new CI

docs/contributing.rst

@@ -146,6 +146,7 @@ MultiscaleRun relies on ``setuptools-scm`` utility to infer the Python package v
 
   * ``multiscale_run/data/config/rat_sscxS1HL_V6/simulation_config.json``
   * ``multiscale_run/data/config/rat_sscxS1HL_V10/simulation_config.json``
+  * ``multiscale_run/data/config/tiny_CI/simulation_config.json``
 
 2. Ensure the Sphinx documentation is up-to-date. The fastest way is to check the artifacts of the ``docs`` stage in the CI.
 3. Ensure the *Releases Notes* section is completed for this version.

docs/simulation_config.rst

@@ -51,6 +51,7 @@ Preprocessor
 
   - **filter_neuron**: Boolean. Determines if the neurons connected to astrocytes must be filtered out when generating the mesh.
   - **neuron_population_name**: String. Name of the neuron population to use. Typically: "All".
+  - **astrocyte_population_name**: String. Name of the astrocyte population to use. Typically: "astrocytes".
 
 Connections among simulators
 ============================

multiscale_run/cli.py

@@ -674,7 +674,7 @@ def main(**kwargs):
         try:
             callback(**args)
         except Exception as e:
-            LOGGER.error(str(e))
+            LOGGER.error(str(e), exc_info=True)
             if size() > 1:
                 comm().Abort(errorcode=1)
             else:

multiscale_run/config.py

@@ -66,6 +66,14 @@ def json(self):
             time="10:00:00",
         ),
     ),
+    "tiny_CI": NamedCircuit(
+        path=CONFIG_DIR / "tiny_CI",
+        sbatch_parameters=dict(
+            job_name="msr_tiny_CI",
+            nodes=1,
+            time="01:00:00",
+        ),
+    ),
     "rat_sscxS1HL_V10_CI": NamedCircuit(
         path=CONFIG_DIR / "rat_sscxS1HL_V10",
         sbatch_parameters=dict(
@@ -83,7 +91,7 @@ def json(self):
     ),
 }
 
-DEFAULT_CIRCUIT = "rat_sscxS1HL_V10_CI"
+DEFAULT_CIRCUIT = "tiny_CI"
 
 
 class MsrConfigException(Exception):

multiscale_run/connection_manager.py

@@ -473,7 +473,7 @@ def remove_gids(self, failed_cells: list[int]):
         ndam_m = self.managers["neurodamus"]
         metab_m = self.managers.get("metabolism", None)
 
-        gids = ndam_m.gids
+        gids = ndam_m.gids()
         failed_gids = {
             gids[igid]: e for igid, e in enumerate(failed_cells) if e is not None
         }

multiscale_run/data/config/msr.schema.json

@@ -106,7 +106,11 @@
             "neuron_population_name": {
               "description": "Name of the neuron population to use. Typically: \"All\".",
               "type": "string"
-            }
+            },
+            "astrocyte_population_name": {
+                "description": "Name of the astrocyte population to use. Typically: \"astrocytes\".",
+                "type": "string"
+              }
           },
           "required": [
             "filter_neuron",

multiscale_run/data/config/rat_sscxS1HL_V10/simulation_config.json

@@ -19,7 +19,8 @@
             },
             "node_sets": {
                 "filter_neuron": false,
-                "neuron_population_name": "All"
+                "neuron_population_name": "All",
+                "astrocyte_population_name": "astrocytes"
             }
         },
         "connections": {

multiscale_run/data/config/rat_sscxS1HL_V6/simulation_config.json

@@ -19,7 +19,8 @@
             },
             "node_sets": {
                 "filter_neuron": false,
-                "neuron_population_name": "All"
+                "neuron_population_name": "All",
+                "astrocyte_population_name": "astrocytes"
             }
         },
         "connections": {

multiscale_run/data/config/tiny_CI/circuit_config.json

@@ -0,0 +1,103 @@
+{
+  "version": 2,
+  "manifest": {
+    "$BASE_DIR": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/build"
+  },
+  "networks": {
+    "nodes": [
+      {
+        "nodes_file": "$BASE_DIR/sonata/networks/nodes/neocortex_neurons/nodes.h5",
+        "populations": {
+          "neocortex_neurons": {
+            "type": "biophysical",
+            "biophysical_neuron_models_dir": "$BASE_DIR/../emodels/hoc",
+            "spatial_segment_index_dir": "$BASE_DIR/sonata/networks/nodes/neocortex_neurons/spatial_segment_index",
+            "provenance": {
+              "bioname_dir": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/bioname"
+            },
+            "alternate_morphologies": {
+              "h5v1": "/gpfs/bbp.cscs.ch/project/proj66/entities/morphologies/2018.02.16/h5v1",
+              "neurolucida-asc": "/gpfs/bbp.cscs.ch/project/proj66/entities/morphologies/2018.02.16/ascii"
+            }
+          }
+        }
+      },
+      {
+        "nodes_file": "$BASE_DIR/sonata/networks/nodes/astrocytes/nodes.h5",
+        "populations": {
+          "astrocytes": {
+            "type": "astrocyte",
+            "alternate_morphologies": {
+              "h5v1": "$BASE_DIR/morphologies/astrocytes/h5"
+            },
+            "microdomains_file": "$BASE_DIR/sonata/networks/nodes/astrocytes/microdomains.h5",
+            "provenance": {
+              "bioname_dir": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/bioname"
+            }
+          }
+        }
+      },
+      {
+        "nodes_file": "$BASE_DIR/sonata/networks/nodes/vasculature/nodes.h5",
+        "populations": {
+          "vasculature": {
+            "type": "vasculature",
+            "vasculature_file": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/atlas/vasculature.h5",
+            "vasculature_mesh": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/atlas/vasculature.obj",
+            "provenance": {
+              "bioname_dir": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/bioname"
+            }
+          }
+        }
+      }
+    ],
+    "edges": [
+      {
+        "edges_file": "$BASE_DIR/sonata/networks/edges/functional/neocortex_neurons__chemical_synapse/edges.h5",
+        "populations": {
+          "neocortex_neurons__chemical_synapse": {
+            "type": "chemical",
+            "provenance": {
+              "bioname_dir": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/bioname"
+            },
+            "spatial_synapse_index_dir": "$BASE_DIR/sonata/networks/edges/functional/neocortex_neurons__chemical_synapse/spatial_synapse_index"
+          }
+        }
+      },
+      {
+        "edges_file": "$BASE_DIR/sonata/networks/edges/neuroglial/edges.h5",
+        "populations": {
+          "neuroglial": {
+            "type": "synapse_astrocyte",
+            "provenance": {
+              "bioname_dir": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/bioname"
+            }
+          }
+        }
+      },
+      {
+        "edges_file": "$BASE_DIR/sonata/networks/edges/glialglial/edges.h5",
+        "populations": {
+          "glialglial": {
+            "type": "glialglial",
+            "provenance": {
+              "bioname_dir": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/bioname"
+            }
+          }
+        }
+      },
+      {
+        "edges_file": "$BASE_DIR/sonata/networks/edges/gliovascular/edges.h5",
+        "populations": {
+          "gliovascular": {
+            "type": "endfoot",
+            "endfeet_meshes_file": "$BASE_DIR/sonata/networks/edges/gliovascular/endfeet_meshes.h5",
+            "provenance": {
+              "bioname_dir": "/gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/tiny_circuit/bioname"
+            }
+          }
+        }
+      }
+    ]
+  }
+}

multiscale_run/data/config/tiny_CI/node_sets.json

@@ -0,0 +1,59 @@
+{
+  "All": [
+        "Neurons",
+        "Astrocytes"
+  ],
+  "Neurons": {
+    "population": "neocortex_neurons"
+  },
+  "Astrocytes": {
+    "population": "astrocytes"
+  },
+  "Excitatory": {
+    "synapse_class": "EXC"
+  },
+  "Inhibitory": {
+    "synapse_class": "INH"
+  },
+  "L23_MC": {
+    "mtype": "L23_MC"
+  },
+  "L5_TPC:A": {
+    "mtype": "L5_TPC:A"
+  },
+  "bAC": {
+    "etype": "bAC"
+  },
+  "bNAC": {
+    "etype": "bNAC"
+  },
+  "cADpyr": {
+    "etype": "cADpyr"
+  },
+  "L3": {
+    "region": "L3"
+  },
+  "L5": {
+    "region": "L5"
+  },
+  "L3_MC": {
+    "mtype": "L23_MC",
+    "region": {
+      "$regex": ".*3"
+    }
+  },
+  "L5_CUSTOM": {
+    "layer": "5"
+  },
+  "L5_TPC": {
+    "mtype": [
+      "L5_TPC:A"
+    ]
+  },
+  "left": {
+    "mtype": "L5_TPC:A"
+  },
+  "right": {
+    "mtype": "L23_MC"
+  }
+}