Installation¶
Requirements¶
phys2bids
requires python 3.6 or above, as well as the modules:
numpy >= 1.9.3
matplotlib >= 3.1.1
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.