Sklearn SGDClassifier partial fit

I have finally found the answer. You need to shuffle the training data between each iteration, as setting shuffle=True when instantiating the model will NOT shuffle the data when using partial_fit (it only applies to fit). Note: it would have been helpful to find this information on the sklearn.linear_model.SGDClassifier page.

The amended code reads as follows:

from sklearn.linear_model import SGDClassifier
import random
clf2 = SGDClassifier(loss="log") # shuffle=True is useless here
shuffledRange = range(len(X))
n_iter = 5
for n in range(n_iter):
    random.shuffle(shuffledRange)
    shuffledX = [X[i] for i in shuffledRange]
    shuffledY = [Y[i] for i in shuffledRange]
    for batch in batches(range(len(shuffledX)), 10000):
        clf2.partial_fit(shuffledX[batch[0]:batch[-1]+1], shuffledY[batch[0]:batch[-1]+1], classes=numpy.unique(Y))