TL;DR: If you want tf.cond() to perform a side effect (like an assignment) in one of the branches, you must create the op that performs the side effect inside the function that you pass to tf.cond().
The behavior of tf.cond() is a little unintuitive. Because execution in a TensorFlow graph flows forward through the graph, all operations that you refer to in either branch must execute before the conditional is evaluated. This means that both the true and the false branches receive a control dependency on the tf.assign() op, and so y always gets set to 2, even if pred is False.
The solution is to create the tf.assign() op inside the function that defines the true branch. For example, you could structure your code as follows:
pred = tf.placeholder(tf.bool, shape=[])
x = tf.Variable([1])
def update_x_2():
with tf.control_dependencies([tf.assign(x, [2])]):
return tf.identity(x)
y = tf.cond(pred, update_x_2, lambda: tf.identity(x))
with tf.Session() as session:
session.run(tf.initialize_all_variables())
print(y.eval(feed_dict={pred: False})) # ==> [1]
print(y.eval(feed_dict={pred: True})) # ==> [2]