dynamicrouting-processing-template

This template sets up a starting point for processing NWB files attached in a DynamicRouting "datacube" data asset.

Using this template

This is a template in two ways:

• a github repository template (from which new repos can be created in github)
• a capsule template (from which new capsules can be created in codeocean) It can be used in either way, described below.

Developing a capsule in codeocean is a lot like developing in a local git repository:

• you can clone from a remote (github) to get started
• changes are tracked as commits, with commit messages
• changes can be pushed or pulled from a remote

Like local git, version-control is opt-in and requires some effort.

For throwaway analyses:

Get up and running quickly by creating a capsule from this repository in codeocean.

This will give you a copy of the capsule defined in this repo, which you can edit and use. However it won't be connected to a remote (github), so all work must be done in codeocean itself.

• open codeocean in a new tab here
• hit the + icon (top left) and select "Capsule" > "Copy from public Git" and paste the URL for this repo: https://github.com/AllenNeuralDynamics/dynamicrouting-processing-template
• the capsule should open at this readme

For more-permanent, collaborative capsule development:

Create a new repo from this template, which can serve as the remote for one or more capsules.

This will allow you to sync changes between github/codeocean (including changes to the environment):

• open this repository on github here
• hit the big green button to Use this template: a new repo will be created after you decide its name
• follow the cloning instructions as for throwaway analyses, but use "Capsule" > "Clone from Git" and supply the link to your new repo
• the capsule can now pull changes from github, so you can add or edit your files anywhere, push to github, then pull in codeocean
• to push changes from codeocean to github:
  • generate a personal access token for your account in github
  • add it to your account in codeocean

Adding your processing code to your copy of the capsule

run_script.py is a skeleton script for processing with utility functions and advice. It just needs two modifications:

• the body of process_session() should be updated where indicated to add processing code that operates on a single NWB file
• the fields in the Params dataclass need to be updated to specify any parameters used in process_session()
  • in addition, if you need to pass parameters via the App Builder interface, add them as named parameters there with exactly the same variable name as in Params (they will be picked up automatically in run_script.py)