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Merge pull request #95 from openworm/ow_test_ruff
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To v0.9.0
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@pgleeson
pgleeson authored Jan 14, 2025
2 parents a733611 + 3aa642a commit 8aa97bb
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Showing 121 changed files with 373 additions and 347 deletions.
2 changes: 2 additions & 0 deletions .gitignore
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/examples/test/images/c302_C1_Syns.net.nml
*ken.sh
/examples/parametersweep/IClamp_GenericNeuronCellX__lems.xml
/examples/parametersweep/LEMS_SimCanonical_X.png
/examples/parametersweep/Canonical_X__lems.xml
1 change: 0 additions & 1 deletion c302/NeuroMLUtilities.py
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############################################################



from c302.ConnectomeReader import analyse_connections


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2 changes: 1 addition & 1 deletion c302/__version__.py
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@@ -1 +1 @@
__version__ = "0.8.1"
__version__ = "0.9.0"
1 change: 0 additions & 1 deletion c302/c302_info.py
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@@ -1,4 +1,3 @@

import c302


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24 changes: 23 additions & 1 deletion c302/custom_synapses.xml
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@@ -1,6 +1,28 @@
<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_v2beta4.xsd" id="cell_C">

<!-- Definition of new synapse model type-->
<!-- Definition of new synapse model types-->



<ComponentType name="outputSynapse"
extends="baseGradedSynapse"
description="For Worm2D...">

<Property name="weight" dimension="none" defaultValue="1"/>

<Constant name="PAMP_SCALE" dimension="current" value="1pA"/>

<Exposure name="i" dimension="current"/>

<Requirement name="state" dimension="none"/>

<InstanceRequirement name="peer" type="outputSynapse"/>

<Dynamics>
<DerivedVariable name="outputpeer" dimension="none" select="peer/state"/>
<DerivedVariable name="i" exposure="i" value="weight * outputpeer * PAMP_SCALE"/>
</Dynamics>
</ComponentType>


<ComponentType name="gradedSynapse2"
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1 change: 0 additions & 1 deletion c302/parameters_D1.py
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"""


from neuroml import GapJunction

from c302.parameters_D import ParameterisedModel as ParameterisedModel_D
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_A_Full.xml
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Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: All cells
Cell stimulated: ['PLML', 'PLMR']
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_A_IClamp.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['ADAL', 'PVCL']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_A_Muscles.xml
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Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
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: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_A_Oscillator.xml
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Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR']
Cell stimulated: ['AVBL', 'AVBR']
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_A_Pharyngeal.xml
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Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
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: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_A_Social.xml
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Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_A_Syns.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_B_Full.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: All cells
Cell stimulated: ['PLML', 'PLMR']
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_B_IClamp.xml
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Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['ADAL', 'PVCL']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_B_Muscles.xml
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Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
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: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_B_Oscillator.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR']
Cell stimulated: ['AVBL', 'AVBR']
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_B_Pharyngeal.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
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: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_B_Social.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_B_Syns.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C0_Full.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: All cells
Cell stimulated: ['PLML', 'PLMR']
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C0_IClamp.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['ADAL', 'PVCL']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C0_Muscles.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
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: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C0_Oscillator.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR']
Cell stimulated: ['AVBL', 'AVBR']
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C0_Pharyngeal.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
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: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C0_Social.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C0_Syns.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C1_Full.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: All cells
Cell stimulated: ['PLML', 'PLMR']
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C1_IClamp.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
Cells: ['ADAL', 'PVCL']
Cell stimulated: []
Connection: []
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6 changes: 3 additions & 3 deletions examples/LEMS_c302_C1_Muscles.xml
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Expand Up @@ -6,9 +6,9 @@
Parameters and setting used to generate this network:
Data reader: SpreadsheetDataReader
c302 version: 0.8.0
owmeta version: 0.12.3
owmeta_core version: 0.13.5
c302 version: 0.9.0
owmeta version: - not installed -
owmeta_core version: - not installed -
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: []
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