How to make an animation - ZigyTheBird/ZigysPlayerAnimatorAPI GitHub Wiki
I want to apologize about this page being so ugly, this is just a wall of resources which you would normally be expected to find yourself.
You can either use Blockbench or Blender to animate the player.
You will need the GeckoLib plugin for BlockBench in order to animate the player that way.
The base models for both Blockbench and Blender can be found here.
If you want to use blender this might help.
This Blockbench model has bones for animating the items.
Blender has the advantage of being able to bend limbs when bendy-lib is installed.
You can get help for animating the player here. (specially with blender)
This provides some information about animating in Blender.
You can get help with Blockbench here and maybe here.
Once you export your animation you have to place it at the assets/<namespace>/player_animation directory and that's about it. (With namespace being replaced with your mod ID)
Caution
THE NAME OF A BLOCKBENCH ANIMATION USED TO ACTUALLY PLAY IT IS THE ONE SET IN BLOCKBENCH NOT THE FILE NAME!