From 04d747c6f95ba3d4119e728a078e9982f4bee23c Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Thu, 4 May 2023 11:08:58 +0100 Subject: [PATCH 1/4] chore(plotting): note that `theme` is not used for 2d --- pyneuroml/plot/PlotMorphology.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyneuroml/plot/PlotMorphology.py b/pyneuroml/plot/PlotMorphology.py index 7d3a17e9..61f01140 100644 --- a/pyneuroml/plot/PlotMorphology.py +++ b/pyneuroml/plot/PlotMorphology.py @@ -104,7 +104,7 @@ def process_args(): type=str, metavar="", default=DEFAULTS["theme"], - help="Theme to use for interactive 3d plotting", + help="Theme to use for interactive 3d plotting (not used for 2d plotting)", ) parser.add_argument( "-minWidth", From a77c5057f9828722b54791a206384662e57b9837 Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Thu, 4 May 2023 11:15:25 +0100 Subject: [PATCH 2/4] feat(plotting): use lowecase for plot types Ref: https://github.com/NeuroML/pyNeuroML/issues/220 --- pyneuroml/plot/PlotMorphology.py | 62 +++++++++++++++--------------- tests/plot/test_morphology_plot.py | 8 ++-- 2 files changed, 35 insertions(+), 35 deletions(-) diff --git a/pyneuroml/plot/PlotMorphology.py b/pyneuroml/plot/PlotMorphology.py index 61f01140..d65c0612 100644 --- a/pyneuroml/plot/PlotMorphology.py +++ b/pyneuroml/plot/PlotMorphology.py @@ -53,7 +53,7 @@ "plane2d": "xy", "minWidth": 0.8, "square": False, - "plotType": "Constant", + "plotType": "constant", "theme": "light", } @@ -95,7 +95,7 @@ def process_args(): parser.add_argument( "-plotType", type=str, - metavar="", + metavar="", default=DEFAULTS["plotType"], help="Level of detail to plot in", ) @@ -180,7 +180,7 @@ def plot_interactive_3D( nml_file: str, min_width: float = DEFAULTS["minWidth"], verbose: bool = False, - plot_type: str = "Constant", + plot_type: str = "constant", title: typing.Optional[str] = None, theme: str = "light", nogui: bool = False, @@ -198,10 +198,10 @@ def plot_interactive_3D( :type verbose: bool :param plot_type: type of plot, one of: - - "Detailed": show detailed morphology taking into account each segment's + - "detailed": show detailed morphology taking into account each segment's width - - "Constant": show morphology, but use constant line widths - - "Schematic": only plot each unbranched segment group as a straight + - "constant": show morphology, but use constant line widths + - "schematic": only plot each unbranched segment group as a straight line, not following each segment This is only applicable for neuroml.Cell cells (ones with some @@ -215,9 +215,9 @@ def plot_interactive_3D( :param nogui: toggle showing gui (for testing only) :type nogui: bool """ - if plot_type not in ["Detailed", "Constant", "Schematic"]: + if plot_type not in ["detailed", "constant", "schematic"]: raise ValueError( - "plot_type must be one of 'Detailed', 'Constant', or 'Schematic'" + "plot_type must be one of 'detailed', 'constant', or 'schematic'" ) if verbose: @@ -322,7 +322,7 @@ def plot_interactive_3D( marker_sizes.extend([radius]) marker_colors.extend([color]) else: - if plot_type == "Schematic": + if plot_type == "schematic": plot_3D_schematic( offset=pos, cell=cell, @@ -373,7 +373,7 @@ def plot_2D( nogui: bool = False, save_to_file: typing.Optional[str] = None, square: bool = False, - plot_type: str = "Detailed", + plot_type: str = "detailed", title: typing.Optional[str] = None, close_plot: bool = False, ): @@ -403,10 +403,10 @@ def plot_2D( :type square: bool :param plot_type: type of plot, one of: - - "Detailed": show detailed morphology taking into account each segment's + - "detailed": show detailed morphology taking into account each segment's width - - "Constant": show morphology, but use constant line widths - - "Schematic": only plot each unbranched segment group as a straight + - "constant": show morphology, but use constant line widths + - "schematic": only plot each unbranched segment group as a straight line, not following each segment This is only applicable for neuroml.Cell cells (ones with some @@ -419,9 +419,9 @@ def plot_2D( :type close_plot: bool """ - if plot_type not in ["Detailed", "Constant", "Schematic"]: + if plot_type not in ["detailed", "constant", "schematic"]: raise ValueError( - "plot_type must be one of 'Detailed', 'Constant', or 'Schematic'" + "plot_type must be one of 'detailed', 'constant', or 'schematic'" ) if verbose: @@ -479,7 +479,7 @@ def plot_2D( nogui=True, ) else: - if plot_type == "Schematic": + if plot_type == "schematic": plot_2D_schematic( offset=pos, cell=cell, @@ -533,7 +533,7 @@ def plot_3D_cell_morphology_plotly( verbose: bool = False, nogui: bool = False, save_to_file: typing.Optional[str] = None, - plot_type: str = "Detailed", + plot_type: str = "detailed", ): """Plot NeuroML2 cell morphology interactively using Plot.ly @@ -557,15 +557,15 @@ def plot_3D_cell_morphology_plotly( :type save_to_file: str :param plot_type: type of plot, one of: - - Detailed: show detailed morphology taking into account each segment's + - detailed: show detailed morphology taking into account each segment's width - - Constant: show morphology, but use constant line widths + - constant: show morphology, but use constant line widths :type plot_type: str """ - if plot_type not in ["Detailed", "Constant"]: + if plot_type not in ["detailed", "constant"]: raise ValueError( - "plot_type must be one of 'Detailed', 'Constant', or 'Schematic'" + "plot_type must be one of 'detailed', 'constant', or 'schematic'" ) nml_model = read_neuroml2_file(nml_file) @@ -584,7 +584,7 @@ def plot_3D_cell_morphology_plotly( width = max(p.diameter, d.diameter) if width < min_width: width = min_width - if plot_type == "Constant": + if plot_type == "constant": width = min_width fig.add_trace( go.Scatter3d( @@ -654,7 +654,7 @@ def plot_2D_cell_morphology( nogui: bool = True, autoscale: bool = True, square: bool = False, - plot_type: str = "Detailed", + plot_type: str = "detailed", save_to_file: typing.Optional[str] = None, close_plot: bool = False, overlay_data: typing.Dict[int, float] = None, @@ -788,7 +788,7 @@ def plot_2D_cell_morphology( if width < min_width: width = min_width - if plot_type == "Constant": + if plot_type == "constant": width = min_width if overlay_data and acolormap and norm: @@ -910,7 +910,7 @@ def plot_3D_cell_morphology( min_width: float = DEFAULTS["minWidth"], axis_min_max: typing.List = [float("inf"), -1 * float("inf")], nogui: bool = True, - plot_type: str = "Constant", + plot_type: str = "constant", theme="light", ): """Plot the detailed 3D morphology of a cell using vispy. @@ -960,11 +960,11 @@ def plot_3D_cell_morphology( :type current_view: ViewBox :param plot_type: type of plot, one of: - - "Detailed": show detailed morphology taking into account each segment's + - "detailed": show detailed morphology taking into account each segment's width. This is not performant, because a new line is required for each segment. To only be used for cells with small numbers of segments - - "Constant": show morphology, but use constant line widths + - "constant": show morphology, but use constant line widths This is only applicable for neuroml.Cell cells (ones with some morphology) @@ -1033,7 +1033,7 @@ def plot_3D_cell_morphology( if width < min_width: width = min_width - if plot_type == "Constant": + if plot_type == "constant": width = min_width seg_color = "white" @@ -1066,14 +1066,14 @@ def plot_3D_cell_morphology( marker_colors.append(seg_color) marker_sizes.append(p.diameter) - if plot_type == "Constant": + if plot_type == "constant": points.append([offset[0] + p.x, offset[1] + p.y, offset[2] + p.z]) colors.append(seg_color) points.append([offset[0] + d.x, offset[1] + d.y, offset[2] + d.z]) colors.append(seg_color) toconnect.append([len(points) - 2, len(points) - 1]) # every segment plotted individually - elif plot_type == "Detailed": + elif plot_type == "detailed": points = [] toconnect = [] colors = [] @@ -1090,7 +1090,7 @@ def plot_3D_cell_morphology( width=width, ) - if plot_type == "Constant": + if plot_type == "constant": scene.Line( pos=points, color=colors, diff --git a/tests/plot/test_morphology_plot.py b/tests/plot/test_morphology_plot.py index c7ba0330..67831da0 100644 --- a/tests/plot/test_morphology_plot.py +++ b/tests/plot/test_morphology_plot.py @@ -148,7 +148,7 @@ def test_2d_constant_plotter_network(self): nogui=True, plane2d=plane, save_to_file=filename, - plot_type="Constant", + plot_type="constant", ) self.assertIsFile(filename) @@ -171,7 +171,7 @@ def test_2d_schematic_plotter_network(self): nogui=True, plane2d=plane, save_to_file=filename, - plot_type="Schematic", + plot_type="schematic", ) self.assertIsFile(filename) @@ -202,7 +202,7 @@ def test_3d_plotter_vispy(self): nml_doc = read_neuroml2_file(nml_file) cell = nml_doc.cells[0] # type: neuroml.Cell plot_3D_cell_morphology( - cell=cell, nogui=True, color="Groups", verbose=True, plot_type="Constant" + cell=cell, nogui=True, color="Groups", verbose=True, plot_type="constant" ) # test a circular soma @@ -210,7 +210,7 @@ def test_3d_plotter_vispy(self): nml_doc = read_neuroml2_file(nml_file) cell = nml_doc.cells[0] # type: neuroml.Cell plot_3D_cell_morphology( - cell=cell, nogui=True, color="Groups", verbose=True, plot_type="Constant" + cell=cell, nogui=True, color="Groups", verbose=True, plot_type="constant" ) def test_3d_plotter_plotly(self): From 22dbdfd5d4aac06db51b83bf0a7e3f1e2dc3a348 Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Thu, 4 May 2023 11:17:10 +0100 Subject: [PATCH 3/4] chore: regenerate man pages --- man/man1/pynml-archive.1 | 8 ++++---- man/man1/pynml-channelanalysis.1 | 8 ++++---- man/man1/pynml-channelml2nml.1 | 8 ++++---- man/man1/pynml-modchananalysis.1 | 8 ++++---- man/man1/pynml-plotmorph.1 | 26 ++++++++++++++++++-------- man/man1/pynml-plotspikes.1 | 8 ++++---- man/man1/pynml-povray.1 | 8 ++++---- man/man1/pynml-sonata.1 | 8 ++++---- man/man1/pynml-summary.1 | 8 ++++---- man/man1/pynml-tune.1 | 8 ++++---- man/man1/pynml.1 | 8 ++++---- man/man1/version.h2m | 2 +- 12 files changed, 59 insertions(+), 49 deletions(-) diff --git a/man/man1/pynml-archive.1 b/man/man1/pynml-archive.1 index bad3905a..2949375a 100644 --- 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 ] .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 index 811298c6..5c6f8b1e 100644 --- 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 ] [\-maxV ] .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 index 219b5229..3916cc44 100644 --- 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 ] .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 index 0b782442..5f46ebae 100644 --- 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 ] .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 index 8f2d3edc..4b8b2a01 100644 --- 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 ] .TP -[\-minWidth] [\-interactive3d] +[\-plotType ] +[\-theme ] +[\-minWidth ] [\-interactive3d] [\-saveToFile ] [\-square] .PP @@ -28,20 +30,28 @@ Don't open plot window \fB\-plane2d\fR Plane to plot on for 2D plot .TP -\fB\-minWidth\fR +\fB\-plotType\fR +Level of detail to plot in +.TP +\fB\-theme\fR +Theme to use for interactive 3d plotting (not used for +2d plotting) +.TP +\fB\-minWidth\fR Minimum width of lines to use .TP \fB\-interactive3d\fR Show interactive 3D plot .TP \fB\-saveToFile\fR -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 index 51f5514c..ef748513 100644 --- 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 ] [\-rates] [\-showPlotsAlready] .TP @@ -42,7 +42,7 @@ 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 index 43b6525d..a094c223 100644 --- 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 ] [\-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 index 79553a1a..11abbec0 100644 --- 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 index d108acc5..97b91b43 100644 --- 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 index 05bcb634..2eea4bb5 100644 --- 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 ] [\-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 index 48ffab4c..774d676c 100644 --- 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] [] .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 index d49eb9cc..e8d53c7b 100644 --- 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) From 1d25aae948e127217d1869de0facca2a82eb64a8 Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Thu, 4 May 2023 11:23:19 +0100 Subject: [PATCH 4/4] chore: regen man --- man/man1/pynml-plotspikes.1 | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/man/man1/pynml-plotspikes.1 b/man/man1/pynml-plotspikes.1 index ef748513..7a9b0848 100644 --- a/man/man1/pynml-plotspikes.1 +++ b/man/man1/pynml-plotspikes.1 @@ -22,7 +22,9 @@ show this help message and exit \fB\-format\fR 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