Description
As reported downstream in PyImageJ, scyjava sets the m2_repo to ~/.m2/repository by default. Although you can override it using scyjava.config.set_m2_repo, the upstream jgo library has a function jgo.m2_path which does as follows:
def m2_path():
return os.getenv("M2_REPO", (pathlib.Path.home() / ".m2").absolute())In other words: it looks also at the M2_REPO environment variable, before falling back to ~/.m2.
This behavior in jgo is actually wrong because M2_REPO is supposed to point to the actual local Maven repository cache directory e.g. ~/.m2/repository, not the parent ~/.m2. So a fix is needed in jgo; see also scijava/jgo#99 which covers essentially the same issue for M2_HOME. Probably the m2_path function should be deprecated in favor of two functions m2_home and m2_repo instead.
And then what scyjava should do is ask jgo—once jgo yields the correct answer—what its default should be, so that it matches.