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      headline:Error when running debugging using pytest in IDE with geopandas
      articleBody:I 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. ```python 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 ```
      author:
         url:https://github.com/arengel
         type:Person
         name:arengel
      datePublished:2022-03-19T01:23:55.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:5
      url:https://github.com/9791/pytest/issues/9791
      context:https://schema.org
      headline:Error when running debugging using pytest in IDE with geopandas
      articleBody:I 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. ```python 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 ```
      author:
         url:https://github.com/arengel
         type:Person
         name:arengel
      datePublished:2022-03-19T01:23:55.000Z
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      url:https://github.com/9791/pytest/issues/9791
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