Closed bgyori closed 2 years ago
I suspect the issue is with the pybel>=0.15.0,<0.16.0
dependency which in turn pulls in pyobo
and bioregistry
. However, in itself, pip install pybel
works in a clean virtualenv.
Do you think making a new release of PyBEL with no version constraint on the bioregistry would solve this?
I don't think that there's anything particularly wrong with this version pin and this might be a bug in pip's resolver, though
update: I looked into this then made a new release of PyBEL (v0.15.5) that did the following:
pyobo
and protmapper
into extras, since these aren't part of the main functionality and not anything that INDRA uses. It turns out that pyobo
also has a bioregistry version pin, and maybe that's what got pip upset (though they shouldn't have actually conflicted)Looks like that worked!
Recent versions of pip attempt to resolve dependency conflicts by backtracking in version history to find versions of dependencies that are compatible. It appears a simple
pip install indra
is working fine but when trying to dopip install indra[all]
to install all extra dependencies, we get into a seemingly endless backtracking situation like:This is currently causing Github Actions runs to fail but I could also reproduce it locally in a clean virtualenv. Though the behavior is slightly different with pip 21.x vs 22.x, both end up endlessly backtracking.