вторник, 27 декември 2022 г.

Conda wouldn't install sundials and scikits.odes

I wanted to install a new integrator for my dear python, since scipi odeint was running crappy on my equations.  I tried to install scikits, but I kept on running into errors:

"ImportError: No module named 'scikits'"

Then after trying to install it, I got:

"Conda package install [Errno 13] Permission denied"

and then after upgrading pip:

"fatal error: sundials/sundials_types.h: No such file or directory"

First, I tried to manually install sundials from https://github.com/certik/sundials which I did with configure, make and make install, but the error in conda persisted. Then I did "export SUNDIALS_INST=/usr/local/include/sundials/" but conda didn't like it. After some digging, I've found it's better to install sundials with pip. So I first had to remove my manual installation:

sudo rm -R /usr/local/include/sundials  

unset SUNDIALS_INST=/usr/local/include/sundials/
 

Then I decided to clean up conda a bit:

conda clean -a -y 

Then I upgraded pip:

pip3 install --user --upgrade pip #that didn't work so:

sudo pacman -S pip
conda install pip 

Then I installed sundials:

pip3 install --user Sundials

sudo pacman -S sundials #that worked
 

Then installed just in case scikit-learn:

sudo pacman -S python-scikit-learn
 

To install it from pacman:

sudo pacman -S sundials

conda -c install conda-forge sundials

conda install -c conda-forge cython  

conda install -c conda-forge scikits.odes #see here for the explanation

sudo conda install -c conda-forge scikits.odes #this took super long because it verified dependencies

pip3 install --user scikits.odes #this one did it
And now, it's installed and loadable.
(see also https://github.com/bmcage/odes/issues/43)

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