[Neuroimaging] Looking for advice regarding releasing some analysis software

vanessa sochat vsochat at stanford.edu
Thu Jun 16 15:03:36 EDT 2016

In case it hasn't been mentioned, I would recommend a documentation
strategy that can parse your code and including comments and arguments from
functions, etc. If you use read the docs
<http://read-the-docs.readthedocs.io/en/latest/getting_started.html> you
can have the build happen automatically with pushes to the repo, and it's a
familiar, clean interface.

On Thu, Jun 16, 2016 at 6:44 AM, Frederick, Blaise B. <
bbfrederick at mclean.harvard.edu> wrote:

> Hi all,
> For the last few years my lab has been doing time delay analysis on fMRI
> and concurrent fMRI/NIRS data, and I’ve written a number of python tools
> for performing the analysis, and they’ve been refined for several years at
> this point, and I think they could be generally useful to people, so I’m
> looking to release the software.  I’m fairly new at this, and I’ve found a
> bunch of recommendations on how to do this, some of which are
> contradictory.  I’d appreciate any help I could get on this.
> What I’ve done so far:
> 1) Chosen a license (Apache 2, based on a lot of reading and some
> conversations)
> 2) Put the core programs up on github (
> https://github.com/bbfrederick/delaytools)
> 3) Tried to put together rudimentary documentation and installation
> directions.
> As things exist now, if you install the prerequisites, download the code,
> and add the main directory to your path, you should be able to run the
> tools, which is a fine start, but there seems to be a lot more to
> installation than that (automatically installing dependancies and all that)
> that I’m unable to figure out. I’d appreciate any feedback on this.  I’m a
> little mystified by the vagaries of constructing a setup.py file, and what
> constitutes a ‘package’ and a ‘module’.
> Some of the questions I have:
> 1) In addition to the main program, I have scads of command line utilities
> that make preparing and interpreting the data easier - do I just put them
> all in the top level directory, or in a bin directory?
> 2) The dependancies for the majority of the tools are very simple (numpy,
> scipy, scikits-learn, matplotlib, nibabel), but there’s a kind of useful
> gui tool that requires pyqt4 and pyqtgraph - pyqt does not seem to be
> installable with pip, so I’m not sure how to handle that (installing it all
> with anaconda is easy though). How should I handle this?
> 3) What’s the best way to publicize this?  This won’t be useful if nobody
> can find it.
> Thanks,
> Blaise
> --------------
> Blaise Frederick
> Associate Professor of Psychiatry/Biophysicist
> Harvard Medical School/McLean Hospital
> bbfrederick at mclean.harvard.edu
> http://www.nirs-fmri.net
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Vanessa Villamia Sochat
Stanford University
(603) 321-0676
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