In order to manage all my python paths for my project and have them available as soon as I start python interpreter, I created a project.pth in the project home directory having relative paths in it,
Actually, to be read, I need to do a site.addsitedir(my_project_home_dir) each time I start the interpreter. 
I tried setting PYTHONPATH or create a .pth in site-packages pointing to my project home directory, but project.pth is still not read automatically when I start the interpreter.
The only thing that works is to put my project.pth in site-packages, but by doing that, I have to transform my project relative paths to absolute paths.
So it there a master .pth file where I can specify my project home directory so I can have my project.pth located in that directory to be read automatically ?
Finally I found 2 ways : 
1) First, note that .pth files also accept lines beginning with 'import' and execute them. So the solution was to create project.pth inside site-packages importing a module in my project home dir that do actually the site.addsitedir()
2) Other possibility : use the environment variable PYTHONSTARTUP : it will execute any module you want at python startup. You can specify a module that do the site.addsitedir() or even directly add paths into sys.path
Is possible to add a python site directory permanently?