NeuroML · sanjayankur31 · Sep 4, 2024 · Jul 18, 2024 · Jul 18, 2024 · Jul 18, 2024
diff --git a/.gitignore b/.gitignore
@@ -138,7 +138,7 @@ examples/results/*.dat
 .mypy_cache/
 /examples/test_data/TwoCell.net.png
 /examples/test_data/Purk2M9s.png
-/.coverage
+**/.coverage
 /Nav.channel.nml
 /iv_izh2007RS0.net.nml
 /leak_chan.channel.nml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,9 +4,10 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-added-large-files
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-added-large-files
+      args: [ "--maxkb=5000"]
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: v0.4.1
   hooks:

diff --git a/man/man1/common.h2m b/man/man1/common.h2m
@@ -11,6 +11,7 @@
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-archive.1 b/man/man1/pynml-archive.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-ARCHIVE "1" "August 2024" "pynml-archive v1.3.9" "User Commands"
+.TH PYNML-ARCHIVE "1" "September 2024" "pynml-archive v1.3.9" "User Commands"
 .SH NAME
 pynml-archive \- manual page for pynml-archive v1.3.9
 .SH DESCRIPTION
@@ -45,6 +45,7 @@ master file.
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-channelanalysis.1 b/man/man1/pynml-channelanalysis.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELANALYSIS "1" "August 2024" "pynml-channelanalysis v1.3.9" "User Commands"
+.TH PYNML-CHANNELANALYSIS "1" "September 2024" "pynml-channelanalysis v1.3.9" "User Commands"
 .SH NAME
 pynml-channelanalysis \- manual page for pynml-channelanalysis v1.3.9
 .SH DESCRIPTION
@@ -105,6 +105,7 @@ plot current vs voltage for ion channel
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-channelml2nml.1 b/man/man1/pynml-channelml2nml.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELML2NML "1" "August 2024" "pynml-channelml2nml v1.3.9" "User Commands"
+.TH PYNML-CHANNELML2NML "1" "September 2024" "pynml-channelml2nml v1.3.9" "User Commands"
 .SH NAME
 pynml-channelml2nml \- manual page for pynml-channelml2nml v1.3.9
 .SH DESCRIPTION
@@ -36,6 +36,7 @@ Name of the outputfile file
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-modchananalysis.1 b/man/man1/pynml-modchananalysis.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-MODCHANANALYSIS "1" "August 2024" "pynml-modchananalysis v1.3.9" "User Commands"
+.TH PYNML-MODCHANANALYSIS "1" "September 2024" "pynml-modchananalysis v1.3.9" "User Commands"
 .SH NAME
 pynml-modchananalysis \- manual page for pynml-modchananalysis v1.3.9
 .SH DESCRIPTION
@@ -70,6 +70,7 @@ Name of the mod file containing the channel
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-plotchan.1 b/man/man1/pynml-plotchan.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTCHAN "1" "August 2024" "pynml-plotchan v1.3.9" "User Commands"
+.TH PYNML-PLOTCHAN "1" "September 2024" "pynml-plotchan v1.3.9" "User Commands"
 .SH NAME
 pynml-plotchan \- manual page for pynml-plotchan v1.3.9
 .SH DESCRIPTION
@@ -36,6 +36,7 @@ Do not show plots as they are generated
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-plotmorph.1 b/man/man1/pynml-plotmorph.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTMORPH "1" "August 2024" "pynml-plotmorph v1.3.9" "User Commands"
+.TH PYNML-PLOTMORPH "1" "September 2024" "pynml-plotmorph v1.3.9" "User Commands"
 .SH NAME
 pynml-plotmorph \- manual page for pynml-plotmorph v1.3.9
 .SH DESCRIPTION
@@ -79,6 +79,7 @@ Scale axes so that image is approximately square, for
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-plotspikes.1 b/man/man1/pynml-plotspikes.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTSPIKES "1" "August 2024" "pynml-plotspikes v1.3.9" "User Commands"
+.TH PYNML-PLOTSPIKES "1" "September 2024" "pynml-plotspikes v1.3.9" "User Commands"
 .SH NAME
 pynml-plotspikes \- manual page for pynml-plotspikes v1.3.9
 .SH DESCRIPTION
@@ -58,6 +58,7 @@ Number of bins for rate histogram
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-plottimeseries.1 b/man/man1/pynml-plottimeseries.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTTIMESERIES "1" "August 2024" "pynml-plottimeseries v1.3.9" "User Commands"
+.TH PYNML-PLOTTIMESERIES "1" "September 2024" "pynml-plottimeseries v1.3.9" "User Commands"
 .SH NAME
 pynml-plottimeseries \- manual page for pynml-plottimeseries v1.3.9
 .SH DESCRIPTION
@@ -36,6 +36,7 @@ Name of the image file to save plot to
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-povray.1 b/man/man1/pynml-povray.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-POVRAY "1" "August 2024" "pynml-povray v1.3.9" "User Commands"
+.TH PYNML-POVRAY "1" "September 2024" "pynml-povray v1.3.9" "User Commands"
 .SH NAME
 pynml-povray \- manual page for pynml-povray v1.3.9
 .SH DESCRIPTION
@@ -107,6 +107,7 @@ Show segment ids
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-sonata.1 b/man/man1/pynml-sonata.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SONATA "1" "August 2024" "pynml-sonata v1.3.9" "User Commands"
+.TH PYNML-SONATA "1" "September 2024" "pynml-sonata v1.3.9" "User Commands"
 .SH NAME
 pynml-sonata \- manual page for pynml-sonata v1.3.9
 .SH DESCRIPTION
@@ -45,6 +45,7 @@ jNeuroML_NEURON
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-summary.1 b/man/man1/pynml-summary.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SUMMARY "1" "August 2024" "pynml-summary v1.3.9" "User Commands"
+.TH PYNML-SUMMARY "1" "September 2024" "pynml-summary v1.3.9" "User Commands"
 .SH NAME
 pynml-summary \- manual page for pynml-summary v1.3.9
 .SH DESCRIPTION
@@ -30,6 +30,7 @@ print this help text and exit
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-swc2nml.1 b/man/man1/pynml-swc2nml.1
@@ -0,0 +1,45 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-SWC2NML "1" "September 2024" "pynml-swc2nml v1.3.9" "User Commands"
+.SH NAME
+pynml-swc2nml \- manual page for pynml-swc2nml v1.3.9
+.SH DESCRIPTION
+usage: pynml\-swc2nml [\-h] [\-neuromlFile <NeuroML file>] [\-morphOnly]
+.IP
+<SWC file>
+.PP
+Convert provided SWC file to NeuroML2
+.SS "positional arguments:"
+.TP
+<SWC file>
+Name of the input SWC file
+.SS "options:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-neuromlFile\fR <NeuroML file>
+Name of the output NeuroML file
+.TP
+\fB\-morphOnly\fR
+Export as standalone Morphology, not as a Cell
+.SH "SEE-ALSO"
+.BR pynml (1),
+.BR pynml-archive (1),
+.BR pynml-channelanalysis (1),
+.BR pynml-channelml2nml (1),
+.BR pynml-modchananalysis (1),
+.BR pynml-plotchan (1),
+.BR pynml-plotmorph (1),
+.BR pynml-plotspikes (1),
+.BR pynml-plottimeseries (1),
+.BR pynml-povray (1),
+.BR pynml-sonata (1),
+.BR pynml-summary (1),
+.BR pynml-swc2nml (1),
+.BR pynml-tune (1),
+.BR pynml-xpp (1),
+.PP
+Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
+.SH ENVIRONMENT
+.PP
+pyNeuroML v1.3.9 (libNeuroML v0.6.4, jNeuroML v0.13.3)
diff --git a/man/man1/pynml-tune.1 b/man/man1/pynml-tune.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-TUNE "1" "August 2024" "pynml-tune v1.3.9" "User Commands"
+.TH PYNML-TUNE "1" "September 2024" "pynml-tune v1.3.9" "User Commands"
 .SH NAME
 pynml-tune \- manual page for pynml-tune v1.3.9
 .SH DESCRIPTION
@@ -143,6 +143,7 @@ as optimisation progresses?
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml-xpp.1 b/man/man1/pynml-xpp.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-XPP "1" "August 2024" "pynml-xpp v1.3.9" "User Commands"
+.TH PYNML-XPP "1" "September 2024" "pynml-xpp v1.3.9" "User Commands"
 .SH NAME
 pynml-xpp \- manual page for pynml-xpp v1.3.9
 .SH DESCRIPTION
@@ -45,6 +45,7 @@ Plot saved variables
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/man/man1/pynml.1 b/man/man1/pynml.1
@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML "1" "August 2024" "pynml v1.3.9" "User Commands"
+.TH PYNML "1" "September 2024" "pynml v1.3.9" "User Commands"
 .SH NAME
 pynml \- manual page for pynml v1.3.9
 .SH DESCRIPTION
@@ -219,6 +219,7 @@ Load NeuroML file(s), and convert it to swc format
 .BR pynml-povray (1),
 .BR pynml-sonata (1),
 .BR pynml-summary (1),
+.BR pynml-swc2nml (1),
 .BR pynml-tune (1),
 .BR pynml-xpp (1),
 .PP

diff --git a/pyneuroml/plot/PlotMorphologyVispy.py b/pyneuroml/plot/PlotMorphologyVispy.py
@@ -725,11 +725,18 @@ def plot_interactive_3D(
         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 random.choice(get_color_names())
-            )
+
+            # use color if specified in property
+            try:
+                color = pop_id_vs_color[pop_id]
+            except KeyError:
+                # if single cell only, use default groups
+                if total_cells == 1:
+                    color = "default groups"
+                # if multiple cells, use different colors for each cell
+                else:
+                    color = random.choice(get_color_names())
+
             # if hightlight spec has a color for the cell, use that
             try:
                 color = highlight_spec[cell.id]["cell_color"]