@jsmnbom Alright I've made the changes you requested and fixed the 4 pytest failures and flake8 error. Two points to note though:

I am not sure if i named the arguments correctly (maybe job needs to be changed to something else?), so let me know what should be changed.
I didn't include context=context on handler.handle_update because it failed one of the tests. I have included the log below:

_____________________________________________________________________ TestConversationHandler.test_conversation_handler_timeout_state ______________________________________________________________________
self = <tests.test_conversationhandler.TestConversationHandler object at 0x10b635048>, dp = <telegram.ext.dispatcher.Dispatcher object at 0x10b5ed7b8>, bot = <telegram.bot.Bot object at 0x10afa4f98>
user1 = <telegram.user.User object at 0x10b5f0320>
    def test_conversation_handler_timeout_state(self, dp, bot, user1):
        states = self.states
        states.update({ConversationHandler.TIMEOUT: [
            CommandHandler('brew', self.passout),
            MessageHandler(~Filters.regex('oding'), self.passout2)
        ]})
        handler = ConversationHandler(entry_points=self.entry_points, states=states,
                                      fallbacks=self.fallbacks, conversation_timeout=0.5)
        dp.add_handler(handler)
        # CommandHandler timeout
        message = Message(0, user1, None, self.group, text='/start',
                          entities=[MessageEntity(type=MessageEntity.BOT_COMMAND, offset=0,
                                                  length=len('/start'))],
                          bot=bot)
        dp.process_update(Update(update_id=0, message=message))
        message.text = '/brew'
        message.entities[0].length = len('/brew')
        dp.process_update(Update(update_id=0, message=message))
        sleep(0.5)
        dp.job_queue.tick()
>       assert handler.conversations.get((self.group.id, user1.id)) is None
E       assert 1 is None
E        +  where 1 = <built-in method get of dict object at 0x10b67f4c8>((0, 123))
E        +    where <built-in method get of dict object at 0x10b67f4c8> = {(0, 123): 1}.get
E        +      where {(0, 123): 1} = <telegram.ext.conversationhandler.ConversationHandler object at 0x10b635b38>.conversations
tests/test_conversationhandler.py:531: AssertionError
-------------------------------------------------------------------------------------------- Captured log call ---------------------------------------------------------------------------------------------
jobqueue.py                264 ERROR    An uncaught error was raised while executing job _trigger_timeout
Traceback (most recent call last):
  File ".../python-telegram-bot/telegram/ext/jobqueue.py", line 260, in tick
    job.run(self._dispatcher)
  File ".../python-telegram-bot/telegram/ext/jobqueue.py", line 390, in run
    self.callback(dispatcher.bot, self)
  File ".../python-telegram-bot/telegram/ext/conversationhandler.py", line 368, in _trigger_timeout
    handler.handle_update(context.update, context.dispatcher, check, context=context)
  File ".../python-telegram-bot/telegram/ext/handler.py", line 117, in handle_update
    return self.callback(update, context)
  File ".../python-telegram-bot/tests/test_conversationhandler.py", line 100, in passout
    assert update.message.text == '/brew'
AttributeError: '_ConversationTimeoutContext' object has no attribute 'message'