dask-image
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Published
20 hours ago •
dask
dask
Flake8 problems
There are two problems:
- I don't think pytest is running flake8 like it should be, and
- When you do force flake8 to run with pytest manually, there are failures. Something is wrong with the pytest flake8 hook (maybe a version mismatch between pytest, flake8, and pytest-flake8?)
Describe the issue:
We have --flake8 as a pytest addopts extra:
[tool:pytest]
addopts = --flake8
...which I think is equivalent to the command line call
pytest --flake8
But when I run just pytest from the command line, it doesn't seem to pick up the extra addopts bit. All the tests pass with just pytest, but there are failures when I run pytest --flake8 explicitly.
Minimal Complete Verifiable Example:
- Install a development version of dask-image, including the test requirements. Also pip install pandas, as that is a test requirement for the new-ish find_objects function.
- Run
pytest, and observe the tests passing. - Run
pytest --flake8(which should be equivalent to the above, given we are using addopts "--flake8"), but this time observe some tests failing due to flake8.
Details (click to expand):
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <_pytest.config.PytestPluginManager object at 0x1052391e0>
hook_name = 'pytest_runtest_call'
methods = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/Users/genevieb/mambaforge/envs/daskimg/lib/pyt...ion' from '/Users/genevieb/mambaforge/envs/daskimg/lib/python3.10/site-packages/_pytest/unraisableexception.py'>>, ...]
kwargs = {'item': <Flake8Item flake-8>}, firstresult = False
def _hookexec(self, hook_name, methods, kwargs, firstresult):
# called from all hookcaller instances.
# enable_tracing will set its own wrapping function at self._inner_hookexec
> return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/pluggy/_manager.py:80:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_name = 'pytest_runtest_call'
hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/Users/genevieb/mambaforge/envs/daskimg/lib/pyt...ion' from '/Users/genevieb/mambaforge/envs/daskimg/lib/python3.10/site-packages/_pytest/unraisableexception.py'>>, ...]
caller_kwargs = {'item': <Flake8Item flake-8>}, firstresult = False
def _multicall(hook_name, hook_impls, caller_kwargs, firstresult):
"""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(
f"hook call must provide argument {argname!r}"
)
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()
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/pluggy/_callers.py:60:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pluggy._result._Result object at 0x138fdbca0>
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
> raise ex[1].with_traceback(ex[2])
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/pluggy/_result.py:60:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
hook_name = 'pytest_runtest_call'
hook_impls = [<HookImpl plugin_name='runner', plugin=<module '_pytest.runner' from '/Users/genevieb/mambaforge/envs/daskimg/lib/pyt...ion' from '/Users/genevieb/mambaforge/envs/daskimg/lib/python3.10/site-packages/_pytest/unraisableexception.py'>>, ...]
caller_kwargs = {'item': <Flake8Item flake-8>}, firstresult = False
def _multicall(hook_name, hook_impls, caller_kwargs, firstresult):
"""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(
f"hook call must provide argument {argname!r}"
)
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)
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/pluggy/_callers.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <Flake8Item flake-8>
def pytest_runtest_call(item: Item) -> None:
_update_current_test_var(item, "call")
try:
del sys.last_type
del sys.last_value
del sys.last_traceback
except AttributeError:
pass
try:
item.runtest()
except Exception as e:
# Store trace info to allow postmortem debugging
sys.last_type = type(e)
sys.last_value = e
assert e.__traceback__ is not None
# Skip *this* frame
sys.last_traceback = e.__traceback__.tb_next
> raise e
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/_pytest/runner.py:175:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
item = <Flake8Item flake-8>
def pytest_runtest_call(item: Item) -> None:
_update_current_test_var(item, "call")
try:
del sys.last_type
del sys.last_value
del sys.last_traceback
except AttributeError:
pass
try:
> item.runtest()
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/_pytest/runner.py:167:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Flake8Item flake-8>
def runtest(self):
with BytesIO() as bo, TextIOWrapper(bo, encoding='utf-8') as to, \
BytesIO() as be, TextIOWrapper(be, encoding='utf-8') as te, \
redirect_stdout(to), redirect_stderr(te):
> found_errors = check_file(
self.fspath,
self.flake8ignore,
self.maxlength,
self.maxdoclength,
self.maxcomplexity,
self.showsource,
self.statistics
)
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/pytest_flake8.py:136:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
path = local('/Users/genevieb/Documents/GitHub/dask-image/tests/test_dask_image/test_ndmorph/test_ndmorph.py')
flake8ignore = [], maxlength = '', maxdoclenght = '', maxcomplexity = ''
showsource = [], statistics = []
def check_file(path, flake8ignore, maxlength, maxdoclenght, maxcomplexity,
showsource, statistics):
"""Run flake8 over a single file, and return the number of failures."""
args = []
if maxlength:
args += ['--max-line-length', maxlength]
if maxdoclenght:
args += ['--max-doc-length', maxdoclenght]
if maxcomplexity:
args += ['--max-complexity', maxcomplexity]
if showsource:
args += ['--show-source']
if statistics:
args += ['--statistics']
app = application.Application()
> prelim_opts, remaining_args = app.parse_preliminary_options(args)
E AttributeError: 'Application' object has no attribute 'parse_preliminary_options'
../../../mambaforge/envs/daskimg/lib/python3.10/site-packages/pytest_flake8.py:216: AttributeError
FAILED dask_image/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/_version.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/dispatch/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/dispatch/_dispatch_ndfilters.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/dispatch/_dispatch_ndinterp.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/dispatch/_dispatch_ndmorph.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/dispatch/_dispatcher.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/dispatch/_utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/imread/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_conv.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_diff.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_edge.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_gaussian.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_generic.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_order.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_smooth.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_threshold.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfilters/_utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfourier/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndfourier/_utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndinterp/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndmeasure/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndmeasure/_utils/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndmeasure/_utils/_find_objects.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndmeasure/_utils/_label.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndmorph/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndmorph/_ops.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED dask_image/ndmorph/_utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED docs/conf.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED docs/release/generate_release_notes.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_imread/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_imread/test_core.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_imread/test_cupy_imread.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__conv.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__diff.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__edge.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__gaussian.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__generic.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__order.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__smooth.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__threshold.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test__utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test_cupy_ndfilters.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfilters/test_cupy_threshold.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfourier/test__utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndfourier/test_core.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndinterp/test_affine_transformation.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndinterp/test_spline_filter.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmeasure/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmeasure/test__utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmeasure/test_core.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmeasure/test_find_objects.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmorph/__init__.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmorph/test__utils.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmorph/test_cupy_ndmorph.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
FAILED tests/test_dask_image/test_ndmorph/test_ndmorph.py::flake-8::FLAKE8 - AttributeError: 'Application' object has no attribute 'parse_preliminary_op...
Anything else we need to know?:
I've noticed the same problem in https://github.com/dask/dask-image/pull/306
I might have done something silly by adding a separate pytest.ini file in https://github.com/dask/dask-image/pull/151, which might override or conflict with the pytest section in setup.cfg. So this might have masked the problem for a while, but since I see the same problems with the new pyrpoject.toml configuration (https://github.com/dask/dask-image/pull/306) that can't explain everything.
Environment:
- Dask version: 2023.03.2
- dask-image version: main branch version (2022.9.0+30.gb08d494)
- Python version: 3.10
- Operating System: Mac Monterey
- Install method (conda, pip, source): pip installed into a conda virtual environment
conda list (click to expand):
# Name Version Build Channel
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
attrs 22.2.0 pypi_0 pypi
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bzip2 1.0.8 h3422bc3_4 conda-forge
ca-certificates 2022.12.7 h4653dfc_0 conda-forge
click 8.1.3 pypi_0 pypi
cloudpickle 2.2.1 pypi_0 pypi
dask 2023.3.2 pypi_0 pypi
dask-image 2022.9.0+30.gb08d494 dev_0 <develop>
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.1.1 pypi_0 pypi
executing 1.2.0 pyhd8ed1ab_0 conda-forge
flake8 6.0.0 pypi_0 pypi
fsspec 2023.3.0 pypi_0 pypi
imageio 2.27.0 pypi_0 pypi
importlib-metadata 6.1.0 pypi_0 pypi
iniconfig 2.0.0 pypi_0 pypi
ipython 8.11.0 pyhd1c38e8_0 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libsqlite 3.40.0 h76d750c_0 conda-forge
libzlib 1.2.13 h03a7124_4 conda-forge
locket 1.0.0 pypi_0 pypi
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mccabe 0.7.0 pypi_0 pypi
ncurses 6.3 h07bb92c_1 conda-forge
numpy 1.24.2 pypi_0 pypi
openssl 3.1.0 h03a7124_0 conda-forge
packaging 23.0 pypi_0 pypi
pandas 1.5.3 pypi_0 pypi
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.3.0 pypi_0 pypi
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.4.0 pypi_0 pypi
pims 0.6.1 pypi_0 pypi
pip 23.0.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pypi_0 pypi
prompt-toolkit 3.0.38 pyha770c72_0 conda-forge
prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycodestyle 2.10.0 pypi_0 pypi
pyflakes 3.0.1 pypi_0 pypi
pygments 2.14.0 pyhd8ed1ab_0 conda-forge
pytest 7.2.2 pypi_0 pypi
pytest-flake8 1.1.1 pypi_0 pypi
pytest-timeout 2.1.0 pypi_0 pypi
python 3.10.10 h3ba56d0_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
pytz 2023.3 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
readline 8.2 h92ec313_1 conda-forge
scipy 1.10.1 pypi_0 pypi
setuptools 67.6.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
slicerator 1.1.0 pypi_0 pypi
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
tifffile 2023.3.21 pypi_0 pypi
tk 8.6.12 he1e0b03_0 conda-forge
tomli 2.0.1 pypi_0 pypi
toolz 0.12.0 pypi_0 pypi
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h57fd34a_0 conda-forge
zipp 3.15.0 pypi_0 pypi
