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navis-org / navis

Python library for analysis of neuroanatomical data.
https://navis.readthedocs.io
GNU General Public License v3.0
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igraph usage #139

Open clbarnes opened 4 months ago

clbarnes commented 4 months ago

As igraph is now a non-optional dependency, would it be possible to remove a lot of the infrastructure involved in switching it on and off?

At present, we run a "no-igraph" CI job but it actually does use igraph, so it's not testing anything. Case in point: using scipy's sparse array for geodesic distance calculation is currently broken, but not tested in navis, so it just breaks in pymaid (which switches off igraph in a different way).

schlegelp commented 4 months ago

I fixed the issue in geodesic_matrix with a5d4b72b439b0df6eb75e865167963287e15ad23 but your point is still well taken.

We could probably just rip out the alternative networkx-based implementations that exist in some of the functions and nobody would notice. I'm trying to find a reason to keep them but the only thing I can come up with is a future regression in igraph (or an improvement in networkx) that would cause us to favour a networkx-based implementation over igraph. Probably not a strong argument against dropping the code that's currently effectively dead.

schlegelp commented 4 months ago

Oh I guess you mentioned yourself that we could test that results from igraph- and networkx-based implementations have the same result?