No module named 'pytest' while executing bidsmapper

[mateuszpawlik]

Describe the bug
When executing bidsmapper I get No module named 'pytest' error. I see pytest in the optional dependencies.

To reproduce
Steps to reproduce the behavior:

1. Execute bidsmapper
2. See error in the bidsmapper.log:

   ERROR | Could not import /root/.local/pipx/venvs/bidscoin/lib/python3.11/site-packages/bidscoin/plugins/dcm2niix2bids.py: No module named 'pytest'
   

Expected behavior
I guess pytest should be installed as a dependency and the error shouldn't then happen.

Software version

• BIDScoin version: development 2899e04
• installed with pipx install git+https://github.com/Donders-Institute/bidscoin.git@2899e04
• OS: Debian 12 in Docker on Debian 11

[mateuszpawlik]

Maybe pipx causes troubles.

[marcelzwiers]

Thanks for reporting this, I will look into it when I am back from my holidays (the 10th of August)...

…

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[mateuszpawlik]

I used pipx to install BIDScoin in a Docker container. This is a recommended way to install Python applications by, for example, Debian 12. pipx creates a virtual environment in which it installs the application and all its Python dependencies. My guess is, pipx didn't know about the pytest dependency.

pipx kindly allows to install manually (pipx inject command) a missing module. Executing pipx inject bidscoin pytest solved the problem for me.

[marcelzwiers]

Mhhh, pytest is no longer used in bidscoin, but only when running bidscoin tests:

https://github.com/search?q=repo%3ADonders-Institute%2Fbidscoin%20%22import%20pytest%22&type=code

But this line in the dcm2niix2bids plugin has a pytest dependency, for which I now added a work-around (e558982). Does this solve your error?

[mateuszpawlik]

It seems to be fine now. I installed BIDScoin with pipx install git+https://github.com/Donders-Institute/bidscoin.git@e558982 and executed it. There were no complaints on pytest missing.

[mateuszpawlik]

Btw. pipx allows for a very quick installation and testing :-)