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Update installation instructions
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rossant committed Jun 15, 2023
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Expand Up @@ -30,52 +30,35 @@ Phy provides two GUIs:
* [Mailing list](https://groups.google.com/forum/#!forum/phy-users)


## Installation instructions
## Hardware requirements

Phy requires a recent GPU and an SSD for storing your data (the GUI may be slow if the data is on an HDD).
It is recommanded to store the data on a SSD for performance reasons.

1. You need a recent Python distribution.
There are no specific GPU requirements as long as relatively recent graphics and OpenGL drivers are installed on the system.

2. Open a terminal and type:

```bash
pip install phy --pre --upgrade
# If you plan to use the Kwik GUI, type the following without the leading hash # character:
# pip install klusta klustakwik2
```
## Installation instructions

3. Phy should now be installed. Open the GUI on a dataset as follows (the phy2 environment should still be activated):
Run the following commands in a terminal:

```bash
cd path/to/my/spikesorting/output
phy template-gui params.py
1. Create a new conda environment with the conda dependencies:

```
conda create -n phy2 -y cython dask h5py joblib matplotlib numpy pillow pip pyopengl pyqt pyqtwebengine pytest python qtconsole requests responses scikit-learn scipy traitlets
```

### Dependencies
2. Activate the new conda environment with `conda activate phy2`

For your information, here are the Python dependencies of phy (as found in `requirements.txt`):
3. Install the development version of phy: `pip install git+https://github.com/cortex-lab/phy.git`

```
phylib
mtscomp
numpy
matplotlib
scipy
h5py
dask
cython
pillow
colorcet
pyopengl
requests
qtconsole
tqdm
joblib
click
mkdocs
PyQtWebEngine
```
4. [OPTIONAL] If you plan to use the Kwik GUI, type `pip install klusta klustakwik2`

5. Phy should now be installed. Open the GUI on a dataset as follows (the phy2 environment should still be activated):

```bash
cd path/to/my/spikesorting/output
phy template-gui params.py
```


### Dealing with the error `ModuleNotFoundError: No module named 'PyQt5.QtWebEngineWidget`
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