Commit 037422f7 authored by Yueqi Wang's avatar Yueqi Wang Committed by GitHub

Add stfio Mac install instruction for non-MacPorts Python

parent fb3b9e03
Building the stfio Python Module Only
:Author: Yueqi Wang
:Date: |today|
This documentation describes how to install the standalone Python file i/o module for Mac OS.
For details on how to use the *stfio* module, see :doc:`/stfio/index`.
Installing stfio for MacPorts Python
Download and install MacPorts from `here <>`_.
$ sudo port install py27-stfio py34-stfio
Using this method, the stfio module can only be imported using MacPorts Python.
Installing stfio for non-MacPorts Python distributions
Note: The officially-supported *stfio* module is not currently available for non-MacPorts Python distributions. You can either link the MacPorts *stfio* to your favorite Python distribution or build the module from source.
Linking the MacPorts stfio module to your Python PATH
Note: This works most of the times, but is not always recommended.
First, install the *stfio* module using MacPorts as described above. Then find the path where *stfio* is installed
$ port content py27-stfio
The install path will look something like this: */opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/stfio/*
There are two ways of adding the MacPorts stfio module to the Python PATH of your non-MacPorts Python distribution:
1) open *$HOME/.bash_profile*, add the following line to the file, and save the file:
export PATHONPATH=$PYTHONPATH:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/stfio/
- Then, update the bash profile:
$ source $HOME/.bash_profile
2) Alternatively, you can soft link the MacPorts *stfio* module folder to the *site-packages* folder of your favorite Python distribution. The following example will link MacPorts *stfio* to Anaconda Python 2.7:
$ ln -s /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/stfio/ $HOME/anaconda/lib/python2.7/site-packages/
Finally, run python to test the module, as described in :doc:`/stfio/index`.
Building the stfio module from source
Install `Homebrew <>`_
$ /usr/bin/ruby -e "$(curl -fsSL"
Install dependencies using Homebrew
$ brew update
$ brew install boost
$ brew install boost-python
$ brew install autoconf
$ brew install automake
$ brew install libtool
$ brew install fftw
$ brew install homebrew/science/hdf5
If you want support for extra biomedical file formats, install the *libbiosig* library:
$ brew tap schloegl/biosig
$ brew install libbiosig
Now download the stimfit source code:
$ cd $HOME
$ git clone
Next, Generate the build system and configure:
$ cd stimfit
$ ./
$ mkdir build
$ mkdir build/module
$ cd build/module
$ ../../configure --enable-module
Add the argument *--with-biosiglite* to the configure script if you want extra biomedical fileformats for *stfio*, but did not install the full *libbiosig* library.
If you want to install the stfio module for a non-default Python distribution, such as **Anaconda Python**, use the argument *--prefix=* to specify the installation path as the *site-packages* folder of your favorite Python distribution. The following example will install stfio for Anaconda Python 2.7:
$ ../../configure --enable-module --prefix=$HOME/anaconda/lib/python2.7/site-packages
Then, build and install:
$ make -j 4
$ make install
Finally, run python to test the module, as described in :doc:`/stfio/index`.
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