Console Output
Started by GitHub push by severinsimmler
Building remotely on Rechenknecht 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 004872f7293fe7d2e78d69da08c4e16fef8637ae (origin/testing)
> /usr/bin/git config core.sparsecheckout # timeout=10
> /usr/bin/git checkout -f 004872f7293fe7d2e78d69da08c4e16fef8637ae
Commit message: "chore: tune version number"
> /usr/bin/git rev-list --no-walk 9c12e8be225b79655c8ce435058a7f8bc9f543cb # timeout=10
[cophi_toolbox] $ /bin/sh -xe /tmp/jenkins9135758770907031571.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-1.0.9.zip
py35 installed: atomicwrites==1.2.1,attrs==18.2.0,cophi==1.0.9,coverage==4.5.2,lxml==4.2.5,more-itertools==4.3.0,numpy==1.15.4,pandas==0.23.4,pathlib2==2.3.2,pkg-resources==0.0.0,pluggy==0.8.0,py==1.7.0,pytest==4.0.0,pytest-cov==2.6.0,python-dateutil==2.7.5,pytz==2018.7,regex==2018.11.22,six==1.11.0
py35 runtests: PYTHONHASHSEED='3354600420'
py35 runtests: commands[0] | pytest
============================= test session starts ==============================
platform linux -- Python 3.5.3, pytest-4.0.0, py-1.7.0, pluggy-0.8.0
rootdir: /mnt/data/jenkins/workspace/cophi_toolbox, inifile: setup.cfg
plugins: cov-2.6.0
collected 90 items
tests/test_api.py .. [ 2%]
tests/test_complexity.py ...................... [ 26%]
tests/test_model.py ..F.F...............F......F...FFFF................. [ 84%]
.......FF [ 94%]
tests/test_utils.py ..... [100%]
=================================== FAILURES ===================================
____________________________ TestTextfile.test_xml _____________________________
self = <test_model.TestTextfile object at 0x7fbb402ac128>
textfile_xml = <cophi.model.Textfile object at 0x7fbb402ac588>
tmpdir = local('/tmp/pytest-of-jenkins/pytest-4/test_xml0')
def test_xml(self, textfile_xml, tmpdir):
assert str(textfile_xml.filepath) == str(tmpdir.join("sub", "document.xml"))
assert textfile_xml.title == "document"
assert textfile_xml.suffix == ".xml"
assert textfile_xml.parent == str(tmpdir.join("sub"))
assert textfile_xml.encoding == "utf-8"
assert textfile_xml.treat_as == ".xml"
> assert textfile_xml.content == DOCUMENT
tests/test_model.py:71:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <cophi.model.Textfile object at 0x7fbb402ac588>
@property
def content(self):
"""Content of text file.
"""
if (self.treat_as is None and self.suffix == ".txt") or (self.treat_as == ".txt"):
return self.filepath.read_text(encoding=self.encoding)
elif (self.treat_as is None and self.suffix == ".xml") or (self.treat_as == ".xml"):
tree = self.parse_xml()
> return self.stringify(tree)
E TypeError: stringify() takes 1 positional argument but 2 were given
src/cophi/model.py:91: TypeError
_________________________ TestTextfile.test_stringify __________________________
self = <test_model.TestTextfile object at 0x7fbb4024f240>
textfile_xml = <cophi.model.Textfile object at 0x7fbb4024f550>
def test_stringify(self, textfile_xml):
tree = textfile_xml.parse_xml()
> assert textfile_xml.stringify(tree) == "AAABBCCCDEF"
E TypeError: stringify() takes 1 positional argument but 2 were given
tests/test_model.py:79: TypeError
____________________________ TestDocument.test_drop ____________________________
self = <test_model.TestDocument object at 0x7fbb402841d0>
document = <cophi.model.Document object at 0x7fbb402842b0>
def test_drop(self, document):
features = ["a", "b", "c"]
> tokens = document.drop(LOWERCASE_TOKENS, features)
E TypeError: drop() takes 2 positional arguments but 3 were given
tests/test_model.py:147: TypeError
_________________________ TestCorpus.test_map_metadata _________________________
self = <test_model.TestCorpus object at 0x7fbb40284f60>
corpus = <cophi.model.Corpus object at 0x7fbb40284828>
def test_map_metadata(self, corpus):
metadata = pd.DataFrame({"uuid": "document", "A": "metadata"}, index=[1])
> matrix = corpus.map_metadata(corpus.dtm, metadata, fields=["A"])
tests/test_model.py:186:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
data = <class 'cophi.model.Corpus'>
metadata = a b c d e f
document 3 2 3 1 1 1
uuid = A uuid
1 metadata document, fields = ['A'], sep = '_'
@classmethod
def map_metadata(data, metadata, uuid="uuid", fields=["title"], sep="_"):
"""Map metadata with a UUID.
Parameters:
data: Data (e.g. a pandas DataFrame) to map with.
metadata: Matrix with metadata, one row corresponds
to one document.
uuid (str): The connecting UUID between `data`
and `metadata` (optional).
fields (list): One or more columns of `metadata` (optional).
sep (str): Glue multiple `fields` with this
separator together (optional).
"""
> data = data.copy() # do not work on original object itself
E AttributeError: type object 'Corpus' has no attribute 'copy'
src/cophi/model.py:382: AttributeError
_____________________________ TestCorpus.test_sort _____________________________
self = <test_model.TestCorpus object at 0x7fbb4014a208>
corpus = <cophi.model.Corpus object at 0x7fbb4014a9e8>
def test_sort(self, corpus):
> assert corpus.sort(corpus.dtm).sum().sum() == len(TOKENS)
E TypeError: sort() takes 1 positional argument but 2 were given
tests/test_model.py:201: TypeError
_____________________________ TestCorpus.test_mfw ______________________________
self = <test_model.TestCorpus object at 0x7fbb4024f8d0>
corpus = <cophi.model.Corpus object at 0x7fbb5e1522b0>
def test_mfw(self, corpus):
> assert corpus.mfw(1, as_list=False, rel=False).sum() == 3
tests/test_model.py:204:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <cophi.model.Corpus object at 0x7fbb5e1522b0>, n = 1, rel = False
as_list = False
def mfw(self, n=100, rel=False, as_list=True):
"""Most frequent words.
Parameters:
n (int): Number of most frequent words (optional).
rel (int): If True, use relative frequencies for
sorting (optional).
as_list: If True, return just tokens in a list (optional).
"""
> dtm = self.sort(self.dtm)
E TypeError: sort() takes 1 positional argument but 2 were given
src/cophi/model.py:431: TypeError
_____________________________ TestCorpus.test_drop _____________________________
self = <test_model.TestCorpus object at 0x7fbb4014af60>
corpus = <cophi.model.Corpus object at 0x7fbb4014a908>
def test_drop(self, corpus):
> matrix = corpus.drop(corpus.dtm, ["a"])
E TypeError: drop() takes 2 positional arguments but 3 were given
tests/test_model.py:209: TypeError
_____________________________ TestCorpus.test_cull _____________________________
self = <test_model.TestCorpus object at 0x7fbb402acb38>
corpus = <cophi.model.Corpus object at 0x7fbb4024fac8>
def test_cull(self, corpus):
> assert corpus.cull(corpus.dtm, 1).sum().sum() == len(TOKENS)
tests/test_model.py:213:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src/cophi/model.py:469: in cull
if ratio > 1:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = a b c d e f
document True True True False False False
def __nonzero__(self):
raise ValueError("The truth value of a {0} is ambiguous. "
"Use a.empty, a.bool(), a.item(), a.any() or a.all()."
> .format(self.__class__.__name__))
E ValueError: The truth value of a DataFrame is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
.tox/py35/lib/python3.5/site-packages/pandas/core/generic.py:1576: ValueError
___________________________ TestCorpus.test_svmlight ___________________________
self = <test_model.TestCorpus object at 0x7fbb401608d0>
corpus = <cophi.model.Corpus object at 0x7fbb40160c50>
def test_svmlight(self, corpus):
output = pathlib.Path("corpus.svmlight")
> corpus.svmlight(corpus.dtm, output)
E TypeError: svmlight() takes 2 positional arguments but 3 were given
tests/test_model.py:292: TypeError
__________________________ TestCorpus.test_plaintext ___________________________
self = <test_model.TestCorpus object at 0x7fbb4016b748>
corpus = <cophi.model.Corpus object at 0x7fbb4016b518>
def test_plaintext(self, corpus):
output = pathlib.Path("corpus.txt")
> corpus.plaintext(corpus.dtm, output)
E TypeError: plaintext() takes 2 positional arguments but 3 were given
tests/test_model.py:299: TypeError
--- generated xml file: /mnt/data/jenkins/workspace/cophi_toolbox/tests.xml ----
----------- coverage: platform linux, python 3.5.3-final-0 -----------
Coverage HTML written to dir htmlcov
Coverage XML written to file coverage.xml
===================== 10 failed, 80 passed in 0.89 seconds =====================
ERROR: InvocationError: '/mnt/data/jenkins/workspace/cophi_toolbox/.tox/py35/bin/pytest'
py36 create: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/py36
ERROR: InterpreterNotFound: python3.6
py37 create: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/py37
ERROR: InterpreterNotFound: python3.7
docs inst-nodeps: /mnt/data/jenkins/workspace/cophi_toolbox/.tox/dist/cophi-1.0.9.zip
docs installed: alabaster==0.7.12,Babel==2.6.0,certifi==2018.10.15,chardet==3.0.4,cophi==1.0.9,docutils==0.14,idna==2.7,imagesize==1.1.0,Jinja2==2.10,lxml==4.2.5,MarkupSafe==1.1.0,numpy==1.15.4,packaging==18.0,pandas==0.23.4,pkg-resources==0.0.0,Pygments==2.2.0,pyparsing==2.3.0,python-dateutil==2.7.5,pytz==2018.7,regex==2018.11.22,requests==2.20.1,six==1.11.0,snowballstemmer==1.2.1,Sphinx==1.8.2,sphinxcontrib-websupport==1.1.0,urllib3==1.24.1
docs runtests: PYTHONHASHSEED='3354600420'
docs runtests: commands[0] | sphinx-build -E -b html docs dist/docs
Running Sphinx v1.8.2
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 v1.8.2
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
SKIPPED: py36: InterpreterNotFound: python3.6
SKIPPED: py37: InterpreterNotFound: python3.7
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@1de618d2[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 18:55:54 GMT], ETag=[W/"8f3d18e90b605baa166ca7a69d01591b"], Last-Modified=[Sun, 23 Dec 2018 18:50:07 GMT], OkHttp-Received-Millis=[1545591354196], OkHttp-Response-Source=[CONDITIONAL_CACHE 200], OkHttp-Selected-Protocol=[http/1.1], OkHttp-Sent-Millis=[1545591353903], 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=[E372:1F57:3B8D6C2:83C49EA:5C1FDA39], X-OAuth-Scopes=[admin:repo_hook, repo, repo:status], X-RateLimit-Limit=[5000], X-RateLimit-Remaining=[4947], X-RateLimit-Reset=[1545592091], X-XSS-Protection=[1; mode=block]},url=https://api.github.com/repos/cophi-wue/cophi-toolbox,id=113045733]] (sha:004872f) with context:cophi_toolbox
Setting commit status on GitHub for https://github.com/cophi-wue/cophi-toolbox/commit/004872f7293fe7d2e78d69da08c4e16fef8637ae
[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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