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Installation guide

  1. Install Anaconda or Miniconda

    Anaconda is the standard package manager for Python in the scientific community. It comes with a GUI for user-friendly package installation and management. However, here we describe its use through the terminal. Miniconda is a lightweight implementation of Anaconda without the GUI.

  2. Open a terminal

    Roughly speaking, a terminal is a text-based way to run instructions. On Windows, use the Anaconda prompt, you can find it by searching for it. On macOS or Linux you can use the default Terminal app.

  3. Clone the source code with the following command:

    git clone https://github.com/ElpadoCan/ChromRings.git

    Important

    On Windows, if you get the error ERROR: Cannot find the command 'git' you need to install git first. Close the terminal and install it from here. After installation, you can restart from here, but remember to activate the acdc environment first with the command conda activate acdc.

  4. Navigate to the ChromRings folder with the following command:

    cd ChromRings

    The command cd stands for "change directory" and it allows you to move between directories in the terminal.

  5. Update conda with the following command:

    conda update conda

    This will update all packages that are part of conda.

  6. Create a virtual environment with the following command:

    conda create -n acdc python=3.10

    This will create a virtual environment, which is an isolated folder where the required libraries will be installed. The virtual environment is called acdc in this case.

  7. Activate the virtual environment with the following command:

    conda activate acdc

    This will activate the environment and the terminal will know where to install packages. If the activation of the environment was successful, this should be indicated to the left of the active path (you should see (acdc) before the path).

    Important

    Before moving to the next steps make sure that you always activate the acdc environment. If you close the terminal and reopen it, always run the command conda activate acdc before installing any package. To know whether the right environment is active, the line on the terminal where you type commands should start with the text (acdc).

  8. Update pip with the following command:

    python -m pip install --upgrade pip

    While we could use conda to install packages, Cell-ACDC is not available on conda yet, hence we will use pip. Pip the default package manager for Python. Here we are updating pip itself.

  9. Install ChromRings with the following command:

    pip install -e "."

    The . at the end of the command means that you want to install from the current folder in the term