Merge branch 'development' into experimental

doc/component-list.json

@@ -0,0 +1 @@
+{"Cells": ["baseCell", "baseSpikingCell", "baseCellMembPot", "baseCellMembPotDL", "baseChannelPopulation", "channelPopulation", "channelPopulationNernst", "baseChannelDensity", "baseChannelDensityCond", "variableParameter", "inhomogeneousValue", "channelDensityNonUniform", "channelDensityNonUniformNernst", "channelDensityNonUniformGHK", "channelDensity", "channelDensityVShift", "channelDensityNernst", "channelDensityNernstCa2", "channelDensityGHK", "channelDensityGHK2", "pointCellCondBased", "pointCellCondBasedCa", "distal", "proximal", "parent", "segment", "segmentGroup", "member", "from", "to", "include", "path", "subTree", "inhomogeneousParameter", "proximalDetails", "distalDetails", "morphology", "specificCapacitance", "initMembPotential", "spikeThresh", "membraneProperties", "membraneProperties2CaPools", "biophysicalProperties", "biophysicalProperties2CaPools", "intracellularProperties", "intracellularProperties2CaPools", "resistivity", "concentrationModel", "decayingPoolConcentrationModel", "fixedFactorConcentrationModel", "fixedFactorConcentrationModelTraub", "species", "cell", "cell2CaPools", "baseCellMembPotCap", "baseIaf", "iafTauCell", "iafTauRefCell", "baseIafCapCell", "iafCell", "iafRefCell", "izhikevichCell", "izhikevich2007Cell", "adExIaFCell", "fitzHughNagumoCell", "pinskyRinzelCA3Cell", "hindmarshRose1984Cell"], "Synapses": ["baseSynapse", "baseVoltageDepSynapse", "baseSynapseDL", "baseCurrentBasedSynapse", "alphaCurrentSynapse", "baseConductanceBasedSynapse", "baseConductanceBasedSynapseTwo", "expOneSynapse", "alphaSynapse", "expTwoSynapse", "expThreeSynapse", "baseBlockMechanism", "voltageConcDepBlockMechanism", "basePlasticityMechanism", "tsodyksMarkramDepMechanism", "tsodyksMarkramDepFacMechanism", "blockingPlasticSynapse", "doubleSynapse", "stdpSynapse", "gapJunction", "baseGradedSynapse", "silentSynapse", "linearGradedSynapse", "gradedSynapse"], "Channels": ["baseVoltageDepRate", "baseVoltageConcDepRate", "baseHHRate", "HHExpRate", "HHSigmoidRate", "HHExpLinearRate", "baseVoltageDepVariable", "baseVoltageConcDepVariable", "baseHHVariable", "HHExpVariable", "HHSigmoidVariable", "HHExpLinearVariable", "baseVoltageDepTime", "baseVoltageConcDepTime", "fixedTimeCourse", "baseQ10Settings", "q10Fixed", "q10ExpTemp", "baseConductanceScaling", "q10ConductanceScaling", "baseConductanceScalingCaDependent", "baseGate", "gate", "gateHHrates", "gateHHtauInf", "gateHHInstantaneous", "gateHHratesTau", "gateHHratesInf", "gateHHratesTauInf", "gateFractional", "subGate", "baseIonChannel", "ionChannelPassive", "ionChannelHH", "ionChannel", "ionChannelVShift", "KSState", "closedState", "openState", "ionChannelKS", "KSTransition", "forwardTransition", "reverseTransition", "vHalfTransition", "tauInfTransition", "gateKS"], "Inputs": ["basePointCurrent", "baseVoltageDepPointCurrent", "baseVoltageDepPointCurrentSpiking", "basePointCurrentDL", "baseVoltageDepPointCurrentDL", "baseSpikeSource", "spikeGenerator", "spikeGeneratorRandom", "spikeGeneratorPoisson", "spikeGeneratorRefPoisson", "poissonFiringSynapse", "transientPoissonFiringSynapse", "timedSynapticInput", "spikeArray", "spike", "pulseGenerator", "compoundInput", "compoundInputDL", "pulseGeneratorDL", "sineGenerator", "sineGeneratorDL", "rampGenerator", "rampGeneratorDL", "voltageClamp", "voltageClampTriple"], "Networks": ["network", "networkWithTemperature", "basePopulation", "population", "populationList", "instance", "location", "region", "rectangularExtent", "projection", "explicitConnection", "connection", "synapticConnection", "synapticConnectionWD", "connectionWD", "electricalConnection", "electricalConnectionInstance", "electricalConnectionInstanceW", "electricalProjection", "continuousConnection", "continuousConnectionInstance", "continuousConnectionInstanceW", "continuousProjection", "explicitInput", "inputList", "input", "inputW"], "PyNN": ["basePyNNCell", "basePyNNIaFCell", "basePyNNIaFCondCell", "IF_curr_alpha", "IF_curr_exp", "IF_cond_alpha", "IF_cond_exp", "EIF_cond_exp_isfa_ista", "EIF_cond_alpha_isfa_ista", "HH_cond_exp", "basePynnSynapse", "expCondSynapse", "expCurrSynapse", "alphaCondSynapse", "alphaCurrSynapse", "SpikeSourcePoisson"], "NeuroMLCoreDimensions": [], "NeuroMLCoreCompTypes": ["notes", "annotation", "property", "baseStandalone", "rdf_RDF", "rdf_Description", "baseBqbiol", "bqbiol_encodes", "bqbiol_hasPart", "bqbiol_hasProperty", "bqbiol_hasVersion", "bqbiol_is", "bqbiol_isDescribedBy", "bqbiol_isEncodedBy", "bqbiol_isHomologTo", "bqbiol_isPartOf", "bqbiol_isPropertyOf", "bqbiol_isVersionOf", "bqbiol_occursIn", "bqbiol_hasTaxon", "bqmodel_is", "bqmodel_isDescribedBy", "bqmodel_isDerivedFrom", "rdf_Bag", "rdf:li", "point3DWithDiam"], "Simulation": ["Simulation", "Display", "Line", "OutputFile", "OutputColumn", "EventOutputFile", "EventSelection", "Meta"]}

doc/helpers/nml-core-docs.py

@@ -7,10 +7,42 @@
 Copyright 2023 NeuroML authors
 """
 
+import json
 import textwrap
 
 print("Generating list of nml classes")
 
+component_type_list = None
+with open("../component-list.json", "r") as f:
+    component_type_list = json.load(f)
+
+component_type_list["Other"] = []
+
+output_files = {}
+comp_num_dict = {}
+
+for ctype in component_type_list.keys():
+    fwrite = open(f"../userdocs/{ctype}_list.rst", "w")
+    output_files[ctype] = fwrite
+    print(ctype, file=fwrite)
+    print("#" * len(ctype), file=fwrite)
+    print("\n", file=fwrite)
+    print("\n", file=fwrite)
+    print(
+        f"This documentation is auto-generated from the `NeuroML schema <https://docs.neuroml.org/Userdocs/Schemas/{ctype}.html>`__.",
+        file=fwrite,
+    )
+    print("\n", file=fwrite)
+    print("\n", file=fwrite)
+    print(".. Generated using nml-core-docs.py", file=fwrite)
+
+    comp_num_dict[ctype] = 0
+
+comp_to_file_map = {}
+for file, ctypes in component_type_list.items():
+    for ctype in ctypes:
+        comp_to_file_map[ctype[0].capitalize() + ctype[1:]] = file
+
 classes = {}
 files = {
     "generatedssupersuper.py": [],
@@ -24,10 +56,6 @@
         "PlasticityTypes",
         "ZeroOrOne",
         "allowedSpaces",
-        "channelTypes",
-        "gateTypes",
-        "networkTypes",
-        "populationTypes",
         "_FixedOffsetTZ",
         "GdsCollector_",
         "GeneratedsSuperSuper",
@@ -52,47 +80,77 @@
     classlist.sort()
     classes[f] = classlist
 
-with open("../userdocs/coreclasses_list.txt", "w") as fwrite:
-    print(".. Generated using nml-core-docs.py", file=fwrite)
-    for module, clist in classes.items():
-        f = module.split(".")[0]
-        for aclass in clist:
-            # do not print all the internal methods in GeneratedsSuper
-            if aclass == "GeneratedsSuper":
-                towrite = textwrap.dedent(
-                    """
-                    {}
-                    {}
-
-                    .. autoclass:: neuroml.nml.{}.{}
-                       :show-inheritance:
-
-                    """.format(
-                        aclass,
-                        "#" * len(aclass),
-                        f,
-                        aclass,
-                    )
+
+total_classes = 0
+for module, clist in classes.items():
+    total_classes += len(clist)
+    f = module.split(".")[0]
+    for aclass in clist:
+        # do not print all the internal methods in GeneratedsSuper
+        if aclass == "GeneratedsSuper":
+            towrite = textwrap.dedent(
+                """
+                {}
+                {}
+
+                .. autoclass:: neuroml.nml.{}.{}
+                   :show-inheritance:
+
+                """.format(
+                    aclass,
+                    "^" * len(aclass),
+                    f,
+                    aclass,
                 )
-            else:
-                towrite = textwrap.dedent(
-                    """
-                    {}
-                    {}
-
-                    .. autoclass:: neuroml.nml.{}.{}
-                       :members:
-                       :undoc-members:
-                       :show-inheritance:
-                       :inherited-members:
-
-                    """.format(
-                        aclass,
-                        "#" * len(aclass),
-                        f,
-                        aclass,
-                    )
+            )
+        else:
+            towrite = textwrap.dedent(
+                """
+                {}
+                {}
+
+                .. autoclass:: neuroml.nml.{}.{}
+                   :members:
+                   :undoc-members:
+                   :show-inheritance:
+                   :inherited-members:
+
+                """.format(
+                    aclass,
+                    "^" * len(aclass),
+                    f,
+                    aclass,
                 )
+            )
+        try:
+            category = comp_to_file_map[aclass]
+        except KeyError:
+            if "cell" in aclass.lower():
+                category = "Cells"
+            elif "gate" in aclass.lower():
+                category = "Channels"
+            elif "hh" in aclass.lower():
+                category = "Channels"
+            elif "q10" in aclass.lower():
+                category = "Channels"
+            elif "channel" in aclass.lower():
+                category = "Channels"
+            elif "network" in aclass.lower():
+                category = "Networks"
+            elif "population" in aclass.lower():
+                category = "Networks"
+            else:
+                print(f"{aclass} fits nowhere, putting in Other")
+                category = "Other"
+        finally:
+            comp_num_dict[category] += 1
+            fwrite = output_files[category]
             print(towrite, file=fwrite)
 
-print("Saved to userdocs/coreclasses_list.txt")
+print("Done")
+print(comp_num_dict)
+
+print(f"Total classes read from libNeuroML: {total_classes}")
+
+for comp, num in comp_num_dict.items():
+    output_files[comp].close()