Synapse parameterization task

[chr-pok]

Implement of an obi-one task which runs a physiological parameterization of an anatomical synaptome. It uses a synaptome (with or without synaptic physiology) from entitycore as an input and generates a (re-)parameterized synaptome as an output which will be registered as a new entity in entitycore.

Implementation details:

• Added a random seed for reproducibility
• Added an explicit overwrite option for re-parameterization
• Added explicit node property by which pathways are defined
• Added entity cache option: If the staged synaptome already exists in the cache, it will be copied to the output folder. Otherwise, it will be directly staged in the output folder and modified in-place.
• Refactored code into commonly used helper functions, to be shared between EM synapse mapping and parameterization tasks
• Changed compression to tarfile for consistency with what we use with all other circuits
• Added a derivation link of type “circuit_rewiring” from the input to the parameterized output synaptome; perhaps we would need a new derivation type for that?

Related issue: #437

[chr-pok]

Hi @james-isbister and @MWolfR! This is my initial implementation proposal, as a basis for further iterations/discussions.

[chr-pok]

@MWolfR, I noticed that the input synaptomes (produced by the EM synapse mapping task) are missing a node_sets.json file but which is referenced in the circuit_config.json. It would be good to add that file (even if empty) since the missing file breaks certain bluepysnap operations.

[james-isbister]

I think there might be some different ways we can specify these different dictionaries using Blocks. But maybe easier if we discuss over a call or in person