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Merge branch 'feat/channelml2nml2' into experimental
* feat/channelml2nml2: docs(channelml): add to sphinx docs docs(channelml): add note about Channelpedia xml converter test(channelml): add test files chore: regenerate man pages feat(channeml2nml): add script end point test(channelml2nml): add test feat(channelml): add to setup.py feat(channeml2nml): add function to convert channelml to neuroml
2 parents 633452c + b1d4794 commit b51558e

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‎docs/source/pyneuroml.channelml.rst‎

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pyneuroml.channelml package
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===========================
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.. automodule:: pyneuroml.channelml
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:members:
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:undoc-members:
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:show-inheritance:
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‎man/man1/common.h2m‎

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[see also]
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.BR pynml (1),
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.BR pynml-channelanalysis (1),
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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (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" "August 2022" "pynml-channelanalysis v0.7.1" "User Commands"
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.TH PYNML-CHANNELANALYSIS "1" "August 2022" "pynml-channelanalysis v0.7.2" "User Commands"
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.SH NAME
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pynml-channelanalysis \- manual page for pynml-channelanalysis v0.7.1
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pynml-channelanalysis \- manual page for pynml-channelanalysis v0.7.2
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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 v0.7.1 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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pyNeuroML v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (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" "August 2022" "pynml-channelml2nml v0.7.2" "User Commands"
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.SH NAME
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pynml-channelml2nml \- manual page for pynml-channelml2nml v0.7.2
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.SH DESCRIPTION
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usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
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.TP
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[\-saveToFile <Output file name>]
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<ChannelML file>
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.PP
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A script to convert ChannelML files to NeuroML2
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.SS "positional arguments:"
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.TP
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<ChannelML file>
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Path of the ChannelML file
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.SS "options:"
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.TP
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\fB\-h\fR, \fB\-\-help\fR
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show this help message and exit
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.TP
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\fB\-xsltfile\fR <XSLT file>
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Path to the XSLT file
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.TP
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\fB\-saveToFile\fR <Output file name>
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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 v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (1),
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.BR pynml-povray (1),
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.BR pynml-sonata (1),
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.BR pynml-summary (1),
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.BR pynml-tune (1).
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.PP
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Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.

‎man/man1/pynml-modchananalysis.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
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.TH PYNML-MODCHANANALYSIS "1" "December 2021" "pynml-modchananalysis v0.5.18" "User Commands"
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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" "August 2022" "pynml-modchananalysis v0.7.2" "User Commands"
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.SH NAME
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pynml-modchananalysis \- manual page for pynml-modchananalysis v0.5.18
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pynml-modchananalysis \- manual page for pynml-modchananalysis v0.7.2
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.SH DESCRIPTION
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usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
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<channel name>
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Name of the channel as used by NEURON (i.e. in SUFFIX
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statement)
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.SS "optional arguments:"
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.SS "options:"
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.TP
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\fB\-h\fR, \fB\-\-help\fR
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show this help message and exit
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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 v0.5.18 (libNeuroML v0.3.1, jNeuroML v0.11.0)
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pyNeuroML v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (1),
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.BR pynml-povray (1),
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.BR pynml-sonata (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" "August 2022" "pynml-plotmorph v0.7.1" "User Commands"
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.TH PYNML-PLOTMORPH "1" "August 2022" "pynml-plotmorph v0.7.2" "User Commands"
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.SH NAME
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pynml-plotmorph \- manual page for pynml-plotmorph v0.7.1
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pynml-plotmorph \- manual page for pynml-plotmorph v0.7.2
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.SH DESCRIPTION
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usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d] [\-interactive3d]
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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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[\-saveToFile <Image file name>]
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[\-minWidth] [\-interactive3d]
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[\-saveToFile <Image file name>] [\-square]
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<NeuroML 2 file>
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.PP
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A script which can generate plots of morphologies in NeuroML 2
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\fB\-nogui\fR
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Don't open plot window
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.TP
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\fB\-plane2d\fR
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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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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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.TP
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\fB\-square\fR
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Scale axes so that image is approximately square
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.7.1 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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pyNeuroML v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (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" "August 2022" "pynml-plotspikes v0.7.1" "User Commands"
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.TH PYNML-PLOTSPIKES "1" "August 2022" "pynml-plotspikes v0.7.2" "User Commands"
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.SH NAME
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pynml-plotspikes \- manual page for pynml-plotspikes v0.7.1
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pynml-plotspikes \- manual page for pynml-plotspikes v0.7.2
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.SH DESCRIPTION
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usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
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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 v0.7.1 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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pyNeuroML v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (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" "August 2022" "pynml-povray v0.7.1" "User Commands"
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.TH PYNML-POVRAY "1" "August 2022" "pynml-povray v0.7.2" "User Commands"
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.SH NAME
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pynml-povray \- manual page for pynml-povray v0.7.1
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pynml-povray \- manual page for pynml-povray v0.7.2
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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 v0.7.1 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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pyNeuroML v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (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" "August 2022" "pynml-summary v0.7.1" "User Commands"
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.TH PYNML-SUMMARY "1" "August 2022" "pynml-summary v0.7.2" "User Commands"
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.SH NAME
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pynml-summary \- manual page for pynml-summary v0.7.1
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pynml-summary \- manual page for pynml-summary v0.7.2
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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 v0.7.1 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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pyNeuroML v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (1),

‎man/man1/pynml-tune.1‎

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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
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.TH PYNML-TUNE "1" "December 2021" "pynml-tune v0.5.18" "User Commands"
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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" "August 2022" "pynml-tune v0.7.2" "User Commands"
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.SH NAME
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pynml-tune \- manual page for pynml-tune v0.5.18
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pynml-tune \- manual page for pynml-tune v0.7.2
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.SH DESCRIPTION
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usage: pynml\-tune [\-h] [\-simTime <simTime>] [\-dt <dt>]
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.IP
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[\-numParallelEvaluations <numParallelEvaluations>]
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[\-showPlotAlready] [\-saveToFile] [\-saveToFileScatter]
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[\-saveToFileHist] [\-saveToFileOutput] [\-verbose] [\-dryRun]
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[\-extraReportInfo <extraReportInfo>] [\-cleanup]
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<prefix> <neuromlFile> <target> <parameters>
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<weights>
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.SS "options:"
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\fB\-h\fR, \fB\-\-help\fR
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show this help message and exit
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\fB\-saveToFile\fR
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Name of file to save generated fitness plot to,
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default: skip.
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\fB\-saveToFileScatter\fR
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Name of file to save generated scatter plot to,
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default: skip.
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.TP
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\fB\-saveToFileHist\fR
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Name of file to save generated histogram plot to,
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default: skip.
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.TP
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\fB\-saveToFileOutput\fR
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Name of file to save generated output plot to,
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default: skip.
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Verbose mode
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as optimisation progresses?
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.SH ENVIRONMENT
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.PP
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pyNeuroML v0.5.18 (libNeuroML v0.3.1, jNeuroML v0.11.0)
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pyNeuroML v0.7.2 (libNeuroML v0.4.0, jNeuroML v0.12.0)
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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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.BR pynml-channelml2nml (1),
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.BR pynml-plotspikes (1),
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.BR pynml-plotmorph (1),
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.BR pynml-modchannelanalysis (1),
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.BR pynml-povray (1),
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.BR pynml-sonata (1),

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