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Merge pull request #222 from NeuroML/feat/update-plotting-220
Plotting fixes related to #220, and regenerates man pages
2 parents e7a0ca6 + 1d25aae commit af3ff6d

14 files changed

+98
-86
lines changed

‎man/man1/pynml-archive.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
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.TH PYNML-ARCHIVE "1" "December 2022" "pynml-archive v0.7.5" "User Commands"
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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.TH PYNML-ARCHIVE "1" "May 2023" "pynml-archive v1.0.0" "User Commands"
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.SH NAME
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pynml-archive \- manual page for pynml-archive v0.7.5
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pynml-archive \- manual page for pynml-archive v1.0.0
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.SH DESCRIPTION
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usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
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.TP
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Explicit list of files to create archive of.
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
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pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
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.SH "SEE ALSO"
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.BR pynml (1),
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.BR pynml-channelanalysis (1),

‎man/man1/pynml-channelanalysis.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
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.TH PYNML-CHANNELANALYSIS "1" "December 2022" "pynml-channelanalysis v0.7.5" "User Commands"
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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.TH PYNML-CHANNELANALYSIS "1" "May 2023" "pynml-channelanalysis v1.0.0" "User Commands"
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.SH NAME
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pynml-channelanalysis \- manual page for pynml-channelanalysis v0.7.5
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pynml-channelanalysis \- manual page for pynml-channelanalysis v1.0.0
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.SH DESCRIPTION
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usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
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.TP
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plot current vs voltage for ion channel
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
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pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
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.SH "SEE ALSO"
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.BR pynml (1),
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.BR pynml-channelanalysis (1),

‎man/man1/pynml-channelml2nml.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
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.TH PYNML-CHANNELML2NML "1" "December 2022" "pynml-channelml2nml v0.7.5" "User Commands"
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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.TH PYNML-CHANNELML2NML "1" "May 2023" "pynml-channelml2nml v1.0.0" "User Commands"
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.SH NAME
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pynml-channelml2nml \- manual page for pynml-channelml2nml v0.7.5
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pynml-channelml2nml \- manual page for pynml-channelml2nml v1.0.0
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.SH DESCRIPTION
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usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
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Name of the outputfile file
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
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pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
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.SH "SEE ALSO"
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.BR pynml (1),
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.BR pynml-channelanalysis (1),

‎man/man1/pynml-modchananalysis.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
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.TH PYNML-MODCHANANALYSIS "1" "December 2022" "pynml-modchananalysis v0.7.5" "User Commands"
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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.TH PYNML-MODCHANANALYSIS "1" "May 2023" "pynml-modchananalysis v1.0.0" "User Commands"
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.SH NAME
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pynml-modchananalysis \- manual page for pynml-modchananalysis v0.7.5
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pynml-modchananalysis \- manual page for pynml-modchananalysis v1.0.0
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.SH DESCRIPTION
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usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
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.TP
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Name of the mod file containing the channel
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
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pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
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.SH "SEE ALSO"
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.BR pynml (1),
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.BR pynml-channelanalysis (1),

‎man/man1/pynml-plotmorph.1‎

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

‎man/man1/pynml-plotspikes.1‎

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

‎man/man1/pynml-povray.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
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.TH PYNML-POVRAY "1" "December 2022" "pynml-povray v0.7.5" "User Commands"
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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.TH PYNML-POVRAY "1" "May 2023" "pynml-povray v1.0.0" "User Commands"
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.SH NAME
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pynml-povray \- manual page for pynml-povray v0.7.5
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pynml-povray \- manual page for pynml-povray v1.0.0
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.SH DESCRIPTION
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usage: pynml\-povray [\-h] [\-split] [\-background <background colour>] [\-movie]
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Show segment ids
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
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pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
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.SH "SEE ALSO"
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.BR pynml (1),
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.BR pynml-channelanalysis (1),

‎man/man1/pynml-sonata.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
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.TH PYNML-SONATA "1" "December 2022" "pynml-sonata v0.7.5" "User Commands"
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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.TH PYNML-SONATA "1" "May 2023" "pynml-sonata v1.0.0" "User Commands"
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.SH NAME
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pynml-sonata \- manual page for pynml-sonata v0.7.5
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pynml-sonata \- manual page for pynml-sonata v1.0.0
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.SH DESCRIPTION
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usage: pynml\-sonata [\-h] [\-h5] [\-jnml] [\-neuron]
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jNeuroML_NEURON
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
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pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
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.SH "SEE ALSO"
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.BR pynml (1),
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.BR pynml-channelanalysis (1),

‎man/man1/pynml-summary.1‎

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

‎man/man1/pynml-tune.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.2.
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.TH PYNML-TUNE "1" "December 2022" "pynml-tune v0.7.5" "User Commands"
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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.TH PYNML-TUNE "1" "May 2023" "pynml-tune v1.0.0" "User Commands"
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.SH NAME
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pynml-tune \- manual page for pynml-tune v0.7.5
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pynml-tune \- manual page for pynml-tune v1.0.0
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.SH DESCRIPTION
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usage: pynml\-tune [\-h] [\-simTime <simTime>] [\-dt <dt>]
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as optimisation progresses?
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.5 (libNeuroML v0.4.2, jNeuroML v0.12.1)
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pyNeuroML v1.0.0 (libNeuroML v0.5.0, jNeuroML v0.12.1)
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.SH "SEE ALSO"
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.BR pynml (1),
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.BR pynml-channelanalysis (1),

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