Merge pull request #259 from NeuroML/development

To 1.1.2

man/man1/pynml-archive.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-ARCHIVE "1" "August 2023" "pynml-archive v1.0.10" "User Commands"
+.TH PYNML-ARCHIVE "1" "September 2023" "pynml-archive v1.1.2" "User Commands"
 .SH NAME
-pynml-archive \- manual page for pynml-archive v1.0.10
+pynml-archive \- manual page for pynml-archive v1.1.2
 .SH DESCRIPTION
 usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
 .TP
@@ -29,7 +29,7 @@ Extension to use for archive.
 Explicit list of files to create archive of.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-channelanalysis.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELANALYSIS "1" "August 2023" "pynml-channelanalysis v1.0.10" "User Commands"
+.TH PYNML-CHANNELANALYSIS "1" "September 2023" "pynml-channelanalysis v1.1.2" "User Commands"
 .SH NAME
-pynml-channelanalysis \- manual page for pynml-channelanalysis v1.0.10
+pynml-channelanalysis \- manual page for pynml-channelanalysis v1.1.2
 .SH DESCRIPTION
 usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
 .TP
@@ -94,7 +94,7 @@ Save currents through voltage clamp at each level &
 plot current vs voltage for ion channel
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-channelml2nml.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELML2NML "1" "August 2023" "pynml-channelml2nml v1.0.10" "User Commands"
+.TH PYNML-CHANNELML2NML "1" "September 2023" "pynml-channelml2nml v1.1.2" "User Commands"
 .SH NAME
-pynml-channelml2nml \- manual page for pynml-channelml2nml v1.0.10
+pynml-channelml2nml \- manual page for pynml-channelml2nml v1.1.2
 .SH DESCRIPTION
 usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
 .TP
@@ -25,7 +25,7 @@ Path to the XSLT file
 Name of the outputfile file
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-modchananalysis.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-MODCHANANALYSIS "1" "August 2023" "pynml-modchananalysis v1.0.10" "User Commands"
+.TH PYNML-MODCHANANALYSIS "1" "September 2023" "pynml-modchananalysis v1.1.2" "User Commands"
 .SH NAME
-pynml-modchananalysis \- manual page for pynml-modchananalysis v1.0.10
+pynml-modchananalysis \- manual page for pynml-modchananalysis v1.1.2
 .SH DESCRIPTION
 usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
 .TP
@@ -56,7 +56,7 @@ in mM)
 Name of the mod file containing the channel
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-plotchan.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTCHAN "1" "August 2023" "pynml-plotchan v1.0.10" "User Commands"
+.TH PYNML-PLOTCHAN "1" "September 2023" "pynml-plotchan v1.1.2" "User Commands"
 .SH NAME
-pynml-plotchan \- manual page for pynml-plotchan v1.0.10
+pynml-plotchan \- manual page for pynml-plotchan v1.1.2
 .SH DESCRIPTION
 usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
 .IP
@@ -25,7 +25,7 @@ Do not generate distance plots
 Do not show plots as they are generated
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-plotmorph.1

@@ -1,11 +1,12 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTMORPH "1" "August 2023" "pynml-plotmorph v1.0.10" "User Commands"
+.TH PYNML-PLOTMORPH "1" "September 2023" "pynml-plotmorph v1.1.2" "User Commands"
 .SH NAME
-pynml-plotmorph \- manual page for pynml-plotmorph v1.0.10
+pynml-plotmorph \- manual page for pynml-plotmorph v1.1.2
 .SH DESCRIPTION
 usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
 .TP
-[\-plotType <type: detailed, constant, or schematic>]
+[\-pointFraction <fraction of each population to plot as point cells>]
+[\-plotType <type: detailed, constant, schematic, or point>]
 [\-theme <theme: light, dark>]
 [\-minWidth <min width of lines>] [\-interactive3d]
 [\-saveToFile <Image file name>] [\-square]
@@ -30,7 +31,10 @@ Don't open plot window
 \fB\-plane2d\fR <plane, e.g. xy, yz, zx>
 Plane to plot on for 2D plot
 .TP
-\fB\-plotType\fR <type: detailed, constant, or schematic>
+\fB\-pointFraction\fR <fraction of each population to plot as point cells>
+Fraction of network to plot as point cells
+.TP
+\fB\-plotType\fR <type: detailed, constant, schematic, or point>
 Level of detail to plot in
 .TP
 \fB\-theme\fR <theme: light, dark>
@@ -51,7 +55,7 @@ Scale axes so that image is approximately square, for
 2D plot
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-plotspikes.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTSPIKES "1" "August 2023" "pynml-plotspikes v1.0.10" "User Commands"
+.TH PYNML-PLOTSPIKES "1" "September 2023" "pynml-plotspikes v1.1.2" "User Commands"
 .SH NAME
-pynml-plotspikes \- manual page for pynml-plotspikes v1.0.10
+pynml-plotspikes \- manual page for pynml-plotspikes v1.1.2
 .SH DESCRIPTION
 usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
 .TP
@@ -44,7 +44,7 @@ Window for rate calculation in ms
 Number of bins for rate histogram
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-povray.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-POVRAY "1" "August 2023" "pynml-povray v1.0.10" "User Commands"
+.TH PYNML-POVRAY "1" "September 2023" "pynml-povray v1.1.2" "User Commands"
 .SH NAME
-pynml-povray \- manual page for pynml-povray v1.0.10
+pynml-povray \- manual page for pynml-povray v1.1.2
 .SH DESCRIPTION
 usage: pynml\-povray [\-h] [\-split] [\-background <background colour>] [\-movie]
 .TP
@@ -96,7 +96,7 @@ cell/network
 Show segment ids
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-sonata.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SONATA "1" "August 2023" "pynml-sonata v1.0.10" "User Commands"
+.TH PYNML-SONATA "1" "September 2023" "pynml-sonata v1.1.2" "User Commands"
 .SH NAME
-pynml-sonata \- manual page for pynml-sonata v1.0.10
+pynml-sonata \- manual page for pynml-sonata v1.1.2
 .SH DESCRIPTION
 usage: pynml\-sonata [\-h] [\-h5] [\-jnml] [\-neuron]
 .IP
@@ -34,7 +34,7 @@ Execute the generated LEMS/NeuroML2 model with
 jNeuroML_NEURON
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-summary.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SUMMARY "1" "August 2023" "pynml-summary v1.0.10" "User Commands"
+.TH PYNML-SUMMARY "1" "September 2023" "pynml-summary v1.1.2" "User Commands"
 .SH NAME
-pynml-summary \- manual page for pynml-summary v1.0.10
+pynml-summary \- manual page for pynml-summary v1.1.2
 .SH DESCRIPTION
 Usage:
 .PP
@@ -19,7 +19,7 @@ enable verbose mode
 print this help text and exit
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml-tune.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-TUNE "1" "August 2023" "pynml-tune v1.0.10" "User Commands"
+.TH PYNML-TUNE "1" "September 2023" "pynml-tune v1.1.2" "User Commands"
 .SH NAME
-pynml-tune \- manual page for pynml-tune v1.0.10
+pynml-tune \- manual page for pynml-tune v1.1.2
 .SH DESCRIPTION
 usage: pynml\-tune [\-h] [\-simTime <simTime>] [\-dt <dt>]
 .IP
@@ -132,7 +132,7 @@ Should (some) generated files, e.g. *.dat, be deleted
 as optimisation progresses?
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/pynml.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML "1" "August 2023" "pynml v1.0.10" "User Commands"
+.TH PYNML "1" "September 2023" "pynml v1.1.2" "User Commands"
 .SH NAME
-pynml \- manual page for pynml v1.0.10
+pynml \- manual page for pynml v1.1.2
 .SH DESCRIPTION
 usage: pynml [\-h|\-\-help] [<shared options>] <one of the mutually\-exclusive options>
 .PP
@@ -180,7 +180,7 @@ latest Schema
 v1.8.1 Schema
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

man/man1/version.h2m

@@ -1,3 +1,3 @@
 [environment]
 .PP
-pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+pyNeuroML v1.1.2 (libNeuroML v0.5.3, jNeuroML v0.12.4)

pyneuroml/plot/PlotMorphology.py

@@ -261,13 +261,24 @@ def plot_2D(
             verbose=False,
             optimized=True,
         )
-
+        if title is None:
+            try:
+                title = f"{nml_model.networks[0].id} from {nml_file}"
+            except IndexError:
+                title = f"{nml_model.cells[0].id} from {nml_file}"
     elif isinstance(nml_file, Cell):
         nml_model = NeuroMLDocument(id="newdoc")
         nml_model.add(nml_file)
+        if title is None:
+            title = f"{nml_model.cells[0].id}"
 
     elif isinstance(nml_file, NeuroMLDocument):
         nml_model = nml_file
+        if title is None:
+            try:
+                title = f"{nml_model.networks[0].id} from {nml_file.id}"
+            except IndexError:
+                title = f"{nml_model.cells[0].id} from {nml_file.id}"
     else:
         raise TypeError(
             "Passed model is not a NeuroML file path, nor a neuroml.Cell, nor a neuroml.NeuroMLDocument"
@@ -283,19 +294,16 @@ def plot_2D(
         nml_model, verbose, nml_file if type(nml_file) is str else ""
     )
 
-    if title is None:
-        if len(nml_model.networks) > 0:
-            title = "2D plot of %s from %s" % (nml_model.networks[0].id, nml_file)
-        else:
-            title = "2D plot of %s" % (nml_model.cells[0].id)
-
     if verbose:
         logger.debug(f"positions: {positions}")
         logger.debug(f"pop_id_vs_cell: {pop_id_vs_cell}")
         logger.debug(f"cell_id_vs_cell: {cell_id_vs_cell}")
         logger.debug(f"pop_id_vs_color: {pop_id_vs_color}")
         logger.debug(f"pop_id_vs_radii: {pop_id_vs_radii}")
 
+    # not used, clear up
+    del cell_id_vs_cell
+
     fig, ax = get_new_matplotlib_morph_plot(title, plane2d)
     axis_min_max = [float("inf"), -1 * float("inf")]
 
@@ -322,7 +330,8 @@ def plot_2D(
         except KeyError:
             pass
 
-    for pop_id, cell in pop_id_vs_cell.items():
+    while pop_id_vs_cell:
+        pop_id, cell = pop_id_vs_cell.popitem()
         pos_pop = positions[pop_id]  # type: typing.Dict[typing.Any, typing.List[float]]
 
         # reinit point_cells for each loop
@@ -337,7 +346,8 @@ def plot_2D(
             except KeyError:
                 pass
 
-        for cell_index, pos in pos_pop.items():
+        while pos_pop:
+            cell_index, pos = pos_pop.popitem()
             radius = pop_id_vs_radii[pop_id] if pop_id in pop_id_vs_radii else 10
             color = pop_id_vs_color[pop_id] if pop_id in pop_id_vs_color else None