Running gpd.read_file() kills my Jupyter kernel

[gerardbarbalich]

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of geopandas.

---

The kernel of my Jupyter Notebook crashes whenever I try to run gpd.read_file() on a package dataset or local shapefile. The package installed fine, and I can access the package's modules, but running this code snipped crashes my kernel:

import geopandas as gpd 
world = gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'))

I installed GeoPandas following this process - installing the most recent version upon a separate conda environment.

Neither this question nor this question resolved my issue.

Output of geopandas.show_versions()

SYSTEM INFO
-----------
python     : 3.10.6 | packaged by conda-forge | (main, Aug 22 2022, 20:30:19) [MSC v.1929 64 bit (AMD64)]
executable : C:\tools\Anaconda3\envs\geo_env\python.exe
machine    : Windows-10-10.0.19044-SP0

GEOS, GDAL, PROJ INFO
---------------------
GEOS       : None
GEOS lib   : None
GDAL       : 3.5.2
GDAL data dir: None
PROJ       : 8.2.1
PROJ data dir: C:\Users\barger\AppData\Roaming\Python\Python310\site-packages\pyproj\proj_dir\share\proj

PYTHON DEPENDENCIES
-------------------
geopandas  : 0.11.1
numpy      : 1.22.2
pandas     : 1.4.1
pyproj     : 3.3.1
shapely    : 1.8.2
fiona      : 1.8.21
geoalchemy2: None
geopy      : None
matplotlib : 3.5.3
mapclassify: 2.4.3
pygeos     : None
pyogrio    : None
psycopg2   : None
pyarrow    : None
rtree      : 1.0.0

Conda environment installed:

argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310he2412df_2    conda-forge
asttokens                 2.0.8              pyhd8ed1ab_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
blosc                     1.21.1               h74325e0_3    conda-forge
boost-cpp                 1.78.0               h9f4b32c_1    conda-forge
branca                    0.5.0              pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h8ffe710_7    conda-forge
brotli-bin                1.0.9                h8ffe710_7    conda-forge
brotlipy                  0.7.0           py310he2412df_1004    conda-forge
bzip2                     1.0.8                h8ffe710_4    conda-forge
ca-certificates           2022.6.15.2          h5b45459_0    conda-forge
cairo                     1.16.0            hd694305_1013    conda-forge
certifi                   2022.6.15.2        pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310hcbf9ad4_0    conda-forge
cfitsio                   4.1.0                h5a969a9_0    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           py310h5588dad_0    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
cligj                     0.7.2              pyhd8ed1ab_1    conda-forge
colorama                  0.4.5              pyhd8ed1ab_0    conda-forge
cryptography              37.0.4          py310ha857299_0    conda-forge
curl                      7.83.1               h789b8ee_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
debugpy                   1.6.3           py310h8a704f9_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.0.0              pyhd8ed1ab_0    conda-forge
expat                     2.4.8                h39d44d4_0    conda-forge
fiona                     1.8.21          py310hfed10a5_2    conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
folium                    0.12.1.post1       pyhd8ed1ab_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.0               hce3cb01_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.37.1          py310he2412df_0    conda-forge
freetype                  2.12.1               h546665d_0    conda-forge
freexl                    1.0.6                ha8e266a_0    conda-forge
gdal                      3.5.2           py310h198874d_0    conda-forge
geopandas                 0.11.1             pyhd8ed1ab_0    conda-forge
geopandas-base            0.11.1             pyha770c72_0    conda-forge
geos                      3.11.0               h39d44d4_0    conda-forge
geotiff                   1.7.1                h714bc5f_3    conda-forge
gettext                   0.19.8.1          ha2e2712_1008    conda-forge
glib                      2.72.1               h7755175_0    conda-forge
glib-tools                2.72.1               h7755175_0    conda-forge
gst-plugins-base          1.20.3               h001b923_1    conda-forge
gstreamer                 1.20.3               h6b5321d_1    conda-forge
hdf4                      4.2.15               h0e5069d_4    conda-forge
hdf5                      1.12.2          nompi_h2a0e4a3_100    conda-forge
icu                       70.1                 h0e60522_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4          py310h5588dad_0    conda-forge
importlib_resources       5.9.0              pyhd8ed1ab_0    conda-forge
intel-openmp              2022.1.0          h57928b3_3787    conda-forge
ipykernel                 6.15.3             pyh025b116_0    conda-forge
ipython                   8.5.0              pyh08f2357_1    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.2              pyhd8ed1ab_1    conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h8ffe710_2    conda-forge
jsonschema                4.16.0             pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0           py310h5588dad_7    conda-forge
jupyter_client            7.3.5              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.4              pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.1          py310h5588dad_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.3              pyhd8ed1ab_0    conda-forge
kealib                    1.4.15               hdf81f3a_1    conda-forge
kiwisolver                1.4.4           py310h476a331_0    conda-forge
krb5                      1.19.3               h1176d77_0    conda-forge
lcms2                     2.12                 h2a16943_0    conda-forge
lerc                      4.0.0                h63175ca_0    conda-forge
libblas                   3.9.0              16_win64_mkl    conda-forge
libbrotlicommon           1.0.9                h8ffe710_7    conda-forge
libbrotlidec              1.0.9                h8ffe710_7    conda-forge
libbrotlienc              1.0.9                h8ffe710_7    conda-forge
libcblas                  3.9.0              16_win64_mkl    conda-forge
libclang                  14.0.6          default_h77d9078_0    conda-forge
libclang13                14.0.6          default_h77d9078_0    conda-forge
libcurl                   7.83.1               h789b8ee_0    conda-forge
libdeflate                1.14                 hcfcfb64_0    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libgdal                   3.5.2                hc386656_0    conda-forge
libglib                   2.72.1               h3be07f2_0    conda-forge
libiconv                  1.16                 he774522_0    conda-forge
libkml                    1.3.0             hf2ab4e4_1015    conda-forge
liblapack                 3.9.0              16_win64_mkl    conda-forge
libnetcdf                 4.8.1           nompi_h85765be_104    conda-forge
libogg                    1.3.4                h8ffe710_1    conda-forge
libpng                    1.6.37               h1d00b33_4    conda-forge
libpq                     14.5                 hfcc5ef8_0    conda-forge
librttopo                 1.1.0               h2842628_11    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libspatialindex           1.9.3                h39d44d4_4    conda-forge
libspatialite             5.0.1               ha17912d_18    conda-forge
libsqlite                 3.39.3               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h680486a_3    conda-forge
libtiff                   4.4.0                h8e97e67_4    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libwebp-base              1.2.4                h8ffe710_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.9.14               hf5bbc77_4    conda-forge
libxslt                   1.1.35               h34f844d_0    conda-forge
libzip                    1.9.2                hfed4ece_1    conda-forge
libzlib                   1.2.12               hcfcfb64_3    conda-forge
lxml                      4.9.1           py310he2412df_0    conda-forge
lz4-c                     1.9.3                h8ffe710_1    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
mapclassify               2.4.3              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1           py310he2412df_1    conda-forge
matplotlib-base           3.5.3           py310h7329aa0_2    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munch                     2.5.0                      py_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.6.8              pyhd8ed1ab_0    conda-forge
nbconvert                 7.0.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.0.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.0.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.5.0              pyhd8ed1ab_0    conda-forge
nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge
networkx                  2.8.6              pyhd8ed1ab_0    conda-forge
notebook                  6.4.12             pyha770c72_0    conda-forge
numpy                     1.23.3          py310h4a8f9c9_0    conda-forge
openjpeg                  2.5.0                hc9384bd_1    conda-forge
openssl                   1.1.1q               h8ffe710_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.4           py310h1c4a608_0    conda-forge
pandoc                    2.19.2               h57928b3_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h0e60522_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.2.0           py310h52929f7_2    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h8ffe710_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
poppler                   22.04.0              hb57f792_3    conda-forge
poppler-data              0.4.11               hd8ed1ab_0    conda-forge
postgresql                14.5                 h1c22c4f_0    conda-forge
proj                      9.0.1                h1cfcee9_1    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.31             pyha770c72_0    conda-forge
prompt_toolkit            3.0.31               hd8ed1ab_0    conda-forge
psutil                    5.9.2           py310h8d17308_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyproj                    3.4.0           py310h6377384_0    conda-forge
pyqt                      5.15.7          py310hbabf5d4_0    conda-forge
pyqt5-sip                 12.11.0         py310h8a704f9_0    conda-forge
pyrsistent                0.18.1          py310he2412df_1    conda-forge
pysocks                   1.7.1              pyh0701188_6    conda-forge
python                    3.10.6          h9a09f29_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.1             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pytz                      2022.2.1           pyhd8ed1ab_0    conda-forge
pywin32                   303             py310he2412df_0    conda-forge
pywinpty                  2.0.7           py310h00ffb61_0    conda-forge
pyzmq                     23.2.1          py310h73ada01_0    conda-forge
qt-main                   5.15.6               hf0cf448_0    conda-forge
qtconsole                 5.3.2              pyhd8ed1ab_0    conda-forge
qtconsole-base            5.3.2              pyha770c72_0    conda-forge
qtpy                      2.2.0              pyhd8ed1ab_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
rtree                     1.0.0           py310h1cbd46b_1    conda-forge
scikit-learn              1.1.2           py310h3a564e9_0    conda-forge
scipy                     1.9.1           py310h578b7cb_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.3.0             pyhd8ed1ab_1    conda-forge
shapely                   1.8.4           py310h523c7d9_0    conda-forge
sip                       6.6.2           py310h8a704f9_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.9                h82413e6_1    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlite                    3.39.3               hcfcfb64_0    conda-forge
stack_data                0.5.0              pyhd8ed1ab_0    conda-forge
tbb                       2021.5.0             h91493d7_2    conda-forge
terminado                 0.15.0          py310h5588dad_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tiledb                    2.11.2               h5689973_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h8ffe710_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tornado                   6.2             py310he2412df_0    conda-forge
traitlets                 5.4.0              pyhd8ed1ab_0    conda-forge
typing_extensions         4.3.0              pyha770c72_0    conda-forge
tzdata                    2022c                h191b570_0    conda-forge
ucrt                      10.0.20348.0         h57928b3_0    conda-forge
unicodedata2              14.0.0          py310he2412df_1    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
vc                        14.2                 hb210afc_7    conda-forge
vs2015_runtime            14.29.30139          h890b9b1_7    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.3              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0           py310h5588dad_4    conda-forge
winpty                    0.4.3                         4    conda-forge
xerces-c                  3.2.3                h0e60522_5    conda-forge
xorg-libxau               1.0.9                hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xyzservices               2022.6.0           pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zipp                      3.8.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               hcfcfb64_3    conda-forge
zstd                      1.5.2                h7755175_4    conda-forge

[martinfleis]

Hello, thanks for the report. It is a bit hard to debug this one... Have you fixed that in the meantime? Can you try installing pyogrio and trying to read a file with that engine?

gpd.read_file(gpd.datasets.get_path('naturalearth_lowres'), engine="pyogrio")

I believe this is an installation issue on fiona side. It may be already fixed on conda-forge side.

[GurgelR]

Had the same issue, but using the VSCode's Shell, that didn't show any error message.

Correctly solved using the engine="pyogrio"

[ScriptsRemote]

Thanks @martinfleis. You helped me and the whole community

In the morning the gdf was running and then out of nowhere, it stopped.