Setup part 3: CoLRev

Extend the $PATH environment variable enabling all pip packages to run correctly (using the shell / Ctrl+Alt+T):

# Add $HOME/.local/bin to the beginning of $PATH environment variable and make it persistent within ~/.bashrc
echo 'export PATH="$HOME/.local/bin:$PATH"' >> $HOME/.bashrc

# Source the adjusted $PATH environment variable into the current terminal session with source
# Or simply open a new terminal session to enable the new $PATH
source ~/.bashrc

Install the following tools mandatory for CoLRev (using the shell / Ctrl+Alt+T):

# Install git, gitk and vim
sudo apt install git
sudo apt install gitk
sudo apt install vim

# Install visual studio code as snap package
sudo snap install --classic code
# If you are using Ubuntu with WSL2, please run the command "code" afterwards
# It will add Visual Studio Code (aka VS Code Server for x64) to your Windows Start Menu with WSL2 compatibility
# if you prefer to install a .deb package, please follow the official instructions: https://code.visualstudio.com/docs/setup/linux

# install python and pip package manager
sudo apt install python3-full
sudo apt install python-is-python3
sudo apt install python3-pip

Note

In the following, we assume that the colrev directory and the test directory are located on the Desktop. If you have chosen a different location, please adjust the paths accordingly.

Clone CoLRev with the following commands (using the shell / Ctrl+Alt+T):

# Clone CoLRev on your Desktop
# Make sure you have registered your SSH key on GitHub beforehand, see "Setup part 2: Git and SSH"
mkdir -p ~/Desktop
cd ~/Desktop
git clone git@github.com:CoLRev-Environment/colrev.git

Create and activate a virtual environment (venv) in Python (using the shell / Ctrl+Alt+T):

# Create a virtual environment called "venv-colrev" and activate it (you can use any other name or create multiple virtual environments)
cd ~/Desktop
python -m venv venv-colrev
source venv-colrev/bin/activate

Note

In the following, we assume that the virtual environment “venv-colrev” is activated. (venv-colrev) should be precede the prompt. The active virtual environment can be deactivated with the command deactivate

Install CoLRev with the following commands (using the shell / Ctrl+Alt+T):

# Install CoLRev
cd ~/Desktop/colrev
pip install -e .[dev,docs]
pre-commit install

# Run the pre-commit hooks
pre-commit run --all

# Run the tests separately (optional)
pytest tests

# Build the docs locally (optional)
cd ~/Desktop/colrev/docs
make html

Test CoLRev in a demo project with the following commands (using the shell / Ctrl+Alt+T):

# Create a test directory on Desktop and change directory into ~/Desktop/test
mkdir ~/Desktop/test
cd ~/Desktop/test

# Complete run to pull the Docker images, this may be time consuming
colrev init --example

# The status operation will guide you through the whole process
colrev status

Pull the newest changes from the main repository and update CoLRev with the following commands (using the shell / Ctrl+Alt+T):

# Switch to colrev directory. Path may differ, if colrev was setup elsewhere
cd ~/Desktop/colrev

# Pull the newest changes and apply the update
git pull
pip install -e .[dev,docs]