Unable to import pymeos (conda installation)

[mitirmizi]

I created a new virtual environment and installed Pymeos using: conda install conda-forge::pymeos. Conda Page for pymeos: https://anaconda.org/conda-forge/pymeos.

Issue:

When I import pymeos I get the following error:

>>> import pymeos as pm
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/teemo/anaconda3/envs/pym2/lib/python3.12/site-packages/pymeos/_init_.py", line 1, in <module>
    from .aggregators import *
  File "/home/teemo/anaconda3/envs/pym2/lib/python3.12/site-packages/pymeos/aggregators/_init_.py", line 1, in <module>
    from .bool_aggregators import *
  File "/home/teemo/anaconda3/envs/pym2/lib/python3.12/site-packages/pymeos/aggregators/bool_aggregators.py", line 1, in <module>
    from pymeos_cffi import *
  File "/home/teemo/anaconda3/envs/pym2/lib/python3.12/site-packages/pymeos_cffi/_init_.py", line 1, in <module>
    from .functions import *
  File "/home/teemo/anaconda3/envs/pym2/lib/python3.12/site-packages/pymeos_cffi/functions.py", line 5, in <module>
    import _meos_cffi
ImportError: libgsl.so.25: cannot open shared object file: No such file or directory

[Diviloper]

I'm unable to reproduce this issue. When installing pymeos in a clean environment (using the miniconda docker image), gsl gets installed when installing pymeos, and it seems to be working properly.
Could you provide more details of your environment to try and reproduce your issue?

[mitirmizi]

When I install it with Anaconda version: 22.9.0. I get the following (image below). I though initially that this was due to me using python 3.12. But I got the same behavior with python 3.11 and 3.10 as can be seen below.

If you think this issue is not because of Pymeos, and maybe conda has something to do with this then I can close this issue. Regardless do you have any suggestion on how to fix conda?

[Diviloper]

I've been able to reproduce the issue. It seems like a dependency mismatch caused by the different conda channels and their priorities. When installing pymeos through conda-forge, conda is getting some packages from the defaults channel and others from the conda-forge channel, when ideally, it should get them all from the latter.
To fix this, just run this to set conda-forge as the first option and try to install again:

conda config --add channels conda-forge
conda config --set channel_priority strict

These instructions are indicated in the feedstock repo, but missing from the PyMEOS documentation.
I will add them there to avoid these problems in the future.

Please confirm whether this solved the issue.

[Diviloper]

The documentation has been updated in #51, which will be merged as soon as this issue is closed

[mitirmizi]

@Diviloper you were correct about this going back to my installations I see that indeed previously I conda install conda-forge::pymeos install packages from different channels.
Packages installed previously:

The following NEW packages will be INSTALLED:

  c-ares             conda-forge/linux-64::c-ares-1.28.1-hd590300_0 None
  cffi               pkgs/main/linux-64::cffi-1.16.0-py310h5eee18b_0 None
  geos               conda-forge/linux-64::geos-3.12.1-h59595ed_0 None
  gsl                pkgs/main/linux-64::gsl-2.7.1-h6e86dc7_1 None
  json-c             conda-forge/linux-64::json-c-0.17-h7ab15ed_0 None
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 None
  krb5               conda-forge/linux-64::krb5-1.21.2-h659d440_0 None
  lerc               conda-forge/linux-64::lerc-4.0.0-h27087fc_0 None
  libblas            conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas None
  libcblas           conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas None
  libcurl            conda-forge/linux-64::libcurl-8.7.1-hca28451_0 None
  libdeflate         conda-forge/linux-64::libdeflate-1.20-hd590300_0 None
  libedit            pkgs/main/linux-64::libedit-3.1.20230828-h5eee18b_0 None
  libev              pkgs/main/linux-64::libev-4.33-h7f8727e_1 None
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1 None
  libgfortran5       pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1 None
  libjpeg-turbo      conda-forge/linux-64::libjpeg-turbo-3.0.0-hd590300_1 None
  liblapack          conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas None
  libnghttp2         conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1 None
  libopenblas        pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0 None
  libpq              conda-forge/linux-64::libpq-16.2-h33b98f1_1 None
  libsqlite          conda-forge/linux-64::libsqlite-3.45.3-h2797004_0 None
  libssh2            conda-forge/linux-64::libssh2-1.11.0-h0841786_0 None
  libtiff            conda-forge/linux-64::libtiff-4.6.0-h1dd3fc0_3 None
  libwebp-base       pkgs/main/linux-64::libwebp-base-1.3.2-h5eee18b_0 None
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5 None
  llvm-openmp        pkgs/main/linux-64::llvm-openmp-14.0.6-h9e868ea_0 None
  lz4-c              pkgs/main/linux-64::lz4-c-1.9.4-h6a678d5_0 None
  meos               conda-forge/linux-64::meos-1.1.1-h8518783_0 None
  numpy              conda-forge/linux-64::numpy-1.26.4-py310hb13e2d6_0 None
  proj               conda-forge/linux-64::proj-9.4.0-h1d62c97_0 None
  pycparser          pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0 None
  pymeos             conda-forge/noarch::pymeos-1.1.3-pyhd8ed1ab_0 None
  pymeos-cffi        conda-forge/linux-64::pymeos-cffi-1.1.1-py310h2372a71_0 None
  python-dateutil    pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0 None
  python_abi         conda-forge/linux-64::python_abi-3.10-2_cp310 None
  shapely            conda-forge/linux-64::shapely-2.0.4-py310hc3e127f_0 None
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1 None
  zstd               pkgs/main/linux-64::zstd-1.5.5-hc292b87_0 None

But after this fix:

conda config --add channels conda-forge
conda config --set channel_priority strict

Packages INSTALLED were:

  c-ares             conda-forge/linux-64::c-ares-1.28.1-hd590300_0 None
  cffi               conda-forge/linux-64::cffi-1.16.0-py310h2fee648_0 None
  geos               conda-forge/linux-64::geos-3.12.1-h59595ed_0 None
  gsl                conda-forge/linux-64::gsl-2.7-he838d99_0 None
  json-c             conda-forge/linux-64::json-c-0.17-h7ab15ed_0 None
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 None
  krb5               conda-forge/linux-64::krb5-1.21.2-h659d440_0 None
  lerc               conda-forge/linux-64::lerc-4.0.0-h27087fc_0 None
  libblas            conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas None
  libcblas           conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas None
  libcurl            conda-forge/linux-64::libcurl-8.7.1-hca28451_0 None
  libdeflate         conda-forge/linux-64::libdeflate-1.20-hd590300_0 None
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 None
  libev              conda-forge/linux-64::libev-4.33-hd590300_2 None
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_5 None
  libgfortran5       conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_5 None
  libjpeg-turbo      conda-forge/linux-64::libjpeg-turbo-3.0.0-hd590300_1 None
  liblapack          conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas None
  libnghttp2         conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1 None
  libopenblas        conda-forge/linux-64::libopenblas-0.3.27-pthreads_h413a1c8_0 None
  libpq              conda-forge/linux-64::libpq-16.2-h33b98f1_1 None
  libssh2            conda-forge/linux-64::libssh2-1.11.0-h0841786_0 None
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_5 None
  libtiff            conda-forge/linux-64::libtiff-4.6.0-h1dd3fc0_3 None
  libwebp-base       conda-forge/linux-64::libwebp-base-1.4.0-hd590300_0 None
  meos               conda-forge/linux-64::meos-1.1.1-h8518783_0 None
  numpy              conda-forge/linux-64::numpy-1.26.4-py310hb13e2d6_0 None
  proj               conda-forge/linux-64::proj-9.4.0-h1d62c97_0 None
  pycparser          conda-forge/noarch::pycparser-2.22-pyhd8ed1ab_0 None
  pymeos             conda-forge/noarch::pymeos-1.1.3-pyhd8ed1ab_0 None
  pymeos-cffi        conda-forge/linux-64::pymeos-cffi-1.1.1-py310h2372a71_0 None
  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 None
  python_abi         conda-forge/linux-64::python_abi-3.10-4_cp310 None
  shapely            conda-forge/linux-64::shapely-2.0.4-py310hc3e127f_0 None
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 None
  sqlite             conda-forge/linux-64::sqlite-3.45.3-h2c6b66d_0 None
  zstd               conda-forge/linux-64::zstd-1.5.5-hfc55251_0 None

This fixed the issue. Now I can successfully import pymeos.