nbval
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Published
20 hours ago •
computationalmodelling
computationalmodelling
nbval and cov do not play nicely together
Steps to reproduce:
- Clone
uarray: https://github.com/Quansight-Labs/uarray - Create a conda env from
.conda/environment.yml - Install
nbval - Comment out the
addoptsline inpytest.ini - Run
pytest --cov --nbval .
Actual output
nbval stalls, then errors with a timeout error.
Expected output
nbval should test the notebooks without a timeout.
OS/environment:
macOS 10.14
conda list
# packages in environment at /Users/hameerabbasi/anaconda/envs/uarray:
#
# Name Version Build Channel
alabaster 0.7.12 py37_0
appdirs 1.4.3 py37h28b3542_0
appnope 0.1.0 py37_0
asn1crypto 0.24.0 py37_0
atomicwrites 1.3.0 py37_1
attrs 19.1.0 py37_1
autopep8 1.4.3 py37_0
babel 2.6.0 py37_0
backcall 0.1.0 py37_0
blas 1.0 mkl
bleach 3.1.0 py37_0
ca-certificates 2019.1.23 0
certifi 2019.3.9 py37_0
cffi 1.12.2 py37hb5b8e2f_1
chardet 3.0.4 py37_1
click 7.0 py37_0
coverage 4.5.3 py37h1de35cc_0
cryptography 2.6.1 py37ha12b0ac_0
decorator 4.4.0 py37_1
defusedxml 0.5.0 py37_1
doc8 0.8.0 py_1 conda-forge
docutils 0.14 py37_0
entrypoints 0.3 py37_0
flake8 3.7.7 py37_0
gumath 0.2.0dev3 py37_243_gd686a36 xnd/label/dev
idna 2.8 py37_0
imagesize 1.1.0 py37_0
intel-openmp 2019.3 199
ipykernel 5.1.0 py37h39e3cac_0
ipython 7.4.0 py37h39e3cac_0
ipython_genutils 0.2.0 py37_0
jedi 0.13.3 py37_0
jinja2 2.10 py37_0
jsonschema 3.0.1 py37_0
jupyter_client 5.2.4 py37_0
jupyter_core 4.4.0 py37_0
jupyterlab 0.35.4 py37hf63ae98_0
jupyterlab_server 0.2.0 py37_0
libcxx 4.0.1 hcfea43d_1
libcxxabi 4.0.1 hcfea43d_1
libedit 3.1.20181209 hb402a30_0
libffi 3.2.1 h475c297_4
libgfortran 3.0.1 h93005f0_2
libgumath 0.2.0dev3 py37_243_gd686a36 xnd/label/dev
libndtypes 0.2.0dev3 py37_228_gcb364d0 xnd/label/dev
libsodium 1.0.16 h3efe00b_0
libxnd 0.2.0dev3 py37_229_g5fdc53b xnd/label/dev
markupsafe 1.1.1 py37h1de35cc_0
mccabe 0.6.1 py37_1
mistune 0.8.4 py37h1de35cc_0
mkl 2019.3 199
mkl_fft 1.0.10 py37h5e564d8_0
mkl_random 1.0.2 py37h27c97d8_0
more-itertools 6.0.0 py37_0
mypy 0.670 py_0
mypy-extensions 0.4.1 pypi_0 pypi
mypy_extensions 0.4.1 py37_0
nbconvert 5.4.1 py37_3
nbformat 4.4.0 py37_0
nbval 0.9.1 py_0 conda-forge
ncurses 6.1 h0a44026_1
ndtypes 0.2.0dev3 py37_228_gcb364d0 xnd/label/dev
ninja 1.9.0 py37h04f5b5a_0
notebook 5.7.8 py37_0
numpy 1.16.2 py37hacdab7b_0
numpy-base 1.16.2 py37h6575580_0
openssl 1.1.1b h1de35cc_1
packaging 19.0 py37_0
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py37_1
parso 0.3.4 py37_0
pbr 5.1.3 py_0
pexpect 4.6.0 py37_0
pickleshare 0.7.5 py37_0
pip 19.0.3 py37_0
pluggy 0.9.0 py37_0
prometheus_client 0.6.0 py37_0
prompt_toolkit 2.0.9 py37_0
psutil 5.4.8 py37h1de35cc_0
ptyprocess 0.6.0 py37_0
py 1.8.0 py37_0
pycodestyle 2.5.0 py37_0
pycparser 2.19 py37_0
pyflakes 2.1.1 py37_0
pygments 2.3.1 py37_0
pyopenssl 19.0.0 py37_0
pyparsing 2.3.1 py37_0
pyrsistent 0.14.11 py37h1de35cc_0
pysocks 1.6.8 py37_0
pytest 4.3.1 py37_0
pytest-cov 2.6.1 py37_0
pytest-flake8 1.0.4 py37_0 conda-forge
pytest-mypy 0.3.2 pypi_0 pypi
python 3.7.3 h359304d_0
python-dateutil 2.8.0 py37_0
pytorch-cpu 1.0.1 py37h0a44026_0 conda-forge
pytz 2018.9 py37_0
pyzmq 18.0.0 py37h0a44026_0
readline 7.0 h1de35cc_5
requests 2.21.0 py37_0
restructuredtext_lint 1.3.0 py_0 conda-forge
rope 0.12.0 py37_0
scipy 1.2.1 py37h1410ff5_0
send2trash 1.5.0 py37_0
setuptools 40.8.0 py37_0
six 1.12.0 py37_0
snowballstemmer 1.2.1 py37_0
sphinx 1.8.5 py37_0
sphinx_rtd_theme 0.4.3 py_0
sphinxcontrib 1.0 py37_1
sphinxcontrib-websupport 1.1.0 py37_1
sqlite 3.27.2 ha441bb4_0
stevedore 1.30.1 py_0 conda-forge
terminado 0.8.1 py37_1
testpath 0.4.2 py37_0
tk 8.6.8 ha441bb4_0
toml 0.10.0 py37h28b3542_0
tornado 6.0.2 py37h1de35cc_0
traitlets 4.3.2 py37_0
typed-ast 1.3.1 pypi_0 pypi
typing 3.6.4 py37_0
uarray 0.4+205.g2e0e01a.dirty dev_0 <develop>
urllib3 1.24.1 py37_0
wcwidth 0.1.7 py37_0
webencodings 0.5.1 py37_1
wheel 0.33.1 py37_0
xnd 0.2.0dev3 py37_229_g5fdc53b xnd/label/dev
xz 5.2.4 h1de35cc_4
zeromq 4.3.1 h0a44026_3
zlib 1.2.11 h1de35cc_3
Full output:
============================= test session starts ==============================
platform darwin -- Python 3.7.3, pytest-4.3.1, py-1.8.0, pluggy-0.9.0
rootdir: /Users/hameerabbasi/Quansight/uarray, inifile: pytest.ini
plugins: mypy-0.3.2, flake8-1.0.4, cov-2.6.1, nbval-0.9.1
collected 69 items
notebooks/01_user_facing.ipynb EEEEEE [ 8%]
notebooks/02_basic_dev_tutorial.ipynb ^C
==================================== ERRORS ====================================
___________ ERROR at setup of notebooks/01_user_facing.ipynb::Cell 0 ___________
cls = <class '_pytest.runner.CallInfo'>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7fd2e97fee18>
when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:226:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = ()
kwargs = {'item': <IPyNbCell Cell 0>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7fd2f801fc18>
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 0>}
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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 0>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 0>}, 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()
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7fd2f9419668>
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])
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 0>}, 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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 0>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:398:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile notebooks/01_user_facing.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x7fd2f868c470>
kernel = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
floc = local('/Users/hameerabbasi/Quansight/uarray/notebooks/01_user_facing.ipynb')
output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
parent_id = 'bd9664d3-cf832aedeafd439954386d8b', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>, stream = 'iopub'
timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x7fd2fb085b38>
args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x7fd2f8d02b38>
block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
___________ ERROR at setup of notebooks/01_user_facing.ipynb::Cell 1 ___________
cls = <class '_pytest.runner.CallInfo'>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7fd2fb1b79d8>
when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:226:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = ()
kwargs = {'item': <IPyNbCell Cell 1>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7fd2f801fc18>
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 1>}
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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 1>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 1>}, 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()
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7fd318711518>
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])
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 1>}, 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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 1>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 1>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
> six.reraise(*col._prepare_exc)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:394:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tp = <class '_queue.Empty'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
../../anaconda/envs/uarray/lib/python3.7/site-packages/six.py:692:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:398:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile notebooks/01_user_facing.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x7fd2f868c470>
kernel = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
floc = local('/Users/hameerabbasi/Quansight/uarray/notebooks/01_user_facing.ipynb')
output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
parent_id = 'bd9664d3-cf832aedeafd439954386d8b', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>, stream = 'iopub'
timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x7fd2fb085b38>
args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x7fd2f8d02b38>
block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
___________ ERROR at setup of notebooks/01_user_facing.ipynb::Cell 2 ___________
cls = <class '_pytest.runner.CallInfo'>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7fd2fb18f400>
when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:226:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = ()
kwargs = {'item': <IPyNbCell Cell 2>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7fd2f801fc18>
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 2>}
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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 2>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 2>}, 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()
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7fd2e99e6550>
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])
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 2>}, 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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 2>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 2>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
> six.reraise(*col._prepare_exc)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:394:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tp = <class '_queue.Empty'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
../../anaconda/envs/uarray/lib/python3.7/site-packages/six.py:692:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:398:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile notebooks/01_user_facing.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x7fd2f868c470>
kernel = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
floc = local('/Users/hameerabbasi/Quansight/uarray/notebooks/01_user_facing.ipynb')
output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
parent_id = 'bd9664d3-cf832aedeafd439954386d8b', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>, stream = 'iopub'
timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x7fd2fb085b38>
args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x7fd2f8d02b38>
block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
___________ ERROR at setup of notebooks/01_user_facing.ipynb::Cell 3 ___________
cls = <class '_pytest.runner.CallInfo'>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7fd2f947d8c8>
when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:226:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = ()
kwargs = {'item': <IPyNbCell Cell 3>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7fd2f801fc18>
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 3>}
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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 3>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 3>}, 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()
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7fd2e9953c88>
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])
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 3>}, 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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 3>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 3>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
> six.reraise(*col._prepare_exc)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:394:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tp = <class '_queue.Empty'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
../../anaconda/envs/uarray/lib/python3.7/site-packages/six.py:692:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:398:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile notebooks/01_user_facing.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x7fd2f868c470>
kernel = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
floc = local('/Users/hameerabbasi/Quansight/uarray/notebooks/01_user_facing.ipynb')
output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
parent_id = 'bd9664d3-cf832aedeafd439954386d8b', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>, stream = 'iopub'
timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x7fd2fb085b38>
args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x7fd2f8d02b38>
block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
___________ ERROR at setup of notebooks/01_user_facing.ipynb::Cell 4 ___________
cls = <class '_pytest.runner.CallInfo'>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7fd318653f28>
when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:226:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = ()
kwargs = {'item': <IPyNbCell Cell 4>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7fd2f801fc18>
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 4>}
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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 4>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 4>}, 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()
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7fd3186ce2e8>
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])
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 4>}, 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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 4>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 4>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
> six.reraise(*col._prepare_exc)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:394:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tp = <class '_queue.Empty'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
../../anaconda/envs/uarray/lib/python3.7/site-packages/six.py:692:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:398:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile notebooks/01_user_facing.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x7fd2f868c470>
kernel = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
floc = local('/Users/hameerabbasi/Quansight/uarray/notebooks/01_user_facing.ipynb')
output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
parent_id = 'bd9664d3-cf832aedeafd439954386d8b', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>, stream = 'iopub'
timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x7fd2fb085b38>
args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x7fd2f8d02b38>
block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
___________ ERROR at setup of notebooks/01_user_facing.ipynb::Cell 5 ___________
cls = <class '_pytest.runner.CallInfo'>
func = <function call_runtest_hook.<locals>.<lambda> at 0x7fd2e9815400>
when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:226:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:198:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = ()
kwargs = {'item': <IPyNbCell Cell 5>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x7fd2f801fc18>
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 5>}
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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
kwargs = {'item': <IPyNbCell Cell 5>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 5>}, 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()
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x7fd2fb2277b8>
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])
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/Users/hameerabbasi/anaconda/envs/uarray/lib/python....py'>>, <HookImpl plugin_name='capturemanager', plugin=<_pytest.capture.CaptureManager object at 0x7fd2f85bfc88>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 5>}, 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)
../../anaconda/envs/uarray/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 5>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:116:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 5>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
> six.reraise(*col._prepare_exc)
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:394:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tp = <class '_queue.Empty'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
../../anaconda/envs/uarray/lib/python3.7/site-packages/six.py:692:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x7fd2f807a438>
colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
../../anaconda/envs/uarray/lib/python3.7/site-packages/_pytest/runner.py:398:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile notebooks/01_user_facing.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x7fd2f868c470>
kernel = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
floc = local('/Users/hameerabbasi/Quansight/uarray/notebooks/01_user_facing.ipynb')
output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>
parent_id = 'bd9664d3-cf832aedeafd439954386d8b', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x7fd2fb085a58>, stream = 'iopub'
timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
../../anaconda/envs/uarray/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x7fd2fb085b38>
args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x7fd2f8d02b38>
block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
../../anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
=============================== warnings summary ===============================
notebooks/01_user_facing.ipynb::Cell 0
/Users/hameerabbasi/anaconda/envs/uarray/lib/python3.7/site-packages/jupyter_client/manager.py:62: DeprecationWarning: KernelManager._kernel_spec_manager_changed is deprecated in traitlets 4.1: use @observe and @unobserve instead.
def _kernel_spec_manager_changed(self):
-- Docs: https://docs.pytest.org/en/latest/warnings.html
---------- coverage: platform darwin, python 3.7.3-final-0 -----------
Name Stmts Miss Branch BrPart Cover
----------------------------------------------------------------
uarray/__init__.py 5 0 0 0 100%
uarray/backend.py 179 95 54 4 38%
uarray/tests/test_backend.py 37 25 0 0 32%
----------------------------------------------------------------
TOTAL 221 120 54 4 38%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! KeyboardInterrupt !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
zmq/backend/cython/checkrc.pxd:12: KeyboardInterrupt
(to show a full traceback on KeyboardInterrupt use --fulltrace)
===================== 1 warnings, 6 error in 64.87 seconds =====================
I am getting this same error as well. I tried downgrading notebook from 5.7.8 to 5.7.0 to see if that would help, but to no avail...
@saulshanabrook Are you getting the same error with the same notebooks, or with different ones?
@vidartf Different notebooks. In https://github.com/quansight-labs/metadsl
Are either one of you able to produce a minimal working example? Its hard to debug behavior in a completely unknown repository.
I was able to reproduce this in an minimal conda environment created like this:
conda create -n tmp -c conda-forge jupyterlab
conda activate tmp
pip install pytest pytest-cov nbval
# Create notebook file `Untitled.ipynb`
pytest --cov --nbval Untitled.ipynb
Output:
========================================================= test session starts =========================================================
platform darwin -- Python 3.7.3, pytest-4.5.0, py-1.8.0, pluggy-0.11.0
rootdir: /Users/saul/p/tmp
plugins: cov-2.7.1, nbval-0.9.1
collected 2 items
Untitled.ipynb EE [100%]Coverage.py warning: No data was collected. (no-data-collected)
WARNING: Failed to generate report: No data to report.
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pytest_cov/plugin.py:229: PytestWarning: Failed to generate report: No data to report.
self.cov_controller.finish()
=============================================================== ERRORS ================================================================
______________________________________________ ERROR at setup of Untitled.ipynb::Cell 0 _______________________________________________
cls = <class '_pytest.runner.CallInfo'>, func = <function call_runtest_hook.<locals>.<lambda> at 0x10a1ed730>, when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:197:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = (), kwargs = {'item': <IPyNbCell Cell 0>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x106ab4128>, hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 0>>>, ...]
kwargs = {'item': <IPyNbCell Cell 0>}
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)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 0>>>, ...]
kwargs = {'item': <IPyNbCell Cell 0>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 0>>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 0>}, 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()
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x10a22de10>
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])
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 0>>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 0>}, 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)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 0>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:115:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x10a1e8f28>, colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:361:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile Untitled.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x10794a0f0>, kernel = <nbval.kernel.RunningKernel object at 0x10a2372b0>
floc = local('/Users/saul/p/tmp/Untitled.ipynb'), output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x10a2372b0>, parent_id = '38a50b57-0eb629018ade829489b5c38f', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x10a2372b0>, stream = 'iopub', timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x10a7398d0>, args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x10a739a90>, block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
______________________________________________ ERROR at setup of Untitled.ipynb::Cell 1 _______________________________________________
cls = <class '_pytest.runner.CallInfo'>, func = <function call_runtest_hook.<locals>.<lambda> at 0x10a21ba60>, when = 'setup'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
@classmethod
def from_call(cls, func, when, reraise=None):
#: context of invocation: one of "setup", "call",
#: "teardown", "memocollect"
start = time()
excinfo = None
try:
> result = func()
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:225:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> lambda: ihook(item=item, **kwds), when=when, reraise=reraise
)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:197:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_HookCaller 'pytest_runtest_setup'>, args = (), kwargs = {'item': <IPyNbCell Cell 1>}, notincall = set()
def __call__(self, *args, **kwargs):
if args:
raise TypeError("hook calling supports only keyword arguments")
assert not self.is_historic()
if self.spec and self.spec.argnames:
notincall = (
set(self.spec.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.get_hookimpls(), kwargs)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/hooks.py:289:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x106ab4128>, hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 1>>>, ...]
kwargs = {'item': <IPyNbCell Cell 1>}
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)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/manager.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook = <_HookCaller 'pytest_runtest_setup'>
methods = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 1>>>, ...]
kwargs = {'item': <IPyNbCell Cell 1>}
self._inner_hookexec = lambda hook, methods, kwargs: hook.multicall(
methods,
kwargs,
> firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/manager.py:62:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 1>>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 1>}, 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()
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/callers.py:208:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy.callers._Result object at 0x10a8e39e8>
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])
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/callers.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_impls = [<HookImpl plugin_name='nose', plugin=<module '_pytest.nose' from '/usr/local/miniconda3/envs/tmp/lib/python3.7/site-p...apture 0 oldfd=5 _state='started'> _state='suspended' _in_suspended='<UNSET>'> _current_item=<IPyNbCell Cell 1>>>, ...]
caller_kwargs = {'item': <IPyNbCell Cell 1>}, 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)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/pluggy/callers.py:187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <IPyNbCell Cell 1>
def pytest_runtest_setup(item):
_update_current_test_var(item, "setup")
> item.session._setupstate.prepare(item)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:115:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x10a1e8f28>, colitem = <IPyNbCell Cell 1>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
> six.reraise(*col._prepare_exc)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:357:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tp = <class '_queue.Empty'>, value = None, tb = None
def reraise(tp, value, tb=None):
try:
if value is None:
value = tp()
if value.__traceback__ is not tb:
> raise value.with_traceback(tb)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/six.py:692:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.runner.SetupState object at 0x10a1e8f28>, colitem = <IPyNbCell Cell 0>
def prepare(self, colitem):
""" setup objects along the collector chain to the test-method
and teardown previously setup objects."""
needed_collectors = colitem.listchain()
self._teardown_towards(needed_collectors)
# check if the last collection node has raised an error
for col in self.stack:
if hasattr(col, "_prepare_exc"):
six.reraise(*col._prepare_exc)
for col in needed_collectors[len(self.stack) :]:
self.stack.append(col)
try:
> col.setup()
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/_pytest/runner.py:361:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <IPyNbFile Untitled.ipynb>
def setup(self):
"""
Called by pytest to setup the collector cells in .
Here we start a kernel and setup the sanitize patterns.
"""
if self.parent.config.option.current_env:
kernel_name = CURRENT_ENV_KERNEL_NAME
else:
kernel_name = self.nb.metadata.get(
'kernelspec', {}).get('name', 'python')
self.kernel = RunningKernel(kernel_name, str(self.fspath.dirname))
self.setup_sanitize_files()
if getattr(self.parent.config.option, 'cov_source', None):
> setup_coverage(self.parent.config, self.kernel, getattr(self, "fspath", None))
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/plugin.py:235:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
config = <_pytest.config.Config object at 0x10794a0f0>, kernel = <nbval.kernel.RunningKernel object at 0x10a2372b0>
floc = local('/Users/saul/p/tmp/Untitled.ipynb'), output_loc = None
def setup_coverage(config, kernel, floc, output_loc=None):
"""Start coverage reporting in kernel.
Currently supported kernel languages are:
- Python
"""
language = kernel.language
if language.startswith('python'):
# Get the pytest-cov coverage object
cov = get_cov(config)
if cov:
# If present, copy the data file location used by pytest-cov
data_file = os.path.abspath(cov.config.data_file)
else:
# Fall back on output_loc and current dir if not
data_file = os.path.abspath(os.path.join(output_loc or os.getcwd(), '.coverage'))
# Get options from pytest-cov's command line arguments:
source = config.option.cov_source
config_file = config.option.cov_config
if isinstance(config_file, str) and os.path.isfile(config_file):
config_file = os.path.abspath(config_file)
# Copy the suffix of plugin if available
suffix = _make_suffix(cov)
if suffix is True:
# Cannot merge data with autogen suffix, so turn off warning
# for missing data in pytest-cov collector
cov._warn_no_data = False
# Build setup command and execute in kernel:
cmd = _python_setup % (data_file, source, config_file, suffix)
msg_id = kernel.kc.execute(cmd, stop_on_error=False)
> kernel.await_idle(msg_id, 60) # A minute should be plenty to enable coverage
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/cover.py:67:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x10a2372b0>, parent_id = '38a50b57-0eb629018ade829489b5c38f', timeout = 60
def await_idle(self, parent_id, timeout):
"""Poll the iopub stream until an idle message is received for the given parent ID"""
while True:
# Get a message from the kernel iopub channel
> msg = self.get_message(timeout=timeout, stream='iopub') # raises Empty on timeout!
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/kernel.py:170:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <nbval.kernel.RunningKernel object at 0x10a2372b0>, stream = 'iopub', timeout = 60
def get_message(self, stream, timeout=None):
"""
Function is used to get a message from the iopub channel.
Timeout is None by default
When timeout is reached
"""
try:
if stream == 'iopub':
> msg = self.kc.get_iopub_msg(timeout=timeout)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/nbval/kernel.py:123:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.client.BlockingKernelClient object at 0x10a7398d0>, args = (), kwargs = {'timeout': 60}
def get_iopub_msg(self, *args, **kwargs):
"""Get a message from the iopub channel"""
> return self.iopub_channel.get_msg(*args, **kwargs)
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/jupyter_client/client.py:81:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <jupyter_client.blocking.channels.ZMQSocketChannel object at 0x10a739a90>, block = True, timeout = 60000
def get_msg(self, block=True, timeout=None):
""" Gets a message if there is one that is ready. """
if block:
if timeout is not None:
timeout *= 1000 # seconds to ms
ready = self.socket.poll(timeout)
else:
ready = self.socket.poll(timeout=0)
if ready:
return self._recv()
else:
> raise Empty
E _queue.Empty
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/jupyter_client/blocking/channels.py:57: Empty
========================================================== warnings summary ===========================================================
Untitled.ipynb::Cell 0
/usr/local/miniconda3/envs/tmp/lib/python3.7/site-packages/jupyter_client/manager.py:62: DeprecationWarning: KernelManager._kernel_spec_manager_changed is deprecated in traitlets 4.1: use @observe and @unobserve instead.
def _kernel_spec_manager_changed(self):
-- Docs: https://docs.pytest.org/en/latest/warnings.html
---------- coverage: platform darwin, python 3.7.3-final-0 -----------
Name Stmts Miss Cover
---------------------------
================================================ 1 warnings, 2 error in 62.50 seconds =================================================
Environment:
$ pip freeze
appnope==0.1.0
atomicwrites==1.3.0
attrs==19.1.0
backcall==0.1.0
bleach==3.1.0
certifi==2019.3.9
coverage==4.5.3
decorator==4.4.0
defusedxml==0.5.0
entrypoints==0.3
flake8==3.6.0
ipykernel==5.1.0
ipython==7.5.0
ipython-genutils==0.2.0
jedi==0.13.3
Jinja2==2.10.1
jsonschema==3.0.1
jupyter-client==5.2.4
jupyter-core==4.4.0
jupyterlab==0.35.6
jupyterlab-server==0.2.0
MarkupSafe==1.1.1
mccabe==0.6.1
mistune==0.8.4
more-itertools==7.0.0
mypy-extensions==0.4.1
nbconvert==5.5.0
nbformat==4.4.0
nbval==0.9.1
notebook==5.7.8
pandocfilters==1.4.2
parso==0.4.0
pexpect==4.7.0
pickleshare==0.7.5
pluggy==0.11.0
prometheus-client==0.6.0
prompt-toolkit==2.0.9
ptyprocess==0.6.0
py==1.8.0
pycodestyle==2.4.0
pyflakes==2.0.0
Pygments==2.4.0
pyrsistent==0.15.2
pytest==4.5.0
pytest-cov==2.7.1
python-dateutil==2.8.0
pyzmq==18.0.1
Send2Trash==1.5.0
six==1.12.0
terminado==0.8.2
testpath==0.4.2
tornado==6.0.2
traitlets==4.3.2
wcwidth==0.1.7
webencodings==0.5.1
$ conda info
active environment : tmp
active env location : /usr/local/miniconda3/envs/tmp
shell level : 1
user config file : /Users/saul/.condarc
populated config files :
conda version : 4.6.12
conda-build version : not installed
python version : 3.6.8.final.0
base environment : /usr/local/miniconda3 (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/osx-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /usr/local/miniconda3/pkgs
/Users/saul/.conda/pkgs
envs directories : /usr/local/miniconda3/envs
/Users/saul/.conda/envs
platform : osx-64
user-agent : conda/4.6.12 requests/2.18.4 CPython/3.6.8 Darwin/17.7.0 OSX/10.13.6
UID:GID : 501:20
netrc file : /Users/saul/.netrc
offline mode : False
$ cat Untitled.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"1 + 1"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
Weird, I cannot reproduce. Diff from pip freeze:
- appnope==0.1.0
+colorama==0.4.1
- mccabe==0.6.1
- mypy-extensions==0.4.1
- pexpect==4.7.0
- ptyprocess==0.6.0
- pycodestyle==2.4.0
- pyflakes==2.0.0
+wincertstore==0.2
The package diff is mostly platform-based (I assume). Speaking of platform, I see that both of you are on OSX. Are you able to reproduce this on other platforms? I'm running on Windows here.
Specifying a module to cover means it won't hang, but also it won't actually pick up coverage:
pytest --cov=mymod --cov-report=term --nbval tests/test_mymod.ipynb
...
tests/test_mymod::ipynb::Cell 0 PASSED
Coverage.py warning: Module mymod was never imported. (module-not-imported)
Coverage.py warning: No data was collected. (no-data-collected)
WARNING: Failed to generate report: No data to report.
PytestWarning: Failed to generate report: No data to report.
...
EDIT: this seems to be because nbval can't handle when test_mymod.ipynb is in a different directory from mymod (i.e. a workaround is mv tests/test_mymod.ipynb ./)
Note that with normal python files (*.py) coverage is picked up fine by comparison.
