From a7c827fcde863876478c9209e4648185bf9cbc7c Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Wed, 14 Aug 2024 17:04:29 +0100 Subject: [PATCH] docs: correctly populate "others" Need to use a `finally` block, not an `else` block. --- doc/helpers/nml-core-docs.py | 17 +- doc/userdocs/Cells_list.rst | 77 +++++ doc/userdocs/Channels_list.rst | 154 ++++++++++ doc/userdocs/Networks_list.rst | 22 ++ doc/userdocs/Other_list.rst | 545 +++++++++++++++++++++++++++++++++ doc/userdocs/coreclasses.rst | 1 + 6 files changed, 815 insertions(+), 1 deletion(-) diff --git a/doc/helpers/nml-core-docs.py b/doc/helpers/nml-core-docs.py index 4de678b..781f376 100644 --- a/doc/helpers/nml-core-docs.py +++ b/doc/helpers/nml-core-docs.py @@ -81,7 +81,9 @@ classes[f] = classlist +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 @@ -127,9 +129,20 @@ 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" - else: + finally: comp_num_dict[category] += 1 fwrite = output_files[category] print(towrite, file=fwrite) @@ -137,5 +150,7 @@ 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() diff --git a/doc/userdocs/Cells_list.rst b/doc/userdocs/Cells_list.rst index 85437ed..f73f687 100644 --- a/doc/userdocs/Cells_list.rst +++ b/doc/userdocs/Cells_list.rst @@ -88,6 +88,17 @@ Cell2CaPools +CellSet +^^^^^^^ + +.. autoclass:: neuroml.nml.nml.CellSet + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + ChannelDensity ^^^^^^^^^^^^^^ @@ -220,6 +231,39 @@ DistalDetails +ExtracellularProperties +^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExtracellularProperties + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +ExtracellularPropertiesLocal +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.ExtracellularPropertiesLocal + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +FitzHughNagumo1969Cell +^^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.FitzHughNagumo1969Cell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + FitzHughNagumoCell ^^^^^^^^^^^^^^^^^^ @@ -547,3 +591,36 @@ VariableParameter :undoc-members: :show-inheritance: :inherited-members: + + + +basePyNNCell +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.basePyNNCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +basePyNNIaFCell +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.basePyNNIaFCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +basePyNNIaFCondCell +^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.basePyNNIaFCondCell + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/Channels_list.rst b/doc/userdocs/Channels_list.rst index 2f5cdcf..e264b50 100644 --- a/doc/userdocs/Channels_list.rst +++ b/doc/userdocs/Channels_list.rst @@ -44,6 +44,17 @@ GateFractional +GateFractionalSubgate +^^^^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateFractionalSubgate + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + GateHHInstantaneous ^^^^^^^^^^^^^^^^^^^ @@ -55,6 +66,72 @@ GateHHInstantaneous +GateHHRates +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateHHRates + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateHHRatesInf +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateHHRatesInf + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateHHRatesTau +^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateHHRatesTau + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateHHRatesTauInf +^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateHHRatesTauInf + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateHHTauInf +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateHHTauInf + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +GateHHUndetermined +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.GateHHUndetermined + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + GateKS ^^^^^^ @@ -66,6 +143,39 @@ GateKS +HHRate +^^^^^^ + +.. autoclass:: neuroml.nml.nml.HHRate + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +HHTime +^^^^^^ + +.. autoclass:: neuroml.nml.nml.HHTime + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +HHVariable +^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.HHVariable + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + IonChannel ^^^^^^^^^^ @@ -99,6 +209,17 @@ IonChannelKS +IonChannelScalable +^^^^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.IonChannelScalable + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + IonChannelVShift ^^^^^^^^^^^^^^^^ @@ -132,6 +253,17 @@ Q10ConductanceScaling +Q10Settings +^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.Q10Settings + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + ReverseTransition ^^^^^^^^^^^^^^^^^ @@ -151,3 +283,25 @@ TauInfTransition :undoc-members: :show-inheritance: :inherited-members: + + + +channelTypes +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.channelTypes + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +gateTypes +^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.gateTypes + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/Networks_list.rst b/doc/userdocs/Networks_list.rst index a188dd0..393265e 100644 --- a/doc/userdocs/Networks_list.rst +++ b/doc/userdocs/Networks_list.rst @@ -239,3 +239,25 @@ SynapticConnection :undoc-members: :show-inheritance: :inherited-members: + + + +networkTypes +^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.networkTypes + :members: + :undoc-members: + :show-inheritance: + :inherited-members: + + + +populationTypes +^^^^^^^^^^^^^^^ + +.. autoclass:: neuroml.nml.nml.populationTypes + :members: + :undoc-members: + :show-inheritance: + :inherited-members: diff --git a/doc/userdocs/Other_list.rst b/doc/userdocs/Other_list.rst index 5496c29..465df8a 100644 --- a/doc/userdocs/Other_list.rst +++ b/doc/userdocs/Other_list.rst @@ -10,3 +10,548 @@ This documentation is auto-generated from the `NeuroML schema