pip install omnipath does not install the package properly

[elmbeech]

Hi There,

I am running Python 3.11 with the latest pip ~ version 25.1.1 on a Linux (Ubuntu-based Pop!_OS 22.04 LTS)

I tried to pip install omnipath.
Everything seems to work fine. No dependency error, nothing.

When I fire up ipython and try:

import omnipath as op

I get the error: ModuleNotFoundError: No module named 'omnipath'.

So I check: .local/lib/python3.11/site-packages/.
There is a omnipath-1.0.10.dist-info folder, but the omnipath folder is missing.

Other packages installed flawless.
I wonder what the problem causes. Do have any insights?

Thank you, Elmar

[elmbeech]

Workaround:

git clone https://github.com/saezlab/omnipath.git
cd omnipath
pip install .

After that :

import omnipath as op

Is throwing the error:

AttributeError: _ARRAY_API not found

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

So ...

pip install 'numpy<2'

Now all works fine!

I think the problem might be that you net enforce a numpy version < 2.0?!

[elmbeech]

hmmm ....
I checked pyproject.toml.
You are not really requiring numpy.
So It might be one of your dependencies that causes the error?

[lincw]

I encountered a similar issue with the error "No module named 'omnipath' in version 1.0.10.
The issue was resolved by downgrading to 1.0.9.

[AaronNing]

same. I encountered a similar issue with the error "No module named 'omnipath' in version 1.0.10.
The issue was resolved by downgrading to 1.0.7.