Prattbuw documentation #19
Conversation
| @@ -1,10 +1,93 @@ | |||
| # Aind.Behavior.Pirouette | |||
|
|
|||
| A repository with source code for long-term, freely moving, electrophisiology recordings in mice | |||
There was a problem hiding this comment.
I would keep a high-level description of the repo in the readme. Feel free to change it, but it would be great to leave one.
README.md
Outdated
| # Aind.Behavior.Pirouette | ||
|
|
||
| A repository with source code for long-term, freely moving, electrophisiology recordings in mice | ||
| Authors: Bruno Cruz, Brandon Pratt, and Carl Schoonover |
There was a problem hiding this comment.
I generally avoid adding this to the readme since the repository already keeps track of contributors. If you want to add Carl, he just has to push a single commit, or you can add him as a co-author in one of them.
README.md
Outdated
| Authors: Bruno Cruz, Brandon Pratt, and Carl Schoonover | ||
|
|
||
| ## Getting started | ||
| Last Updated: 05/15/2025 |
There was a problem hiding this comment.
Last Updated is also redundant since this is one of the major perks of using Github for documentation. Changes are tracked for free.
README.md
Outdated
| ### 3. Lifealert | ||
| ### 4. Neural activity visualization | ||
| --- | ||
| ### 1. Getting started |
There was a problem hiding this comment.
This sounds like instructions to setup the experiment in the Allen. As we discussed previously, it would be nice to leave the entry-point to the repo somewhat agnostic. Wouldnt it make more sense to put these instructions in a separate docs file? We can also just trigger the build of the sphinx website and move this there.
You should also consider linking, or reproducing the following deployment scipt: https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/blob/main/scripts/install_dependencies.ps1
This is what I use for all tasks and it is what SIPE is using as reference for automatic deployment
README.md
Outdated
| --- | ||
| ### 1. Getting started | ||
| 1. If using a new computer, contact IT to set up the "svc_aind_chronic" service account, which is the account that all Pirouette systems use. | ||
| 2. Clone this repository using git clone (may need to generate an ssh key and link it with your GitHub account -- https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent). |
There was a problem hiding this comment.
The repo is public, i dont think this is needed
README.md
Outdated
| 8. Generate the rig.json, session.json, and task.json configuration files by running example.py found within the examples directory (update the content to reflect current experimental parameters, like device IDs). | ||
| --- | ||
| ### 2. Pirouette Bonsai workflow | ||
| 1.Open Git Bash, navigate to the Aind.Behavior.Pirouette remote directory, and luanch visual studio. |
There was a problem hiding this comment.
This is confusing. In the previous section you tell people to use uv, but know you are telling them to run the workflow using a different tool?
I can see two solutions:
- Always tell them to use uv
- Explain the different ways to start bonsai, including passing the schema files as inputs
- Wrap the whole experiment in a launcher that takes care of the life-alert + launching bonsai with one command
There was a problem hiding this comment.
I added the third point as an issue in the repo because a launcher that takes care of both life-alert and Bonsai is something I would like to add in the future.
@bruno-f-cruz, I updated the pirouette documentation with the focus of documenting how experiments are run. The documentation will likely change in the future, but will serve as a good reference for those wanting to us our system.