Installation

Requirements

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

numpy >=1.9.3, !=*rc*
matplotlib >=3.1.1, !=3.3.0rc1
PyYAML >=5.1, !=*rc*

Depending on the processed files, it might require the manual installation of extra modules. At the moment, those modules are:

  • bioread, for AcqKnowledge (.acq) files.

Linux and mac installation

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.

Install phys2bids alone

Pypi has the latest stable release of phys2bids as a package. Just run:

pip3 install phys2bids

If you want the latest development version of the program, download the package from github and uncompress it. Alternatively, if you have git, use the command:

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

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

pip3 install .

Install extra modules

If you are planning to use file formats other than plain txt, you need to install extra modules to have the right interface. Extra modules installation can be done with the syntax:

pip3 install <package>[<extra>]

Where <package>> is either phys2bids or ., depending on whether you want to use pip or git for the installation, and <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 the interfaces, run:

pip3 install phys2bids[interfaces]

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 the 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

You might still need to install extra dependencies listed at the beginning of the page.

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 1.3.0-beta or similar, phys2bids is ready to be used.