PyCharm: The project at ... uses a non-standard layout and cannot be attached to this project

As mentioned by norok2, for Pycharm 2019.1, first open the project in a new window.

Afterward, try to attach it to the existing window.

I created a new project in PyCharm and had this problem. Following this solution, I found the new project did not have a .iml file in the new project's .idea folder. I copied and pasted the .iml from another project and just changed the .iml file name to match the project. Problem solved.

PyCharm support suggested that I comment out the ProjectModuleManager component from ~/.PyCharm2017.1/config/options/project.default.xml. After restarting PyCharm (2017.1.3) and removing any .idea/ directories from the modules I wanted to open, I no longer had this issue.