When content is in file.py from branch2 that is no longer applies to branch1, it requires picking some changes and leaving others. For full control do an interactive merge using the --patch switch:
$ git checkout --patch branch2 file.py
The interactive mode section in the man page for git-add(1) explains the keys that are to be used:
y - stage this hunk
n - do not stage this hunk
q - quit; do not stage this hunk nor any of the remaining ones
a - stage this hunk and all later hunks in the file
d - do not stage this hunk nor any of the later hunks in the file
g - select a hunk to go to
/ - search for a hunk matching the given regex
j - leave this hunk undecided, see next undecided hunk
J - leave this hunk undecided, see next hunk
k - leave this hunk undecided, see previous undecided hunk
K - leave this hunk undecided, see previous hunk
s - split the current hunk into smaller hunks
e - manually edit the current hunk
? - print help
The split command is particularly useful.