mouse_connectivity_models
mouse_connectivity_models is a Python module for constructing and testing mesoscale connectivity models using data from the Allen Institute for Brain Science.
It provides models written in Scikit-Learn
estimator
style, and has been used in the following publications:
Website: http://mouse-connectivity-models.readthedocs.io/en/latest/
Installation
Dependencies
mouse_connectivity_models requires:
- Python (>=2.7 or >= 3.4)
- scikit-learn (>= 0.22.1)
- allensdk (>= 2.10.1)
For running the examples Matplotlib >= 1.3.1 is required.
We have only tested and used this package on Linux.
User installation
We use Git for our version control and Github for hosting our main repository.
You can check out the latest sources and install using pip
:
$ git clone https://github.com/AllenInstitute/mouse_connectivity_models.git $ cd mouse_connectivity_models $ pip install .
Level of Support
We are not currently supporting this code, but simply releasing it to the community AS IS but are not able to provide any guarantees of support. The community is welcome to submit issues, but you should not expect an active response.
Contrubuting
We encourage the community to contribute! Please first review the Allen Institute Contributing Agreement, then refer to the contributing guide.
dev
requirements
Installing the Use pipenv to install the dev
dependencies. If you do not have pipenv
currently installed
$ pip install pipenv
Then install dev
dependencies
$ pipenv install --dev
This will create a virtual environment on your machine for this project. To activate the virtual environment (to develop)
$ pipenv shell
Testing
After installation, you can launch the test suite from outside the source
directory (mcmodels
) using pytest
$ pytest mcmodels
Help and Support
Documentation
The documentation that supports mouse_connectivity_models can be found at the Website.