enabling conda within neurodesktop

[fphsFischmeister]

Dear all,

We are currently implementing some custom Python scripts to analyze our fMRI data. While implementing, I noticed that conda is within the search path when using the JupyterLab environment but not when utilizing the Neurodesk platform. While I currently simply run /opt/conda/bin/conda init to initialize, I was wandering if there is any reason for not having conda within the search path of Neurodesktop. Additionally, just to make sure, is the /opt/conda path the same instance within JupyterLab and Neurodesk?

Thanks in advance,

Florian

[stebo85]

Dear Florian, this sounds like bug. I investigate and get back to you. Which version of neurodesk are you using? Thank you Steffen

…

-- W: https://mri.sbollmann.net<https://mri.sbollmann.net/> | W: https://www.neurodesk.org<https://www.neurodesk.org/> | T: https://twitter.com/sbollmann_MRI | G: https://github.com/stebo85 Book meeting: https://calendly.com/s-bollmann/meeting

________________________________ From: Florian Ph.S Fischmeister ***@***.***> Sent: Monday, October 30, 2023 6:17:57 AM To: NeuroDesk/neurodesk.github.io ***@***.***> Cc: Subscribed ***@***.***> Subject: [Neurodesk Organisation] enabling conda within neurodesktop (Discussion #377) Dear all, We are currently implementing some custom Python scripts to analyze our fMRI data. While implementing, I noticed that conda is within the search path when using the JupyterLab environment but not when utilizing the Neurodesk platform. While I currently simply run /opt/conda/bin/conda init to initialize, I was wandering if there is any reason for not having conda within the search path of Neurodesktop. Additionally, just to make sure, is the /opt/conda path the same instance within JupyterLab and Neurodesk? Thanks in advance, Florian — Reply to this email directly, view it on GitHub<#377>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA6V2W4D722FTGM2X3K36R3YB2TWLAVCNFSM6AAAAAA6VCLCWKVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZVG44TCOBXGI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[fphsFischmeister]

We are using vnmd/neurodesktop:20230830.

Thanks,

Florian

[stebo85]

Dear @fphsFischmeister - I can confirm it's a bug. I just fixed it and we will create a new release.

[stebo85]

Dear @fphsFischmeister,

we created a new release. Can you try to the new release from here? https://www.neurodesk.org/docs/getting-started/neurodesktop/

when you use conda environments in neurodesktop make sure to follow these instructions to set it up: https://www.neurodesk.org/tutorials-examples/tutorials/programming/conda/

Let us know if this works as expected for you :)

[fphsFischmeister]

Dear @stebo85,
Tested the 2023-10-30 version and thanks everything works perfectly now.
Best, Florian

[stebo85]

That's great to hear! Thank you for finding the bug and reporting it :) Let us know if there is anything else that comes up!