mindscope-utilities 0.1.9

Utilities for loading, manipulating and visualizing data from the Allen Institute Mindscope program

mindscope_utilities

Utilities for loading, manipulating and visualizing data from the Allen Institute Mindscope program.

Functions in this repository depend on the AllenSDK https://github.com/AllenInstitute/AllenSDK

Installation

Set up a dedicated conda environment:

conda create -n mindscope_utilities python=3.8 

Activate the new environment:

conda activate mindscope_utilities

Make the new environment visible in the Jupyter

pip install ipykernel
python -m ipykernel install --user --name mindscope_utilities

Install mindscope_utilities

pip install mindscope_utilities

Or if you intend to edit the source code, install in developer mode:

git clone https://github.com/AllenInstitute/mindscope_utilities.git
cd mindscope_utilities
pip install -e .

Testing

Tests are run on CircleCI on every github commit.

Tests can be run locally by running the following at the command line:

flake8 mindscope_utilities
pytest

Level of Support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.