Merge branch 'development' into feat/nsgr-integration

man/man1/common.h2m

@@ -2,6 +2,7 @@
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (1),

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" "May 2023" "pynml-archive v1.0.1" "User Commands"
+.TH PYNML-ARCHIVE "1" "August 2023" "pynml-archive v1.0.10" "User Commands"
 .SH NAME
-pynml-archive \- manual page for pynml-archive v1.0.1
+pynml-archive \- manual page for pynml-archive v1.0.10
 .SH DESCRIPTION
 usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
 .TP
@@ -29,11 +29,12 @@ Extension to use for archive.
 Explicit list of files to create archive of.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-channelanalysis v1.0.1" "User Commands"
+.TH PYNML-CHANNELANALYSIS "1" "August 2023" "pynml-channelanalysis v1.0.10" "User Commands"
 .SH NAME
-pynml-channelanalysis \- manual page for pynml-channelanalysis v1.0.1
+pynml-channelanalysis \- manual page for pynml-channelanalysis v1.0.10
 .SH DESCRIPTION
 usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
 .TP
@@ -94,11 +94,12 @@ Save currents through voltage clamp at each level &
 plot current vs voltage for ion channel
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-channelml2nml v1.0.1" "User Commands"
+.TH PYNML-CHANNELML2NML "1" "August 2023" "pynml-channelml2nml v1.0.10" "User Commands"
 .SH NAME
-pynml-channelml2nml \- manual page for pynml-channelml2nml v1.0.1
+pynml-channelml2nml \- manual page for pynml-channelml2nml v1.0.10
 .SH DESCRIPTION
 usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
 .TP
@@ -25,11 +25,12 @@ Path to the XSLT file
 Name of the outputfile file
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-modchananalysis v1.0.1" "User Commands"
+.TH PYNML-MODCHANANALYSIS "1" "August 2023" "pynml-modchananalysis v1.0.10" "User Commands"
 .SH NAME
-pynml-modchananalysis \- manual page for pynml-modchananalysis v1.0.1
+pynml-modchananalysis \- manual page for pynml-modchananalysis v1.0.10
 .SH DESCRIPTION
 usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
 .TP
@@ -56,11 +56,12 @@ in mM)
 Name of the mod file containing the channel
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (1),

man/man1/pynml-plotchan.1

@@ -0,0 +1,42 @@
+.\" 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"
+.SH NAME
+pynml-plotchan \- manual page for pynml-plotchan v1.0.10
+.SH DESCRIPTION
+usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
+.IP
+<NeuroML 2 Cell file> [<NeuroML 2 Cell file> ...]
+.PP
+A script to generate channel density plotsfor different ion channels on a
+NeuroML2cell
+.SS "positional arguments:"
+.TP
+<NeuroML 2 Cell file>
+Name of the NeuroML 2 file(s)
+.SS "options:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-noDistancePlots\fR
+Do not generate distance plots
+.TP
+\fB\-nogui\fR
+Do not show plots as they are generated
+.SH ENVIRONMENT
+.PP
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
+.SH "SEE ALSO"
+.BR pynml (1),
+.BR pynml-channelanalysis (1),
+.BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
+.BR pynml-plotspikes (1),
+.BR pynml-plotmorph (1),
+.BR pynml-modchannelanalysis (1),
+.BR pynml-povray (1),
+.BR pynml-sonata (1),
+.BR pynml-summary (1),
+.BR pynml-tune (1).
+.PP
+Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.

man/man1/pynml-plotmorph.1

@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTMORPH "1" "May 2023" "pynml-plotmorph v1.0.1" "User Commands"
+.TH PYNML-PLOTMORPH "1" "August 2023" "pynml-plotmorph v1.0.10" "User Commands"
 .SH NAME
-pynml-plotmorph \- manual page for pynml-plotmorph v1.0.1
+pynml-plotmorph \- manual page for pynml-plotmorph v1.0.10
 .SH DESCRIPTION
 usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
 .TP
@@ -51,11 +51,12 @@ Scale axes so that image is approximately square, for
 2D plot
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-plotspikes v1.0.1" "User Commands"
+.TH PYNML-PLOTSPIKES "1" "August 2023" "pynml-plotspikes v1.0.10" "User Commands"
 .SH NAME
-pynml-plotspikes \- manual page for pynml-plotspikes v1.0.1
+pynml-plotspikes \- manual page for pynml-plotspikes v1.0.10
 .SH DESCRIPTION
 usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
 .TP
@@ -44,11 +44,12 @@ Window for rate calculation in ms
 Number of bins for rate histogram
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-povray v1.0.1" "User Commands"
+.TH PYNML-POVRAY "1" "August 2023" "pynml-povray v1.0.10" "User Commands"
 .SH NAME
-pynml-povray \- manual page for pynml-povray v1.0.1
+pynml-povray \- manual page for pynml-povray v1.0.10
 .SH DESCRIPTION
 usage: pynml\-povray [\-h] [\-split] [\-background <background colour>] [\-movie]
 .TP
@@ -96,11 +96,12 @@ cell/network
 Show segment ids
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-sonata v1.0.1" "User Commands"
+.TH PYNML-SONATA "1" "August 2023" "pynml-sonata v1.0.10" "User Commands"
 .SH NAME
-pynml-sonata \- manual page for pynml-sonata v1.0.1
+pynml-sonata \- manual page for pynml-sonata v1.0.10
 .SH DESCRIPTION
 usage: pynml\-sonata [\-h] [\-h5] [\-jnml] [\-neuron]
 .IP
@@ -34,11 +34,12 @@ Execute the generated LEMS/NeuroML2 model with
 jNeuroML_NEURON
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-summary v1.0.1" "User Commands"
+.TH PYNML-SUMMARY "1" "August 2023" "pynml-summary v1.0.10" "User Commands"
 .SH NAME
-pynml-summary \- manual page for pynml-summary v1.0.1
+pynml-summary \- manual page for pynml-summary v1.0.10
 .SH DESCRIPTION
 Usage:
 .PP
@@ -19,11 +19,12 @@ enable verbose mode
 print this help text and exit
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml-tune v1.0.1" "User Commands"
+.TH PYNML-TUNE "1" "August 2023" "pynml-tune v1.0.10" "User Commands"
 .SH NAME
-pynml-tune \- manual page for pynml-tune v1.0.1
+pynml-tune \- manual page for pynml-tune v1.0.10
 .SH DESCRIPTION
 usage: pynml\-tune [\-h] [\-simTime <simTime>] [\-dt <dt>]
 .IP
@@ -132,11 +132,12 @@ Should (some) generated files, e.g. *.dat, be deleted
 as optimisation progresses?
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (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" "May 2023" "pynml v1.0.1" "User Commands"
+.TH PYNML "1" "August 2023" "pynml v1.0.10" "User Commands"
 .SH NAME
-pynml \- manual page for pynml v1.0.1
+pynml \- manual page for pynml v1.0.10
 .SH DESCRIPTION
 usage: pynml [\-h|\-\-help] [<shared options>] <one of the mutually\-exclusive options>
 .PP
@@ -180,11 +180,12 @@ latest Schema
 v1.8.1 Schema
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),
 .BR pynml-channelml2nml (1),
+.BR pynml-plotchan (1),
 .BR pynml-plotspikes (1),
 .BR pynml-plotmorph (1),
 .BR pynml-modchannelanalysis (1),

man/man1/version.h2m

@@ -1,3 +1,3 @@
 [environment]
 .PP
-pyNeuroML v1.0.1 (libNeuroML v0.5.0, jNeuroML v0.12.2)
+pyNeuroML v1.0.10 (libNeuroML v0.5.3, jNeuroML v0.12.2)