Remember, Jason, software like PyCharm might be commercial, but what distinguishes it from other editors/IDEs you mention is that it's "proprietary". That's the opposite of free and open source, which can be (and often is) quite commercial.
You can probably achieve that with the open source Gitlab (like having your own Github, although you can also pay for a hosted instance - see https://gitlab.com) which supports submitting help requests via email and has the ability to incorporate a kanban board: http://kanban.leanlabs.io/
Remember, Jason, software like PyCharm might be commercial, but what distinguishes it from other editors/IDEs you mention is that it's "proprietary". That's the opposite of free and open source, which can be (and often is) quite commercial.