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  • 🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 · 8 ✖

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  • CONTRIBUTOR · 8 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1320956883 https://github.com/pydata/xarray/issues/7259#issuecomment-1320956883 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85OvDPT hmaarrfk 90008 2022-11-19T19:51:27Z 2022-11-19T19:51:27Z CONTRIBUTOR

I'm really not sure. It seems to happen with a large swath of versions from my recent search.

Also running from the python REPL, i don't see the warning. which makes me feel like numpy/cython/netcdf4 are trying to suppress the harmless warning.

https://github.com/cython/cython/blob/0.29.x/Cython/Utility/ImportExport.c#L365

 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995
1320953994 https://github.com/pydata/xarray/issues/7259#issuecomment-1320953994 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85OvCiK hmaarrfk 90008 2022-11-19T19:33:37Z 2022-11-19T19:33:37Z CONTRIBUTOR

one or the other.

 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995
1320953155 https://github.com/pydata/xarray/issues/7259#issuecomment-1320953155 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85OvCVD hmaarrfk 90008 2022-11-19T19:28:20Z 2022-11-19T19:28:53Z CONTRIBUTOR

I think it is a numpy thing bash mamba create --name np numpy netcdf4 --channel conda-forge --override-channels conda activate np python -c "import numpy; import warnings; warnings.filterwarnings('error'); import netCDF4" python Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/mark/mambaforge/envs/np/lib/python3.11/site-packages/netCDF4/__init__.py", line 3, in <module> from ._netCDF4 import * File "src/netCDF4/_netCDF4.pyx", line 1, in init netCDF4._netCDF4 RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject

``` $ mamba list # packages in environment at /home/mark/mambaforge/envs/np: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.9.24 ha878542_0 conda-forge cftime 1.6.2 py311h4c7f6c3_1 conda-forge curl 7.86.0 h2283fc2_1 conda-forge hdf4 4.2.15 h9772cbc_5 conda-forge hdf5 1.12.2 nompi_h4df4325_100 conda-forge icu 70.1 h27087fc_0 conda-forge jpeg 9e h166bdaf_2 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.19.3 h08a2579_0 conda-forge ld_impl_linux-64 2.39 hc81fddc_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcurl 7.86.0 h2283fc2_1 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge libnghttp2 1.47.0 hff17c54_1 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 hf14f497_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libxml2 2.10.3 h7463322_0 conda-forge libzip 1.9.2 hc929e4a_1 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge ncurses 6.3 h27087fc_1 conda-forge netcdf4 1.6.2 nompi_py311hc6fcf29_100 conda-forge numpy 1.23.4 py311h7d28db0_1 conda-forge openssl 3.0.7 h166bdaf_0 conda-forge pip 22.3.1 pyhd8ed1ab_0 conda-forge python 3.11.0 ha86cf86_0_cpython conda-forge python_abi 3.11 2_cp311 conda-forge readline 8.1.2 h0f457ee_0 conda-forge setuptools 65.5.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tzdata 2022f h191b570_0 conda-forge wheel 0.38.4 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge ``` 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995
1320950377 https://github.com/pydata/xarray/issues/7259#issuecomment-1320950377 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85OvBpp hmaarrfk 90008 2022-11-19T19:14:04Z 2022-11-19T19:14:04Z CONTRIBUTOR

mamba create --name xr numpy pandas xarray netcdf4 --channel conda-forge --override-channels conda activate xr python -c "import xarray; import warnings; warnings.filterwarnings('error'); import netCDF4"

Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/mark/mambaforge/envs/xr/lib/python3.11/site-packages/netCDF4/__init__.py", line 3, in <module> from ._netCDF4 import * File "src/netCDF4/_netCDF4.pyx", line 1, in init netCDF4._netCDF4 RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject

`mamba list` ``` mamba list # packages in environment at /home/mark/mambaforge/envs/xr: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.9.24 ha878542_0 conda-forge cftime 1.6.2 py311h4c7f6c3_1 conda-forge curl 7.86.0 h2283fc2_1 conda-forge hdf4 4.2.15 h9772cbc_5 conda-forge hdf5 1.12.2 nompi_h4df4325_100 conda-forge icu 70.1 h27087fc_0 conda-forge jpeg 9e h166bdaf_2 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.19.3 h08a2579_0 conda-forge ld_impl_linux-64 2.39 hc81fddc_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcurl 7.86.0 h2283fc2_1 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge libnghttp2 1.47.0 hff17c54_1 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 hf14f497_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libxml2 2.10.3 h7463322_0 conda-forge libzip 1.9.2 hc929e4a_1 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge ncurses 6.3 h27087fc_1 conda-forge netcdf4 1.6.2 nompi_py311hc6fcf29_100 conda-forge numpy 1.23.4 py311h7d28db0_1 conda-forge openssl 3.0.7 h166bdaf_0 conda-forge packaging 21.3 pyhd8ed1ab_0 conda-forge pandas 1.5.1 py311h8b32b4d_1 conda-forge pip 22.3.1 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge python 3.11.0 ha86cf86_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.11 2_cp311 conda-forge pytz 2022.6 pyhd8ed1ab_0 conda-forge readline 8.1.2 h0f457ee_0 conda-forge setuptools 65.5.1 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tzdata 2022f h191b570_0 conda-forge wheel 0.38.4 pyhd8ed1ab_0 conda-forge xarray 2022.11.0 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge ``` 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995
1320945794 https://github.com/pydata/xarray/issues/7259#issuecomment-1320945794 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85OvAiC hmaarrfk 90008 2022-11-19T18:51:01Z 2022-11-19T18:51:01Z CONTRIBUTOR

It is also reproducible on binder:

It seems that the binder uses conda-forge, which is why i'm commenting here.

It is really strange in the sense that xarray doesn't compile anything.

https://github.com/conda-forge/xarray-feedstock/blob/main/recipe/meta.yaml#L16

So it must be something that gets lazy loaded that triggers things.

 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995
1306334761 https://github.com/pydata/xarray/issues/7259#issuecomment-1306334761 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85N3RYp s-weigand 9513634 2022-11-07T22:54:11Z 2022-11-07T22:54:11Z CONTRIBUTOR

It is also reproducible locally only xarray makes the difference, for the git bisect I used a fresh env.

 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995
1306146088 https://github.com/pydata/xarray/issues/7259#issuecomment-1306146088 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85N2jUo s-weigand 9513634 2022-11-07T20:25:50Z 2022-11-07T20:26:02Z CONTRIBUTOR

Yeah we first saw it on the CI, which moved it from bad local install (as pretty much all accepted StackOverflow answers also suggest) to

I have no idea what is going wrong ...

😅

 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995
1305984239 https://github.com/pydata/xarray/issues/7259#issuecomment-1305984239 https://api.github.com/repos/pydata/xarray/issues/7259 IC_kwDOAMm_X85N17zv s-weigand 9513634 2022-11-07T17:59:38Z 2022-11-07T17:59:38Z CONTRIBUTOR

We were/are also entirely baffled and have no clue what kind of black magic is going is going on with this 😅

 
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   🐛 NetCDF4 RuntimeWarning if xarray is imported before netCDF4 1437481995

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