For some projects we use 2-spaces indentation and for others 4-spaces. I know how to change the indentation size in PyDev settings, but I don't know how to set it on a per-project basis.
So my questions are:
You can go to the preferences (PyDev > Editor > Tabs), configure the tab-length to the value you want and use the
Save to ...>
Project settings ...` button to save that configuration to a project (see screenshot below).
It should create a file under project/.settings/org.python.pydev.yaml
with the proper contents (which you should commit to your vcs so that other users will have the setting correct too).