Install Stimfit as a python package

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Sally Kim

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Mar 14, 2017, 11:01:06 AM3/14/17
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Hi Everyone,

First of all, thank you so much for providing the program. It will be extremely helpful and convenient to analyze my ephy's data in OSX. 

I was able to install and open the program on my Mac OS X El Capitan using "sudo port install stimfit py27-stfio py34-stfio" (obviously, I installed Xcode and MacPorts). But, when I import stf in python, it says "No module named stf", suggesting that it cannot be used in python? As an alternative, I could build stimfit from source, but when I attempted to install git-core, MacPorts cannot find git-core (Error: Port git-core not found). So, I updated the local ports tree (selfupdate) and search for the available port installation, but it says "No match for git-core found". My ports version is 2.4.1. 

Anyone who has faced this difficulty in OSX? or knows how to solve this problem. My goal here is to  be able to make a python script with import stf so that I can easily repeat the analysis of multiple traces.

Appreciate for all of your help in advance,
Sally

Christoph Schmidt-Hieber

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Mar 14, 2017, 11:12:46 AM3/14/17
to sti...@googlegroups.com
Hi,

If you just want to use the module that reads various electrophysiology file formats, you need to use the stfio standalone module.

http://www.stimfit.org/doc/sphinx/stfio/index.html

If you want to use the full program including its graphical user interface, you need to open /Applications/MacPorts/stimfit.app

This program (stimfit) has an embedded Python shell. The module to interact with the main program is called “stf” and is already imported.

Christoph
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