README.md

np_workflows

This package contains all the Python code required to run Mindscope Neuropixels experiments.

Experiment workflows and related tasks are coordinated by Jupyter notebooks maintained here: https://github.com/AllenInstitute/np_notebooks

Running the notebooks requires a Python environment with:

• Python >= 3.11
• np_workflows
• Jupyter / JupyterLab

git clone https://github.com/AllenInstitute/np_notebooks
conda create -n workflows python=3.11
pip install np_workflows
pip install jupyterlab

Keep the np_workflows package up-to-date by running pip install np_workflows -U before each use

To develop this package git clone then pdm install

NP. rig setup

.venv is currently used, with PDM to update packages before each experiment:

1. install JupyterLab desktop (Win 64-bit)
2. clone np_notebooks (not np_workflows) cd c:\Users\svc_neuropix\Documents\github & git clone https://github.com/AllenInstitute/np_notebooks
3. find the path to python.exe 3.11.*, or install it manually
4. create a new venv in the np_notebooks dir: cd np_notebooks & path-to-python.exe -m venv .venv
5. activate venv: .venv\scripts\activate (terminal should now report (np_notebooks-3.11))
6. install PDM in venv: path-to-python.exe -m pip install pdm
7. install np_notebooks requirements: pdm install
8. in JupyterLab, set the default to Python environment to use c:\Users\svc_neuropix\Documents\github\np_notebooks\.venv\scripts\python.exe
9. open up any workflow in the np_notebooks dir and check that the initial cell with imports works