diff --git a/scripts/schemas/asttemplates.py b/scripts/schemas/asttemplates.py index d3cd12f2..c538dda9 100644 --- a/scripts/schemas/asttemplates.py +++ b/scripts/schemas/asttemplates.py @@ -567,8 +567,10 @@ def format_math(expr): *Go to the libNeuroML documentation* ```{code-block} python from neuroml import {{ pysig[0] }} + from neuroml.utils import component_factory - variable = {{ pysig[0] }}( + variable = component_factory( + {{ pysig[0] }}, {%- for sig in pysig[1] %} {{ sig | indent(4) }}, {%- endfor %} diff --git a/scripts/schemas/generate-jupyter-ast.py b/scripts/schemas/generate-jupyter-ast.py index b81ea35d..b1b4afa6 100644 --- a/scripts/schemas/generate-jupyter-ast.py +++ b/scripts/schemas/generate-jupyter-ast.py @@ -433,6 +433,11 @@ def main(srcdir, destdir): print("Output files will be written to {} directory".format(destdir)) links_doc_data = {} + for x in ["IncludeType", "NeuroMLDocument"]: + links_doc_data[x.lower()] = ( + f'\n\n- {{ref}}`{x} `' + ) + for comp_definition in comp_definitions: fullpath = "{}/{}.xml".format(tmpsrcdir, comp_definition) diff --git a/source/Userdocs/Schemas/Cells.md b/source/Userdocs/Schemas/Cells.md index 0cfd9ba8..a342932c 100644 --- a/source/Userdocs/Schemas/Cells.md +++ b/source/Userdocs/Schemas/Cells.md @@ -46,8 +46,10 @@ extends *{ref}`schema:basestandalone`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BaseCell +from neuroml.utils import component_factory -variable = BaseCell( +variable = component_factory( + BaseCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -335,8 +337,10 @@ extends *{ref}`schema:basechannelpopulation`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelPopulation +from neuroml.utils import component_factory -variable = ChannelPopulation( +variable = component_factory( + ChannelPopulation, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, number: 'a NonNegativeInteger (required)' = None, @@ -603,8 +607,10 @@ extends *{ref}`schema:basechanneldensity`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import VariableParameter +from neuroml.utils import component_factory -variable = VariableParameter( +variable = component_factory( + VariableParameter, parameter: 'a string (required)' = None, segment_groups: 'a string (required)' = None, inhomogeneous_value: 'a InhomogeneousValue (optional)' = None, @@ -660,8 +666,10 @@ variable = VariableParameter( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import InhomogeneousValue +from neuroml.utils import component_factory -variable = InhomogeneousValue( +variable = component_factory( + InhomogeneousValue, inhomogeneous_parameters: 'a string (required)' = None, value: 'a string (required)' = None, ) @@ -803,8 +811,10 @@ extends *{ref}`schema:basechanneldensity`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityNonUniform +from neuroml.utils import component_factory -variable = ChannelDensityNonUniform( +variable = component_factory( + ChannelDensityNonUniform, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, erev: 'a Nml2Quantity_voltage (required)' = None, @@ -941,8 +951,10 @@ extends *{ref}`schema:basechanneldensity`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityNonUniformNernst +from neuroml.utils import component_factory -variable = ChannelDensityNonUniformNernst( +variable = component_factory( + ChannelDensityNonUniformNernst, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, ion: 'a NmlId (required)' = None, @@ -1069,8 +1081,10 @@ extends *{ref}`schema:basechanneldensity`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityNonUniformGHK +from neuroml.utils import component_factory -variable = ChannelDensityNonUniformGHK( +variable = component_factory( + ChannelDensityNonUniformGHK, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, ion: 'a NmlId (required)' = None, @@ -1205,8 +1219,10 @@ extends *{ref}`schema:basechanneldensitycond`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensity +from neuroml.utils import component_factory -variable = ChannelDensity( +variable = component_factory( + ChannelDensity, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, cond_density: 'a Nml2Quantity_conductanceDensity (optional)' = None, @@ -1311,8 +1327,10 @@ extends {ref}`schema:channeldensity` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityVShift +from neuroml.utils import component_factory -variable = ChannelDensityVShift( +variable = component_factory( + ChannelDensityVShift, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, cond_density: 'a Nml2Quantity_conductanceDensity (optional)' = None, @@ -1468,8 +1486,10 @@ extends *{ref}`schema:basechanneldensitycond`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityNernst +from neuroml.utils import component_factory -variable = ChannelDensityNernst( +variable = component_factory( + ChannelDensityNernst, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, cond_density: 'a Nml2Quantity_conductanceDensity (optional)' = None, @@ -1613,8 +1633,10 @@ extends *{ref}`schema:basechanneldensitycond`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityNernstCa2 +from neuroml.utils import component_factory -variable = ChannelDensityNernstCa2( +variable = component_factory( + ChannelDensityNernstCa2, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, cond_density: 'a Nml2Quantity_conductanceDensity (optional)' = None, @@ -1757,8 +1779,10 @@ extends *{ref}`schema:basechanneldensity`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityGHK +from neuroml.utils import component_factory -variable = ChannelDensityGHK( +variable = component_factory( + ChannelDensityGHK, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, permeability: 'a Nml2Quantity_permeability (required)' = None, @@ -1909,8 +1933,10 @@ extends *{ref}`schema:basechanneldensitycond`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ChannelDensityGHK2 +from neuroml.utils import component_factory -variable = ChannelDensityGHK2( +variable = component_factory( + ChannelDensityGHK2, id: 'a NmlId (required)' = None, ion_channel: 'a NmlId (required)' = None, cond_density: 'a Nml2Quantity_conductanceDensity (optional)' = None, @@ -2500,8 +2526,10 @@ extends {ref}`schema:point3dwithdiam` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Segment +from neuroml.utils import component_factory -variable = Segment( +variable = component_factory( + Segment, id: 'a NonNegativeInteger (required)' = None, name: 'a string (optional)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, @@ -2610,8 +2638,10 @@ variable = Segment( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SegmentGroup +from neuroml.utils import component_factory -variable = SegmentGroup( +variable = component_factory( + SegmentGroup, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, notes: 'a string (optional)' = None, @@ -2684,8 +2714,10 @@ variable = SegmentGroup( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Member +from neuroml.utils import component_factory -variable = Member( +variable = component_factory( + Member, segments: 'a NonNegativeInteger (required)' = None, ) ``` @@ -2829,8 +2861,10 @@ variable = Member( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Include +from neuroml.utils import component_factory -variable = Include( +variable = component_factory( + Include, segment_groups: 'a NmlId (required)' = None, ) ``` @@ -2891,8 +2925,10 @@ variable = Include( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Path +from neuroml.utils import component_factory -variable = Path( +variable = component_factory( + Path, from_: 'a SegmentEndPoint (optional)' = None, to: 'a SegmentEndPoint (optional)' = None, ) @@ -2950,8 +2986,10 @@ variable = Path( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SubTree +from neuroml.utils import component_factory -variable = SubTree( +variable = component_factory( + SubTree, from_: 'a SegmentEndPoint (optional)' = None, to: 'a SegmentEndPoint (optional)' = None, ) @@ -3022,8 +3060,10 @@ variable = SubTree( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import InhomogeneousParameter +from neuroml.utils import component_factory -variable = InhomogeneousParameter( +variable = component_factory( + InhomogeneousParameter, id: 'a NmlId (required)' = None, variable: 'a string (required)' = None, metric: 'a Metric (required)' = None, @@ -3083,8 +3123,10 @@ variable = InhomogeneousParameter( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ProximalDetails +from neuroml.utils import component_factory -variable = ProximalDetails( +variable = component_factory( + ProximalDetails, translation_start: 'a double (required)' = None, ) ``` @@ -3129,8 +3171,10 @@ variable = ProximalDetails( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import DistalDetails +from neuroml.utils import component_factory -variable = DistalDetails( +variable = component_factory( + DistalDetails, normalization_end: 'a double (required)' = None, ) ``` @@ -3180,8 +3224,10 @@ variable = DistalDetails( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Morphology +from neuroml.utils import component_factory -variable = Morphology( +variable = component_factory( + Morphology, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -3345,8 +3391,10 @@ variable = Morphology( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpecificCapacitance +from neuroml.utils import component_factory -variable = SpecificCapacitance( +variable = component_factory( + SpecificCapacitance, value: 'a Nml2Quantity_specificCapacitance (required)' = None, segment_groups: 'a NmlId (optional)' = 'all', ) @@ -3405,8 +3453,10 @@ variable = SpecificCapacitance( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import InitMembPotential +from neuroml.utils import component_factory -variable = InitMembPotential( +variable = component_factory( + InitMembPotential, value: 'a Nml2Quantity_voltage (required)' = None, segment_groups: 'a NmlId (optional)' = 'all', ) @@ -3462,8 +3512,10 @@ variable = InitMembPotential( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpikeThresh +from neuroml.utils import component_factory -variable = SpikeThresh( +variable = component_factory( + SpikeThresh, value: 'a Nml2Quantity_voltage (required)' = None, segment_groups: 'a NmlId (optional)' = 'all', ) @@ -3594,8 +3646,10 @@ variable = SpikeThresh( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import MembraneProperties +from neuroml.utils import component_factory -variable = MembraneProperties( +variable = component_factory( + MembraneProperties, channel_populations: 'list of ChannelPopulation(s) (optional)' = None, channel_densities: 'list of ChannelDensity(s) (optional)' = None, channel_density_v_shifts: 'list of ChannelDensityVShift(s) (optional)' = None, @@ -3756,8 +3810,10 @@ extends {ref}`schema:membraneproperties` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import MembraneProperties2CaPools +from neuroml.utils import component_factory -variable = MembraneProperties2CaPools( +variable = component_factory( + MembraneProperties2CaPools, channel_populations: 'list of ChannelPopulation(s) (optional)' = None, channel_densities: 'list of ChannelDensity(s) (optional)' = None, channel_density_v_shifts: 'list of ChannelDensityVShift(s) (optional)' = None, @@ -3850,8 +3906,10 @@ variable = MembraneProperties2CaPools( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BiophysicalProperties +from neuroml.utils import component_factory -variable = BiophysicalProperties( +variable = component_factory( + BiophysicalProperties, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -3985,8 +4043,10 @@ variable = BiophysicalProperties( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BiophysicalProperties2CaPools +from neuroml.utils import component_factory -variable = BiophysicalProperties2CaPools( +variable = component_factory( + BiophysicalProperties2CaPools, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -4075,8 +4135,10 @@ variable = BiophysicalProperties2CaPools( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IntracellularProperties +from neuroml.utils import component_factory -variable = IntracellularProperties( +variable = component_factory( + IntracellularProperties, species: 'list of Species(s) (optional)' = None, resistivities: 'list of Resistivity(s) (optional)' = None, extensiontype_=None, @@ -4183,8 +4245,10 @@ extends {ref}`schema:intracellularproperties` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IntracellularProperties2CaPools +from neuroml.utils import component_factory -variable = IntracellularProperties2CaPools( +variable = component_factory( + IntracellularProperties2CaPools, species: 'list of Species(s) (optional)' = None, resistivities: 'list of Resistivity(s) (optional)' = None, ) @@ -4242,8 +4306,10 @@ variable = IntracellularProperties2CaPools( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Resistivity +from neuroml.utils import component_factory -variable = Resistivity( +variable = component_factory( + Resistivity, value: 'a Nml2Quantity_resistivity (required)' = None, segment_groups: 'a NmlId (optional)' = 'all', ) @@ -4485,8 +4551,10 @@ extends {ref}`schema:concentrationmodel` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import DecayingPoolConcentrationModel +from neuroml.utils import component_factory -variable = DecayingPoolConcentrationModel( +variable = component_factory( + DecayingPoolConcentrationModel, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -4630,8 +4698,10 @@ extends {ref}`schema:concentrationmodel` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import FixedFactorConcentrationModel +from neuroml.utils import component_factory -variable = FixedFactorConcentrationModel( +variable = component_factory( + FixedFactorConcentrationModel, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -4857,8 +4927,10 @@ extends {ref}`schema:concentrationmodel` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Species +from neuroml.utils import component_factory -variable = Species( +variable = component_factory( + Species, id: 'a NmlId (required)' = None, concentration_model: 'a NmlId (required)' = None, ion: 'a NmlId (optional)' = None, @@ -5034,8 +5106,10 @@ extends *{ref}`schema:basecellmembpot`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Cell +from neuroml.utils import component_factory -variable = Cell( +variable = component_factory( + Cell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -5319,8 +5393,10 @@ extends {ref}`schema:cell` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Cell2CaPools +from neuroml.utils import component_factory -variable = Cell2CaPools( +variable = component_factory( + Cell2CaPools, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -5410,8 +5486,10 @@ extends *{ref}`schema:basecellmembpot`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BaseCellMembPotCap +from neuroml.utils import component_factory -variable = BaseCellMembPotCap( +variable = component_factory( + BaseCellMembPotCap, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -5585,8 +5663,10 @@ extends *{ref}`schema:baseiaf`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IafTauCell +from neuroml.utils import component_factory -variable = IafTauCell( +variable = component_factory( + IafTauCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -5721,8 +5801,10 @@ extends {ref}`schema:iaftaucell` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IafTauRefCell +from neuroml.utils import component_factory -variable = IafTauRefCell( +variable = component_factory( + IafTauRefCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -5928,8 +6010,10 @@ extends *{ref}`schema:baseiafcapcell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IafCell +from neuroml.utils import component_factory -variable = IafCell( +variable = component_factory( + IafCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -6091,8 +6175,10 @@ extends {ref}`schema:iafcell` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IafRefCell +from neuroml.utils import component_factory -variable = IafRefCell( +variable = component_factory( + IafRefCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -6262,8 +6348,10 @@ extends *{ref}`schema:basecellmembpot`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IzhikevichCell +from neuroml.utils import component_factory -variable = IzhikevichCell( +variable = component_factory( + IzhikevichCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -6431,8 +6519,10 @@ extends *{ref}`schema:basecellmembpotcap`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Izhikevich2007Cell +from neuroml.utils import component_factory -variable = Izhikevich2007Cell( +variable = component_factory( + Izhikevich2007Cell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -6613,8 +6703,10 @@ extends *{ref}`schema:basecellmembpotcap`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import AdExIaFCell +from neuroml.utils import component_factory -variable = AdExIaFCell( +variable = component_factory( + AdExIaFCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -6743,8 +6835,10 @@ extends *{ref}`schema:basecellmembpotdl`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import FitzHughNagumoCell +from neuroml.utils import component_factory -variable = FitzHughNagumoCell( +variable = component_factory( + FitzHughNagumoCell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -6986,8 +7080,10 @@ extends *{ref}`schema:basecellmembpot`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import PinskyRinzelCA3Cell +from neuroml.utils import component_factory -variable = PinskyRinzelCA3Cell( +variable = component_factory( + PinskyRinzelCA3Cell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -7201,8 +7297,10 @@ extends *{ref}`schema:basecellmembpotcap`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import HindmarshRose1984Cell +from neuroml.utils import component_factory -variable = HindmarshRose1984Cell( +variable = component_factory( + HindmarshRose1984Cell, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, diff --git a/source/Userdocs/Schemas/Channels.md b/source/Userdocs/Schemas/Channels.md index f3eaddd0..bd3a0af1 100644 --- a/source/Userdocs/Schemas/Channels.md +++ b/source/Userdocs/Schemas/Channels.md @@ -1283,8 +1283,10 @@ extends *{ref}`schema:baseconductancescaling`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Q10ConductanceScaling +from neuroml.utils import component_factory -variable = Q10ConductanceScaling( +variable = component_factory( + Q10ConductanceScaling, q10_factor: 'a Nml2Quantity_none (required)' = None, experimental_temp: 'a Nml2Quantity_temperature (required)' = None, ) @@ -1465,8 +1467,10 @@ extends *{ref}`schema:basegate`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateHHUndetermined +from neuroml.utils import component_factory -variable = GateHHUndetermined( +variable = component_factory( + GateHHUndetermined, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, type: 'a gateTypes (required)' = None, @@ -1612,8 +1616,10 @@ extends {ref}`schema:gate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateHHRates +from neuroml.utils import component_factory -variable = GateHHRates( +variable = component_factory( + GateHHRates, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, @@ -1772,8 +1778,10 @@ extends {ref}`schema:gate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateHHTauInf +from neuroml.utils import component_factory -variable = GateHHTauInf( +variable = component_factory( + GateHHTauInf, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, @@ -1890,8 +1898,10 @@ extends {ref}`schema:gate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateHHInstantaneous +from neuroml.utils import component_factory -variable = GateHHInstantaneous( +variable = component_factory( + GateHHInstantaneous, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, @@ -2034,8 +2044,10 @@ extends {ref}`schema:gate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateHHRatesTau +from neuroml.utils import component_factory -variable = GateHHRatesTau( +variable = component_factory( + GateHHRatesTau, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, @@ -2180,8 +2192,10 @@ extends {ref}`schema:gate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateHHRatesInf +from neuroml.utils import component_factory -variable = GateHHRatesInf( +variable = component_factory( + GateHHRatesInf, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, @@ -2329,8 +2343,10 @@ extends {ref}`schema:gate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateHHRatesTauInf +from neuroml.utils import component_factory -variable = GateHHRatesTauInf( +variable = component_factory( + GateHHRatesTauInf, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, @@ -2438,8 +2454,10 @@ extends {ref}`schema:gate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateFractional +from neuroml.utils import component_factory -variable = GateFractional( +variable = component_factory( + GateFractional, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, @@ -2572,8 +2590,10 @@ variable = GateFractional( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateFractionalSubgate +from neuroml.utils import component_factory -variable = GateFractionalSubgate( +variable = component_factory( + GateFractionalSubgate, id: 'a NmlId (required)' = None, fractional_conductance: 'a Nml2Quantity_none (required)' = None, notes: 'a string (optional)' = None, @@ -2841,8 +2861,10 @@ extends *{ref}`schema:baseionchannel`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IonChannelHH +from neuroml.utils import component_factory -variable = IonChannelHH( +variable = component_factory( + IonChannelHH, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2988,8 +3010,10 @@ extends {ref}`schema:ionchannelhh` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IonChannel +from neuroml.utils import component_factory -variable = IonChannel( +variable = component_factory( + IonChannel, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -3091,8 +3115,10 @@ extends {ref}`schema:ionchannel` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IonChannelVShift +from neuroml.utils import component_factory -variable = IonChannelVShift( +variable = component_factory( + IonChannelVShift, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -3229,8 +3255,10 @@ extends {ref}`schema:ksstate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ClosedState +from neuroml.utils import component_factory -variable = ClosedState( +variable = component_factory( + ClosedState, id: 'a NmlId (required)' = None, ) ``` @@ -3291,8 +3319,10 @@ extends {ref}`schema:ksstate` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import OpenState +from neuroml.utils import component_factory -variable = OpenState( +variable = component_factory( + OpenState, id: 'a NmlId (required)' = None, ) ``` @@ -3412,8 +3442,10 @@ extends *{ref}`schema:baseionchannel`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IonChannelKS +from neuroml.utils import component_factory -variable = IonChannelKS( +variable = component_factory( + IonChannelKS, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -3543,8 +3575,10 @@ extends {ref}`schema:kstransition` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ForwardTransition +from neuroml.utils import component_factory -variable = ForwardTransition( +variable = component_factory( + ForwardTransition, id: 'a NmlId (required)' = None, from_: 'a NmlId (required)' = None, to: 'a NmlId (required)' = None, @@ -3645,8 +3679,10 @@ extends {ref}`schema:kstransition` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ReverseTransition +from neuroml.utils import component_factory -variable = ReverseTransition( +variable = component_factory( + ReverseTransition, id: 'a NmlId (required)' = None, from_: 'a NmlId (required)' = None, to: 'a NmlId (required)' = None, @@ -3826,8 +3862,10 @@ extends {ref}`schema:kstransition` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import TauInfTransition +from neuroml.utils import component_factory -variable = TauInfTransition( +variable = component_factory( + TauInfTransition, id: 'a NmlId (required)' = None, from_: 'a NmlId (required)' = None, to: 'a NmlId (required)' = None, @@ -3938,8 +3976,10 @@ extends *{ref}`schema:basegate`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GateKS +from neuroml.utils import component_factory -variable = GateKS( +variable = component_factory( + GateKS, id: 'a NmlId (required)' = None, instances: 'a PositiveInteger (required)' = None, notes: 'a string (optional)' = None, diff --git a/source/Userdocs/Schemas/Index.md b/source/Userdocs/Schemas/Index.md index 4ad887f2..28de6882 100644 --- a/source/Userdocs/Schemas/Index.md +++ b/source/Userdocs/Schemas/Index.md @@ -474,6 +474,9 @@ - {ref}`include ` + + +- {ref}`IncludeType ` - {ref}`inhomogeneousParameter ` @@ -561,6 +564,9 @@ - {ref}`networkWithTemperature ` + + +- {ref}`NeuroMLDocument ` - {ref}`notes ` diff --git a/source/Userdocs/Schemas/Inputs.md b/source/Userdocs/Schemas/Inputs.md index a71318d7..7e4b2a3c 100644 --- a/source/Userdocs/Schemas/Inputs.md +++ b/source/Userdocs/Schemas/Inputs.md @@ -344,8 +344,10 @@ extends *{ref}`schema:basespikesource`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpikeGenerator +from neuroml.utils import component_factory -variable = SpikeGenerator( +variable = component_factory( + SpikeGenerator, id: 'a NonNegativeInteger (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -488,8 +490,10 @@ extends *{ref}`schema:basespikesource`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpikeGeneratorRandom +from neuroml.utils import component_factory -variable = SpikeGeneratorRandom( +variable = component_factory( + SpikeGeneratorRandom, id: 'a NonNegativeInteger (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -636,8 +640,10 @@ extends *{ref}`schema:basespikesource`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpikeGeneratorPoisson +from neuroml.utils import component_factory -variable = SpikeGeneratorPoisson( +variable = component_factory( + SpikeGeneratorPoisson, id: 'a NonNegativeInteger (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -786,8 +792,10 @@ extends {ref}`schema:spikegeneratorpoisson` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpikeGeneratorRefPoisson +from neuroml.utils import component_factory -variable = SpikeGeneratorRefPoisson( +variable = component_factory( + SpikeGeneratorRefPoisson, id: 'a NonNegativeInteger (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1008,8 +1016,10 @@ extends *{ref}`schema:basevoltagedeppointcurrentspiking`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import PoissonFiringSynapse +from neuroml.utils import component_factory -variable = PoissonFiringSynapse( +variable = component_factory( + PoissonFiringSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1236,8 +1246,10 @@ extends *{ref}`schema:basevoltagedeppointcurrentspiking`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import TransientPoissonFiringSynapse +from neuroml.utils import component_factory -variable = TransientPoissonFiringSynapse( +variable = component_factory( + TransientPoissonFiringSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1425,8 +1437,10 @@ extends *{ref}`schema:basevoltagedeppointcurrentspiking`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import TimedSynapticInput +from neuroml.utils import component_factory -variable = TimedSynapticInput( +variable = component_factory( + TimedSynapticInput, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1568,8 +1582,10 @@ extends *{ref}`schema:basespikesource`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpikeArray +from neuroml.utils import component_factory -variable = SpikeArray( +variable = component_factory( + SpikeArray, id: 'a NonNegativeInteger (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1706,8 +1722,10 @@ extends *{ref}`schema:basespikesource`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Spike +from neuroml.utils import component_factory -variable = Spike( +variable = component_factory( + Spike, id: 'a NonNegativeInteger (required)' = None, time: 'a Nml2Quantity_time (required)' = None, ) @@ -1849,8 +1867,10 @@ extends *{ref}`schema:basepointcurrent`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import PulseGenerator +from neuroml.utils import component_factory -variable = PulseGenerator( +variable = component_factory( + PulseGenerator, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1987,8 +2007,10 @@ extends *{ref}`schema:basepointcurrent`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import CompoundInput +from neuroml.utils import component_factory -variable = CompoundInput( +variable = component_factory( + CompoundInput, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2123,8 +2145,10 @@ extends *{ref}`schema:basepointcurrentdl`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import CompoundInputDL +from neuroml.utils import component_factory -variable = CompoundInputDL( +variable = component_factory( + CompoundInputDL, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2261,8 +2285,10 @@ extends *{ref}`schema:basepointcurrentdl`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import PulseGeneratorDL +from neuroml.utils import component_factory -variable = PulseGeneratorDL( +variable = component_factory( + PulseGeneratorDL, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2403,8 +2429,10 @@ extends *{ref}`schema:basepointcurrent`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SineGenerator +from neuroml.utils import component_factory -variable = SineGenerator( +variable = component_factory( + SineGenerator, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2555,8 +2583,10 @@ extends *{ref}`schema:basepointcurrentdl`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SineGeneratorDL +from neuroml.utils import component_factory -variable = SineGeneratorDL( +variable = component_factory( + SineGeneratorDL, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2701,8 +2731,10 @@ extends *{ref}`schema:basepointcurrent`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import RampGenerator +from neuroml.utils import component_factory -variable = RampGenerator( +variable = component_factory( + RampGenerator, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2852,8 +2884,10 @@ extends *{ref}`schema:basepointcurrentdl`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import RampGeneratorDL +from neuroml.utils import component_factory -variable = RampGeneratorDL( +variable = component_factory( + RampGeneratorDL, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -3005,8 +3039,10 @@ extends *{ref}`schema:basevoltagedeppointcurrent`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import VoltageClamp +from neuroml.utils import component_factory -variable = VoltageClamp( +variable = component_factory( + VoltageClamp, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -3163,8 +3199,10 @@ extends *{ref}`schema:basevoltagedeppointcurrent`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import VoltageClampTriple +from neuroml.utils import component_factory -variable = VoltageClampTriple( +variable = component_factory( + VoltageClampTriple, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, diff --git a/source/Userdocs/Schemas/Networks.md b/source/Userdocs/Schemas/Networks.md index 95b5e466..004b20dc 100644 --- a/source/Userdocs/Schemas/Networks.md +++ b/source/Userdocs/Schemas/Networks.md @@ -79,8 +79,10 @@ extends *{ref}`schema:basestandalone`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Network +from neuroml.utils import component_factory -variable = Network( +variable = component_factory( + Network, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -280,8 +282,10 @@ extends *{ref}`schema:basepopulation`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Population +from neuroml.utils import component_factory -variable = Population( +variable = component_factory( + Population, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -392,8 +396,10 @@ extends *{ref}`schema:basepopulation`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Instance +from neuroml.utils import component_factory -variable = Instance( +variable = component_factory( + Instance, id: 'a nonNegativeInteger (optional)' = None, i: 'a nonNegativeInteger (optional)' = None, j: 'a nonNegativeInteger (optional)' = None, @@ -464,8 +470,10 @@ variable = Instance( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Location +from neuroml.utils import component_factory -variable = Location( +variable = component_factory( + Location, x: 'a float (required)' = None, y: 'a float (required)' = None, z: 'a float (required)' = None, @@ -527,8 +535,10 @@ variable = Location( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Region +from neuroml.utils import component_factory -variable = Region( +variable = component_factory( + Region, id: 'a NmlId (required)' = None, spaces: 'a NmlId (optional)' = None, anytypeobjs_=None, @@ -631,8 +641,10 @@ variable = Region( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Projection +from neuroml.utils import component_factory -variable = Projection( +variable = component_factory( + Projection, id: 'a NmlId (required)' = None, presynaptic_population: 'a NmlId (required)' = None, postsynaptic_population: 'a NmlId (required)' = None, @@ -747,8 +759,10 @@ variable = Projection( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Connection +from neuroml.utils import component_factory -variable = Connection( +variable = component_factory( + Connection, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell_id: 'a Nml2PopulationReferencePath (required)' = None, @@ -841,8 +855,10 @@ extends {ref}`schema:explicitconnection` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SynapticConnection +from neuroml.utils import component_factory -variable = SynapticConnection( +variable = component_factory( + SynapticConnection, neuro_lex_id: 'a NeuroLexId (optional)' = None, from_: 'a Nml2PopulationReferencePath (required)' = None, to: 'a Nml2PopulationReferencePath (required)' = None, @@ -962,8 +978,10 @@ extends {ref}`schema:connection` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ConnectionWD +from neuroml.utils import component_factory -variable = ConnectionWD( +variable = component_factory( + ConnectionWD, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell_id: 'a Nml2PopulationReferencePath (required)' = None, @@ -1029,8 +1047,10 @@ variable = ConnectionWD( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ElectricalConnection +from neuroml.utils import component_factory -variable = ElectricalConnection( +variable = component_factory( + ElectricalConnection, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell: 'a string (required)' = None, @@ -1112,8 +1132,10 @@ variable = ElectricalConnection( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ElectricalConnectionInstance +from neuroml.utils import component_factory -variable = ElectricalConnectionInstance( +variable = component_factory( + ElectricalConnectionInstance, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell: 'a string (required)' = None, @@ -1201,8 +1223,10 @@ extends {ref}`schema:electricalconnectioninstance` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ElectricalConnectionInstanceW +from neuroml.utils import component_factory -variable = ElectricalConnectionInstanceW( +variable = component_factory( + ElectricalConnectionInstanceW, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell: 'a string (required)' = None, @@ -1274,8 +1298,10 @@ variable = ElectricalConnectionInstanceW( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ElectricalProjection +from neuroml.utils import component_factory -variable = ElectricalProjection( +variable = component_factory( + ElectricalProjection, id: 'a NmlId (required)' = None, presynaptic_population: 'a NmlId (required)' = None, postsynaptic_population: 'a NmlId (required)' = None, @@ -1340,8 +1366,10 @@ variable = ElectricalProjection( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ContinuousConnection +from neuroml.utils import component_factory -variable = ContinuousConnection( +variable = component_factory( + ContinuousConnection, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell: 'a string (required)' = None, @@ -1428,8 +1456,10 @@ variable = ContinuousConnection( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ContinuousConnectionInstance +from neuroml.utils import component_factory -variable = ContinuousConnectionInstance( +variable = component_factory( + ContinuousConnectionInstance, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell: 'a string (required)' = None, @@ -1513,8 +1543,10 @@ extends {ref}`schema:continuousconnectioninstance` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ContinuousConnectionInstanceW +from neuroml.utils import component_factory -variable = ContinuousConnectionInstanceW( +variable = component_factory( + ContinuousConnectionInstanceW, id: 'a NonNegativeInteger (required)' = None, neuro_lex_id: 'a NeuroLexId (optional)' = None, pre_cell: 'a string (required)' = None, @@ -1592,8 +1624,10 @@ variable = ContinuousConnectionInstanceW( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ContinuousProjection +from neuroml.utils import component_factory -variable = ContinuousProjection( +variable = component_factory( + ContinuousProjection, id: 'a NmlId (required)' = None, presynaptic_population: 'a NmlId (required)' = None, postsynaptic_population: 'a NmlId (required)' = None, @@ -1685,8 +1719,10 @@ variable = ContinuousProjection( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ExplicitInput +from neuroml.utils import component_factory -variable = ExplicitInput( +variable = component_factory( + ExplicitInput, target: 'a Nml2PopulationReferencePath (required)' = None, input: 'a NmlId (required)' = None, destination: 'a NmlId (optional)' = None, @@ -1771,8 +1807,10 @@ variable = ExplicitInput( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import InputList +from neuroml.utils import component_factory -variable = InputList( +variable = component_factory( + InputList, id: 'a NonNegativeInteger (required)' = None, populations: 'a NmlId (required)' = None, component: 'a NmlId (required)' = None, @@ -1853,8 +1891,10 @@ variable = InputList( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Input +from neuroml.utils import component_factory -variable = Input( +variable = component_factory( + Input, id: 'a NonNegativeInteger (required)' = None, target: 'a Nml2PopulationReferencePath (required)' = None, destination: 'a NmlId (required)' = None, @@ -1940,8 +1980,10 @@ extends {ref}`schema:input` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import InputW +from neuroml.utils import component_factory -variable = InputW( +variable = component_factory( + InputW, id: 'a NonNegativeInteger (required)' = None, target: 'a Nml2PopulationReferencePath (required)' = None, destination: 'a NmlId (required)' = None, diff --git a/source/Userdocs/Schemas/NeuroMLCoreCompTypes.md b/source/Userdocs/Schemas/NeuroMLCoreCompTypes.md index 3deb885c..0119eaf9 100644 --- a/source/Userdocs/Schemas/NeuroMLCoreCompTypes.md +++ b/source/Userdocs/Schemas/NeuroMLCoreCompTypes.md @@ -103,8 +103,10 @@ Please file any issues or questions at the [issue tracker here](https://github.c *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Annotation +from neuroml.utils import component_factory -variable = Annotation( +variable = component_factory( + Annotation, anytypeobjs_=None, ) ``` @@ -166,8 +168,10 @@ variable = Annotation( *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Property +from neuroml.utils import component_factory -variable = Property( +variable = component_factory( + Property, tag: 'a string (required)' = None, value: 'a string (required)' = None, ) @@ -736,8 +740,10 @@ extends *{ref}`schema:basebqbiol`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import Point3DWithDiam +from neuroml.utils import component_factory -variable = Point3DWithDiam( +variable = component_factory( + Point3DWithDiam, x: 'a double (required)' = None, y: 'a double (required)' = None, z: 'a double (required)' = None, diff --git a/source/Userdocs/Schemas/NeuroMLDocument.md b/source/Userdocs/Schemas/NeuroMLDocument.md new file mode 100644 index 00000000..cedf46ee --- /dev/null +++ b/source/Userdocs/Schemas/NeuroMLDocument.md @@ -0,0 +1,199 @@ +(schema:neuroml_main_)= +# NeuroMLDocument + +**The main NeuroML container class, and other associated types that do not fit into the other categories** + +--- + + +Schema against which NeuroML based on these should be valid: [NeuroML_v2.3.xsd](https://github.com/NeuroML/NeuroML2/tree/master/Schemas/NeuroML2/NeuroML_v2.3.xsd). +Please file any issues or questions at the [issue tracker here](https://github.com/NeuroML/NeuroML2/issues). + +--- + +(schema:neuromldocument)= +## NeuroMLDocument + +`````{tab-set} +````{tab-item} Schema +```{code-block} xml + + + The root NeuroML element. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +``` +```` + +````{tab-item} Usage: Python +*Go to the libNeuroML documentation* +```{code-block} python +from neuroml import NeuroMLDocument +from neuroml.utils import component_factory + +variable = component_factory( + NeuroMLDocument, + id: 'a NmlId (required)' = None + metaid: 'a MetaId (optional)' = None + notes: 'a string (optional)' = None + properties: 'list of Property(s) (optional)' = None + annotation: 'a Annotation (optional)' = None + includes: 'list of IncludeType(s) (optional)' = None + extracellular_properties: 'list of ExtracellularProperties(s) (optional)' = None + intracellular_properties: 'list of IntracellularProperties(s) (optional)' = None + morphology: 'list of Morphology(s) (optional)' = None + ion_channel: 'list of IonChannel(s) (optional)' = None + ion_channel_hhs: 'list of IonChannelHH(s) (optional)' = None + ion_channel_v_shifts: 'list of IonChannelVShift(s) (optional)' = None + ion_channel_kses: 'list of IonChannelKS(s) (optional)' = None + decaying_pool_concentration_models: 'list of DecayingPoolConcentrationModel(s) (optional)' = None + fixed_factor_concentration_models: 'list of FixedFactorConcentrationModel(s) (optional)' = None + alpha_current_synapses: 'list of AlphaCurrentSynapse(s) (optional)' = None + alpha_synapses: 'list of AlphaSynapse(s) (optional)' = None + exp_one_synapses: 'list of ExpOneSynapse(s) (optional)' = None + exp_two_synapses: 'list of ExpTwoSynapse(s) (optional)' = None + exp_three_synapses: 'list of ExpThreeSynapse(s) (optional)' = None + blocking_plastic_synapses: 'list of BlockingPlasticSynapse(s) (optional)' = None + double_synapses: 'list of DoubleSynapse(s) (optional)' = None + gap_junctions: 'list of GapJunction(s) (optional)' = None + silent_synapses: 'list of SilentSynapse(s) (optional)' = None + linear_graded_synapses: 'list of LinearGradedSynapse(s) (optional)' = None + graded_synapses: 'list of GradedSynapse(s) (optional)' = None + biophysical_properties: 'list of BiophysicalProperties(s) (optional)' = None + cells: 'list of Cell(s) (optional)' = None + cell2_ca_poolses: 'list of Cell2CaPools(s) (optional)' = None + base_cells: 'list of BaseCell(s) (optional)' = None + iaf_tau_cells: 'list of IafTauCell(s) (optional)' = None + iaf_tau_ref_cells: 'list of IafTauRefCell(s) (optional)' = None + iaf_cells: 'list of IafCell(s) (optional)' = None + iaf_ref_cells: 'list of IafRefCell(s) (optional)' = None + izhikevich_cells: 'list of IzhikevichCell(s) (optional)' = None + izhikevich2007_cells: 'list of Izhikevich2007Cell(s) (optional)' = None + ad_ex_ia_f_cells: 'list of AdExIaFCell(s) (optional)' = None + fitz_hugh_nagumo_cells: 'list of FitzHughNagumoCell(s) (optional)' = None + fitz_hugh_nagumo1969_cells: 'list of FitzHughNagumo1969Cell(s) (optional)' = None + pinsky_rinzel_ca3_cells: 'list of PinskyRinzelCA3Cell(s) (optional)' = None + hindmarshRose1984Cell: 'list of HindmarshRose1984Cell(s) (optional)' = None + pulse_generators: 'list of PulseGenerator(s) (optional)' = None + pulse_generator_dls: 'list of PulseGeneratorDL(s) (optional)' = None + sine_generators: 'list of SineGenerator(s) (optional)' = None + sine_generator_dls: 'list of SineGeneratorDL(s) (optional)' = None + ramp_generators: 'list of RampGenerator(s) (optional)' = None + ramp_generator_dls: 'list of RampGeneratorDL(s) (optional)' = None + compound_inputs: 'list of CompoundInput(s) (optional)' = None + compound_input_dls: 'list of CompoundInputDL(s) (optional)' = None + voltage_clamps: 'list of VoltageClamp(s) (optional)' = None + voltage_clamp_triples: 'list of VoltageClampTriple(s) (optional)' = None + spike_arrays: 'list of SpikeArray(s) (optional)' = None + timed_synaptic_inputs: 'list of TimedSynapticInput(s) (optional)' = None + spike_generators: 'list of SpikeGenerator(s) (optional)' = None + spike_generator_randoms: 'list of SpikeGeneratorRandom(s) (optional)' = None + spike_generator_poissons: 'list of SpikeGeneratorPoisson(s) (optional)' = None + spike_generator_ref_poissons: 'list of SpikeGeneratorRefPoisson(s) (optional)' = None + poisson_firing_synapses: 'list of PoissonFiringSynapse(s) (optional)' = None + transient_poisson_firing_synapses: 'list of TransientPoissonFiringSynapse(s) (optional)' = None + IF_curr_alpha: 'list of IF_curr_alpha(s) (optional)' = None + IF_curr_exp: 'list of IF_curr_exp(s) (optional)' = None + IF_cond_alpha: 'list of IF_cond_alpha(s) (optional)' = None + IF_cond_exp: 'list of IF_cond_exp(s) (optional)' = None + EIF_cond_exp_isfa_ista: 'list of EIF_cond_exp_isfa_ista(s) (optional)' = None + EIF_cond_alpha_isfa_ista: 'list of EIF_cond_alpha_isfa_ista(s) (optional)' = None + HH_cond_exp: 'list of HH_cond_exp(s) (optional)' = None + exp_cond_synapses: 'list of ExpCondSynapse(s) (optional)' = None + alpha_cond_synapses: 'list of AlphaCondSynapse(s) (optional)' = None + exp_curr_synapses: 'list of ExpCurrSynapse(s) (optional)' = None + alpha_curr_synapses: 'list of AlphaCurrSynapse(s) (optional)' = None + SpikeSourcePoisson: 'list of SpikeSourcePoisson(s) (optional)' = None + networks: 'list of Network(s) (optional)' = None + ComponentType: 'list of ComponentType(s) (optional)' = None +``` +```` + +````{tab-item} Usage: XML +```{code-block} xml + + + + Simple pulse generator + + + + + + + + + + + + + + +``` +```` +````` + +(schema:includetype)= +## IncludeType + + +Used to include other documents into each other. + +`````{tab-set} +````{tab-item} Schema +```{code-block} xml + + + +``` +```` + +````{tab-item} Usage: Python +*Go to the libNeuroML documentation* +```{code-block} python +from neuroml import IncludeType +from neuroml.utils import component_factory + +variable = component_factory( + IncludeType, + href: 'a anyURI (required)' = None) +``` +```` + +````{tab-item} Usage: XML +```{code-block} xml + + + .. + +``` +```` +````` diff --git a/source/Userdocs/Schemas/PyNN.md b/source/Userdocs/Schemas/PyNN.md index cd18d324..8835b718 100644 --- a/source/Userdocs/Schemas/PyNN.md +++ b/source/Userdocs/Schemas/PyNN.md @@ -391,8 +391,10 @@ extends *{ref}`schema:basepynniafcell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IF_curr_alpha +from neuroml.utils import component_factory -variable = IF_curr_alpha( +variable = component_factory( + IF_curr_alpha, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -555,8 +557,10 @@ extends *{ref}`schema:basepynniafcell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IF_curr_exp +from neuroml.utils import component_factory -variable = IF_curr_exp( +variable = component_factory( + IF_curr_exp, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -721,8 +725,10 @@ extends *{ref}`schema:basepynniafcondcell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IF_cond_alpha +from neuroml.utils import component_factory -variable = IF_cond_alpha( +variable = component_factory( + IF_cond_alpha, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -892,8 +898,10 @@ extends *{ref}`schema:basepynniafcondcell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import IF_cond_exp +from neuroml.utils import component_factory -variable = IF_cond_exp( +variable = component_factory( + IF_cond_exp, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1095,8 +1103,10 @@ extends *{ref}`schema:basepynniafcondcell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import EIF_cond_exp_isfa_ista +from neuroml.utils import component_factory -variable = EIF_cond_exp_isfa_ista( +variable = component_factory( + EIF_cond_exp_isfa_ista, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1299,8 +1309,10 @@ extends *{ref}`schema:basepynniafcondcell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import EIF_cond_alpha_isfa_ista +from neuroml.utils import component_factory -variable = EIF_cond_alpha_isfa_ista( +variable = component_factory( + EIF_cond_alpha_isfa_ista, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1489,8 +1501,10 @@ extends *{ref}`schema:basepynncell`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import HH_cond_exp +from neuroml.utils import component_factory -variable = HH_cond_exp( +variable = component_factory( + HH_cond_exp, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1610,8 +1624,10 @@ extends *{ref}`schema:basevoltagedepsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BasePynnSynapse +from neuroml.utils import component_factory -variable = BasePynnSynapse( +variable = component_factory( + BasePynnSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1754,8 +1770,10 @@ extends *{ref}`schema:basepynnsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ExpCondSynapse +from neuroml.utils import component_factory -variable = ExpCondSynapse( +variable = component_factory( + ExpCondSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1901,8 +1919,10 @@ extends *{ref}`schema:basepynnsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ExpCurrSynapse +from neuroml.utils import component_factory -variable = ExpCurrSynapse( +variable = component_factory( + ExpCurrSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2052,8 +2072,10 @@ extends *{ref}`schema:basepynnsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import AlphaCondSynapse +from neuroml.utils import component_factory -variable = AlphaCondSynapse( +variable = component_factory( + AlphaCondSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2202,8 +2224,10 @@ extends *{ref}`schema:basepynnsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import AlphaCurrSynapse +from neuroml.utils import component_factory -variable = AlphaCurrSynapse( +variable = component_factory( + AlphaCurrSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2368,8 +2392,10 @@ extends *{ref}`schema:basespikesource`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SpikeSourcePoisson +from neuroml.utils import component_factory -variable = SpikeSourcePoisson( +variable = component_factory( + SpikeSourcePoisson, id: 'a NonNegativeInteger (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, diff --git a/source/Userdocs/Schemas/Synapses.md b/source/Userdocs/Schemas/Synapses.md index 58064830..29a7f772 100644 --- a/source/Userdocs/Schemas/Synapses.md +++ b/source/Userdocs/Schemas/Synapses.md @@ -70,8 +70,10 @@ extends *{ref}`schema:basepointcurrent`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BaseSynapse +from neuroml.utils import component_factory -variable = BaseSynapse( +variable = component_factory( + BaseSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -149,8 +151,10 @@ extends *{ref}`schema:basesynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BaseVoltageDepSynapse +from neuroml.utils import component_factory -variable = BaseVoltageDepSynapse( +variable = component_factory( + BaseVoltageDepSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -257,8 +261,10 @@ extends *{ref}`schema:basesynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BaseCurrentBasedSynapse +from neuroml.utils import component_factory -variable = BaseCurrentBasedSynapse( +variable = component_factory( + BaseCurrentBasedSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -394,8 +400,10 @@ extends *{ref}`schema:basecurrentbasedsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import AlphaCurrentSynapse +from neuroml.utils import component_factory -variable = AlphaCurrentSynapse( +variable = component_factory( + AlphaCurrentSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -490,8 +498,10 @@ extends *{ref}`schema:basevoltagedepsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BaseConductanceBasedSynapse +from neuroml.utils import component_factory -variable = BaseConductanceBasedSynapse( +variable = component_factory( + BaseConductanceBasedSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -589,8 +599,10 @@ extends *{ref}`schema:basevoltagedepsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BaseConductanceBasedSynapseTwo +from neuroml.utils import component_factory -variable = BaseConductanceBasedSynapseTwo( +variable = component_factory( + BaseConductanceBasedSynapseTwo, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -738,8 +750,10 @@ extends *{ref}`schema:baseconductancebasedsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ExpOneSynapse +from neuroml.utils import component_factory -variable = ExpOneSynapse( +variable = component_factory( + ExpOneSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -900,8 +914,10 @@ extends *{ref}`schema:baseconductancebasedsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import AlphaSynapse +from neuroml.utils import component_factory -variable = AlphaSynapse( +variable = component_factory( + AlphaSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1082,8 +1098,10 @@ extends *{ref}`schema:baseconductancebasedsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ExpTwoSynapse +from neuroml.utils import component_factory -variable = ExpTwoSynapse( +variable = component_factory( + ExpTwoSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1293,8 +1311,10 @@ extends *{ref}`schema:baseconductancebasedsynapsetwo`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import ExpThreeSynapse +from neuroml.utils import component_factory -variable = ExpThreeSynapse( +variable = component_factory( + ExpThreeSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -1840,8 +1860,10 @@ extends {ref}`schema:exptwosynapse` *Go to the libNeuroML documentation* ```{code-block} python from neuroml import BlockingPlasticSynapse +from neuroml.utils import component_factory -variable = BlockingPlasticSynapse( +variable = component_factory( + BlockingPlasticSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2035,8 +2057,10 @@ extends *{ref}`schema:basevoltagedepsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import DoubleSynapse +from neuroml.utils import component_factory -variable = DoubleSynapse( +variable = component_factory( + DoubleSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2322,8 +2346,10 @@ extends *{ref}`schema:basesynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GapJunction +from neuroml.utils import component_factory -variable = GapJunction( +variable = component_factory( + GapJunction, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2489,8 +2515,10 @@ extends *{ref}`schema:basegradedsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import SilentSynapse +from neuroml.utils import component_factory -variable = SilentSynapse( +variable = component_factory( + SilentSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2620,8 +2648,10 @@ extends *{ref}`schema:basegradedsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import LinearGradedSynapse +from neuroml.utils import component_factory -variable = LinearGradedSynapse( +variable = component_factory( + LinearGradedSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, @@ -2786,8 +2816,10 @@ extends *{ref}`schema:basegradedsynapse`* *Go to the libNeuroML documentation* ```{code-block} python from neuroml import GradedSynapse +from neuroml.utils import component_factory -variable = GradedSynapse( +variable = component_factory( + GradedSynapse, id: 'a NmlId (required)' = None, metaid: 'a MetaId (optional)' = None, notes: 'a string (optional)' = None, diff --git a/source/_toc.yml b/source/_toc.yml index 12047a10..7419f978 100644 --- a/source/_toc.yml +++ b/source/_toc.yml @@ -48,6 +48,7 @@ parts: sections: - file: Userdocs/NeuroMLv2 sections: + - file: Userdocs/Schemas/NeuroMLDocument - file: Userdocs/Schemas/NeuroMLCoreDimensions - file: Userdocs/Schemas/NeuroMLCoreCompTypes - file: Userdocs/Schemas/Cells