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NSLS-II / scipy-binder

Binder-compatible repo including scipy stack and databroker
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Add `shadow3`, `srwpy`, `edrixs` #41

Closed mrakitin closed 2 years ago

mrakitin commented 2 years ago

NSLS-II TES users (@bnash and @nickgoldring) requested access to the Shadow3 and SRW codes in Jupyter to perform a comparison of the simulated data with the experimental one. This PR adds both packages.

I sorted the dependencies and removed duplicates (3 scikit-learn - was it meant to have scikit-beam?)

Update on 2022-09-15: added recently built edrixs to check if it builds without any conflicts. The build was successful.

mrakitin commented 2 years ago

Looks like there is an issue with nbserverproxy:

  ERROR conda.core.link:_execute(698): An error occurred while installing package 'conda-forge::nbserverproxy-0.8.8-py_1000'.
  Rolling back transaction: ...working... done

  LinkError: post-link script failed for package conda-forge::nbserverproxy-0.8.8-py_1000
  location of failed script: /srv/conda/envs/notebook/bin/.nbserverproxy-post-link.sh

Will try to power-cycle the CI to see if it helps.

mrakitin commented 2 years ago

@danielballan, how would you run it locally? I'd like to experiment with it to see if it's something package-related or an infrastructure issue.

mrakitin commented 2 years ago

Turned out that the shadow3 package from conda-forge has some conflicts preventing from using the latest scipy. I think it's due to the gfortran compiler v7 that restricts installs of the scipy versions built with a newer compiler. We'll have to postpone this addition to the environment. Sorry, @nickgoldring.

bnash commented 2 years ago

Thanks for trying @mrakitin. I recall that Rob had to do something special to get it compiled and installed on the RadiaSoft server. For comparing just a few images it's not crucial but for large data sets it's certainly easier to have the simulation code and the experimental data on the same server to avoid having to do large data transfers.

danielballan commented 2 years ago

Sorry for missing that notificaiton @mrakitin. You can run these locally with docker run.

danielballan commented 2 years ago

@mrakitin needs rebase

mrakitin commented 2 years ago

I started fresh off the main branch. Added srwpy and shadow3, let's see if they can be added easier now 🙂.

mrakitin commented 2 years ago

Looks like it's doing its job now! @danielballan, mind re-reviewing it and merging?

mrakitin commented 2 years ago

I bundled edrixs here to add all three packages in one shot. @danielballan, please review/merge when you have a moment. Thanks!