No bike gets it spark from the battery. The spark is from a voltage dramatically higher than any lead acid battery can produce on its own. Same goes for getting spark from alternator. Now a magneto is different. That can produce the power needed to start a mototcycle without a battery installed. It uses permanent magnets to help generate the power.
For your Yamaha, you have already stated that you know the bike starts a lot easier when the battery is fully charged. Why not just charge the battery and see if perhaps it does indeed start easier this way. For a CDI ignition system, it requires power from an external source, like a battery, for it to work. The battery is not suppling the spark, it is suppling the power to the ignition system, so it can provide the spark.
So, as others have suggesting, charge the battery, ensure the carb fuel bowl has fresh fuel in it, set the choke to the suggested setting for a cold engine, make sure the kill switch is not in the off position, make sure the bike is in neutral, pull the clutch in if your manual says to do that, and kick away.
This is not rocket science, it is simply starting a motorcycle, even girls can do it.