data/jenkins/workspace/cophi_toolbox/tests.xml ----
----------- coverage: platform linux, python 3.5.6-final-0 -----------
Coverage HTML written to dir htmlcov
Coverage XML written to file coverage.xml
===================== 1 failed, 90 passed in 0.85 seconds ======================
ERROR: InvocationError: '/mnt/data/jenkins/workspace/cophi_toolbox/.tox/py35/bin/pytest'
py36 inst-nodeps: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/dist/cophi-1.1.0.zip
py36 installed: atomicwrites==1.2.1,attrs==18.2.0,cophi==1.1.0,coverage==4.5.1,lxml==4.2.5,more-itertools==4.3.0,numpy==1.15.3,pandas==0.23.4,pluggy==0.8.0,py==1.7.0,pytest==3.9.3,pytest-cov==2.6.0,python-dateutil==2.7.5,pytz==2018.6,regex==2018.8.29,six==1.11.0
py36 runtests: PYTHONHASHSEED='3605800431'
py36 runtests: commands[0] | pytest
============================= test session starts ==============================
platform linux -- Python 3.6.7, pytest-3.9.3, py-1.7.0, pluggy-0.8.0
rootdir: /mnt/data/jenkins/workspace/cophi_toolbox, inifile: setup.cfg
plugins: cov-2.6.0
collected 91 items
tests/test_api.py ..F [ 3%]
tests/test_complexity.py ...................... [ 27%]
tests/test_model.py .................................................... [ 84%]
......... [ 94%]
tests/test_utils.py ..... [100%]
=================================== FAILURES ===================================
_________________________________ test_export __________________________________
corpus = <cophi.model.Corpus object at 0x7f897b217dd8>
def test_export(corpus):
output = pathlib.Path("corpus.svmlight")
> cophi.export(corpus.dtm, output, "svmlight")
tests/test_api.py:35:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src/cophi/api.py:98: in export
cophi.model.Corpus.svmlight(corpus, filepath)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'cophi.model.Corpus'>, dtm = <function corpus at 0x7f897c88e400>
filepath = PosixPath('corpus.svmlight')
@classmethod
def svmlight(cls, dtm, filepath):
"""Export corpus to SVMLight format.
Parameters:
dtm: Document-term matrix.
filepath: Path to output file.
"""
with pathlib.Path(filepath).open("w", encoding="utf-8") as file:
> for title, document in dtm.iterrows():
E AttributeError: 'function' object has no attribute 'iterrows'
src/cophi/model.py:689: AttributeError
--- generated xml file: /mnt/data/jenkins/workspace/cophi_toolbox/tests.xml ----
----------- coverage: platform linux, python 3.6.7-final-0 -----------
Coverage HTML written to dir htmlcov
Coverage XML written to file coverage.xml
===================== 1 failed, 90 passed in 0.91 seconds ======================
ERROR: InvocationError: '/mnt/data/jenkins/workspace/cophi_toolbox/.tox/py36/bin/pytest'
py37 inst-nodeps: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/dist/cophi-1.1.0.zip
py37 installed: atomicwrites==1.2.1,attrs==18.2.0,cophi==1.1.0,coverage==4.5.1,lxml==4.2.5,more-itertools==4.3.0,numpy==1.15.3,pandas==0.23.4,pluggy==0.8.0,py==1.7.0,pytest==3.9.3,pytest-cov==2.6.0,python-dateutil==2.7.5,pytz==2018.6,regex==2018.8.29,six==1.11.0
py37 runtests: PYTHONHASHSEED='3605800431'
py37 runtests: commands[0] | pytest
============================= test session starts ==============================
platform linux -- Python 3.7.1, pytest-3.9.3, py-1.7.0, pluggy-0.8.0
rootdir: /mnt/data/jenkins/workspace/cophi_toolbox, inifile: setup.cfg
plugins: cov-2.6.0
collected 91 items
tests/test_api.py ..F [ 3%]
tests/test_complexity.py ...................... [ 27%]
tests/test_model.py .................................................... [ 84%]
......... [ 94%]
tests/test_utils.py ..... [100%]
=================================== FAILURES ===================================
_________________________________ test_export __________________________________
corpus = <cophi.model.Corpus object at 0x7f589dc5cb00>
def test_export(corpus):
output = pathlib.Path("corpus.svmlight")
> cophi.export(corpus.dtm, output, "svmlight")
tests/test_api.py:35:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src/cophi/api.py:98: in export
cophi.model.Corpus.svmlight(corpus, filepath)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
cls = <class 'cophi.model.Corpus'>, dtm = <function corpus at 0x7f589e9e9f28>
filepath = PosixPath('corpus.svmlight')
@classmethod
def svmlight(cls, dtm, filepath):
"""Export corpus to SVMLight format.
Parameters:
dtm: Document-term matrix.
filepath: Path to output file.
"""
with pathlib.Path(filepath).open("w", encoding="utf-8") as file:
> for title, document in dtm.iterrows():
E AttributeError: 'function' object has no attribute 'iterrows'
src/cophi/model.py:689: AttributeError
--- generated xml file: /mnt/data/jenkins/workspace/cophi_toolbox/tests.xml ----
----------- coverage: platform linux, python 3.7.1-final-0 -----------
Coverage HTML written to dir htmlcov
Coverage XML written to file coverage.xml
=============================== warnings summary ===============================
.tox/py37/lib/python3.7/site-packages/pandas/core/dtypes/inference.py:6
/mnt/data/jenkins/workspace/cophi_toolbox/.tox/py37/lib/python3.7/site-packages/pandas/core/dtypes/inference.py:6: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import Iterable
.tox/py37/lib/python3.7/site-packages/pandas/core/tools/datetimes.py:3
/mnt/data/jenkins/workspace/cophi_toolbox/.tox/py37/lib/python3.7/site-packages/pandas/core/tools/datetimes.py:3: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
from collections import MutableMapping
tests/test_model.py::TestCorpus::()::test_map_metadata
/mnt/data/jenkins/workspace/cophi_toolbox/.tox/py37/lib/python3.7/site-packages/pandas/core/common.py:471: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
if not issubclass(into, collections.Mapping):
-- Docs: https://docs.pytest.org/en/latest/warnings.html
=============== 1 failed, 90 passed, 3 warnings in 0.80 seconds ================
ERROR: InvocationError: '/mnt/data/jenkins/workspace/cophi_toolbox/.tox/py37/bin/pytest'
docs inst-nodeps: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/dist/cophi-1.1.0.zip
docs installed: alabaster==0.7.12,Babel==2.6.0,certifi==2018.10.15,chardet==3.0.4,cophi==1.1.0,docutils==0.14,idna==2.7,imagesize==1.1.0,Jinja2==2.10,lxml==4.2.5,MarkupSafe==1.0,numpy==1.15.3,packaging==18.0,pandas==0.23.4,Pygments==2.2.0,pyparsing==2.2.2,python-dateutil==2.7.5,pytz==2018.6,regex==2018.8.29,requests==2.20.0,six==1.11.0,snowballstemmer==1.2.1,Sphinx==1.8.1,sphinxcontrib-websupport==1.1.0,urllib3==1.24
docs runtests: PYTHONHASHSEED='3605800431'
docs runtests: commands[0] | sphinx-build -E -b html docs dist/docs
Running Sphinx v1.8.1
loading intersphinx inventory from https://docs.python.org/objects.inv...
intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 3 source files that are out of date
updating environment: 3 added, 0 changed, 0 removed
reading sources... [ 33%] index
reading sources... [ 66%] reference/cophi-toolbox
reading sources... [100%] reference/index
/mnt/data/jenkins/workspace/cophi_toolbox/docs/reference/cophi-toolbox.rst:3: WARNING: Unknown directive type "testsetup".
.. testsetup::
from cophi import *
WARNING: autodoc: failed to import module 'preprocessing' from module 'cophi_toolbox'; the following exception was raised:
No module named 'cophi_toolbox'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /mnt/data/jenkins/workspace/cophi_toolbox/docs/reference/cophi-toolbox.rst: WARNING: document isn't included in any toctree
/mnt/data/jenkins/workspace/cophi_toolbox/docs/reference/index.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 33%] index
writing output... [ 66%] reference/cophi-toolbox
writing output... [100%] reference/index
generating indices... genindex
writing additional pages... search
copying static files... WARNING: html_static_path entry '/mnt/data/jenkins/workspace/cophi_toolbox/docs/_static' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 5 warnings.
The HTML pages are in dist/docs.
docs runtests: commands[1] | sphinx-build -b linkcheck docs dist/docs
Running Sphinx v1.8.1
loading pickled environment... done
building [mo]: targets for 0 po files that are out of date
building [linkcheck]: targets for 3 source files that are out of date
updating environment: [] 0 added, 1 changed, 0 removed
reading sources... [100%] reference/cophi-toolbox
/mnt/data/jenkins/workspace/cophi_toolbox/docs/reference/cophi-toolbox.rst:3: WARNING: Unknown directive type "testsetup".
.. testsetup::
from cophi import *
WARNING: autodoc: failed to import module 'preprocessing' from module 'cophi_toolbox'; the following exception was raised:
No module named 'cophi_toolbox'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /mnt/data/jenkins/workspace/cophi_toolbox/docs/reference/cophi-toolbox.rst: WARNING: document isn't included in any toctree
/mnt/data/jenkins/workspace/cophi_toolbox/docs/reference/index.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 33%] index
writing output... [ 66%] reference/cophi-toolbox
writing output... [100%] reference/index
build succeeded, 4 warnings.
Look for any errors in the above output or in dist/docs/output.txt
___________________________________ summary ____________________________________
SKIPPED: py34: InterpreterNotFound: python3.4
ERROR: py35: commands failed
ERROR: py36: commands failed
ERROR: py37: commands failed
docs: commands succeeded
Build step 'Execute shell' marked build as failure
[TASKS] Skipping publisher since build result is 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@421b7bf5[description=A repository containing general functions for processing and accessing text corpora,homepage=<null>,name=cophi-toolbox,license=<null>,fork=false,size=461,milestones={},language=Jupyter Notebook,commits={},source=<null>,parent=<null>,responseHeaderFields={null=[HTTP/1.1 200 OK], Access-Control-Allow-Origin=[*], Access-Control-Expose-Headers=[ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type], Cache-Control=[private, max-age=60, s-maxage=60], Content-Encoding=[gzip], Content-Security-Policy=[default-src 'none'], Content-Type=[application/json; charset=utf-8], Date=[Sun, 23 Dec 2018 19:24:04 GMT], ETag=[W/"a165fc65197e9cd202840b2aa5293f3d"], Last-Modified=[Sun, 23 Dec 2018 19:08:12 GMT], OkHttp-Received-Millis=[1545593044452], OkHttp-Response-Source=[CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1545593044284], 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=[B3AB:1F57:3B9BA3D:83E4A51:5C1FE0D3], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4998], X-RateLimit-Reset=[1545595708], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/cophi-wue/cophi-toolbox,id=113045733]] (sha:eba6bd7) with context:cophi_toolbox
Setting commit status on GitHub for https://github.com/cophi-wue/cophi-toolbox/commit/eba6bd7ce1631c22ee2e56ffbc2c251f1521f858
[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
Finished: FAILURE
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