Bug on Windows/Mac - partially initialized module 'fiona' has no attribute '_loading'
See original GitHub issueExpected behavior and actual behavior.
When using geopandas, shapley and fiona, the importing of files breaks on Mac OS. The same problem does not occur on windows or linux. The following error arises:
partially initialized module 'fiona' has no attribute '_loading' (most likely due to a circular import)
File "/Users/runner/work/pypsa-africa/pypsa-africa/Snakefile", line 15, in <module>
File "/Users/runner/work/pypsa-africa/pypsa-africa/scripts/add_electricity.py", line 93, in <module>
File "/Users/runner/miniconda3/envs/pypsa-africa/lib/python3.9/site-packages/fiona/__init__.py", line 85, in <module>
ERROR:snakemake.logging:AttributeError in line 15 of /Users/runner/work/pypsa-africa/pypsa-africa/Snakefile:
partially initialized module 'fiona' has no attribute '_loading' (most likely due to a circular import)
File "/Users/runner/work/pypsa-africa/pypsa-africa/Snakefile", line 15, in <module>
File "/Users/runner/work/pypsa-africa/pypsa-africa/scripts/add_electricity.py", line 93, in <module>
File "/Users/runner/miniconda3/envs/pypsa-africa/lib/python3.9/site-packages/fiona/__init__.py", line 85, in <module>
Error: Process completed with exit code 1.
Steps to reproduce the problem.
This is reproducible in the CI shown in: https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true I attempted various ways, but most likely the errors arise while performing the following series of imports:
import logging
import os
import geopandas as gpd
import numpy as np
import pandas as pd
import powerplantmatching as pm
import pypsa
import xarray as xr
from powerplantmatching.export import map_country_bus
from shapely.validation import make_valid
Operating system
Environment: macos-11 Version: 20220322.1
Fiona and GDAL version and provenance
Installed using the following environment file: https://github.com/pypsa-meets-africa/pypsa-africa/blob/main/envs/environment.yaml
# packages in environment at /Users/runner/miniconda3/envs/pypsa-africa:
#
# Name Version Build Channel
affine 2.3.1 pyhd8ed1ab_0 conda-forge
amply 0.1.4 py_0 conda-forge
anyio 3.5.0 py39h6e9494a_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
appnope 0.1.2 py39h6e9494a_2 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39h89e85a6_1 conda-forge
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
atlite 0.2.5 pyhd8ed1ab_0 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pyh44b3[12](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:12)d_0 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 4.10.0 pyha770c72_0 conda-forge
bleach 4.1.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.0 he49afe7_0 conda-forge
bokeh 2.4.2 py39h6e9494a_0 conda-forge
boost-cpp 1.74.0 hff03dee_4 conda-forge
bottleneck 1.3.4 py39h86b5767_0 conda-forge
branca 0.4.2 pyhd8ed1ab_0 conda-forge
brotli 1.0.9 h0d85af4_6 conda-forge
brotli-bin 1.0.9 h0d85af4_6 conda-forge
brotlipy 0.7.0 py39h89e85a6_1003 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.18.1 h0d85af4_0 conda-forge
ca-certificates 2021.10.8 h033912b_0 conda-forge
cairo 1.16.0 he43a7df_1008 conda-forge
cartopy 0.20.1 py39h6878a05_1 conda-forge
cdsapi 0.5.1 pyhd8ed1ab_0 conda-forge
certifi 2021.10.8 py39h6e9494a_1 conda-forge
cffi 1.15.0 py39he338e87_0 conda-forge
cfgv 3.3.1 pyhd8ed1ab_0 conda-forge
cfitsio 3.470 h01dc385_7 conda-forge
cftime 1.6.0 py39h86b5767_0 conda-forge
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
click 7.1.2 pyh9f0ad1d_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.7.2 pyhd8ed1ab_1 conda-forge
cloudpickle 2.0.0 pyhd8ed1ab_0 conda-forge
coin-or-cbc 2.10.7 hada2c85_0 conda-forge
coin-or-cgl 0.60.3 h1c2bb20_2 conda-forge
coin-or-clp 1.17.6 h79c0eca_3 conda-forge
coin-or-osi 0.108.6 h009c923_2 conda-forge
coin-or-utils 2.11.6 h07ff368_0 conda-forge
coincbc 2.10.7 0_metapackage conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
colorcet 3.0.0 pyhd8ed1ab_0 conda-forge
conda 4.12.0 py39h6e9494a_0 conda-forge
conda-package-handling 1.8.0 py39h63b48b0_0 conda-forge
configargparse 1.5.3 pyhd8ed1ab_0 conda-forge
connection_pool 0.0.3 pyhd3deb0d_0 conda-forge
country_converter 0.7.4 pyhd8ed1ab_0 conda-forge
countrycode 0.2 pypi_0 pypi
cryptography 36.0.2 py39h1644bb1_0 conda-forge
curl 7.82.0 h9f20792_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.11.2 py39h89e85a6_1 conda-forge
dask 2021.3.1 pyhd8ed1ab_0 conda-forge
dask-core 2021.3.1 pyhd8ed1ab_0 conda-forge
datashader 0.[13](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:13).0 pyh6c4a22f_0 conda-forge
datashape 0.5.4 py_1 conda-forge
datrie 0.8.2 py39h89e85a6_3 conda-forge
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decorator 5.1.1 pyhd8ed1ab_0 conda-forge
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deprecation 2.1.0 pyh9f0ad1d_0 conda-forge
descartes 1.1.0 py_4 conda-forge
distlib 0.3.4 pyhd8ed1ab_0 conda-forge
distributed 2021.4.1 py39h6e9494a_1 conda-forge
docutils 0.18.1 py39h6e9494a_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
entsoe-py 0.5.2 pypi_0 pypi
esy-osm-pbf 0.0.1 pypi_0 pypi
esy-osmfilter 1.0.11 pypi_0 pypi
et_xmlfile 1.0.1 py_1001 conda-forge
executing 0.8.3 pyhd8ed1ab_0 conda-forge
expat 2.4.7 h96cf925_0 conda-forge
filelock 3.6.0 pyhd8ed1ab_0 conda-forge
fiona 1.8.20 py39h10412eb_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 2.13.96 h676cef8_2 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.31.2 py39h63b48b0_0 conda-forge
freetype 2.10.4 h4cff582_1 conda-forge
freexl 1.0.6 h0d85af4_0 conda-forge
fsspec 2022.2.0 pyhd8ed1ab_0 conda-forge
gdal 3.3.3 py39he7e3f19_0 conda-forge
geographiclib 1.52 pyhd8ed1ab_0 conda-forge
geopandas 0.10.2 pyhd8ed1ab_1 conda-forge
geopandas-base 0.10.2 pyha770c72_1 conda-forge
geopy 2.2.0 pyhd8ed1ab_0 conda-forge
geos 3.9.1 he49afe7_2 conda-forge
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glpk 5.0 h3cb5acd_0 conda-forge
gmp 6.2.1 h2e338ed_0 conda-forge
googledrivedownloader 0.4 pyhd3deb0d_1 conda-forge
hdf4 4.2.15 hefd3b78_3 conda-forge
hdf5 1.12.1 nompi_ha60fbc9_104 conda-forge
heapdict 1.0.1 py_0 conda-forge
holoviews 1.[14](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:14).8 pyhd8ed1ab_0 conda-forge
hvplot 0.7.3 pyh6c4a22f_0 conda-forge
icu 68.2 he49afe7_0 conda-forge
identify 2.4.12 pyhd8ed1ab_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.3 py39h6e9494a_0 conda-forge
importlib_metadata 4.11.3 hd8ed1ab_0 conda-forge
importlib_resources 5.6.0 pyhd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipopt 3.13.2 h654a6ca_1 conda-forge
ipykernel 6.9.2 py39h71a6800_0 conda-forge
ipython 8.1.1 py39h6e9494a_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jbig 2.1 h0d85af4_2003 conda-forge
jedi 0.18.1 py39h6e9494a_0 conda-forge
jinja2 3.1.1 pyhd8ed1ab_0 conda-forge
joblib 1.1.0 pyhd8ed1ab_0 conda-forge
jpeg 9e h0d85af4_0 conda-forge
json-c 0.[15](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:15) hcb556a6_0 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.4.0 pyhd8ed1ab_0 conda-forge
jupyter_client 7.1.2 pyhd8ed1ab_0 conda-forge
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jupyterlab 3.3.2 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_server 2.11.0 pyhd8ed1ab_0 conda-forge
kealib 1.4.14 ha22a8b1_3 conda-forge
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krb5 1.19.3 hb49756b_0 conda-forge
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libcblas 3.9.0 13_osx64_openblas conda-forge
libcurl 7.82.0 h9f20792_0 conda-forge
libcxx 13.0.1 hc203e6f_0 conda-forge
libdap4 3.20.6 h3e144a0_2 conda-forge
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libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
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libgdal 3.3.3 h053b6da_0 conda-forge
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libglib 2.70.2 hf1fb8c0_4 conda-forge
libiconv 1.[16](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:16) haf1e3a3_0 conda-forge
libkml 1.3.0 h8fd9edb_1014 conda-forge
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libllvm10 10.0.1 h009f743_3 conda-forge
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libpng 1.6.37 h7cec526_2 conda-forge
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librttopo 1.1.0 h5413771_6 conda-forge
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libspatialindex 1.9.3 he49afe7_4 conda-forge
libspatialite 5.0.1 hfc891e7_9 conda-forge
libssh2 1.10.0 h52ee1ee_2 conda-forge
libtiff 4.3.0 h[17](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:17)f2ce3_3 conda-forge
libwebp 1.2.2 h28dabe5_0 conda-forge
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libxslt 1.1.33 h5739fc3_2 conda-forge
libzip 1.8.0 h8b0c345_1 conda-forge
libzlib 1.2.11 h6c3fc93_1014 conda-forge
llvm-openmp 13.0.1 hcb1a161_1 conda-forge
llvmlite 0.36.0 py39h798a4f4_0 conda-forge
locket 0.2.0 py_2 conda-forge
lxml 4.8.0 py39h63b48b0_1 conda-forge
lz4-c 1.9.3 he49afe7_1 conda-forge
lzo 2.10 haf1e3a3_1000 conda-forge
mamba 0.22.1 py39ha435c47_0 conda-forge
mapclassify 2.4.3 pyhd8ed1ab_0 conda-forge
markdown 3.3.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.1 py39h63b48b0_0 conda-forge
matplotlib 3.5.1 py39h6e9494a_0 conda-forge
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metis 5.1.0 h2e338ed_1006 conda-forge
mistune 0.8.4 py39h89e85a6_1005 conda-forge
msgpack-python 1.0.3 py39hf0[18](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:18)cea_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 2.5.0 py_0 conda-forge
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networkx 2.7.1 pyhd8ed1ab_1 conda-forge
nodeenv 1.6.0 pyhd8ed1ab_0 conda-forge
notebook 6.4.10 pyha770c72_0 conda-forge
notebook-shim 0.1.0 pyhd8ed1ab_0 conda-forge
nspr 4.32 hcd9eead_1 conda-forge
nss 3.76 hfce436b_0 conda-forge
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numexpr 2.8.0 py39h4d6be9b_1 conda-forge
numpy 1.22.3 py39hf56e92f_0 conda-forge
openjpeg 2.4.0 h6e7aa92_1 conda-forge
openpyxl 3.0.9 pyhd8ed1ab_0 conda-forge
openssl 1.1.1n h6c3fc93_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.1 pypi_0 pypi
pandoc 2.17.1.1 h694c41f_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
panel 0.12.6 pyhd8ed1ab_0 conda-forge
param 1.12.0 pyh6c4a22f_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.2.0 pyhd8ed1ab_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pcre 8.45 he49afe7_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.0.1 py39hd2c7aa1_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 hbcb3906_0 conda-forge
plac 1.3.4 pyhd8ed1ab_0 conda-forge
platformdirs 2.5.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 py39h6e9494a_2 conda-forge
ply 3.11 py_1 conda-forge
poppler 21.09.0 h9573804_3 conda-forge
poppler-data 0.4.11 hd8ed1ab_0 conda-forge
postgresql 13.5 he8fe76e_1 conda-forge
powerplantmatching 0.4.8 pypi_0 pypi
pre-commit 2.17.0 py39h6e9494a_0 conda-forge
progressbar2 4.0.0 pyhd8ed1ab_0 conda-forge
proj 8.1.1 h1512c50_2 conda-forge
prometheus_client 0.13.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.27 pyha770c72_0 conda-forge
protobuf 3.[19](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:19).4 pypi_0 pypi
psutil 5.9.0 py39h89e85a6_0 conda-forge
pthread-stubs 0.4 hc929b4f_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulp 2.6.0 py39h6e9494a_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py 1.11.0 pyh6c4a22f_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.3 py39h89e85a6_1009 conda-forge
pycountry [20](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:20).7.3 pyh9f0ad1d_0 conda-forge
pycparser 2.[21](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:21) pyhd8ed1ab_0 conda-forge
pyct 0.4.6 py_0 conda-forge
pyct-core 0.4.6 py_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pyomo 6.4.0 py39hfd1d529_0 conda-forge
pyopenssl [22](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:22).0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyproj 3.2.1 py39h5ea97c7_2 conda-forge
pypsa 0.19.2 pyhd8ed1ab_0 conda-forge
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pytest 7.1.1 py39h6e9494a_0 conda-forge
python 3.9.12 h8b4d769_1_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-utils 3.1.0 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyviz_comms 2.1.0 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py39h89e85a6_3 conda-forge
pyzmq 22.3.0 py39h7fec2f1_1 conda-forge
rasterio 1.2.10 py39hf4c83f0_0 conda-forge
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readline 8.1 h05e3726_0 conda-forge
reproc 14.2.3 h0d85af4_0 conda-forge
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requests 2.27.1 pyhd8ed1ab_0 conda-forge
retry 0.9.2 py_0 conda-forge
rioxarray 0.10.2 pyhd8ed1ab_0 conda-forge
rtree 0.9.7 py39h7d0d40a_3 conda-forge
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scikit-learn 1.0.2 py39hd4eea88_0 conda-forge
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setuptools 59.8.0 py39h6e9494a_0 conda-forge
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six 1.16.0 pyh6c4a22f_0 conda-forge
sklearn 0.0 pypi_0 pypi
smart_open 5.2.1 pyhd8ed1ab_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
snakemake-minimal 7.3.2 pyhdfd78af_0 bioconda
sniffio 1.2.0 py39h6e9494a_2 conda-forge
snuggs 1.4.7 py_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
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sqlite 3.37.1 hb516[25](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:25)3_0 conda-forge
stack_data 0.2.0 pyhd8ed1ab_0 conda-forge
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stopit 1.1.2 py_0 conda-forge
tabulate 0.8.9 pyhd8ed1ab_0 conda-forge
tblib 1.7.0 pyhd8ed1ab_0 conda-forge
terminado 0.13.3 py39h6e9494a_0 conda-forge
testpath 0.6.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tiledb 2.3.4 h8370e7a_0 conda-forge
tk 8.6.12 h5dbffcc_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
toolz 0.11.2 pyhd8ed1ab_0 conda-forge
toposort 1.7 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39h89e85a6_2 conda-forge
tqdm 4.63.1 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
tsam 2.0.0 pypi_0 pypi
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzcode 2022a h5eb16cf_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
ukkonen 1.0.1 py39hf018cea_1 conda-forge
unicodedata2 14.0.0 py39h89e85a6_0 conda-forge
urllib3 1.[26](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:26).9 pyhd8ed1ab_0 conda-forge
virtualenv 20.14.0 py39h6e9494a_0 conda-forge
vresutils 0.3.1 pypi_0 pypi
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.3.1 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.14.0 py39h63b48b0_0 conda-forge
xarray 2022.3.1.dev[27](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:27)+g8f42bfd3 pypi_0 pypi
xerces-c 3.2.3 h379762d_3 conda-forge
xlrd 2.0.1 pyhd8ed1ab_3 conda-forge
xorg-libxau 1.0.9 h35c211d_0 conda-forge
xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge
xyzservices 2022.3.0 pyhd8ed1ab_0 conda-forge
xz 5.2.5 haf1e3a3_1 conda-forge
yaml 0.2.5 h0d85af4_2 conda-forge
yaml-cpp 0.6.3 hb1e8[31](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:31)3_4 conda-forge
yte 1.2.0 py[39](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:39)h6e9[49](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:49)4a_0 conda-forge
zeromq 4.3.4 he49afe7_1 conda-forge
zict 2.1.0 pyhd8ed1ab_0 conda-forge
zipp 3.7.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.11 h6c3fc93_1014 conda-forge
zstd 1.5.2 h[58](https://github.com/pypsa-meets-africa/pypsa-africa/runs/5709176725?check_suite_focus=true#step:7:58)2d3a0_0 conda-forge
Issue Analytics
- State:
- Created a year ago
- Reactions:1
- Comments:8 (3 by maintainers)
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Is it possible to configure
fiona
to simply look forlibgdal.dylib
instead of a specific version? Or else, to fall back to a genericlibgdal.dylib
when a specific version e.g.libgdal.28.dylib
can’t be found?The issue seems equivalent to this closed one: https://github.com/Toblerity/Fiona/issues/944 In the updated environment (dash unconstrained), the issue moves from mac back to windows.
However, this simple trick does not work in my case https://github.com/Toblerity/Fiona/issues/944#issuecomment-806362135 Now Fiona breaks on its own and if I try to import it first or alone, the import breaks