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:
- install JupyterLab desktop (Win 64-bit)
- clone
np_notebooks(notnp_workflows)cd c:\Users\svc_neuropix\Documents\github & git clone https://github.com/AllenInstitute/np_notebooks - find the path to python.exe 3.11.*, or install it manually
- create a new venv in the
np_notebooksdir:cd np_notebooks & path-to-python.exe -m venv .venv - activate venv:
.venv\scripts\activate(terminal should now report(np_notebooks-3.11)) - install PDM in venv:
path-to-python.exe -m pip install pdm - install
np_notebooksrequirements:pdm install - in JupyterLab, set the default to Python environment to use
c:\Users\svc_neuropix\Documents\github\np_notebooks\.venv\scripts\python.exe - open up any workflow in the
np_notebooksdir and check that the initial cell with imports works
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Release files for np-workflows 1.6.103
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