To v0.6.1; Update schema to latest - require specCap & init memb pot

NeuralEnsemble · Jun 11, 2024 · bcea5a4 · bcea5a4
1 parent 259505c
commit bcea5a4
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Showing 4 changed files with 59 additions and 14 deletions.
diff --git a/neuroml/nml/NeuroML_v2.3.1.xsd b/neuroml/nml/NeuroML_v2.3.1.xsd
@@ -2118,8 +2118,8 @@
           <xs:element name="channelDensityNonUniformNernst" type="ChannelDensityNonUniformNernst" minOccurs="0" maxOccurs="unbounded"/>
           <xs:element name="channelDensityNonUniformGHK" type="ChannelDensityNonUniformGHK" minOccurs="0" maxOccurs="unbounded"/>
           <xs:element name="spikeThresh" type="SpikeThresh" minOccurs="1" maxOccurs="unbounded"/>
-          <xs:element name="specificCapacitance" type="SpecificCapacitance" minOccurs="0" maxOccurs="unbounded"/>
-          <xs:element name="initMembPotential" type="InitMembPotential" minOccurs="0" maxOccurs="unbounded"/>
+          <xs:element name="specificCapacitance" type="SpecificCapacitance" minOccurs="1" maxOccurs="unbounded"/>
+          <xs:element name="initMembPotential" type="InitMembPotential" minOccurs="1" maxOccurs="unbounded"/>
           <!-- Taking this out until confirmation it's needed
                 <xs:element name="reversalPotential" type="ReversalPotential" minOccurs="0" maxOccurs="unbounded"/>-->
         </xs:sequence>

diff --git a/neuroml/nml/nml.py b/neuroml/nml/nml.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 
 #
-# Generated Tue Jun 11 13:57:16 2024 by generateDS.py version 2.43.3.
+# Generated Tue Jun 11 14:00:16 2024 by generateDS.py version 2.43.3.
 # Python 3.10.9 (main, Jan 11 2023, 15:21:40) [GCC 11.2.0]
 #
 # Command line options:
@@ -24597,10 +24597,10 @@ class MembraneProperties(BaseWithoutId):
             "specific_capacitances",
             "SpecificCapacitance",
             1,
-            1,
+            0,
             {
                 "maxOccurs": "unbounded",
-                "minOccurs": "0",
+                "minOccurs": "1",
                 "name": "specificCapacitance",
                 "type": "SpecificCapacitance",
             },
@@ -24610,10 +24610,10 @@ class MembraneProperties(BaseWithoutId):
             "init_memb_potentials",
             "InitMembPotential",
             1,
-            1,
+            0,
             {
                 "maxOccurs": "unbounded",
-                "minOccurs": "0",
+                "minOccurs": "1",
                 "name": "initMembPotential",
                 "type": "InitMembPotential",
             },
@@ -24635,8 +24635,8 @@ def __init__(
         channel_density_non_uniform_nernsts: "list of ChannelDensityNonUniformNernst(s) (optional)" = None,
         channel_density_non_uniform_ghks: "list of ChannelDensityNonUniformGHK(s) (optional)" = None,
         spike_threshes: "list of SpikeThresh(s) (required)" = None,
-        specific_capacitances: "list of SpecificCapacitance(s) (optional)" = None,
-        init_memb_potentials: "list of InitMembPotential(s) (optional)" = None,
+        specific_capacitances: "list of SpecificCapacitance(s) (required)" = None,
+        init_memb_potentials: "list of InitMembPotential(s) (required)" = None,
         extensiontype_=None,
         gds_collector_=None,
         **kwargs_,
@@ -25088,13 +25088,13 @@ def validate_(self, gds_collector, recursive=False):
         self.gds_check_cardinality_(
             self.specific_capacitances,
             "specific_capacitances",
-            min_occurs=0,
+            min_occurs=1,
             max_occurs=9999999,
         )
         self.gds_check_cardinality_(
             self.init_memb_potentials,
             "init_memb_potentials",
-            min_occurs=0,
+            min_occurs=1,
             max_occurs=9999999,
         )
         if recursive:
@@ -47930,8 +47930,8 @@ def __init__(
         channel_density_non_uniform_nernsts: "list of ChannelDensityNonUniformNernst(s) (optional)" = None,
         channel_density_non_uniform_ghks: "list of ChannelDensityNonUniformGHK(s) (optional)" = None,
         spike_threshes: "list of SpikeThresh(s) (required)" = None,
-        specific_capacitances: "list of SpecificCapacitance(s) (optional)" = None,
-        init_memb_potentials: "list of InitMembPotential(s) (optional)" = None,
+        specific_capacitances: "list of SpecificCapacitance(s) (required)" = None,
+        init_memb_potentials: "list of InitMembPotential(s) (required)" = None,
         channel_density_nernst_ca2s: "list of ChannelDensityNernstCa2(s) (optional)" = None,
         gds_collector_=None,
         **kwargs_,

diff --git a/neuroml/test/test_nml.py b/neuroml/test/test_nml.py
@@ -178,6 +178,8 @@ def test_info(self):
         """Test getting member info."""
         cell = neuroml.Cell(id="testcell")
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         info = cell.info()
         self.assertRegex(info, "morphology")
         self.assertRegex(info, "biophysical_properties")
@@ -214,6 +216,8 @@ def test_parentinfo(self):
         """Test the parent info method"""
         cell = neuroml.Cell(id="testcell")
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         info = cell.parentinfo()
         self.assertRegex(info, "NeuroMLDocument")
 
@@ -240,6 +244,8 @@ def test_add_segment(self):
         """Test adding a segment."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         segment = new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -259,6 +265,8 @@ def test_add_segment_no_group(self):
         """Test adding a segment but without a group."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         segment = new_cell.add_segment(
             (0, 0, 0, 20), (20, 0, 0, 20), name="soma", group_id=None, seg_type="soma"
         )
@@ -274,6 +282,7 @@ def test_setting_init_memb_potential(self):
         """Test adding initial membrane potential."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -296,6 +305,8 @@ def test_setting_spike_thresh(self):
             seg_type="soma",
         )
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
 
         self.assertIsNone(new_cell.validate(True))
 
@@ -327,6 +338,8 @@ def test_setting_resistivity(self):
         )
         new_cell.set_resistivity("2000 ohm_cm")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         self.assertIsNone(new_cell.validate(True))
 
     @unittest.expectedFailure
@@ -347,6 +360,8 @@ def test_setting_specific_capacitance(self):
         """Test setting the specific_capacitance."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -362,6 +377,8 @@ def test_setting_specific_capacitance_should_fail(self):
         """Test setting the specific_capacitance."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -376,6 +393,8 @@ def test_setting_channel_density(self):
         """Test setting the channel_density."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -421,6 +440,8 @@ def test_setting_channel_density_v(self):
         """Test setting the channel_density."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -469,6 +490,8 @@ def test_setting_channel_density_should_fail(self):
         """Test setting the channel_density."""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -502,6 +525,7 @@ def test_setting_membrane_property(self):
         """Test adding a new membrane property"""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -524,6 +548,8 @@ def test_setting_intracellular_property(self):
         """Test adding a new membrane property"""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         new_cell.add_segment(
             (0, 0, 0, 20),
             (20, 0, 0, 20),
@@ -550,6 +576,8 @@ def test_simple_cell(self):
         # test with component_factory
         cell = component_factory("Cell", id="simple_cell")
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         cell.notes = "NeuroML cell created by CellBuilder"
 
         # Add soma segment
@@ -571,6 +599,8 @@ def test_complex_cell(self):
         # with component_factory
         cell = component_factory("Cell", id="complex_cell")  # type: neuroml.Cell
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         cell.notes = "NeuroML cell created by CellBuilder"
 
         # Add soma segment
@@ -600,6 +630,8 @@ def test_component_factory_create_cell(self):
         """Test cell creation"""
         new_cell = component_factory("Cell", id="test_cell")
         new_cell.set_spike_thresh("40mV")
+        new_cell.set_init_memb_potential("-70mV")
+        new_cell.set_specific_capacitance("1 uF_per_cm2")
         self.assertIsInstance(new_cell, neuroml.Cell)
 
         # cell does not have segments: is invalid NeuroML
@@ -611,6 +643,8 @@ def test_add_unbranched_segments(self):
         # test with component_factory
         cell = component_factory("Cell", id="simple_cell")
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         cell.notes = "NeuroML cell created by CellBuilder"
 
         # Add soma segment
@@ -647,6 +681,8 @@ def test_optimise_segment_group(self):
         """Test `optimise_segment_group`"""
         cell = component_factory("Cell", id="simple_cell")  # type: neuroml.Cell
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         cell.notes = "NeuroML cell created by CellBuilder"
 
         # Add soma segment
@@ -688,6 +724,8 @@ def test_create_unbranched_segment_group_branches(self):
         "Test create_unbranched_segment_group_branches"
         cell = component_factory("Cell", id="simple_cell")  # type: neuroml.Cell
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         cell.notes = "NeuroML cell created by CellBuilder"
 
         # Add soma segment
@@ -758,6 +796,8 @@ def test_morphinfo(self):
         # with component_factory
         cell = component_factory("Cell", id="complex_cell")  # type: neuroml.Cell
         cell.set_spike_thresh("40mV")
+        cell.set_init_memb_potential("-70mV")
+        cell.set_specific_capacitance("1 uF_per_cm2")
         cell.notes = "NeuroML cell created by CellBuilder"
 
         # Add soma segment
@@ -797,3 +837,8 @@ def test_class_hierarchy(self):
         print(hier)
         print()
         print_hierarchy(hier)
+
+if __name__ == "__main__":
+    ta = TestNML()
+
+    ta.test_add_segment()
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = libNeuroML
-version = 0.6.0
+version = 0.6.1
 author_email = vellamike@gmail.com, p.gleeson@gmail.com
 author = libNeuroML authors and contributors
 description = A Python library for working with NeuroML descriptions of neuronal models