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As with flashing there are several ways to upload code from your computer to the device.

ESPlorer

The essential multiplatforms tools for any ESP8266 developer from luatool author’s, including Lua for NodeMCU and MicroPython. Also, all AT commands are supported. Requires Java (Standard Edition - SE ver 7 and above) installed.

Source: https://github.com/4refr0nt/ESPlorer

Supported platforms: OS X, Linux, Windows, anything that runs Java

nodemcu-uploader.py

A simple tool for uploading files to the filesystem of an ESP8266 running NodeMCU as well as some other useful commands.

Source: https://github.com/kmpm/nodemcu-uploader

Supported platforms: OS X, Linux, Windows, anything that runs Python

NodeMCU Studio

THIS TOOL IS IN REALLY REALLY REALLY REALLY EARLY STAGE!!!!!!!!!!!!!!!!!!!!!!!!!!!

Source: https://github.com/nodemcu/nodemcu-studio-csharp

Supported platforms: Windows

luatool

Allow easy uploading of any Lua-based script into the ESP8266 flash memory with NodeMcu firmware

Source: https://github.com/4refr0nt/luatool