Merge pull request #48 from openworm/development

Regenerated NeuroML
openworm · Jun 26, 2023 · b2828cd · b2828cd
2 parents 82310f1 + 87e0009
commit b2828cd
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Showing 423 changed files with 3,502 additions and 3,496 deletions.
diff --git a/c302/OpenWormReader.py b/c302/OpenWormReader.py
@@ -35,7 +35,13 @@ def get_cells_in_model(self, net):
     def read_data(self, include_nonconnected_cells=False):
         print_("Initialising OpenWormReader")
 
-        cell_names, pre, post, conns = self._read_connections('neuron')
+        try:
+            cell_names, pre, post, conns = self._read_connections('neuron')
+        except:
+            print('\nProblem loading connections via owmeta! The package is installed however. You may need to try running:'+
+                  "\n\n    owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'\n")
+
+            exit()
 
         if include_nonconnected_cells:
             return cell_names, conns

diff --git a/cells/ADAL_D.cell.nml b/cells/ADAL_D.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.2.xsd" id="ADAL">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="ADAL">
     <cell id="ADAL">
         <notes>Cell model created by c302 with custom electrical parameters</notes>
         <morphology id="morphology_ADAL">
@@ -83,10 +83,10 @@
                 <parent segment="18"/>
                 <distal x="-2.1" y="-275.35" z="53.399998" diameter="0.5"/>
             </segment>
-            <segmentGroup neuroLexId="sao864921383" id="Soma">
+            <segmentGroup id="Soma" neuroLexId="sao864921383">
                 <member segment="0"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Axon">
+            <segmentGroup id="Axon" neuroLexId="sao864921383">
                 <member segment="1"/>
                 <member segment="2"/>
                 <member segment="3"/>
@@ -111,10 +111,10 @@
                 <include segmentGroup="Soma"/>
                 <include segmentGroup="Axon"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0043025" id="soma_group">
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <include segmentGroup="Soma"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030424" id="axon_group">
+            <segmentGroup id="axon_group" neuroLexId="GO:0030424">
                 <include segmentGroup="Axon"/>
             </segmentGroup>
         </morphology>

diff --git a/cells/AIBL_D.cell.nml b/cells/AIBL_D.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.2.xsd" id="AIBL">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="AIBL">
     <cell id="AIBL">
         <notes>Cell model created by c302 with custom electrical parameters</notes>
         <morphology id="morphology_AIBL">
@@ -131,10 +131,10 @@
                 <parent segment="30"/>
                 <distal x="-2.7" y="-272.42502" z="34.45" diameter="0.4387482"/>
             </segment>
-            <segmentGroup neuroLexId="sao864921383" id="Soma">
+            <segmentGroup id="Soma" neuroLexId="sao864921383">
                 <member segment="0"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Axon">
+            <segmentGroup id="Axon" neuroLexId="sao864921383">
                 <member segment="1"/>
                 <member segment="2"/>
                 <member segment="3"/>
@@ -171,10 +171,10 @@
                 <include segmentGroup="Soma"/>
                 <include segmentGroup="Axon"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0043025" id="soma_group">
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <include segmentGroup="Soma"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030424" id="axon_group">
+            <segmentGroup id="axon_group" neuroLexId="GO:0030424">
                 <include segmentGroup="Axon"/>
             </segmentGroup>
         </morphology>

diff --git a/cells/DB5_D.cell.nml b/cells/DB5_D.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.2.xsd" id="DB5">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="DB5">
     <cell id="DB5">
         <notes>Cell model created by c302 with custom electrical parameters</notes>
         <morphology id="morphology_DB5">
@@ -212,10 +212,10 @@
                 <parent segment="50"/>
                 <distal x="-1.4499999" y="279.2" z="-24.0" diameter="0.5"/>
             </segment>
-            <segmentGroup neuroLexId="sao864921383" id="Soma">
+            <segmentGroup id="Soma" neuroLexId="sao864921383">
                 <member segment="0"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Axon">
+            <segmentGroup id="Axon" neuroLexId="sao864921383">
                 <member segment="1"/>
                 <member segment="2"/>
                 <member segment="3"/>
@@ -249,7 +249,7 @@
                 <member segment="31"/>
                 <member segment="32"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Dendrite2">
+            <segmentGroup id="Dendrite2" neuroLexId="sao864921383">
                 <member segment="33"/>
                 <member segment="34"/>
                 <member segment="35"/>
@@ -275,13 +275,13 @@
                 <include segmentGroup="Axon"/>
                 <include segmentGroup="Dendrite2"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0043025" id="soma_group">
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <include segmentGroup="Soma"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030424" id="axon_group">
+            <segmentGroup id="axon_group" neuroLexId="GO:0030424">
                 <include segmentGroup="Axon"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030425" id="dendrite_group">
+            <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">
                 <include segmentGroup="Dendrite2"/>
             </segmentGroup>
         </morphology>

diff --git a/cells/I1L_D.cell.nml b/cells/I1L_D.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.2.xsd" id="I1L">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="I1L">
     <cell id="I1L">
         <notes>Cell model created by c302 with custom electrical parameters</notes>
         <morphology id="morphology_I1L">
@@ -112,10 +112,10 @@
                 <parent segment="25"/>
                 <distal x="0.1" y="-340.55" z="59.149998" diameter="0.42426404"/>
             </segment>
-            <segmentGroup neuroLexId="sao864921383" id="Soma">
+            <segmentGroup id="Soma" neuroLexId="sao864921383">
                 <member segment="0"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Axon">
+            <segmentGroup id="Axon" neuroLexId="sao864921383">
                 <member segment="1"/>
                 <member segment="2"/>
                 <member segment="3"/>
@@ -131,7 +131,7 @@
                 <member segment="13"/>
                 <member segment="14"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Dendrite2">
+            <segmentGroup id="Dendrite2" neuroLexId="sao864921383">
                 <member segment="15"/>
                 <member segment="16"/>
                 <member segment="17"/>
@@ -150,13 +150,13 @@
                 <include segmentGroup="Axon"/>
                 <include segmentGroup="Dendrite2"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0043025" id="soma_group">
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <include segmentGroup="Soma"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030424" id="axon_group">
+            <segmentGroup id="axon_group" neuroLexId="GO:0030424">
                 <include segmentGroup="Axon"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030425" id="dendrite_group">
+            <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">
                 <include segmentGroup="Dendrite2"/>
             </segmentGroup>
         </morphology>

diff --git a/cells/I3_D.cell.nml b/cells/I3_D.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.2.xsd" id="I3">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="I3">
     <cell id="I3">
         <notes>Cell model created by c302 with custom electrical parameters</notes>
         <morphology id="morphology_I3">
@@ -66,15 +66,15 @@
                 <parent segment="13"/>
                 <distal x="-2.05" y="-290.15" z="56.950005" diameter="0.4358899"/>
             </segment>
-            <segmentGroup neuroLexId="sao864921383" id="Soma">
+            <segmentGroup id="Soma" neuroLexId="sao864921383">
                 <member segment="0"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Axon">
+            <segmentGroup id="Axon" neuroLexId="sao864921383">
                 <member segment="8"/>
                 <member segment="9"/>
                 <member segment="10"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Dendrite2">
+            <segmentGroup id="Dendrite2" neuroLexId="sao864921383">
                 <member segment="1"/>
                 <member segment="2"/>
                 <member segment="3"/>
@@ -83,11 +83,11 @@
                 <member segment="6"/>
                 <member segment="7"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Neurite3">
+            <segmentGroup id="Neurite3" neuroLexId="sao864921383">
                 <member segment="11"/>
                 <member segment="12"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Neurite4">
+            <segmentGroup id="Neurite4" neuroLexId="sao864921383">
                 <member segment="13"/>
                 <member segment="14"/>
             </segmentGroup>
@@ -98,13 +98,13 @@
                 <include segmentGroup="Neurite3"/>
                 <include segmentGroup="Neurite4"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0043025" id="soma_group">
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <include segmentGroup="Soma"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030424" id="axon_group">
+            <segmentGroup id="axon_group" neuroLexId="GO:0030424">
                 <include segmentGroup="Axon"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030425" id="dendrite_group">
+            <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">
                 <include segmentGroup="Dendrite2"/>
                 <include segmentGroup="Neurite3"/>
                 <include segmentGroup="Neurite4"/>

diff --git a/cells/PVCR_D.cell.nml b/cells/PVCR_D.cell.nml
@@ -1,4 +1,4 @@
-<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.2.xsd" id="PVCR">
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="PVCR">
     <cell id="PVCR">
         <notes>Cell model created by c302 with custom electrical parameters</notes>
         <morphology id="morphology_PVCR">
@@ -243,10 +243,10 @@
                 <parent segment="58"/>
                 <distal x="-2.3" y="-275.35" z="53.399998" diameter="0.5"/>
             </segment>
-            <segmentGroup neuroLexId="sao864921383" id="Soma">
+            <segmentGroup id="Soma" neuroLexId="sao864921383">
                 <member segment="0"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="sao864921383" id="Axon">
+            <segmentGroup id="Axon" neuroLexId="sao864921383">
                 <member segment="1"/>
                 <member segment="2"/>
                 <member segment="3"/>
@@ -311,10 +311,10 @@
                 <include segmentGroup="Soma"/>
                 <include segmentGroup="Axon"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0043025" id="soma_group">
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                 <include segmentGroup="Soma"/>
             </segmentGroup>
-            <segmentGroup neuroLexId="GO:0030424" id="axon_group">
+            <segmentGroup id="axon_group" neuroLexId="GO:0030424">
                 <include segmentGroup="Axon"/>
             </segmentGroup>
         </morphology>

diff --git a/examples/LEMS_c302_A_Full.xml b/examples/LEMS_c302_A_Full.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          All cells
     Cell stimulated:                ['PLML', 'PLMR']
     Connection:                     []

diff --git a/examples/LEMS_c302_A_IClamp.xml b/examples/LEMS_c302_A_IClamp.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          ['ADAL', 'PVCL']
     Cell stimulated:                []
     Connection:                     []

diff --git a/examples/LEMS_c302_A_Muscles.xml b/examples/LEMS_c302_A_Muscles.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

diff --git a/examples/LEMS_c302_A_Oscillator.xml b/examples/LEMS_c302_A_Oscillator.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR']
     Cell stimulated:                ['AVBL', 'AVBR']
     Connection:                     []

diff --git a/examples/LEMS_c302_A_Pharyngeal.xml b/examples/LEMS_c302_A_Pharyngeal.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR']
     Cell stimulated:                ['M1', 'M3R', 'M4', 'M5', 'I1L', 'I4', 'I5', 'I6', 'MCL', 'MCR']
     Connection:                     []

diff --git a/examples/LEMS_c302_A_Social.xml b/examples/LEMS_c302_A_Social.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR']
     Cell stimulated:                []
     Connection:                     []

diff --git a/examples/LEMS_c302_A_Syns.xml b/examples/LEMS_c302_A_Syns.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2']
     Cell stimulated:                []
     Connection:                     []

diff --git a/examples/LEMS_c302_B_Full.xml b/examples/LEMS_c302_B_Full.xml
@@ -6,9 +6,9 @@
 Parameters and setting used to generate this network:
 
     Data reader:                    SpreadsheetDataReader
-    c302 version:                   0.7.9
+    c302 version:                   0.7.10
     owmeta version:                 0.12.3
-    owmeta_core version:            0.12.2
+    owmeta_core version:            0.13.5
     Cells:                          All cells
     Cell stimulated:                ['PLML', 'PLMR']
     Connection:                     []