Skip to content

Commit bdd9018

Browse files
sanjayankur31sanjayankur31
authored
Merge pull request #307 from NeuroML/feat/refactor-spike-trace-plots
Feat: Add method and cli to plot time series
2 parents 99b798e + 5168139 commit bdd9018

31 files changed

+1059
-159
lines changed

‎docs/source/pyneuroml.plot.rst‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,14 @@ pyneuroml.plot.Plot module
1414
:undoc-members:
1515
:show-inheritance:
1616

17+
pyneuroml.plot.PlotTimeSeries module
18+
--------------------------------
19+
20+
.. automodule:: pyneuroml.plot.PlotTimeSeries
21+
:members:
22+
:undoc-members:
23+
:show-inheritance:
24+
1725
pyneuroml.plot.PlotSpikes module
1826
--------------------------------
1927

‎docs/source/pyneuroml.utils.rst‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,14 @@ pyneuroml.utils.plot module
2222
:undoc-members:
2323
:show-inheritance:
2424

25+
pyneuroml.utils.misc module
26+
---------------------------
27+
28+
.. automodule:: pyneuroml.utils.misc
29+
:members:
30+
:undoc-members:
31+
:show-inheritance:
32+
2533
pyneuroml.utils.cli module
2634
---------------------------
2735

‎man/man1/common.h2m‎

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,16 @@
1-
[see also]
1+
[see-also]
22
.BR pynml (1),
3+
.BR pynml-archive (1),
34
.BR pynml-channelanalysis (1),
45
.BR pynml-channelml2nml (1),
6+
.BR pynml-modchananalysis (1),
57
.BR pynml-plotchan (1),
6-
.BR pynml-plotspikes (1),
78
.BR pynml-plotmorph (1),
8-
.BR pynml-modchannelanalysis (1),
9+
.BR pynml-plotspikes (1),
10+
.BR pynml-plottimeseries (1),
911
.BR pynml-povray (1),
1012
.BR pynml-sonata (1),
1113
.BR pynml-summary (1),
12-
.BR pynml-tune (1).
14+
.BR pynml-tune (1),
1315
.PP
1416
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.

‎man/man1/generate-man-pages.sh‎

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
#!/bin/bash
22

33
# Copyright 2023 Ankur Sinha
4-
# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
4+
# Author: Ankur Sinha <sanjay DOT ankur AT gmail DOT com>
55
# File : generate-man-pages.sh
66
#
77
# Generate man pages for all pyNeuroML command lines using help2man
@@ -27,6 +27,17 @@ else
2727
echo ".PP" >> version.h2m
2828
echo "${fullversioninfo}" >> version.h2m
2929

30+
echo "Generating common file: common.h2m"
31+
echo "[see-also]" > common.h2m
32+
33+
for f in ${bin_location}/pynml*
34+
do
35+
current_file=$(basename $f)
36+
echo ".BR ${current_file} (1)," >> common.h2m
37+
done
38+
echo ".PP" >> common.h2m
39+
echo "Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem." >> common.h2m
40+
3041
cat common.h2m version.h2m >> common-temp.h2m
3142

3243
for f in ${bin_location}/pynml*
@@ -39,4 +50,3 @@ else
3950

4051
rm common-temp.h2m
4152
fi
42-

‎man/man1/pynml-archive.1‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2-
.TH PYNML-ARCHIVE "1" "February 2024" "pynml-archive v1.2.0" "User Commands"
2+
.TH PYNML-ARCHIVE "1" "February 2024" "pynml-archive v1.2.2" "User Commands"
33
.SH NAME
4-
pynml-archive \- manual page for pynml-archive v1.2.0
4+
pynml-archive \- manual page for pynml-archive v1.2.2
55
.SH DESCRIPTION
66
usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
77
.TP
@@ -27,20 +27,22 @@ Extension to use for archive.
2727
.TP
2828
\fB\-filelist\fR [<explicit list of files to create archive of> ...]
2929
Explicit list of files to create archive of.
30-
.SH ENVIRONMENT
31-
.PP
32-
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
33-
.SH "SEE ALSO"
30+
.SH "SEE-ALSO"
3431
.BR pynml (1),
32+
.BR pynml-archive (1),
3533
.BR pynml-channelanalysis (1),
3634
.BR pynml-channelml2nml (1),
35+
.BR pynml-modchananalysis (1),
3736
.BR pynml-plotchan (1),
38-
.BR pynml-plotspikes (1),
3937
.BR pynml-plotmorph (1),
40-
.BR pynml-modchannelanalysis (1),
38+
.BR pynml-plotspikes (1),
39+
.BR pynml-plottimeseries (1),
4140
.BR pynml-povray (1),
4241
.BR pynml-sonata (1),
4342
.BR pynml-summary (1),
44-
.BR pynml-tune (1).
43+
.BR pynml-tune (1),
4544
.PP
4645
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
46+
.SH ENVIRONMENT
47+
.PP
48+
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)

‎man/man1/pynml-channelanalysis.1‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2-
.TH PYNML-CHANNELANALYSIS "1" "February 2024" "pynml-channelanalysis v1.2.0" "User Commands"
2+
.TH PYNML-CHANNELANALYSIS "1" "February 2024" "pynml-channelanalysis v1.2.2" "User Commands"
33
.SH NAME
4-
pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.0
4+
pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.2
55
.SH DESCRIPTION
66
usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
77
.TP
@@ -92,20 +92,22 @@ the plots for the channel
9292
\fB\-ivCurve\fR
9393
Save currents through voltage clamp at each level &
9494
plot current vs voltage for ion channel
95-
.SH ENVIRONMENT
96-
.PP
97-
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
98-
.SH "SEE ALSO"
95+
.SH "SEE-ALSO"
9996
.BR pynml (1),
97+
.BR pynml-archive (1),
10098
.BR pynml-channelanalysis (1),
10199
.BR pynml-channelml2nml (1),
100+
.BR pynml-modchananalysis (1),
102101
.BR pynml-plotchan (1),
103-
.BR pynml-plotspikes (1),
104102
.BR pynml-plotmorph (1),
105-
.BR pynml-modchannelanalysis (1),
103+
.BR pynml-plotspikes (1),
104+
.BR pynml-plottimeseries (1),
106105
.BR pynml-povray (1),
107106
.BR pynml-sonata (1),
108107
.BR pynml-summary (1),
109-
.BR pynml-tune (1).
108+
.BR pynml-tune (1),
110109
.PP
111110
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
111+
.SH ENVIRONMENT
112+
.PP
113+
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)

‎man/man1/pynml-channelml2nml.1‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2-
.TH PYNML-CHANNELML2NML "1" "February 2024" "pynml-channelml2nml v1.2.0" "User Commands"
2+
.TH PYNML-CHANNELML2NML "1" "February 2024" "pynml-channelml2nml v1.2.2" "User Commands"
33
.SH NAME
4-
pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.0
4+
pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.2
55
.SH DESCRIPTION
66
usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
77
.TP
@@ -23,20 +23,22 @@ Path to the XSLT file
2323
.TP
2424
\fB\-saveToFile\fR <Output file name>
2525
Name of the outputfile file
26-
.SH ENVIRONMENT
27-
.PP
28-
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
29-
.SH "SEE ALSO"
26+
.SH "SEE-ALSO"
3027
.BR pynml (1),
28+
.BR pynml-archive (1),
3129
.BR pynml-channelanalysis (1),
3230
.BR pynml-channelml2nml (1),
31+
.BR pynml-modchananalysis (1),
3332
.BR pynml-plotchan (1),
34-
.BR pynml-plotspikes (1),
3533
.BR pynml-plotmorph (1),
36-
.BR pynml-modchannelanalysis (1),
34+
.BR pynml-plotspikes (1),
35+
.BR pynml-plottimeseries (1),
3736
.BR pynml-povray (1),
3837
.BR pynml-sonata (1),
3938
.BR pynml-summary (1),
40-
.BR pynml-tune (1).
39+
.BR pynml-tune (1),
4140
.PP
4241
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
42+
.SH ENVIRONMENT
43+
.PP
44+
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)

‎man/man1/pynml-modchananalysis.1‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2-
.TH PYNML-MODCHANANALYSIS "1" "February 2024" "pynml-modchananalysis v1.2.0" "User Commands"
2+
.TH PYNML-MODCHANANALYSIS "1" "February 2024" "pynml-modchananalysis v1.2.2" "User Commands"
33
.SH NAME
4-
pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.0
4+
pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.2
55
.SH DESCRIPTION
66
usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
77
.TP
@@ -54,20 +54,22 @@ in mM)
5454
.TP
5555
\fB\-modFile\fR <name of mod file>
5656
Name of the mod file containing the channel
57-
.SH ENVIRONMENT
58-
.PP
59-
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
60-
.SH "SEE ALSO"
57+
.SH "SEE-ALSO"
6158
.BR pynml (1),
59+
.BR pynml-archive (1),
6260
.BR pynml-channelanalysis (1),
6361
.BR pynml-channelml2nml (1),
62+
.BR pynml-modchananalysis (1),
6463
.BR pynml-plotchan (1),
65-
.BR pynml-plotspikes (1),
6664
.BR pynml-plotmorph (1),
67-
.BR pynml-modchannelanalysis (1),
65+
.BR pynml-plotspikes (1),
66+
.BR pynml-plottimeseries (1),
6867
.BR pynml-povray (1),
6968
.BR pynml-sonata (1),
7069
.BR pynml-summary (1),
71-
.BR pynml-tune (1).
70+
.BR pynml-tune (1),
7271
.PP
7372
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
73+
.SH ENVIRONMENT
74+
.PP
75+
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)

‎man/man1/pynml-plotchan.1‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2-
.TH PYNML-PLOTCHAN "1" "February 2024" "pynml-plotchan v1.2.0" "User Commands"
2+
.TH PYNML-PLOTCHAN "1" "February 2024" "pynml-plotchan v1.2.2" "User Commands"
33
.SH NAME
4-
pynml-plotchan \- manual page for pynml-plotchan v1.2.0
4+
pynml-plotchan \- manual page for pynml-plotchan v1.2.2
55
.SH DESCRIPTION
66
usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
77
.IP
@@ -23,20 +23,22 @@ Do not generate distance plots
2323
.TP
2424
\fB\-nogui\fR
2525
Do not show plots as they are generated
26-
.SH ENVIRONMENT
27-
.PP
28-
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
29-
.SH "SEE ALSO"
26+
.SH "SEE-ALSO"
3027
.BR pynml (1),
28+
.BR pynml-archive (1),
3129
.BR pynml-channelanalysis (1),
3230
.BR pynml-channelml2nml (1),
31+
.BR pynml-modchananalysis (1),
3332
.BR pynml-plotchan (1),
34-
.BR pynml-plotspikes (1),
3533
.BR pynml-plotmorph (1),
36-
.BR pynml-modchannelanalysis (1),
34+
.BR pynml-plotspikes (1),
35+
.BR pynml-plottimeseries (1),
3736
.BR pynml-povray (1),
3837
.BR pynml-sonata (1),
3938
.BR pynml-summary (1),
40-
.BR pynml-tune (1).
39+
.BR pynml-tune (1),
4140
.PP
4241
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
42+
.SH ENVIRONMENT
43+
.PP
44+
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)

‎man/man1/pynml-plotmorph.1‎

Lines changed: 11 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2-
.TH PYNML-PLOTMORPH "1" "February 2024" "pynml-plotmorph v1.2.0" "User Commands"
2+
.TH PYNML-PLOTMORPH "1" "February 2024" "pynml-plotmorph v1.2.2" "User Commands"
33
.SH NAME
4-
pynml-plotmorph \- manual page for pynml-plotmorph v1.2.0
4+
pynml-plotmorph \- manual page for pynml-plotmorph v1.2.2
55
.SH DESCRIPTION
66
usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
77
.TP
@@ -53,20 +53,22 @@ Name of the image file, for 2D plot
5353
\fB\-square\fR
5454
Scale axes so that image is approximately square, for
5555
2D plot
56-
.SH ENVIRONMENT
57-
.PP
58-
pyNeuroML v1.2.0 (libNeuroML v0.5.8, jNeuroML v0.13.0)
59-
.SH "SEE ALSO"
56+
.SH "SEE-ALSO"
6057
.BR pynml (1),
58+
.BR pynml-archive (1),
6159
.BR pynml-channelanalysis (1),
6260
.BR pynml-channelml2nml (1),
61+
.BR pynml-modchananalysis (1),
6362
.BR pynml-plotchan (1),
64-
.BR pynml-plotspikes (1),
6563
.BR pynml-plotmorph (1),
66-
.BR pynml-modchannelanalysis (1),
64+
.BR pynml-plotspikes (1),
65+
.BR pynml-plottimeseries (1),
6766
.BR pynml-povray (1),
6867
.BR pynml-sonata (1),
6968
.BR pynml-summary (1),
70-
.BR pynml-tune (1).
69+
.BR pynml-tune (1),
7170
.PP
7271
Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
72+
.SH ENVIRONMENT
73+
.PP
74+
pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)

0 commit comments

Comments
 (0)