So that test case is hard for me to follow since I don't know what a .srctree file is and the file seems to have some magical comments in it.

If my assumptions are correct you are generating a C file that does a relative import in the extension module's init function? Has that actually worked in the past? The error you are seeing suggests that the module is not being inserted into sys.modules before executing the body which I have no control over since that's the purview of imp.load_dynamic(). If you skip the relative imports does the import work otherwise?