Installation

Requirements

phy works better on computers with sufficient RAM, a recent graphics card, and an SSD to store data files.

Dependencies

Main dependencies are NumPy, SciPy, PyQt5, pyopengl, joblib. The full list of dependencies is available in the environment.yml file.

Upgrading from phy 1 to phy 2

  • Never install phy 1 and phy 2 in the same conda environment.
  • It is recommended to delete ~/.phy/TemplateGUI/state.json when upgrading.

Instructions

Minimal installation instructions (to be completed):

  1. Install Anaconda.

  2. Open a terminal and type:

conda create -n phy2 python pip numpy matplotlib scipy h5py pyqt cython -y
conda activate phy2
pip install colorcet pyopengl qtconsole requests traitlets tqdm joblib click mkdocs
pip install git+https://github.com/cortex-lab/phy.git@dev
pip install git+https://github.com/cortex-lab/phylib.git
  1. Phy should now be installed. Open the GUI on a dataset as follows (the phy2 environment should still be activated):
cd path/to/my/spikesorting/output
phy template-gui params.py

Troubleshooting

  • If you receive the error: No module named PyQt5.sip, try to run the following commands in your conda environment (solution found by Claire Ward):
pip uninstall pyqt5 pyqt5-tools
pip install pyqt5 pyqt5-tools pyqt5.sip

How to reset the GUI configuration

This might be useful if the organization of the views in the GUI is incorrect.

Run phy with the --clear-state option. Alternatively, delete both files:

  • Global GUI state: ~/.phy/TemplateGUI/state.json (common to all datasets)
  • Local GUI state: .phy/state.json (within your data directory)