Unable to execute msprime.Demography() following msprime installation

[mshpak76]

I followed the installation instructions for msprime and seemingly successfully completed the installation in Python 3.8.6 using pip, and I was able to execute:

 import msprime   
 testing=msprime.simulate(sample_size=5,Ne=1000000,mutation_rate=3e-7,recombination_rate=3e-7)

However,

demography = msprime.Demography()

gives the error 'module msprime has no attribute Demography(). The same error applies with msprime.sim_ancestry() and various other functions. Something seems to have gone wrong with the installation, but I don't know what it is and how to repair it.

Thank you in advance for any help in trouble-shooting this.

[benjeffery]

Hi @mshpak76!
I've transferred this issue to the msprime repo.
Can you tell us the result of print(msprime.__version__)?

[jeromekelleher]

It's probably a python-and-pip-on-different-versions-issue, I think.

Can you try using python -m pip install msprime rather than pip install msprime @mshpak76? (Where python is whatever the command line you use in order to start the python interpreter.)

[mshpak76]

I think I see where the problem is. I'm attempting a global installation, but for some reason sudo pip install msprime is installing msprime version 1.2.0 in /usr/local/bin rather than the opt/bin where Python 3.8.6 is globally installed. So when I run Python, the old version of msprime 0.7.4 remains (similarly, if I try to use sudo pip uninstall msprime, it will attempt to uninstall msprime 1.2.0 in my local directory). So the problem is with what sudo pip is doing rather than any issue with msprime, though I have no idea why it is doing this.

[benjeffery]

I strongly recommend using a virtual environment. See here for a guide.

[jeromekelleher]

sudo python -m pip should do what you want. It's almost never a good idea to use the pip executable directly.

[mshpak76]

Thanks - I have msprime 1.2 installed both globally and in a conda environment (associated with a newer version of python) now.