docs: minor fixes to improve rtd generation

docs/source/pyneuroml.archive.rst

@@ -0,0 +1,7 @@
+pyneuroml.archive package
+==========================
+
+.. automodule:: pyneuroml.archive
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyneuroml.nsgr.rst

@@ -0,0 +1,7 @@
+pyneuroml.nsgr package
+======================
+
+.. automodule:: pyneuroml.nsgr
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyneuroml.pynml.rst

@@ -0,0 +1,7 @@
+pyneuroml.pynml module
+======================
+
+.. automodule:: pyneuroml.pynml
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pyneuroml.rst

@@ -10,24 +10,17 @@ Subpackages
 -----------
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 1
 
+   pyneuroml.pynml
    pyneuroml.analysis
+   pyneuroml.archive
    pyneuroml.channelml
    pyneuroml.lems
+   pyneuroml.neuron
+   pyneuroml.nsgr
    pyneuroml.plot
    pyneuroml.povray
    pyneuroml.swc
    pyneuroml.tune
-   pyneuroml.neuron
    pyneuroml.utils
-
-
-pyneuroml.pynml module
-----------------------
-
-.. automodule:: pyneuroml.pynml
-   :members:
-   :undoc-members:
-   :show-inheritance:
-

pyneuroml/analysis/__init__.py

@@ -58,7 +58,7 @@ def generate_current_vs_frequency_curve(
     return_axes: bool = False,
     verbose: bool = False,
     segment_id: typing.Optional[str] = None,
-    fraction_along: typing.Optional[float] = None
+    fraction_along: typing.Optional[float] = None,
 ):
     """Generate current vs firing rate frequency curves for provided cell.
 
@@ -81,7 +81,7 @@ def generate_current_vs_frequency_curve(
     stimulus currents.
 
     The various plotting related arguments to this method are passed on to
-    :py:method`pynml.generate_plot`
+    :py:meth:`pyneuroml.plot.generate_plot`
 
     :param nml2_file: name of NeuroML file containing cell definition
     :type nml2_file: str
@@ -251,8 +251,11 @@ def generate_current_vs_frequency_curve(
         # Add these to cells
         input_list = nml.InputList(id=input_id, component=pg.id, populations=pop.id)
         aninput = nml.Input(
-            id="0", target="../%s[%i]" % (pop.id, i), destination="synapses",
-            segment_id=segment_id, fraction_along=fraction_along
+            id="0",
+            target="../%s[%i]" % (pop.id, i),
+            destination="synapses",
+            segment_id=segment_id,
+            fraction_along=fraction_along,
         )
         input_list.input.append(aninput)
 
@@ -378,7 +381,6 @@ def generate_current_vs_frequency_curve(
                 iv_results[stims[i]] = v_end
 
     if plot_voltage_traces:
-
         traces_ax = pynml.generate_plot(
             times_results,
             volts_results,
@@ -505,7 +507,6 @@ def analyse_spiketime_vs_dt(
     save_figure_to=None,
     num_of_last_spikes=None,
 ):
-
     from pyelectro.analysis import max_min
     import numpy as np
 

pyneuroml/nsgr/__init__.py

@@ -67,7 +67,7 @@ def run_on_nsg(
 
     .. versionadded:: 1.0.10
 
-    :param engine: name of engine: suffixes of the run_lems_with.. functions
+    :param engine: name of engine: suffixes of the run_lems_with functions
     :type engine: str
     :param lems_file_name: name of LEMS simulation file
     :type lems_file_name: str
@@ -83,9 +83,9 @@ def run_on_nsg(
         It is good practice to separate directories where simulations are run
         from the source of the model/simulations.
     :type run_dir: str
-    :param *engine_args: positional args to be passed to the engine runner
+    :param engine_args: positional args to be passed to the engine runner
         function
-    :param **engine_kwargs: keyword args to be be passed to the engine runner
+    :param engine_kwargs: keyword args to be be passed to the engine runner
         function
     :param dry_run: do everything but do not submit
     :type dry_run: bool

pyneuroml/pynml.py

@@ -1330,8 +1330,8 @@ def run_lems_with(engine: str, *args: typing.Any, **kwargs: typing.Any):
 
     :param engine: engine to run with
     :type engine: string (valid names are methods)
-    :param *args: postional arguments to pass to run function
-    :param **kwargs: named arguments to pass to run function
+    :param args: postional arguments to pass to run function
+    :param kwargs: named arguments to pass to run function
     :returns: return value of called method
 
     """