Installation and Upgrade

There are several ways to install the software. The application requires python3.

To avoid interference with the other packages, it is recommended to use virtual environments, as described below.

We recommend to install the software using automatic installation scripts provided for Linux/Mac and Windows.

Releases

All releases are listed at Releases. Releases are distributed as executable (for Windows) and through The Python Package Index (PyPI). Due to numerous issues encountered while distributing through Anaconda, we discontinued Anaconda support.

Linux/Mac

To use automatic installation script for Linux/Mac make first sure that you have latest pip installed by running:

python3 -m pip install --user --upgrade pip

Then open terminal and go to folder where you like to install the program. Then run following command:

curl https://gitlab.com/iocbio/kinetics/-/raw/master/install.sh | bash

or

wget -qO - https://gitlab.com/iocbio/kinetics/-/raw/master/install.sh | bash

and run by

iocbio-kinetics/bin/iocbio-kinetics

Windows

Note that for Windows we provide also executable, see below. However, to install IOCBIO Kinetics software using automatic installation script make sure that you have Python installed. More information about installing Python in Windows see Python for Beginners. In addition, install Microsoft Visual C++ Redistributable for Visual Studio 2015, 2017 and 2019. Respective installer can be found here.

When Python is installed open PowerShell and make first sure that Get-ExecutionPolicy is not Restricted. We suggest using Bypass to bypass the policy to get things installed or AllSigned for quite a bit more security. First, run Get-ExecutionPolicy in PowerShell. In case, it returns Restricted, then run Set-ExecutionPolicy AllSigned or Set-ExecutionPolicy Bypass -Scope Process. When this is all set you can install the program by running following command:

Set-ExecutionPolicy Bypass -Scope Process -Force; [System.Net.ServicePointManager]::SecurityProtocol = [System.Net.ServicePointManager]::SecurityProtocol -bor 3072; iex ((New-Object System.Net.WebClient).DownloadString('https://gitlab.com/iocbio/kinetics/-/raw/master/install.ps1'))

pip

To be able to install PySide6 using pip, you have to use python3.5 or higher. If not available in the system, you can replace pip3 command below with python3 -m pip.

To install published version, run

pip3 install --user iocbio.kinetics

This will install all dependencies and it is expected to add a command iocbio-kinetics into your PATH. If the command is missing after installation, check whether the default location of pip3 installation is in your path. For Linux, it should be ~/.local/bin.

To install, use the Git repository directly, for HTTPS users:

pip3 install --user git+https://gitlab.com/iocbio/kinetics

and for SSH users:

python3 -m pip install --user git+ssh://git@gitlab.com/iocbio/kinetics.git

For development, use

pip3 install --user -e .

in the source directory. To install the current version from the source, use

pip3 install --user .

Note that --user is recommended to avoid messing up the system packages.

For upgrade, add --upgrade after install keyword. For example,

pip3 install --upgrade --user git+https://gitlab.com/iocbio/kinetics

or

python3 -m pip install --upgrade --user git+ssh://git@gitlab.com/iocbio/kinetics.git

pip with virtual environment

Sometimes packages for different applications can cause incompatibilities. To avoid it, you could use virtual environment for the software installation. To create virtual python environment, run

python -m venv iocbio-kinetics

This will create folder iocbio-kinetics and install scripts, such as pip, into it. To use the environment, call pip from that folder and install iocbio-kinetics into it

iocbio-kinetics/bin/pip install iocbio.kinetics

and run by

iocbio-kinetics/bin/iocbio-kinetics

Windows ZIP binary

Starting from 1.1.1 release, MS Windows executable is provided in the form of ZIP file. This allows to install and use the program quickly as all the required packages are included in the provided ZIP.

To install, download the ZIP package from the link provided in the corresponding release notes. Unpack the ZIP file which would result in folder Kinetics. You could place this folder as you see fit on your PC. To start IOCBIO Kinetics, enter the folder and start kinetics.bat by double clicking on it.

On the first start, after connecting to the database, you would need to enter "Settings". If you use your own modules, the path to them will have to be specified as well.

Use with R

If iocbio-banova is used, some additional packges are needed. Install R and the following packages in R:

install.packages(c("tidyverse", "BayesFactor", "formula.tools", "ggplot2"))

In addition, you will need to install rpy2 Python package by using pip.