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Regression
notebooks.Visualizations.ipynb./mnt/data/jenkins/workspace/DARIAH-Topics/notebooks/Visualizations.ipynb (from pytest)
Error Message
nbconvert.preprocessors.execute.CellExecutionError: An error occurred while executing the following cell: ------------------ corpus = list(preprocessing.read_files(meta.index)) corpus[0][:255] # printing the first 255 characters of the first document ------------------ #x1B[0;31m---------------------------------------------------------------------------#x1B[0m #x1B[0;31mAttributeError#x1B[0m Traceback (most recent call last) #x1B[0;32m<ipython-input-4-1004dfe5ae0a>#x1B[0m in #x1B[0;36m<module>#x1B[0;34m()#x1B[0m #x1B[0;32m----> 1#x1B[0;31m #x1B[0mcorpus#x1B[0m #x1B[0;34m=#x1B[0m #x1B[0mlist#x1B[0m#x1B[0;34m(#x1B[0m#x1B[0mpreprocessing#x1B[0m#x1B[0;34m.#x1B[0m#x1B[0mread_files#x1B[0m#x1B[0;34m(#x1B[0m#x1B[0mmeta#x1B[0m#x1B[0;34m.#x1B[0m#x1B[0mindex#x1B[0m#x1B[0;34m)#x1B[0m#x1B[0;34m)#x1B[0m#x1B[0;34m#x1B[0m#x1B[0m #x1B[0m#x1B[1;32m 2#x1B[0m #x1B[0mcorpus#x1B[0m#x1B[0;34m[#x1B[0m#x1B[0;36m0#x1B[0m#x1B[0;34m]#x1B[0m#x1B[0;34m[#x1B[0m#x1B[0;34m:#x1B[0m#x1B[0;36m255#x1B[0m#x1B[0;34m]#x1B[0m #x1B[0;31m# printing the first 255 characters of the first document#x1B[0m#x1B[0;34m#x1B[0m#x1B[0m #x1B[0;31mAttributeError#x1B[0m: module 'cophi_toolbox.preprocessing' has no attribute 'read_files' AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
Stacktrace
self = <CallInfo when='call' exception: An error occurred while executing the following cell:
------------------
corpus = lis...ing' has no attribute 'read_files'
AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7f323935d378>
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/python3.5/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds),
when=when,
treat_keyboard_interrupt_as_exception=item.config.getvalue("usepdb"),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/_pytest/runner.py:181:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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.argnames:
notincall = set(self.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._nonwrappers + self._wrappers, kwargs)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:617:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7f3268364390>
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
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/python3.5/site-packages/pluggy/__init__.py:222:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_call'>
methods = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
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'),
)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/pluggy/__init__.py:216:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
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/python3.5/site-packages/pluggy/callers.py:201:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7f323940c898>
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/python3.5/site-packages/pluggy/callers.py:76:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<pluggy.HookImpl object at 0x7f32661d6e80>, <pluggy.HookImpl object at 0x7f32630c7358>, <pluggy.HookImpl object at 0x7f32630570f0>]
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/python3.5/site-packages/pluggy/callers.py:180:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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/python3.5/site-packages/_pytest/runner.py:109:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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/python3.5/site-packages/nbsmoke/__init__.py:274:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f323940cfd0>
nb = {'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}, 'language_info': {'... width=800)\nshow(interactive_barchart_per_document, notebook_handle=True)"}], 'nbformat_minor': 2}
resources = {}
def preprocess(self, nb, resources):
"""
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``.
Returns
-------
nb : NotebookNode
The executed notebook.
resources : dictionary
Additional resources used in the conversion process.
"""
path = resources.get('metadata', {}).get('path', '')
if path == '':
path = None
# clear display_id map
self._display_id_map = {}
# from jupyter_client.manager import start_new_kernel
def start_new_kernel(startup_timeout=60, kernel_name='python', **kwargs):
km = self.kernel_manager_class(kernel_name=kernel_name)
km.start_kernel(**kwargs)
kc = km.client()
kc.start_channels()
try:
kc.wait_for_ready(timeout=startup_timeout)
except RuntimeError:
kc.stop_channels()
km.shutdown_kernel()
raise
return km, kc
kernel_name = nb.metadata.get('kernelspec', {}).get('name', 'python')
if self.kernel_name:
kernel_name = self.kernel_name
self.log.info("Executing notebook with kernel: %s" % kernel_name)
self.km, self.kc = start_new_kernel(
startup_timeout=self.startup_timeout,
kernel_name=kernel_name,
extra_arguments=self.extra_arguments,
cwd=path)
self.kc.allow_stdin = False
self.nb = nb
try:
> nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:262:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f323940cfd0>
nb = {'metadata': {'kernelspec': {'language': 'python', 'name': 'python3', 'display_name': 'Python 3'}, 'language_info': {'... width=800)\nshow(interactive_barchart_per_document, notebook_handle=True)"}], '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/python3.5/site-packages/nbconvert/preprocessors/base.py:69:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbconvert.preprocessors.execute.ExecutePreprocessor object at 0x7f323940cfd0>
cell = {'cell_type': 'code', 'metadata': {}, 'outputs': [{'output_type': 'error', 'ename': 'AttributeError', 'evalue': "modul...list(preprocessing.read_files(meta.index))\ncorpus[0][:255] # printing the first 255 characters of the first document'}
resources = {}, cell_index = 3
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':
return cell, resources
reply, outputs = self.run_cell(cell, cell_index)
cell.outputs = outputs
if not self.allow_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 corpus = list(preprocessing.read_files(meta.index))
E corpus[0][:255] # printing the first 255 characters of the first document
E ------------------
E
E #x1B[0;31m---------------------------------------------------------------------------#x1B[0m
E #x1B[0;31mAttributeError#x1B[0m Traceback (most recent call last)
E #x1B[0;32m<ipython-input-4-1004dfe5ae0a>#x1B[0m in #x1B[0;36m<module>#x1B[0;34m()#x1B[0m
E #x1B[0;32m----> 1#x1B[0;31m #x1B[0mcorpus#x1B[0m #x1B[0;34m=#x1B[0m #x1B[0mlist#x1B[0m#x1B[0;34m(#x1B[0m#x1B[0mpreprocessing#x1B[0m#x1B[0;34m.#x1B[0m#x1B[0mread_files#x1B[0m#x1B[0;34m(#x1B[0m#x1B[0mmeta#x1B[0m#x1B[0;34m.#x1B[0m#x1B[0mindex#x1B[0m#x1B[0;34m)#x1B[0m#x1B[0;34m)#x1B[0m#x1B[0;34m#x1B[0m#x1B[0m
E #x1B[0m#x1B[1;32m 2#x1B[0m #x1B[0mcorpus#x1B[0m#x1B[0;34m[#x1B[0m#x1B[0;36m0#x1B[0m#x1B[0;34m]#x1B[0m#x1B[0;34m[#x1B[0m#x1B[0;34m:#x1B[0m#x1B[0;36m255#x1B[0m#x1B[0;34m]#x1B[0m #x1B[0;31m# printing the first 255 characters of the first document#x1B[0m#x1B[0;34m#x1B[0m#x1B[0m
E
E #x1B[0;31mAttributeError#x1B[0m: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
E AttributeError: module 'cophi_toolbox.preprocessing' has no attribute 'read_files'
../../shiningpanda/jobs/62c67c92/virtualenvs/d41d8cd9/lib/python3.5/site-packages/nbconvert/preprocessors/execute.py:286: CellExecutionError