AllenSDK

This small package creates a basic interface to the AllenSDK python package using PythonCall. It exports the top-level allensdk module, which can be used to import other submodules. For example:

using AllenSDK
using PythonCall
ecephyscache = pyimport("allensdk.brain_observatory.ecephys.ecephys_project_cache")
cache = ecephyscache.EcephysProjectCache # This can be used to access neuropixels data
units = cache.get_units() # E.g. get a python dataframe of neuropixels units

For more complex usage, please see AllenNeuropixels.jl, which builds on this package by providing a more Julia-oriented interface to the AllenSDK.

If CondaPkg has trouble resolving the Python dependencies, you may need to manually install the packages listed in CondaPkg.toml to some Conda environment, then set:

ENV["JULIA_CONDAPKG_ENV"] = "/path/to/some/environment/"
ENV["JULIA_CONDAPKG_OFFLINE"] = true

These environment variables tell CondaPkg.jl to use a manual python installation and avoid updating.