Specified Networkx Version, Fixed Parallel Bug

LinkageIO / Camoco

Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes.

MIT License

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Specified Networkx Version, Fixed Parallel Bug #73

Closed monprin closed 6 years ago

monprin commented 6 years ago

When networkx upgraded to 2.0, it broke something in odo, but their conda recipe has not been updated to reflect this change or their software has not been properly fixed. They are aware of this problem: https://github.com/blaze/odo/issues/579 .

Though we may want to consider assessing alternatives to Blaze and Odo given that Anaconda seems to be less invested in them lately, but I have not seen any official announcement to this effect, and the Repos seem to have awaken over the last couple of days. So who knows. This takes care ofthe problem for the time being.

coveralls commented 6 years ago

Coverage decreased (-0.01%) to 39.336% when pulling 27017ccda27f0448b89ff31de5a010b96e7ec61d on monprin:master into 3adc6203254e417965c1add532be95c1e9edd4c7 on schae234:master.

schae234 commented 6 years ago

What are we currently using blaze and odo for? The out of core stuff?

monprin commented 6 years ago

It is used in COB.py for easier managing of the bcolz data structure. It provides nice ways to access specific columns and what not, a lot like pandas, except for out of memory stuff.

Alot of this stuff can probably be done with just the bcolz functions, but I will have to look into it more. It is a really cool tool, but I am nervous about pace of development.

coveralls commented 6 years ago

Coverage increased (+0.1%) to 39.489% when pulling b547fa06b27fa3eae2441e080c6fc04bfc0b005b on monprin:master into 3adc6203254e417965c1add532be95c1e9edd4c7 on schae234:master.