diff --git a/docs/sphinx/source/api/export_format/NeuroML/ABCD.1.mdf.png b/docs/sphinx/source/api/export_format/NeuroML/ABCD.1.mdf.png index eca473dc5..2972c1bdd 100644 Binary files a/docs/sphinx/source/api/export_format/NeuroML/ABCD.1.mdf.png and b/docs/sphinx/source/api/export_format/NeuroML/ABCD.1.mdf.png differ diff --git a/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png b/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png index 84b763664..2e5ce54c4 100644 Binary files a/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png and b/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png differ diff --git a/docs/sphinx/source/api/export_format/NeuroML/FN.gv.png b/docs/sphinx/source/api/export_format/NeuroML/FN.gv.png index 1d86d21ed..c6d61be82 100644 Binary files a/docs/sphinx/source/api/export_format/NeuroML/FN.gv.png and b/docs/sphinx/source/api/export_format/NeuroML/FN.gv.png differ diff --git a/docs/sphinx/source/api/export_format/NeuroML/FNmulti.png b/docs/sphinx/source/api/export_format/NeuroML/FNmulti.png index 5a2681465..c4bfab28d 100644 Binary files a/docs/sphinx/source/api/export_format/NeuroML/FNmulti.png and b/docs/sphinx/source/api/export_format/NeuroML/FNmulti.png differ diff --git a/docs/sphinx/source/api/export_format/NeuroML/Izh.png b/docs/sphinx/source/api/export_format/NeuroML/Izh.png index 89225233e..88f497920 100644 Binary files a/docs/sphinx/source/api/export_format/NeuroML/Izh.png and b/docs/sphinx/source/api/export_format/NeuroML/Izh.png differ diff --git a/docs/sphinx/source/api/export_format/NeuroML/IzhikevichTest.gv.png b/docs/sphinx/source/api/export_format/NeuroML/IzhikevichTest.gv.png index 1dcf2d0e4..71a39af4a 100644 Binary files a/docs/sphinx/source/api/export_format/NeuroML/IzhikevichTest.gv.png and b/docs/sphinx/source/api/export_format/NeuroML/IzhikevichTest.gv.png differ diff --git a/examples/ACT-R/addition.json b/examples/ACT-R/addition.json index c9d69859d..1414d18d8 100644 --- a/examples/ACT-R/addition.json +++ b/examples/ACT-R/addition.json @@ -1,7 +1,7 @@ { "addition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "addition_graph": { "nodes": { diff --git a/examples/ACT-R/addition.yaml b/examples/ACT-R/addition.yaml index fba4148da..b4c2d84a7 100644 --- a/examples/ACT-R/addition.yaml +++ b/examples/ACT-R/addition.yaml @@ -1,6 +1,6 @@ addition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: addition_graph: nodes: diff --git a/examples/ACT-R/count.json b/examples/ACT-R/count.json index 4cca9a06b..5888b29f9 100644 --- a/examples/ACT-R/count.json +++ b/examples/ACT-R/count.json @@ -1,7 +1,7 @@ { "count": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "count_graph": { "nodes": { diff --git a/examples/ACT-R/count.yaml b/examples/ACT-R/count.yaml index cfda39caf..01b981055 100644 --- a/examples/ACT-R/count.yaml +++ b/examples/ACT-R/count.yaml @@ -1,6 +1,6 @@ count: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: count_graph: nodes: diff --git a/examples/MDF/ABCD.json b/examples/MDF/ABCD.json index 9a5b5c9e1..1750f4c8c 100644 --- a/examples/MDF/ABCD.json +++ b/examples/MDF/ABCD.json @@ -1,7 +1,7 @@ { "ABCD": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "abcd_example": { "nodes": { diff --git a/examples/MDF/ABCD.yaml b/examples/MDF/ABCD.yaml index 277194287..2df48661f 100644 --- a/examples/MDF/ABCD.yaml +++ b/examples/MDF/ABCD.yaml @@ -1,6 +1,6 @@ ABCD: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: abcd_example: nodes: diff --git a/examples/MDF/Arrays.json b/examples/MDF/Arrays.json index c0435c447..65f6e4d95 100644 --- a/examples/MDF/Arrays.json +++ b/examples/MDF/Arrays.json @@ -1,7 +1,7 @@ { "Arrays": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "array_example": { "nodes": { diff --git a/examples/MDF/Arrays.yaml b/examples/MDF/Arrays.yaml index bab803614..1a9094fd5 100644 --- a/examples/MDF/Arrays.yaml +++ b/examples/MDF/Arrays.yaml @@ -1,6 +1,6 @@ Arrays: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: array_example: nodes: diff --git a/examples/MDF/ParametersFunctions.json b/examples/MDF/ParametersFunctions.json index 9189428b9..36a486558 100644 --- a/examples/MDF/ParametersFunctions.json +++ b/examples/MDF/ParametersFunctions.json @@ -1,7 +1,7 @@ { "ParametersFunctions": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "params_funcs_example": { "nodes": { diff --git a/examples/MDF/ParametersFunctions.yaml b/examples/MDF/ParametersFunctions.yaml index e18744055..03538bb9f 100644 --- a/examples/MDF/ParametersFunctions.yaml +++ b/examples/MDF/ParametersFunctions.yaml @@ -1,6 +1,6 @@ ParametersFunctions: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: params_funcs_example: nodes: diff --git a/examples/MDF/RNN/IAF_net.json b/examples/MDF/RNN/IAF_net.json index a2c54994b..7dd1d7394 100644 --- a/examples/MDF/RNN/IAF_net.json +++ b/examples/MDF/RNN/IAF_net.json @@ -1,7 +1,7 @@ { "IAF_net": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "iaf_example": { "nodes": { diff --git a/examples/MDF/RNN/IAF_net.yaml b/examples/MDF/RNN/IAF_net.yaml index b7645fdfb..7a18e31cb 100644 --- a/examples/MDF/RNN/IAF_net.yaml +++ b/examples/MDF/RNN/IAF_net.yaml @@ -1,6 +1,6 @@ IAF_net: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: iaf_example: nodes: diff --git a/examples/MDF/RNN/IAF_net2.json b/examples/MDF/RNN/IAF_net2.json index d5f2d486a..1402dd637 100644 --- a/examples/MDF/RNN/IAF_net2.json +++ b/examples/MDF/RNN/IAF_net2.json @@ -1,7 +1,7 @@ { "IAF_net2": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "iaf_example": { "nodes": { diff --git a/examples/MDF/RNN/IAF_net2.yaml b/examples/MDF/RNN/IAF_net2.yaml index ce90e1201..6972a75c0 100644 --- a/examples/MDF/RNN/IAF_net2.yaml +++ b/examples/MDF/RNN/IAF_net2.yaml @@ -1,6 +1,6 @@ IAF_net2: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: iaf_example: nodes: diff --git a/examples/MDF/RNN/IAFs.json b/examples/MDF/RNN/IAFs.json index 55508ee93..b413bf84a 100644 --- a/examples/MDF/RNN/IAFs.json +++ b/examples/MDF/RNN/IAFs.json @@ -1,7 +1,7 @@ { "IAFs": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "iaf_example": { "nodes": { diff --git a/examples/MDF/RNN/IAFs.yaml b/examples/MDF/RNN/IAFs.yaml index ac8de32a1..b7deecbd3 100644 --- a/examples/MDF/RNN/IAFs.yaml +++ b/examples/MDF/RNN/IAFs.yaml @@ -1,6 +1,6 @@ IAFs: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: iaf_example: nodes: diff --git a/examples/MDF/RNN/RNNs.json b/examples/MDF/RNN/RNNs.json index cc2b35784..7198adda2 100644 --- a/examples/MDF/RNN/RNNs.json +++ b/examples/MDF/RNN/RNNs.json @@ -1,7 +1,7 @@ { "RNNs": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "rnn_example": { "nodes": { diff --git a/examples/MDF/RNN/RNNs.yaml b/examples/MDF/RNN/RNNs.yaml index 12c591c63..2f7235c6d 100644 --- a/examples/MDF/RNN/RNNs.yaml +++ b/examples/MDF/RNN/RNNs.yaml @@ -1,6 +1,6 @@ RNNs: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: rnn_example: nodes: diff --git a/examples/MDF/Simple.bson b/examples/MDF/Simple.bson index 51c202475..c24db249b 100644 Binary files a/examples/MDF/Simple.bson and b/examples/MDF/Simple.bson differ diff --git a/examples/MDF/Simple.json b/examples/MDF/Simple.json index e1f3adb3f..2ab426980 100644 --- a/examples/MDF/Simple.json +++ b/examples/MDF/Simple.json @@ -1,7 +1,7 @@ { "Simple": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "simple_example": { "nodes": { diff --git a/examples/MDF/Simple.yaml b/examples/MDF/Simple.yaml index 7dcd160ba..b212c7532 100644 --- a/examples/MDF/Simple.yaml +++ b/examples/MDF/Simple.yaml @@ -1,6 +1,6 @@ Simple: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: simple_example: nodes: diff --git a/examples/MDF/States.json b/examples/MDF/States.json index dff6cac76..4a9d18397 100644 --- a/examples/MDF/States.json +++ b/examples/MDF/States.json @@ -1,7 +1,7 @@ { "States": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "state_example": { "nodes": { diff --git a/examples/MDF/States.yaml b/examples/MDF/States.yaml index ad25fa31c..18c95af3e 100644 --- a/examples/MDF/States.yaml +++ b/examples/MDF/States.yaml @@ -1,6 +1,6 @@ States: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: state_example: nodes: diff --git a/examples/MDF/abc_conditions.json b/examples/MDF/abc_conditions.json index 608529ab2..1c69081e9 100644 --- a/examples/MDF/abc_conditions.json +++ b/examples/MDF/abc_conditions.json @@ -1,7 +1,7 @@ { "abc_conditions": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "abc_conditions_example": { "nodes": { diff --git a/examples/MDF/abc_conditions.yaml b/examples/MDF/abc_conditions.yaml index f79ed72cd..3e6a5a931 100644 --- a/examples/MDF/abc_conditions.yaml +++ b/examples/MDF/abc_conditions.yaml @@ -1,6 +1,6 @@ abc_conditions: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: abc_conditions_example: nodes: diff --git a/examples/MDF/conditions/Composite_mdf_condition.json b/examples/MDF/conditions/Composite_mdf_condition.json index 487545478..6bd4efed2 100644 --- a/examples/MDF/conditions/Composite_mdf_condition.json +++ b/examples/MDF/conditions/Composite_mdf_condition.json @@ -1,7 +1,7 @@ { "Composite_mdf_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "Composite_mdf_condition_example": { "nodes": { diff --git a/examples/MDF/conditions/Composite_mdf_condition.yaml b/examples/MDF/conditions/Composite_mdf_condition.yaml index 1196a638d..9a4878998 100644 --- a/examples/MDF/conditions/Composite_mdf_condition.yaml +++ b/examples/MDF/conditions/Composite_mdf_condition.yaml @@ -1,6 +1,6 @@ Composite_mdf_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: Composite_mdf_condition_example: nodes: diff --git a/examples/MDF/conditions/everyncalls_condition.json b/examples/MDF/conditions/everyncalls_condition.json index b19807501..f1a3ca25e 100644 --- a/examples/MDF/conditions/everyncalls_condition.json +++ b/examples/MDF/conditions/everyncalls_condition.json @@ -1,7 +1,7 @@ { "everyncalls_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "everyncalls_example": { "nodes": { diff --git a/examples/MDF/conditions/everyncalls_condition.yaml b/examples/MDF/conditions/everyncalls_condition.yaml index 3227361be..79d7cb039 100644 --- a/examples/MDF/conditions/everyncalls_condition.yaml +++ b/examples/MDF/conditions/everyncalls_condition.yaml @@ -1,6 +1,6 @@ everyncalls_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: everyncalls_example: nodes: diff --git a/examples/MDF/conditions/threshold_condition.json b/examples/MDF/conditions/threshold_condition.json index b4a3b8fa3..74f6b60a8 100644 --- a/examples/MDF/conditions/threshold_condition.json +++ b/examples/MDF/conditions/threshold_condition.json @@ -1,7 +1,7 @@ { "threshold_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "threshold_example": { "nodes": { diff --git a/examples/MDF/conditions/threshold_condition.yaml b/examples/MDF/conditions/threshold_condition.yaml index e7e49bca9..2d498c8ee 100644 --- a/examples/MDF/conditions/threshold_condition.yaml +++ b/examples/MDF/conditions/threshold_condition.yaml @@ -1,6 +1,6 @@ threshold_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: threshold_example: nodes: diff --git a/examples/MDF/conditions/timeinterval_condition.json b/examples/MDF/conditions/timeinterval_condition.json index a0c3127bc..1e788cb30 100644 --- a/examples/MDF/conditions/timeinterval_condition.json +++ b/examples/MDF/conditions/timeinterval_condition.json @@ -1,7 +1,7 @@ { "timeinterval_condition": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "timeinterval_example": { "nodes": { diff --git a/examples/MDF/conditions/timeinterval_condition.yaml b/examples/MDF/conditions/timeinterval_condition.yaml index 5a86de430..7df4abb2f 100644 --- a/examples/MDF/conditions/timeinterval_condition.yaml +++ b/examples/MDF/conditions/timeinterval_condition.yaml @@ -1,6 +1,6 @@ timeinterval_condition: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: timeinterval_example: nodes: diff --git a/examples/NeuroML/ABCD.1.mdf.png b/examples/NeuroML/ABCD.1.mdf.png index eca473dc5..2972c1bdd 100644 Binary files a/examples/NeuroML/ABCD.1.mdf.png and b/examples/NeuroML/ABCD.1.mdf.png differ diff --git a/examples/NeuroML/ABCD.json b/examples/NeuroML/ABCD.json index 745323273..ba35670b7 100644 --- a/examples/NeuroML/ABCD.json +++ b/examples/NeuroML/ABCD.json @@ -1,6 +1,6 @@ { "ABCD": { - "version": "NeuroMLlite v0.5.4", + "version": "NeuroMLlite v0.5.5", "notes": "Example of a simplified network", "parameters": { "A_initial": 0.1, diff --git a/examples/NeuroML/ABCD.mdf.json b/examples/NeuroML/ABCD.mdf.json index 5565ac5ac..fc67c977b 100644 --- a/examples/NeuroML/ABCD.mdf.json +++ b/examples/NeuroML/ABCD.mdf.json @@ -17,6 +17,21 @@ 2.0 ] }, + "spike": { + "default_initial_value": [ + 0 + ], + "conditions": { + "condition_0_on": { + "test": "OUTPUT < 0", + "value": 1 + }, + "condition_0_off": { + "test": "spike > 0", + "value": 0 + } + } + }, "V": { "value": 0 }, @@ -28,6 +43,9 @@ "INPUT": {} }, "output_ports": { + "spike": { + "value": "spike" + }, "V": { "value": "V" }, @@ -54,6 +72,21 @@ 2.0 ] }, + "spike": { + "default_initial_value": [ + 0 + ], + "conditions": { + "condition_0_on": { + "test": "OUTPUT < 0", + "value": 1 + }, + "condition_0_off": { + "test": "spike > 0", + "value": 0 + } + } + }, "V": { "value": 0 }, @@ -65,6 +98,9 @@ "INPUT": {} }, "output_ports": { + "spike": { + "value": "spike" + }, "V": { "value": "V" }, @@ -101,17 +137,35 @@ 0.0 ] }, + "spike": { + "default_initial_value": [ + 0 + ], + "conditions": { + "condition_0_on": { + "test": "OUTPUT < 0", + "value": 1 + }, + "condition_0_off": { + "test": "spike > 0", + "value": 0 + } + } + }, "V": { "value": 0 }, "OUTPUT": { - "value": "1/(1+math.exp(-1*gain*(INPUT + bias - x_0)+offset))" + "value": "1/(1+numpy.exp(-1*gain*(INPUT + bias - x_0)+offset))" } }, "input_ports": { "INPUT": {} }, "output_ports": { + "spike": { + "value": "spike" + }, "V": { "value": "V" }, @@ -148,17 +202,35 @@ 0.0 ] }, + "spike": { + "default_initial_value": [ + 0 + ], + "conditions": { + "condition_0_on": { + "test": "OUTPUT < 0", + "value": 1 + }, + "condition_0_off": { + "test": "spike > 0", + "value": 0 + } + } + }, "V": { "value": 0 }, "OUTPUT": { - "value": "scale * math.exp((rate * INPUT) + bias) + offset" + "value": "scale * numpy.exp((rate * INPUT) + bias) + offset" } }, "input_ports": { "INPUT": {} }, "output_ports": { + "spike": { + "value": "spike" + }, "V": { "value": "V" }, @@ -185,8 +257,26 @@ 0.1 ] }, + "spike": { + "default_initial_value": [ + 0 + ], + "conditions": { + "condition_0_on": { + "test": "OUTPUT < 0", + "value": 1 + }, + "condition_0_off": { + "test": "spike > 0", + "value": 0 + } + } + }, "OUTPUT": { - "time_derivative": "(rate * INPUT) / time_step_size" + "time_derivative": "(rate * INPUT) / time_step_size", + "default_initial_value": [ + 0 + ] }, "V": { "value": 0 @@ -196,6 +286,9 @@ "INPUT": {} }, "output_ports": { + "spike": { + "value": "spike" + }, "OUTPUT": { "value": "OUTPUT" }, @@ -204,42 +297,222 @@ } }, "notes": "Cell: [Cell(notes=None, id='d', parameters=None, neuroml2_source_file=None, lems_source_file='PNL.xml', neuroml2_cell=None, pynn_cell=None, arbor_cell=None, bindsnet_node=None)] is defined in PNL.xml and in Lems is: Component, id: d, type: pnlSimpleIntegratorMechanism,\n parameters: {'rate': '0.05', 'time_step_size': '0.1s'}\n parent: None\n" + }, + "proj_input_rsDL": { + "parameters": { + "weight": { + "value": [ + 1.0 + ] + }, + "SEC": { + "value": [ + 1.0 + ] + }, + "rpeer": { + "value": "peer_OUTPUT" + }, + "I": { + "value": "weight * rpeer" + } + }, + "input_ports": { + "peer_OUTPUT": {} + }, + "output_ports": { + "I": { + "value": "I" + } + }, + "notes": "Cell: [Synapse(notes=None, id='rsDL', parameters=None, neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None, pynn_receptor_type=None)] is defined in PNL.xml and in Lems is: Component, id: rsDL, type: synapseDL,\n parameters: {}\n parent: None\n" + }, + "proj0_rsDL": { + "parameters": { + "weight": { + "value": [ + 1.0 + ] + }, + "SEC": { + "value": [ + 1.0 + ] + }, + "rpeer": { + "value": "peer_OUTPUT" + }, + "I": { + "value": "weight * rpeer" + } + }, + "input_ports": { + "peer_OUTPUT": {} + }, + "output_ports": { + "I": { + "value": "I" + } + }, + "notes": "Cell: [Synapse(notes=None, id='rsDL', parameters=None, neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None, pynn_receptor_type=None)] is defined in PNL.xml and in Lems is: Component, id: rsDL, type: synapseDL,\n parameters: {}\n parent: None\n" + }, + "proj1_rsDL": { + "parameters": { + "weight": { + "value": [ + 1.0 + ] + }, + "SEC": { + "value": [ + 1.0 + ] + }, + "rpeer": { + "value": "peer_OUTPUT" + }, + "I": { + "value": "weight * rpeer" + } + }, + "input_ports": { + "peer_OUTPUT": {} + }, + "output_ports": { + "I": { + "value": "I" + } + }, + "notes": "Cell: [Synapse(notes=None, id='rsDL', parameters=None, neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None, pynn_receptor_type=None)] is defined in PNL.xml and in Lems is: Component, id: rsDL, type: synapseDL,\n parameters: {}\n parent: None\n" + }, + "proj2_rsDL": { + "parameters": { + "weight": { + "value": [ + 1.0 + ] + }, + "SEC": { + "value": [ + 1.0 + ] + }, + "rpeer": { + "value": "peer_OUTPUT" + }, + "I": { + "value": "weight * rpeer" + } + }, + "input_ports": { + "peer_OUTPUT": {} + }, + "output_ports": { + "I": { + "value": "I" + } + }, + "notes": "Cell: [Synapse(notes=None, id='rsDL', parameters=None, neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None, pynn_receptor_type=None)] is defined in PNL.xml and in Lems is: Component, id: rsDL, type: synapseDL,\n parameters: {}\n parent: None\n" + }, + "proj3_rsDL": { + "parameters": { + "weight": { + "value": [ + 1.0 + ] + }, + "SEC": { + "value": [ + 1.0 + ] + }, + "rpeer": { + "value": "peer_OUTPUT" + }, + "I": { + "value": "weight * rpeer" + } + }, + "input_ports": { + "peer_OUTPUT": {} + }, + "output_ports": { + "I": { + "value": "I" + } + }, + "notes": "Cell: [Synapse(notes=None, id='rsDL', parameters=None, neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None, pynn_receptor_type=None)] is defined in PNL.xml and in Lems is: Component, id: rsDL, type: synapseDL,\n parameters: {}\n parent: None\n" } }, "edges": { - "Edge A to B": { - "name": "Edge A to B", + "A_TO_proj_input_rsDL": { + "name": "A_TO_proj_input_rsDL", "sender_port": "OUTPUT", - "receiver_port": "INPUT", + "receiver_port": "peer_OUTPUT", "sender": "A", + "receiver": "proj_input_rsDL" + }, + "proj_input_rsDL_TO_B": { + "name": "proj_input_rsDL_TO_B", + "sender_port": "I", + "receiver_port": "INPUT", + "sender": "proj_input_rsDL", "receiver": "B" }, - "Edge A_input to A": { - "name": "Edge A_input to A", + "A_input_TO_proj0_rsDL": { + "name": "A_input_TO_proj0_rsDL", "sender_port": "OUTPUT", - "receiver_port": "INPUT", + "receiver_port": "peer_OUTPUT", "sender": "A_input", + "receiver": "proj0_rsDL" + }, + "proj0_rsDL_TO_A": { + "name": "proj0_rsDL_TO_A", + "sender_port": "I", + "receiver_port": "INPUT", + "sender": "proj0_rsDL", "receiver": "A" }, - "Edge A to C": { - "name": "Edge A to C", + "A_TO_proj1_rsDL": { + "name": "A_TO_proj1_rsDL", "sender_port": "OUTPUT", - "receiver_port": "INPUT", + "receiver_port": "peer_OUTPUT", "sender": "A", + "receiver": "proj1_rsDL" + }, + "proj1_rsDL_TO_C": { + "name": "proj1_rsDL_TO_C", + "sender_port": "I", + "receiver_port": "INPUT", + "sender": "proj1_rsDL", "receiver": "C" }, - "Edge B to D": { - "name": "Edge B to D", + "B_TO_proj2_rsDL": { + "name": "B_TO_proj2_rsDL", "sender_port": "OUTPUT", - "receiver_port": "INPUT", + "receiver_port": "peer_OUTPUT", "sender": "B", + "receiver": "proj2_rsDL" + }, + "proj2_rsDL_TO_D": { + "name": "proj2_rsDL_TO_D", + "sender_port": "I", + "receiver_port": "INPUT", + "sender": "proj2_rsDL", "receiver": "D" }, - "Edge C to D": { - "name": "Edge C to D", + "C_TO_proj3_rsDL": { + "name": "C_TO_proj3_rsDL", "sender_port": "OUTPUT", - "receiver_port": "INPUT", + "receiver_port": "peer_OUTPUT", "sender": "C", + "receiver": "proj3_rsDL" + }, + "proj3_rsDL_TO_D": { + "name": "proj3_rsDL_TO_D", + "sender_port": "I", + "receiver_port": "INPUT", + "sender": "proj3_rsDL", "receiver": "D" } } diff --git a/examples/NeuroML/ABCD.mdf.png b/examples/NeuroML/ABCD.mdf.png index 84b763664..2e5ce54c4 100644 Binary files a/examples/NeuroML/ABCD.mdf.png and b/examples/NeuroML/ABCD.mdf.png differ diff --git a/examples/NeuroML/ABCD.mdf.yaml b/examples/NeuroML/ABCD.mdf.yaml index c7a157c82..c3c214ada 100644 --- a/examples/NeuroML/ABCD.mdf.yaml +++ b/examples/NeuroML/ABCD.mdf.yaml @@ -13,6 +13,16 @@ ABCD: variable: value: - 2.0 + spike: + default_initial_value: + - 0 + conditions: + condition_0_on: + test: OUTPUT < 0 + value: 1 + condition_0_off: + test: spike > 0 + value: 0 V: value: 0 OUTPUT: @@ -20,6 +30,8 @@ ABCD: input_ports: INPUT: {} output_ports: + spike: + value: spike V: value: V OUTPUT: @@ -42,6 +54,16 @@ ABCD: intercept: value: - 2.0 + spike: + default_initial_value: + - 0 + conditions: + condition_0_on: + test: OUTPUT < 0 + value: 1 + condition_0_off: + test: spike > 0 + value: 0 V: value: 0 OUTPUT: @@ -49,6 +71,8 @@ ABCD: input_ports: INPUT: {} output_ports: + spike: + value: spike V: value: V OUTPUT: @@ -77,13 +101,25 @@ ABCD: offset: value: - 0.0 + spike: + default_initial_value: + - 0 + conditions: + condition_0_on: + test: OUTPUT < 0 + value: 1 + condition_0_off: + test: spike > 0 + value: 0 V: value: 0 OUTPUT: - value: 1/(1+math.exp(-1*gain*(INPUT + bias - x_0)+offset)) + value: 1/(1+numpy.exp(-1*gain*(INPUT + bias - x_0)+offset)) input_ports: INPUT: {} output_ports: + spike: + value: spike V: value: V OUTPUT: @@ -112,13 +148,25 @@ ABCD: offset: value: - 0.0 + spike: + default_initial_value: + - 0 + conditions: + condition_0_on: + test: OUTPUT < 0 + value: 1 + condition_0_off: + test: spike > 0 + value: 0 V: value: 0 OUTPUT: - value: scale * math.exp((rate * INPUT) + bias) + offset + value: scale * numpy.exp((rate * INPUT) + bias) + offset input_ports: INPUT: {} output_ports: + spike: + value: spike V: value: V OUTPUT: @@ -141,13 +189,27 @@ ABCD: time_step_size: value: - 0.1 + spike: + default_initial_value: + - 0 + conditions: + condition_0_on: + test: OUTPUT < 0 + value: 1 + condition_0_off: + test: spike > 0 + value: 0 OUTPUT: time_derivative: (rate * INPUT) / time_step_size + default_initial_value: + - 0 V: value: 0 input_ports: INPUT: {} output_ports: + spike: + value: spike OUTPUT: value: OUTPUT V: @@ -158,34 +220,174 @@ ABCD: \ and in Lems is: Component, id: d, type: pnlSimpleIntegratorMechanism,\n\ \ parameters: {'rate': '0.05', 'time_step_size': '0.1s'}\n\ \ parent: None\n" + proj_input_rsDL: + parameters: + weight: + value: + - 1.0 + SEC: + value: + - 1.0 + rpeer: + value: peer_OUTPUT + I: + value: weight * rpeer + input_ports: + peer_OUTPUT: {} + output_ports: + I: + value: I + notes: "Cell: [Synapse(notes=None, id='rsDL', parameters=None,\ + \ neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None,\ + \ pynn_receptor_type=None)] is defined in PNL.xml and in Lems\ + \ is: Component, id: rsDL, type: synapseDL,\n parameters:\ + \ {}\n parent: None\n" + proj0_rsDL: + parameters: + weight: + value: + - 1.0 + SEC: + value: + - 1.0 + rpeer: + value: peer_OUTPUT + I: + value: weight * rpeer + input_ports: + peer_OUTPUT: {} + output_ports: + I: + value: I + notes: "Cell: [Synapse(notes=None, id='rsDL', parameters=None,\ + \ neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None,\ + \ pynn_receptor_type=None)] is defined in PNL.xml and in Lems\ + \ is: Component, id: rsDL, type: synapseDL,\n parameters:\ + \ {}\n parent: None\n" + proj1_rsDL: + parameters: + weight: + value: + - 1.0 + SEC: + value: + - 1.0 + rpeer: + value: peer_OUTPUT + I: + value: weight * rpeer + input_ports: + peer_OUTPUT: {} + output_ports: + I: + value: I + notes: "Cell: [Synapse(notes=None, id='rsDL', parameters=None,\ + \ neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None,\ + \ pynn_receptor_type=None)] is defined in PNL.xml and in Lems\ + \ is: Component, id: rsDL, type: synapseDL,\n parameters:\ + \ {}\n parent: None\n" + proj2_rsDL: + parameters: + weight: + value: + - 1.0 + SEC: + value: + - 1.0 + rpeer: + value: peer_OUTPUT + I: + value: weight * rpeer + input_ports: + peer_OUTPUT: {} + output_ports: + I: + value: I + notes: "Cell: [Synapse(notes=None, id='rsDL', parameters=None,\ + \ neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None,\ + \ pynn_receptor_type=None)] is defined in PNL.xml and in Lems\ + \ is: Component, id: rsDL, type: synapseDL,\n parameters:\ + \ {}\n parent: None\n" + proj3_rsDL: + parameters: + weight: + value: + - 1.0 + SEC: + value: + - 1.0 + rpeer: + value: peer_OUTPUT + I: + value: weight * rpeer + input_ports: + peer_OUTPUT: {} + output_ports: + I: + value: I + notes: "Cell: [Synapse(notes=None, id='rsDL', parameters=None,\ + \ neuroml2_source_file=None, lems_source_file='PNL.xml', pynn_synapse_type=None,\ + \ pynn_receptor_type=None)] is defined in PNL.xml and in Lems\ + \ is: Component, id: rsDL, type: synapseDL,\n parameters:\ + \ {}\n parent: None\n" edges: - Edge A to B: - name: Edge A to B + A_TO_proj_input_rsDL: + name: A_TO_proj_input_rsDL sender_port: OUTPUT - receiver_port: INPUT + receiver_port: peer_OUTPUT sender: A + receiver: proj_input_rsDL + proj_input_rsDL_TO_B: + name: proj_input_rsDL_TO_B + sender_port: I + receiver_port: INPUT + sender: proj_input_rsDL receiver: B - Edge A_input to A: - name: Edge A_input to A + A_input_TO_proj0_rsDL: + name: A_input_TO_proj0_rsDL sender_port: OUTPUT - receiver_port: INPUT + receiver_port: peer_OUTPUT sender: A_input + receiver: proj0_rsDL + proj0_rsDL_TO_A: + name: proj0_rsDL_TO_A + sender_port: I + receiver_port: INPUT + sender: proj0_rsDL receiver: A - Edge A to C: - name: Edge A to C + A_TO_proj1_rsDL: + name: A_TO_proj1_rsDL sender_port: OUTPUT - receiver_port: INPUT + receiver_port: peer_OUTPUT sender: A + receiver: proj1_rsDL + proj1_rsDL_TO_C: + name: proj1_rsDL_TO_C + sender_port: I + receiver_port: INPUT + sender: proj1_rsDL receiver: C - Edge B to D: - name: Edge B to D + B_TO_proj2_rsDL: + name: B_TO_proj2_rsDL sender_port: OUTPUT - receiver_port: INPUT + receiver_port: peer_OUTPUT sender: B + receiver: proj2_rsDL + proj2_rsDL_TO_D: + name: proj2_rsDL_TO_D + sender_port: I + receiver_port: INPUT + sender: proj2_rsDL receiver: D - Edge C to D: - name: Edge C to D + C_TO_proj3_rsDL: + name: C_TO_proj3_rsDL sender_port: OUTPUT - receiver_port: INPUT + receiver_port: peer_OUTPUT sender: C + receiver: proj3_rsDL + proj3_rsDL_TO_D: + name: proj3_rsDL_TO_D + sender_port: I + receiver_port: INPUT + sender: proj3_rsDL receiver: D diff --git a/examples/NeuroML/ABCD.net.nml b/examples/NeuroML/ABCD.net.nml index 8468f154f..fe25999e1 100644 --- a/examples/NeuroML/ABCD.net.nml +++ b/examples/NeuroML/ABCD.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.4 + Generated by NeuroMLlite v0.5.5 Generated network: ABCD Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/NeuroML/FN.gv.png b/examples/NeuroML/FN.gv.png index 1d86d21ed..c6d61be82 100644 Binary files a/examples/NeuroML/FN.gv.png and b/examples/NeuroML/FN.gv.png differ diff --git a/examples/NeuroML/FN.json b/examples/NeuroML/FN.json index 16d809201..8e6a436c3 100644 --- a/examples/NeuroML/FN.json +++ b/examples/NeuroML/FN.json @@ -1,6 +1,6 @@ { "FN": { - "version": "NeuroMLlite v0.5.4", + "version": "NeuroMLlite v0.5.5", "notes": "FitzHugh Nagumo cell model - originally specified in NeuroML/LEMS", "parameters": { "initial_w": 0.0, diff --git a/examples/NeuroML/FN.mdf.json b/examples/NeuroML/FN.mdf.json index 5b003e2a8..5b3b07c7e 100644 --- a/examples/NeuroML/FN.mdf.json +++ b/examples/NeuroML/FN.mdf.json @@ -102,6 +102,11 @@ 0.001 ] }, + "spike": { + "value": [ + 0 + ] + }, "V": { "default_initial_value": "initial_v", "time_derivative": "(a_v*V*V*V + (1+threshold_exc)*b_v*V*V + (-1*threshold_exc)*c_v*V + d_v + e_v*W + f_v*Iext + INPUT) / (time_constant_v*MSEC)" @@ -115,6 +120,9 @@ "INPUT": {} }, "output_ports": { + "spike": { + "value": "spike" + }, "V": { "value": "V" }, diff --git a/examples/NeuroML/FN.mdf.yaml b/examples/NeuroML/FN.mdf.yaml index 9f9851976..2fe6d0350 100644 --- a/examples/NeuroML/FN.mdf.yaml +++ b/examples/NeuroML/FN.mdf.yaml @@ -64,6 +64,9 @@ FN: MSEC: value: - 0.001 + spike: + value: + - 0 V: default_initial_value: initial_v time_derivative: (a_v*V*V*V + (1+threshold_exc)*b_v*V*V @@ -76,6 +79,8 @@ FN: input_ports: INPUT: {} output_ports: + spike: + value: spike V: value: V W: diff --git a/examples/NeuroML/FN.net.nml b/examples/NeuroML/FN.net.nml index b976a5671..bacd03af7 100644 --- a/examples/NeuroML/FN.net.nml +++ b/examples/NeuroML/FN.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.4 + Generated by NeuroMLlite v0.5.5 Generated network: FN Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/NeuroML/FNmulti.png b/examples/NeuroML/FNmulti.png index 5a2681465..c4bfab28d 100644 Binary files a/examples/NeuroML/FNmulti.png and b/examples/NeuroML/FNmulti.png differ diff --git a/examples/NeuroML/Izh.png b/examples/NeuroML/Izh.png index 89225233e..88f497920 100644 Binary files a/examples/NeuroML/Izh.png and b/examples/NeuroML/Izh.png differ diff --git a/examples/NeuroML/Izh_run.py b/examples/NeuroML/Izh_run.py index b4a10c1ff..9e53acd45 100644 --- a/examples/NeuroML/Izh_run.py +++ b/examples/NeuroML/Izh_run.py @@ -17,7 +17,7 @@ def execute(): dt = 0.0005 duration = 0.7 - input_node = mod_graph.get_node("Input_stim_0") + input_node = mod_graph.get_node("InputList_stim") izh_node = mod_graph.get_node("izhPop") num_cells = 1 @@ -82,13 +82,13 @@ def execute(): vv[i].append(v) uu[i].append(u) - ic = eg.enodes["Input_stim_0"].evaluable_parameters["i"].curr_value[i] + ic = eg.enodes[input_node.id].evaluable_parameters["i"].curr_value[i] ii[i].append(ic) print( f" Value at {t}: v={eg.enodes['izhPop'].evaluable_parameters['v'].curr_value }, \ u={eg.enodes['izhPop'].evaluable_parameters['u'].curr_value},\ - i={eg.enodes['Input_stim_0'].evaluable_parameters['i'].curr_value}" + i={eg.enodes[input_node.id].evaluable_parameters['i'].curr_value}" ) t += dt diff --git a/examples/NeuroML/IzhikevichTest.gv.png b/examples/NeuroML/IzhikevichTest.gv.png index 1dcf2d0e4..71a39af4a 100644 Binary files a/examples/NeuroML/IzhikevichTest.gv.png and b/examples/NeuroML/IzhikevichTest.gv.png differ diff --git a/examples/NeuroML/IzhikevichTest.mdf.json b/examples/NeuroML/IzhikevichTest.mdf.json index 33f3612b5..b218c3966 100644 --- a/examples/NeuroML/IzhikevichTest.mdf.json +++ b/examples/NeuroML/IzhikevichTest.mdf.json @@ -57,6 +57,21 @@ 1e-10 ] }, + "spike": { + "default_initial_value": [ + 0 + ], + "conditions": { + "condition_0_on": { + "test": "v > vpeak", + "value": 1 + }, + "condition_0_off": { + "test": "spike > 0", + "value": 0 + } + } + }, "v": { "default_initial_value": "v0", "conditions": { @@ -88,6 +103,9 @@ "synapses_i": {} }, "output_ports": { + "spike": { + "value": "spike" + }, "v": { "value": "v" }, @@ -100,7 +118,7 @@ }, "notes": "Cell: [Cell(notes=None, id='izhCell', parameters={'v0': 'v0', 'C': 'C', 'k': 'k', 'vr': 'vr', 'vt': 'vt', 'vpeak': 'vpeak', 'a': 'a', 'b': 'b', 'c': 'c', 'd': 'd'}, neuroml2_source_file=None, lems_source_file=None, neuroml2_cell='izhikevich2007Cell', pynn_cell=None, arbor_cell=None, bindsnet_node=None)] is defined in None and in Lems is: Component, id: izhCell, type: izhikevich2007Cell,\n parameters: {'v0': '-80mV', 'C': '100 pF', 'k': '0.7 nS_per_mV', 'vr': '-60 mV', 'vt': '-40 mV', 'vpeak': '35 mV', 'a': '0.03 per_ms', 'b': '-2 nS', 'c': '-50 mV', 'd': '100 pA'}\n parent: None\n" }, - "Input_stim_0": { + "InputList_stim": { "parameters": { "amplitude": { "value": [ @@ -117,6 +135,11 @@ 0.5 ] }, + "weight": { + "value": [ + 1 + ] + }, "i": { "conditions": { "condition_0": { @@ -136,12 +159,16 @@ "t": { "default_initial_value": 0, "time_derivative": "1" - }, - "weight": { - "value": 1 } }, - "input_ports": {}, + "input_ports": { + "spike_input": { + "shape": [ + 1 + ], + "reduce": "add" + } + }, "output_ports": { "i": { "value": "i" @@ -151,11 +178,11 @@ } }, "edges": { - "Edge Input_stim_0 to izhPop": { - "name": "Edge Input_stim_0 to izhPop", + "Edge InputList_stim to izhPop": { + "name": "Edge InputList_stim to izhPop", "sender_port": "i", "receiver_port": "synapses_i", - "sender": "Input_stim_0", + "sender": "InputList_stim", "receiver": "izhPop" } } diff --git a/examples/NeuroML/IzhikevichTest.mdf.yaml b/examples/NeuroML/IzhikevichTest.mdf.yaml index 46e176002..12ef35863 100644 --- a/examples/NeuroML/IzhikevichTest.mdf.yaml +++ b/examples/NeuroML/IzhikevichTest.mdf.yaml @@ -36,6 +36,16 @@ IzhikevichTest: d: value: - 1.0e-10 + spike: + default_initial_value: + - 0 + conditions: + condition_0_on: + test: v > vpeak + value: 1 + condition_0_off: + test: spike > 0 + value: 0 v: default_initial_value: v0 conditions: @@ -57,6 +67,8 @@ IzhikevichTest: input_ports: synapses_i: {} output_ports: + spike: + value: spike v: value: v u: @@ -73,7 +85,7 @@ IzhikevichTest: \ 'C': '100 pF', 'k': '0.7 nS_per_mV', 'vr': '-60 mV', 'vt':\ \ '-40 mV', 'vpeak': '35 mV', 'a': '0.03 per_ms', 'b': '-2\ \ nS', 'c': '-50 mV', 'd': '100 pA'}\n parent: None\n" - Input_stim_0: + InputList_stim: parameters: amplitude: value: @@ -84,6 +96,9 @@ IzhikevichTest: duration: value: - 0.5 + weight: + value: + - 1 i: conditions: condition_0: @@ -98,9 +113,11 @@ IzhikevichTest: t: default_initial_value: 0 time_derivative: '1' - weight: - value: 1 - input_ports: {} + input_ports: + spike_input: + shape: + - 1 + reduce: add output_ports: i: value: i @@ -112,9 +129,9 @@ IzhikevichTest: \ '100pA', 'delay': '100ms', 'duration': '500ms'}\n parent:\ \ None\n" edges: - Edge Input_stim_0 to izhPop: - name: Edge Input_stim_0 to izhPop + Edge InputList_stim to izhPop: + name: Edge InputList_stim to izhPop sender_port: i receiver_port: synapses_i - sender: Input_stim_0 + sender: InputList_stim receiver: izhPop diff --git a/examples/NeuroML/IzhikevichTest.net.nml b/examples/NeuroML/IzhikevichTest.net.nml index 34f852e78..8eb844232 100644 --- a/examples/NeuroML/IzhikevichTest.net.nml +++ b/examples/NeuroML/IzhikevichTest.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.4 + Generated by NeuroMLlite v0.5.5 Generated network: IzhikevichTest Generation seed: 1234 NeuroMLlite parameters: diff --git a/examples/NeuroML/IzhikevichTest.nmllite.yaml b/examples/NeuroML/IzhikevichTest.nmllite.yaml index 0f756187a..9865e8784 100644 --- a/examples/NeuroML/IzhikevichTest.nmllite.yaml +++ b/examples/NeuroML/IzhikevichTest.nmllite.yaml @@ -1,5 +1,5 @@ IzhikevichTest: - version: NeuroMLlite v0.5.4 + version: NeuroMLlite v0.5.5 notes: Example Izhikevich parameters: N: 1 diff --git a/examples/NeuroML/LEMS_SimABCD.xml b/examples/NeuroML/LEMS_SimABCD.xml index 86b9d1eba..b4fd77efd 100644 --- a/examples/NeuroML/LEMS_SimABCD.xml +++ b/examples/NeuroML/LEMS_SimABCD.xml @@ -2,7 +2,7 @@ diff --git a/examples/NeuroML/LEMS_SimFN.xml b/examples/NeuroML/LEMS_SimFN.xml index b8d74ec21..e3ae57645 100644 --- a/examples/NeuroML/LEMS_SimFN.xml +++ b/examples/NeuroML/LEMS_SimFN.xml @@ -2,7 +2,7 @@ diff --git a/examples/NeuroML/LEMS_SimIzhikevichTest.xml b/examples/NeuroML/LEMS_SimIzhikevichTest.xml index 0494c1b03..1bf4ac597 100644 --- a/examples/NeuroML/LEMS_SimIzhikevichTest.xml +++ b/examples/NeuroML/LEMS_SimIzhikevichTest.xml @@ -2,7 +2,7 @@ diff --git a/examples/NeuroML/SimABCD.json b/examples/NeuroML/SimABCD.json index c1764defe..35bf02eb3 100644 --- a/examples/NeuroML/SimABCD.json +++ b/examples/NeuroML/SimABCD.json @@ -1,6 +1,6 @@ { "SimABCD": { - "version": "NeuroMLlite v0.5.4", + "version": "NeuroMLlite v0.5.5", "network": "ABCD.json", "duration": 5000.0, "dt": 100.0, diff --git a/examples/NeuroML/SimFN.json b/examples/NeuroML/SimFN.json index a35953b60..cc8efc22c 100644 --- a/examples/NeuroML/SimFN.json +++ b/examples/NeuroML/SimFN.json @@ -1,6 +1,6 @@ { "SimFN": { - "version": "NeuroMLlite v0.5.4", + "version": "NeuroMLlite v0.5.5", "network": "FN.json", "duration": 100.0, "dt": 0.05, diff --git a/examples/NeuroML/SimIzhikevichTest.yaml b/examples/NeuroML/SimIzhikevichTest.yaml index a5f01884e..aa52243c0 100644 --- a/examples/NeuroML/SimIzhikevichTest.yaml +++ b/examples/NeuroML/SimIzhikevichTest.yaml @@ -1,5 +1,5 @@ SimIzhikevichTest: - version: NeuroMLlite v0.5.4 + version: NeuroMLlite v0.5.5 network: IzhikevichTest.nmllite.yaml duration: 700.0 dt: 0.025 diff --git a/examples/ONNX/ab.json b/examples/ONNX/ab.json index 260b05f57..d1531090e 100644 --- a/examples/ONNX/ab.json +++ b/examples/ONNX/ab.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "torch-jit-export": { "nodes": { diff --git a/examples/ONNX/ab.yaml b/examples/ONNX/ab.yaml index d550284eb..68d142f0c 100644 --- a/examples/ONNX/ab.yaml +++ b/examples/ONNX/ab.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: torch-jit-export: nodes: diff --git a/examples/ONNX/abc.json b/examples/ONNX/abc.json index 448106226..28595e844 100644 --- a/examples/ONNX/abc.json +++ b/examples/ONNX/abc.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "torch-jit-export": { "nodes": { diff --git a/examples/ONNX/abc.yaml b/examples/ONNX/abc.yaml index 6ea175c98..53672ce76 100644 --- a/examples/ONNX/abc.yaml +++ b/examples/ONNX/abc.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: torch-jit-export: nodes: diff --git a/examples/ONNX/abcd.json b/examples/ONNX/abcd.json index e2ffef042..a234236dd 100644 --- a/examples/ONNX/abcd.json +++ b/examples/ONNX/abcd.json @@ -1,7 +1,7 @@ { "ONNX Model": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "torch-jit-export": { "nodes": { diff --git a/examples/ONNX/abcd.yaml b/examples/ONNX/abcd.yaml index 625476526..7da067acb 100644 --- a/examples/ONNX/abcd.yaml +++ b/examples/ONNX/abcd.yaml @@ -1,6 +1,6 @@ ONNX Model: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: torch-jit-export: nodes: diff --git a/examples/PyTorch/MDF_PyTorch/ABCD_pytorch.py b/examples/PyTorch/MDF_PyTorch/ABCD_pytorch.py index dfda7dc1e..4e68aad8f 100644 --- a/examples/PyTorch/MDF_PyTorch/ABCD_pytorch.py +++ b/examples/PyTorch/MDF_PyTorch/ABCD_pytorch.py @@ -1,5 +1,5 @@ """ -This script has been generated by modeci_mdf v0.4.5. +This script has been generated by modeci_mdf v0.4.6. It is an export of a MDF model (mdf.s - MDF stateful, i.e. full MDF allowing stateful parameters) to PyTorch """ diff --git a/examples/PyTorch/MDF_PyTorch/Arrays_pytorch.py b/examples/PyTorch/MDF_PyTorch/Arrays_pytorch.py index d776c44bf..446366331 100644 --- a/examples/PyTorch/MDF_PyTorch/Arrays_pytorch.py +++ b/examples/PyTorch/MDF_PyTorch/Arrays_pytorch.py @@ -1,5 +1,5 @@ """ -This script has been generated by modeci_mdf v0.4.5. +This script has been generated by modeci_mdf v0.4.6. It is an export of a MDF model (mdf.s - MDF stateful, i.e. full MDF allowing stateful parameters) to PyTorch """ diff --git a/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py b/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py index 1cee63fef..8b3f2e045 100644 --- a/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py +++ b/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py @@ -1,5 +1,5 @@ """ -This script has been generated by modeci_mdf v0.4.5. +This script has been generated by modeci_mdf v0.4.6. It is an export of a MDF model (mdf.s - MDF stateful, i.e. full MDF allowing stateful parameters) to PyTorch """ diff --git a/examples/PyTorch/inception.json b/examples/PyTorch/inception.json index 30a48aa84..5d555af27 100644 --- a/examples/PyTorch/inception.json +++ b/examples/PyTorch/inception.json @@ -1,7 +1,7 @@ { "InceptionBlocks": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "InceptionBlocksGraph": { "nodes": { diff --git a/examples/PyTorch/mlp_pure_mdf.json b/examples/PyTorch/mlp_pure_mdf.json index b3cb2ae11..23b34c326 100644 --- a/examples/PyTorch/mlp_pure_mdf.json +++ b/examples/PyTorch/mlp_pure_mdf.json @@ -1,7 +1,7 @@ { "mlp_pure_mdf": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "mlp_pure_mdf": { "nodes": { diff --git a/examples/PyTorch/mlp_pure_mdf.yaml b/examples/PyTorch/mlp_pure_mdf.yaml index 10a296af0..b14b3e54b 100644 --- a/examples/PyTorch/mlp_pure_mdf.yaml +++ b/examples/PyTorch/mlp_pure_mdf.yaml @@ -1,6 +1,6 @@ mlp_pure_mdf: format: ModECI MDF v0.4 - generating_application: Python modeci-mdf v0.4.5 + generating_application: Python modeci-mdf v0.4.6 graphs: mlp_pure_mdf: nodes: diff --git a/examples/PyTorch/simple_pytorch_to_mdf.json b/examples/PyTorch/simple_pytorch_to_mdf.json index e6eb73cd9..6e2317a13 100644 --- a/examples/PyTorch/simple_pytorch_to_mdf.json +++ b/examples/PyTorch/simple_pytorch_to_mdf.json @@ -1,7 +1,7 @@ { "SimpleNet": { "format": "ModECI MDF v0.4", - "generating_application": "Python modeci-mdf v0.4.5", + "generating_application": "Python modeci-mdf v0.4.6", "graphs": { "SimpleNetGraph": { "nodes": { diff --git a/src/modeci_mdf/__init__.py b/src/modeci_mdf/__init__.py index 6874bd3f9..0cd984e0c 100644 --- a/src/modeci_mdf/__init__.py +++ b/src/modeci_mdf/__init__.py @@ -13,4 +13,4 @@ MODECI_MDF_VERSION = "0.4" # Version of the Python module. -__version__ = "0.4.5" +__version__ = "0.4.6"