The SpyKING CIRCUS comes as a python package, and it at this stage, note that mostly unix systems have been tested. However, users managed to get the software running on Mac OS X, and on Windows 7,8, or 10. We are doing our best, using your feedbacks, to improve the packaging and make the whole process as smooth as possible on all platforms.
How to install¶
We recommend using Anaconda, with a simple install:
Using with CONDA¶
As an example for linux, just type:
>> wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh >> bash Miniconda-latest-Linux-x86_64.sh
Then install the software itself:
>> conda install -c conda-forge -c spyking-circus spyking-circus
To do so, use the
>> pip install spyking-circus
You might want to add the
--user flag, to install SpyKING CIRCUS for the local user only, which means that you don’t need administrator privileges for the installation.
In principle, the above command also install SpyKING CIRCUS’s dependencies, and CUDA_ support if
nvcc command is found in your environment. Once the install is complete, you need to add the
PATH where SpyKING CIRCUS has been installed into your local
PATH, if not already the case. To do so, simply edit your
$HOME/.bashrc and add the following line:
Then you have to relaunch the shell, and you should now have the SpyKING CIRCUS installed!
Alternatively, you can download the source package directly and uncompress it, or work directly with the git folder https://github.com/spyking-circus/spyking-circus to be in sync with bug fixes. You can then simply run:
>> pip install . --user
Or even better, you can install it with the develop mode:
>> pip install . -e --user
Such that if you do a git pull in the software directory, you do not need to reinstall it.
For those that are not pip users, it is equivalent to:
>> python setup.py install
Or to keep the folder in sync with the install in a develop mode:
>> python setup.py develop
If you want to install
scikit-learn, needed to get the BEER estimates, you need to add
[beer] to any pip install
If you experience some issues with Qt or pyQt, you may need to install it manually on your system. For linux users, simply use your software distribution system (apt for example). For windows user, please see here
Installing phy 2.0¶
If you want to use the phy GUI to visualize your results, you may need to install phy 2.0:
>> pip install colorcet pyopengl joblib >> pip install --upgrade http://github.com/cortex-lab/phy/archive/dev.zip >> pip install --upgrade http://github.com/cortex-lab/phylib/archive/master.zip
During the install, the code creates a
spyking-circus folder in
/home/user where it will copy several probe designs, and a copy of the default parameter file. Note that if you are always using the code with a similar setup, you can edit this template, as this is the one that will be used by default.
If you are planning to use MPI, the best solution is to create a file
$HOME/spyking-circus/circus.hosts with the lists of available nodes (see Configuration of MPI). You should also make sure, for large number of electrodes, that your MPI implementation is compatible recent enough such that it can allow shared memory within processes.
- For information, here is the list of all the dependencies required by the SpyKING CIRCUS: