José Manuel Domínguez

Can the problem be fixed adjusting [setup.py](https://github.com/deeptools/HiCExplorer/blob/67a4f378f3775be24b6829779d3058530b871b8f/setup.py#L112)? In other words, is there a version of `cooler` with which all "sub-tools" work?

I am in fact writing because of the bug report we have received at usegalaxy.eu related to this issue. According to the README, this tool is supposed to work with...

The transitive_hull method won't work here because it is meant to be applied on an already instantiated OntologyEntity. There is however a more primitive method `Graph.transitiveClosure` from rdflib that we...

It looks some kind of evolved version of our YAML. If it's a superset of what our YAML can do, then maybe yes, we should support it. It's a benefit...

I am labelling this also as breaking change as we might want to introduce a new API or do changes to the wrapper API for this.

Related #651.

I started to work on this in the linked pull request, but later I realized that it is only possible to solve this issue in a simple way when the...

> I think it might relate to [this](https://stackoverflow.com/questions/63436496/is-it-possible-to-have-python-ides-offer-autocompletion-for-dynamically-generate)? Exactly, this person wants the same functionality as us.

This should be solved now with [`test_installation.py`](https://github.com/simphony/osp-core/blob/master/tests/test_installation.py), right?

> Does this only test the installation of `city`, or also all the other [included ontologies](https://simphony.readthedocs.io/en/latest/ontologies_included.html#included-ontologies)? > > My point was that if we include some popular ontologies for easier...