Charles Tapley Hoyt comments

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                                            Charles Tapley Hoyt

Passing a dropout value to a model through the pipeline API

After a second look, I'm leaning on the side of rejecting this. It would add more complexity for a special use case - and ultimately make the pipeline less usable...

to_bel_script() invokes a TypeError: make_knowledge_header() missing 1 required positional argument: 'name'

It should give nicer output but to write to bel script you need to set the name of the graph. I think the version as well.

to_bel_script() invokes a TypeError: make_knowledge_header() missing 1 required positional argument: 'name'

Quite strange, maybe you could try and figure out for which annotation there's a `None` as the value (that shouldn't happen...)

ImportError: cannot import name 'write_namespace'

Hi @charalamm I think this is again an artifact due to your issue on the reactome repo (https://github.com/bio2bel/reactome/issues/16) Could you please provide the installed version of pybel for me? You...

collapse_nodes does not apply to members of ListAbundance

Oof that’s a good catch, since those types of nodes store extra copies of the nodes

collapse_nodes does not apply to members of ListAbundance

I wrote unit tests for it a few days ago but no implementation yet. I'll make a draft PR, you can add an implementation if this is urgent

Add reverse of secretion syntax sugar

See: https://github.com/belbio/bep/issues/7

Unit tests for parsing without semantic validation

Initial commit: 30c108864ea078d746bae440ff41d26e73a40030 Still needs testing

Add exporter to a local MongoDB

Needs unit tests!

Troubles with loading .json files created with pybel 14.0.8

I was pretty careful to make sure old files could be loaded. However, there are many flavors of JSON (nodelink JSON, SBEL JSON, GraphDati JSON) so you have to make...