Installation (Linux and Mac OS)

LIFEsim is available for installation from Github. It is compatible with Python 3.8.

Hint

Installation on Mac OS

We recommend the usage of a package manager for mac (e.g. Miniconda). Follow the installation instruction given by the respective package manager, making sure that you use the correct version of python (3.8).

Open a terminal window and activate conda by running

$ conda activate

Virtual Environment

It is highly recommended to install LIFEsim in a virtual environment. This ensures installed packages and changes made do not affect other projects on a system. The package dependencies of LIFEsim are best managed with a package manager like pip.

As a first step, virtualenv is installed with pip

$ pip install virtualenv

Then a virtual environment in the folder new_folder is created in the current directory

$ virtualenv -p python3.8 new_folder

Hint

You might need to deactivate the conda base

$ conda deactivate

To activate and deactivate your new virtual environment use the following statement respectively

$ source path_to_new_folder/new_folder/bin/activate

Check that you are using the correct python version.

$ python --version
Python 3.8.X

$ deactivate

Download from Github

Navigate to the directory in which you desire to place the LIFEsim repository. Then clone the repository from Github by executing

$ git clone https://github.com/fdannert/LIFEsim.git

Hint

If git is not installed on your system run

$ sudo apt install git

The dependencies required by LIFEsim can be installed with

$ pip install -r LIFEsim/requirements.txt

To upgrade already installed dependencies to LIFEsim requirements run

$ pip install --upgrade -r LIFEsim/requirements.txt

Important

LIFEsim need a modified version of the package SpectRes to run. Please install it via the following procedure.

First, make sure that you are in the directory where you want to install SpectRes. Then run

$ git clone https://github.com/fdannert/SpectRes.git

The last step is point the Python install of your virtual environment to LIFEsim and SpectRes. Please do so by running

$ echo "export PYTHONPATH='$PYTHONPATH:/path_to_LIFEsim/LIFEsim/:/path_to_SpectRes/SpectRes/'" >> path_to_new_folder/new_folder/bin/activate

Testing the Installation

To test the installation, open a new console and activate the virtual environment as above. Then open Python and import LIFEsim with

$ python

>>> import lifesim

If the import statement executes, the installation has been successful. As an extra test run

>>> lifesim.util.constants.c
299792000.0

This should return the speed of light in [m s \(^{-1}\) ].

Hint

If the import lifesim command fails, the reason is likely that the the PYTHONPATH is not set correctly. To check for this please run in Python (started with the virtual environment active as above)

>>> import sys
>>> sys.path

If the path to LIFEsim '/path_to_LIFEsim/LIFEsim/' is not returned in the results, please open the file path_to_new_folder/new_folder/bin/activate with a text editor of your choice. Then make sure that the last line of the file reads

  export PYTHONPATH=':/path_to_LIFEsim/LIFEsim/'

The same test can be performed if SpectRes does not import.