If you already have Arduino IDE and Python on your Windows system then you probably already have ESPTool.py as well. It's probably located at
C:\Users\Ty\AppData\Local\Arduino15\packages\esp8266\hardware\esp8266\2.5.2\tools\esptool
(substitute your username for Ty)
You can then run it from the command line using the command shown in the readme. However, for Windows, you have to change the -cp /dev/tty$1 to whatever port Windows assigned to your WeMos (see Device Manager -> Ports)
The other, probably easier option is to get a Windows build of nodemcu-pyflasher from
THIS REPO
. It is a stand-alone Windows .exe with a GUI that's pretty self explanatory. I have not used it extensively, being more of a command line guy, but I have tried it a few times and it seems to work fine. It does not require installation - just download the .exe and run it - and it has no dependencies.