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Replace BlueConfig with SONATA config in ngv test
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## Context
The current ngv unit test uses an old BlueConfig file which needs to be updated to the latest SONATA config file.

## Scope
For the ngv unit test, replace BlueConfig with the latest Sonata simulation config file used by the multiscale run CI (https://bbpgitlab.epfl.ch/molsys/multiscale_run/-/blob/main/simulation_config.json)

## Testing

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or files) are good
* [ ] Unit/Scientific test added 
* [ ] Updated Readme, in-code, developer documentation
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WeinaJi authored and ferdonline committed Jul 12, 2023
1 parent bf3e0cf commit 386445f
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Showing 7 changed files with 257 additions and 265 deletions.
162 changes: 0 additions & 162 deletions tests/simulations/ngv/BlueConfig

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71 changes: 71 additions & 0 deletions tests/simulations/ngv/circuit_config.json
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{
"version": 1,
"manifest": {
"$BASE_DIR": "/gpfs/bbp.cscs.ch/project/proj12/jenkins/subcellular/blueconfigs_test/simulation-sonataconf"
},
"node_sets_file": "node_sets.json",
"networks": {
"nodes": [
{
"nodes_file": "$BASE_DIR/base_circuit/nodes.h5",
"populations": {
"All": {
"type": "biophysical",
"biophysical_neuron_models_dir": "$BASE_DIR/base_circuit/emodels_atp_scan/emodels_atp_1p4",
"alternate_morphologies": {
"neurolucida-asc": "$BASE_DIR/base_circuit/morphologies/fixed_ais_L23PC_20201210/ascii"
}
}
}
},
{
"nodes_file": "$BASE_DIR/astrocytes/nodes.h5",
"populations": {
"astrocytes": {
"type": "astrocyte",
"morphologies_dir": "$BASE_DIR/astrocytes/morphologies/astrocytes/h5",
"biophysical_neuron_models_dir": "$BASE_DIR/emodels",
"microdomains_file": "PLACEHOLDER"
}
}
},
{
"nodes_file": "$BASE_DIR/vasculature/nodes.h5",
"populations": {
"vasculature": {
"type": "vasculature",
"vasculature_file": "PLACEHOLDER",
"vasculature_mesh": "PLACEHOLDER"
}
}
}
],
"edges": [
{
"edges_file": "$BASE_DIR/base_circuit/edges.h5",
"populations": {
"default": {
"type": "chemical"
}
}
},
{
"edges_file": "$BASE_DIR/astrocytes/edges.h5",
"populations": {
"neuroglial": {
"type": "synapse_astrocyte"
}
}
},
{
"edges_file": "$BASE_DIR/vasculature/edges.h5",
"populations": {
"gliovascular": {
"type": "endfoot",
"endfeet_meshes_file" : "PLACEHOLDER"
}
}
}
]
}
}
108 changes: 108 additions & 0 deletions tests/simulations/ngv/node_sets.json
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{
"testNGVSSCX_AstroMini": [
"testNGVSSCX",
"AstroMini"
],
"testNGVSSCX": {
"population": "All",
"node_id": [
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},
"AstroMini": {
"population": "astrocytes",
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]
},
"src_cells": {
"population": "All",
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]
}
}
1 change: 0 additions & 1 deletion tests/simulations/ngv/sim_conf/populations_offset.dat

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