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