NeuroML · pgleeson · May 4, 2023 · May 4, 2023 · May 4, 2023 · May 4, 2023
diff --git a/man/man1/pynml-archive.1 b/man/man1/pynml-archive.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-ARCHIVE "1" "December 2022" "pynml-archive v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-ARCHIVE "1" "May 2023" "pynml-archive v1.0.0" "User Commands"
 .SH NAME
-pynml-archive \- manual page for pynml-archive v0.7.5
+pynml-archive \- manual page for pynml-archive v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-channelanalysis.1 b/man/man1/pynml-channelanalysis.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-CHANNELANALYSIS "1" "December 2022" "pynml-channelanalysis v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-CHANNELANALYSIS "1" "May 2023" "pynml-channelanalysis v1.0.0" "User Commands"
 .SH NAME
-pynml-channelanalysis \- manual page for pynml-channelanalysis v0.7.5
+pynml-channelanalysis \- manual page for pynml-channelanalysis v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-channelml2nml.1 b/man/man1/pynml-channelml2nml.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-CHANNELML2NML "1" "December 2022" "pynml-channelml2nml v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-CHANNELML2NML "1" "May 2023" "pynml-channelml2nml v1.0.0" "User Commands"
 .SH NAME
-pynml-channelml2nml \- manual page for pynml-channelml2nml v0.7.5
+pynml-channelml2nml \- manual page for pynml-channelml2nml v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-modchananalysis.1 b/man/man1/pynml-modchananalysis.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-MODCHANANALYSIS "1" "December 2022" "pynml-modchananalysis v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-MODCHANANALYSIS "1" "May 2023" "pynml-modchananalysis v1.0.0" "User Commands"
 .SH NAME
-pynml-modchananalysis \- manual page for pynml-modchananalysis v0.7.5
+pynml-modchananalysis \- manual page for pynml-modchananalysis v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-plotmorph.1 b/man/man1/pynml-plotmorph.1
@@ -1,11 +1,13 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-PLOTMORPH "1" "December 2022" "pynml-plotmorph v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-PLOTMORPH "1" "May 2023" "pynml-plotmorph v1.0.0" "User Commands"
 .SH NAME
-pynml-plotmorph \- manual page for pynml-plotmorph v0.7.5
+pynml-plotmorph \- manual page for pynml-plotmorph v1.0.0
 .SH DESCRIPTION
 usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
 .TP
-[\-minWidth] [\-interactive3d]
+[\-plotType <type: detailed, constant, or schematic>]
+[\-theme <theme: light, dark>]
+[\-minWidth <min width of lines>] [\-interactive3d]
 [\-saveToFile <Image file name>] [\-square]
 <NeuroML 2 file>
 .PP
@@ -28,20 +30,28 @@ Don't open plot window
 \fB\-plane2d\fR <plane, e.g. xy, yz, zx>
 Plane to plot on for 2D plot
 .TP
-\fB\-minWidth\fR
+\fB\-plotType\fR <type: detailed, constant, or schematic>
+Level of detail to plot in
+.TP
+\fB\-theme\fR <theme: light, dark>
+Theme to use for interactive 3d plotting (not used for
+2d plotting)
+.TP
+\fB\-minWidth\fR <min width of lines>
 Minimum width of lines to use
 .TP
 \fB\-interactive3d\fR
 Show interactive 3D plot
 .TP
 \fB\-saveToFile\fR <Image file name>
-Name of the image file
+Name of the image file, for 2D plot
 .TP
 \fB\-square\fR
-Scale axes so that image is approximately square
+Scale axes so that image is approximately square, for
+2D plot
 .SH ENVIRONMENT
 .PP
-pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-plotspikes.1 b/man/man1/pynml-plotspikes.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-PLOTSPIKES "1" "December 2022" "pynml-plotspikes v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-PLOTSPIKES "1" "May 2023" "pynml-plotspikes v1.0.0" "User Commands"
 .SH NAME
-pynml-plotspikes \- manual page for pynml-plotspikes v0.7.5
+pynml-plotspikes \- manual page for pynml-plotspikes v1.0.0
 .SH DESCRIPTION
 usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
 .TP
@@ -22,7 +22,9 @@ show this help message and exit
 \fB\-format\fR <format>
 How the spiketimes are represented on each line of
 file: id_t: id of cell, space(s) / tab(s), time of
-spike (default); t_id: time of spike, space(s) /
+spike (default); id_t_nest_dat: id of cell, space(s) /
+tab(s), time of spike, allowing NEST dat file
+comments/metadata; t_id: time of spike, space(s) /
 tab(s), id of cell; sonata: SONATA format HDF5 file
 containing spike times
 .TP
@@ -42,7 +44,7 @@ Window for rate calculation in ms
 Number of bins for rate histogram
 .SH ENVIRONMENT
 .PP
-pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-povray.1 b/man/man1/pynml-povray.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-POVRAY "1" "December 2022" "pynml-povray v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-POVRAY "1" "May 2023" "pynml-povray v1.0.0" "User Commands"
 .SH NAME
-pynml-povray \- manual page for pynml-povray v0.7.5
+pynml-povray \- manual page for pynml-povray v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-sonata.1 b/man/man1/pynml-sonata.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-SONATA "1" "December 2022" "pynml-sonata v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-SONATA "1" "May 2023" "pynml-sonata v1.0.0" "User Commands"
 .SH NAME
-pynml-sonata \- manual page for pynml-sonata v0.7.5
+pynml-sonata \- manual page for pynml-sonata v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-summary.1 b/man/man1/pynml-summary.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-SUMMARY "1" "December 2022" "pynml-summary v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-SUMMARY "1" "May 2023" "pynml-summary v1.0.0" "User Commands"
 .SH NAME
-pynml-summary \- manual page for pynml-summary v0.7.5
+pynml-summary \- manual page for pynml-summary v1.0.0
 .SH DESCRIPTION
 Usage:
 .PP
@@ -19,7 +19,7 @@ enable verbose mode
 print this help text and exit
 .SH ENVIRONMENT
 .PP
-pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-tune.1 b/man/man1/pynml-tune.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML-TUNE "1" "December 2022" "pynml-tune v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML-TUNE "1" "May 2023" "pynml-tune v1.0.0" "User Commands"
 .SH NAME
-pynml-tune \- manual page for pynml-tune v0.7.5
+pynml-tune \- manual page for pynml-tune v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml.1 b/man/man1/pynml.1
@@ -1,7 +1,7 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
-.TH PYNML "1" "December 2022" "pynml v0.7.5" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
+.TH PYNML "1" "May 2023" "pynml v1.0.0" "User Commands"
 .SH NAME
-pynml \- manual page for pynml v0.7.5
+pynml \- manual page for pynml v1.0.0
 .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 v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/version.h2m b/man/man1/version.h2m
@@ -1,3 +1,3 @@
 [environment]
 .PP
-pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
+pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)