AllenInstitute / ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes
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documentation request #66

Open WeissShahaf opened 3 years ago

WeissShahaf commented 3 years ago

Hey, great tool you've made.

it is though, very hard to install. -can you please mark in the DOCS, all the paths that must be changed in the code to make it work? or even better, have them all in only one file? otherwise when some one wants to use the tool they have to change it line by line as error messages pop up, which causes some of us to give up on the way.

also, "pipenv" installation and path registering doesn't work (it put's it in your system's python, rather even when specifcially installed with a different version. but this is a minor issue.

thanks, Shahaf

jsiegle commented 3 years ago

Which modules have been difficult to get up and running? There is currently a single file, create_input_json.py, that is used to specify all of the custom file paths, but there may be some that we've overlooked.

simonweiler commented 2 years ago

Hi, concerning the pipenv issue for unexperienced Python users, you should make sure that you have these paths added:

set PATH=%PATH% ;C:\Users\name_user\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\Scripts

set PATH=%PATH%;C:\Users\name_user\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\Scripts

It would be helfpul if this is added to the documentation (or linked to the pipenv installation help)

jsiegle commented 2 years ago

It should be noted that these paths will depend on the specifics of your Python installation, and definitely won't work for everyone. If you installed the pipenv package following the instructions on this page but the pipenv command still won't work, then it will likely be necessary to add the Python "scripts" directory to your system path (as in the example above).

On Windows we've always used Python that was installed using Anaconda/Miniconda, and in that case the pipenv command was immediately accessible.