{"id":13689382,"url":"https://github.com/AllenInstitute/mouse_connectivity_models","last_synced_at":"2025-05-01T23:34:27.468Z","repository":{"id":45692162,"uuid":"119611480","full_name":"AllenInstitute/mouse_connectivity_models","owner":"AllenInstitute","description":"Python package providing mesoscale connectivity models for 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-*- mode: rst -*-\n\n\nmouse_connectivity_models\n=========================\n\n|Travis|_ |Codecov|_ |Readthedocs|_\n\n.. |Travis| image:: https://travis-ci.org/AllenInstitute/mouse_connectivity_models.svg?branch=master\n.. _Travis: https://travis-ci.org/AllenInstitute/mouse_connectivity_models\n\n.. |Codecov| image:: https://codecov.io/gh/AllenInstitute/mouse_connectivity_models/branch/master/graph/badge.svg\n.. _Codecov: https://codecov.io/gh/AllenInstitute/mouse_connectivity_models\n.. |Readthedocs| image:: https://readthedocs.org/projects/mouse-connectivity-models/badge/?version=latest\n.. _Readthedocs: http://mouse-connectivity-models.readthedocs.io/en/latest/?badge=latest\n\n\n.. image:: cortical_projection.gif\n\nmouse_connectivity_models is a Python module for constructing and testing\nmesoscale connectivity models using data from the `Allen Institute for Brain\nScience \u003chttps://brain-map.org\u003e`_.\n\nIt provides models written in `Scikit-Learn \u003chttp://scikit-learn.org\u003e`_\n``estimator`` style, and has been used in the following publications:\n\n- `High resolution data-driven model of the mouse connectome\n  \u003chttps://www.mitpressjournals.org/doi/full/10.1162/netn_a_00066\u003e`_\n\n**Download**: http://download.alleninstitute.org/publications/A_high_resolution_data-driven_model_of_the_mouse_connectome/\n\n**Website**: http://mouse-connectivity-models.readthedocs.io/en/latest/\n\nInstallation\n------------\n\nDependencies\n~~~~~~~~~~~~\n\nmouse_connectivity_models requires:\n\n- Python (\u003e=2.7 or \u003e= 3.4)\n- scikit-learn (\u003e= 0.22.1)\n- allensdk (\u003e= 2.10.1)\n\nFor running the examples Matplotlib \u003e= 1.3.1 is required.\n\nWe have only tested and used this package on Linux.\n\nUser installation\n~~~~~~~~~~~~~~~~~\n\nWe use `Git \u003chttps://git-scm.com/\u003e`_ for our version control and `Github\n\u003chttps://github.com/\u003e`_ for hosting our main repository.\n\nYou can check out the latest sources and install using ``pip``::\n\n    $ git clone git@github.com:AllenInstitute/mouse_connectivity_models.git\n    $ cd mouse_connectivity_models\n    $ pip install .\n\n\nLevel of Support\n----------------\nWe are not currently supporting this code, but simply releasing it to the\ncommunity AS IS but are not able to provide any guarantees of support. The\ncommunity is welcome to submit issues, but you should not expect an active\nresponse.\n\n\nContributing\n------------\nWe encourage the community to contribute! Please first review the `Allen\nInstitute Contributing Agreement \u003chttps://github.com/AllenInstitute/\nmouse_connectivity_models/blob/master/CONTRIBUTING.md\u003e`_, then refer to the\n`contributing guide \u003chttp://AllenInstitute.github.io/mouse_connectivity_models/\ncontributing.html\u003e`_.\n\n\nInstalling the ``dev`` requirements\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nUse `pipenv \u003chttps://github.com/pypa/pipenv\u003e`_ to install the ``dev``\ndependencies. If you do not have ``pipenv`` currently installed ::\n\n   $ pip install pipenv\n\nThen install ``dev`` dependencies ::\n\n   $ pipenv install --dev\n\nThis will create a virtual environment on your machine for this project. To\nactivate the virtual environment (to develop) ::\n\n   $ pipenv shell\n\n\nTesting\n~~~~~~~\n\nAfter installation, you can launch the test suite from outside the source\ndirectory (``mcmodels``) using `pytest \u003chttps://pytest.org\u003e`_ ::\n\n   $ pytest mcmodels\n\n\nHelp and Support\n----------------\n\nDocumentation\n~~~~~~~~~~~~~\nThe documentation that supports mouse_connectivity_models can be found at the\n`Website \u003chttp://mouse-connectivity-models.readthedocs.io/en/latest/\u003e`_.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAllenInstitute%2Fmouse_connectivity_models","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FAllenInstitute%2Fmouse_connectivity_models","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FAllenInstitute%2Fmouse_connectivity_models/lists"}