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Update scripts to use python3 #3

merged 1 commit into from May 28, 2019


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commented Dec 9, 2018

This updates the scripts to use Python3 using 2to3, and updates the shebangs also.

(python2 will reach end-of-life soon).


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commented Dec 20, 2018

Hi Ankur, thanks for the updates to GENESIS. I am particularly interested in
the conversion of the Python 2 scripts in genesis/Scripts/gpython-tools
to Python 3. With the phasing out of Python 2, this is necessary, and these
are the tools that I use for my simulation analysis. I may put the Python 3
versions into a separate directory gpython-tools/python3.

However, I discovered a new problem that will have to be fixed in both
versions. When I upgraded my computer from Fedora 27 to 29, I found that
my favorite plotting program, gipyplot.pyh was broken. This is true with your
python3 version also, and seems to be from a change in matplotlib.

I've found the solution, and sometime before the end of the year will
try to get these changes incorporated.

Are you working with Volker Steuber? Doing anything intesting with


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commented Dec 21, 2018


Thank you for looking into this. Yes, I did feel I was being overly optimistic that a simple 2to3 would be enough. I'd not been able to thoroughly test the scripts myself.

Yes, Volker is my principal PhD supervisor. (I'm just wrapping up my PhD now). Unfortunately, I haven't needed genesis in my work yet. My PhD work is limited to larger network models, so I use NEST at the moment. I knew of Genesis and wanted to make it available in NeuroFedora---I work on it on the side with help from other Fedora community volunteers. (We'll formally announce NeuroFedora once we have documentation up, hopefully, in the first week of the new year)

Genesis is available in neurofedora now, so users should be able to install in on a current Fedora release soon using:

sudo dnf install genesis-simulator

It's currently in testing so it temporarily requires enabling the updates-testing repository. I expect I'll push it to stable when I get back to work after Christmas.

sudo dnf --enablerepo=updates-testing install genesis-simulator

We hope that making well established tools like genesis easily available will enable the research community use them better, and at the same time, get folks interested in helping maintain these tools. If you have any feedback at all, we'd love to hear it :)

@genesis-sim genesis-sim merged commit b3f5497 into genesis-sim:master May 28, 2019

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