Stuck on an issue?
Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.
And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.
Error when running debugging using pytest in IDE with geopandas
See original GitHub issueI ran into an error today while running a test in debug mode using PyCharm (I found the same issue on VS Code as well) when geopandas is imported. Outside of debug mode it seems to work fine. I’ve also found that downgrading pytest to 6.2.4 resolves the issue.
I was able to reproduce the problem by setting up a test environment using conda: A simple test script with a breakpoint set at the assert statement produces the error below
conda create --name test --channel=conda-forge python pytest geopandas
Today when I set it up that command resulted in the following version being installed (full list of packages installed below):
python=3.10.2 pytest=7.1.1 geopandas=0.10.2
I am using an ARM Mac running macOS 12.3, I’ve also gotten the same result on an Intel Mac macOS 11.6.4.
import geopandas
def test_pytest_and_geopandas():
assert False
A simple test script with a breakpoint set at the assert statement like that above produces the following error if the test is run in debug mode in PyCharm:
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/_pytest/main.py", line 268, in wrap_session
INTERNALERROR> session.exitstatus = doit(config, session) or 0
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/_pytest/main.py", line 321, in _main
INTERNALERROR> config.hook.pytest_collection(session=session)
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_hooks.py", line 265, in __call__
INTERNALERROR> return self._hookexec(self.name, self.get_hookimpls(), kwargs, firstresult)
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_manager.py", line 80, in _hookexec
INTERNALERROR> return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_callers.py", line 60, in _multicall
INTERNALERROR> return outcome.get_result()
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_result.py", line 60, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_callers.py", line 39, in _multicall
INTERNALERROR> res = hook_impl.function(*args)
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/_pytest/main.py", line 332, in pytest_collection
INTERNALERROR> session.perform_collect()
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/_pytest/main.py", line 644, in perform_collect
INTERNALERROR> self.ihook.pytest_collectreport(report=rep)
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_hooks.py", line 265, in __call__
INTERNALERROR> return self._hookexec(self.name, self.get_hookimpls(), kwargs, firstresult)
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_manager.py", line 80, in _hookexec
INTERNALERROR> return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_callers.py", line 60, in _multicall
INTERNALERROR> return outcome.get_result()
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_result.py", line 60, in get_result
INTERNALERROR> raise ex[1].with_traceback(ex[2])
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/pluggy/_callers.py", line 39, in _multicall
INTERNALERROR> res = hook_impl.function(*args)
INTERNALERROR> File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/teamcity/pytest_plugin.py", line 328, in pytest_collectreport
INTERNALERROR> self.report_test_failure(test_id, report)
INTERNALERROR> File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/teamcity/pytest_plugin.py", line 223, in report_test_failure
INTERNALERROR> self.ensure_test_start_reported(test_id)
INTERNALERROR> File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/teamcity/pytest_plugin.py", line 186, in ensure_test_start_reported
INTERNALERROR> self.teamcity.testStarted(test_id, flowId=test_id, captureStandardOutput=capture_standard_output, metainfo=metainfo)
INTERNALERROR> File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/_jb_runner_tools.py", line 181, in testStarted
INTERNALERROR> commands = _TREE_MANAGER_HOLDER.manager.level_opened(self._test_to_list(testName), _write_start_message)
INTERNALERROR> File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/_jb_runner_tools.py", line 51, in manager
INTERNALERROR> self._fill_manager()
INTERNALERROR> File "/Applications/PyCharm.app/Contents/plugins/python/helpers/pycharm/_jb_runner_tools.py", line 59, in _fill_manager
INTERNALERROR> from _jb_serial_tree_manager import SerialTreeManager
INTERNALERROR> File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
INTERNALERROR> File "<frozen importlib._bootstrap>", line 1002, in _find_and_load_unlocked
INTERNALERROR> File "<frozen importlib._bootstrap>", line 945, in _find_spec
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/_pytest/assertion/rewrite.py", line 92, in find_spec
INTERNALERROR> if self._early_rewrite_bailout(name, state):
INTERNALERROR> File "/Users/aengel/miniconda3/envs/test/lib/python3.10/site-packages/_pytest/assertion/rewrite.py", line 193, in _early_rewrite_bailout
INTERNALERROR> path = PurePath(os.path.sep.join(parts) + ".py")
INTERNALERROR> AttributeError: module 'posixpath' has no attribute 'sep'
or VS Code
tests[/test_addl.py:10](): in <module>
import geopandas
.[./../miniconda3/envs/test/lib/python3.10/site-packages/geopandas/__init__.py:1](): in <module>
from geopandas._config import options # noqa
.[./../miniconda3/envs/test/lib/python3.10/site-packages/geopandas/_config.py:109](): in <module>
default_value=_default_use_pygeos(),
.[./../miniconda3/envs/test/lib/python3.10/site-packages/geopandas/_config.py:95](): in _default_use_pygeos
import geopandas._compat as compat
.[./../miniconda3/envs/test/lib/python3.10/site-packages/geopandas/_compat.py:9](): in <module>
import pyproj
.[./../miniconda3/envs/test/lib/python3.10/site-packages/pyproj/__init__.py:93](): in <module>
pyproj.network.set_ca_bundle_path()
.[./../miniconda3/envs/test/lib/python3.10/site-packages/pyproj/network.py:51](): in set_ca_bundle_path
ca_bundle_path = certifi.where()
.[./../miniconda3/envs/test/lib/python3.10/site-packages/certifi/core.py:36](): in where
_CACERT_CTX = get_path("certifi", "cacert.pem")
.[./../miniconda3/envs/test/lib/python3.10/importlib/resources.py:119](): in path
reader = _common.get_resource_reader(_common.get_package(package))
.[./../miniconda3/envs/test/lib/python3.10/importlib/_common.py:52](): in get_resource_reader
return reader(spec.name) # type: ignore
<frozen importlib._bootstrap_external>:548: in _check_name_wrapper
???
<frozen importlib._bootstrap_external>:1081: in get_resource_reader
???
<frozen importlib._bootstrap>:1027: in _find_and_load
???
<frozen importlib._bootstrap>:1002: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:945: in _find_spec
???
.[./../miniconda3/envs/test/lib/python3.10/site-packages/_pytest/assertion/rewrite.py:92](): in find_spec
if self._early_rewrite_bailout(name, state):
.[./../miniconda3/envs/test/lib/python3.10/site-packages/_pytest/assertion/rewrite.py:193](): in _early_rewrite_bailout
path = PurePath(os.path.sep.join(parts) + ".py")
E AttributeError: module 'posixpath' has no attribute 'sep'
Package Version
------------------ ------------
attrs 21.4.0
branca 0.4.2
brotlipy 0.7.0
certifi 2021.10.8
cffi 1.15.0
charset-normalizer 2.0.12
click 8.0.4
click-plugins 1.1.1
cligj 0.7.2
cryptography 36.0.1
cycler 0.11.0
Fiona 1.8.21
folium 0.12.1.post1
fonttools 4.31.1
GDAL 3.4.2
geopandas 0.10.2
idna 3.3
iniconfig 1.1.1
Jinja2 3.0.3
joblib 1.1.0
kiwisolver 1.4.0
mapclassify 2.4.3
MarkupSafe 2.1.1
matplotlib 3.5.1
munch 2.5.0
munkres 1.1.4
networkx 2.7.1
numpy 1.22.3
packaging 21.3
pandas 1.4.1
Pillow 9.0.1
pip 22.0.4
pluggy 1.0.0
py 1.11.0
pycparser 2.21
pyOpenSSL 22.0.0
pyparsing 3.0.7
pyproj 3.3.0
PySocks 1.7.1
pytest 7.1.1
python-dateutil 2.8.2
pytz 2021.3
requests 2.27.1
Rtree 0.9.7
scikit-learn 1.0.2
scipy 1.8.0
setuptools 60.10.0
Shapely 1.8.0
six 1.16.0
threadpoolctl 3.1.0
tomli 2.0.1
unicodedata2 14.0.0
urllib3 1.26.9
wheel 0.37.1
xyzservices 2022.3.0
Issue Analytics
- State:
- Created 2 years ago
- Reactions:6
- Comments:5 (1 by maintainers)
Top Results From Across the Web
Running pytest with "debug in test" works correctly but "run in ...
I have a project where I am running tests using the debug menu pull down and they run fine. ... When I do...
Read more >IntelliJ Python plugin pytest code runs but debug doesn't work
I have an issue debugging python tests using pytest on IntelliJ IDE with the python plugin. the tests can be run (they have...
Read more >Debugging — Kedro 0.18.4 documentation
This guide provides examples on how to instantiate a post-mortem debugging session with pdb using Kedro Hooks when an uncaught error occurs during...
Read more >Running Rust on Microcontrollers - mbedded.ninja
Architecture Support; MCU Family Support; IDEs, Programming and the Debugging Experience; RTOSes; Rust Disadvantages. Lets jump straight in!
Read more >conda install geopandas failed with initial frozen solve
I resolved the problem by installing geopandas using ... Currently, I am running conda install geopandas and it is not working, but I...
Read more >
Top Related Medium Post
No results found
Top Related StackOverflow Question
No results found
Troubleshoot Live Code
Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free
Top Related Reddit Thread
No results found
Top Related Hackernoon Post
No results found
Top Related Tweet
No results found
Top Related Dev.to Post
No results found
Top Related Hashnode Post
No results found
Hi,
I have found the same bug after updating project from Python3.9 to Python3.10. Looks like
proj==3.3.0works with Python3.9 debugger and with Python3.10 without debugger, but breaks with 3.10 and debugger. This does not seem to be related to pytest, some code completely breaksos.path, pytest is just the first one to find that attribute is missing. Minimal reproducible example:Stack-trace:
Looks like a bug to me: we should also let
PurePathdo the joining, not hand-rolling string manipulation.(and the error is because there’s no such thing as
os.path.sep, it’s justos.sep… oros.pathsep, but confusingly that’s an entirely different thing.)