Installation

Requirements

phys2bids requires python 3.6 or above, as well as the modules:

numpy >=1.10, <1.24
matplotlib >=3.1.1, !=3.3.0rc1
PyYAML >=5.1

If you are planning to use file formats other than plain txt, you will need to install additional extra modules to have the right interface. At the moment, those modules are:

  • bioread, for AcqKnowledge (.acq) files.

Linux and mac installation

The most convenient option is to use pip, as it allows you to automatically download and install the package from PyPI repository and facilitates upgrading or uninstalling it. Since we use auto to publish the latest features as soon as they are ready, PyPI will always have the latest stable release of phys2bids as a package.

Alternatively, you can get the package directly from GitHub but all download, installation and package handling steps will need to be done manually.

Install with pip

Note

The following instructions are provided assuming that python 3 is not your default version of python. If it is, you might need to use pip instead of pip3, although some OSs do adopt pip3 anyway. If you want to check, type python --version in a terminal.

If you don’t need any of the extra modules listed at the beginning of this page go to Install phys2bids alone. Otherwise, follow the instructions under Install phys2bids with extra modules.

Install phys2bids alone

To install phys2bids along with the basic required modules just run:

pip3 install phys2bids

You can now proceed to check your installation and start using phys2bids!

Install phys2bids with extra modules

The installation of phys2bids along with extra modules can be done with the syntax:

pip3 install phys2bids[<extra>]

Where <extra> is one of the following:

  • acq: if you plan to use native AcqKnowledge files (.acq extension)

  • interfaces: for all the interfaces above.

For instance, if you plan to install phys2bids and use all of the interfaces, run:

pip3 install phys2bids[interfaces]

You can now proceed to check your installation and start using phys2bids!

Note

If you “missed” or skipped this trick when you installed phys2bids the first time, don’t worry! You can do it any time - this will update phys2bids and install all extra modules you want.

Install without pip

Download the latest package release from github and uncompress it. Alternatively, if you have git installed, use the command:

git clone https://github.com/physiopy/phys2bids.git

Open a terminal in the phys2bids folder and execute the command:

python3 setup.py install

This should have installed phys2bids along with the basic required modules. If you need any of the extra modules listed at the beginning of the page you might need to install them manually. Otherwise, you can proceed to check your installation and start using phys2bids.

Note

If python 3 is already your default, you might use python rather than python3

Check your installation!

Type the command:

phys2bids -v

If your output is: phys2bids 2.2.2 or similar, phys2bids is ready to be used.

Windows installation

First of all let’s check you have python installed. Open a windows power shell window in admin mode and type:

python --version

In case you don’t have it, either install it from here or type the command:

python

It will redirect you to the windows store python install (in the creation of this tutorial the newest version of python was 3.8).

Warning

phys2bids supports Python 3.6 and later versions. We can’t guarantee it will work if you use python 2.

Once python is installed, you can follow the instructions to install phys2bids reported above

Note

Remember to open a terminal in admin mode to install libraries!