Merge branch 'development' into feat/py3.12

NeuroML · Feb 6, 2024 · 4f8c799 · 4f8c799
2 parents 273036b + d32fda7
commit 4f8c799
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -36,10 +36,9 @@ jobs:
         echo "github.ref is: ${{ github.ref }}"
         echo "github.base_ref is: ${{ github.base_ref }}"
 
-    - name: Upgrade pip, install inspyred
+    - name: Upgrade pip, install deps
       run: |
         python -m pip install --upgrade pip
-        pip install git+https://github.com/aarongarrett/inspyred.git@master#egg=inspyred
         pip install .[dev]
 
     - name: List packages so far

diff --git a/.gitignore b/.gitignore
@@ -165,3 +165,5 @@ arm64
 /tests/plot/test_schematic_plot_2d_test_cell_nml_xz.png
 /tests/plot/test_schematic_plot_2d_test_cell_nml_yz.png
 /tests/analysis/*png
+*ken.sh
+/tests/plot/test_morphology*.png
diff --git a/examples/Vm_plot.py b/examples/Vm_plot.py
@@ -30,7 +30,6 @@ def generate_Vm_vs_time_plot(
     simulator="jNeuroML",
     include_included=True,
 ):
-
     ref = "Test"
     logger.info(
         "Generating Vm(mV) vs Time(ms) plot for cell %s in %s using %s (Inj %snA / %sms dur after %sms delay)"

diff --git a/examples/component_evaluation.py b/examples/component_evaluation.py
@@ -12,7 +12,6 @@ def main(args=None):
         nml_doc = pynml.read_neuroml2_file(f)
 
         for ct in nml_doc.ComponentType:
-
             ys = []
             for v in vs:
                 req_variables = {"v": "%sV" % v, "vShift": "10mV"}

diff --git a/examples/create_new_lems_file.py b/examples/create_new_lems_file.py
@@ -14,7 +14,6 @@
 
 
 if __name__ == "__main__":
-
     ############################################
     #  Create a LEMS file "manually"...
 

diff --git a/examples/generate_if_curve.py b/examples/generate_if_curve.py
@@ -16,5 +16,5 @@
     plot_voltage_traces=not nogui,
     plot_if=not nogui,
     plot_iv=not nogui,
-    save_if_data_to="if_data.dat"
+    save_if_data_to="if_data.dat",
 )
diff --git a/examples/generate_povray.py b/examples/generate_povray.py
@@ -1,6 +1,5 @@
-
 from pyneuroml.povray.NeuroML2ToPOVRay import generate_povray
 
-#generate_povray(neuroml_file='test_data/ca1/TestOLMNet.net.nml')
+# generate_povray(neuroml_file='test_data/ca1/TestOLMNet.net.nml')
 
-generate_povray(neuroml_file='test_data/Purk2M9s.nml', scalez=3)
+generate_povray(neuroml_file="test_data/Purk2M9s.nml", scalez=3)
diff --git a/examples/quick_plot.py b/examples/quick_plot.py
@@ -14,29 +14,28 @@
 siny = [math.sin(t / 10) for t in ts]
 cosey = [math.exp(t / -80) * math.cos(t / 5) for t in ts]
 
-if '-i' in sys.argv:
+if "-i" in sys.argv:
     from pyneuroml.plot.Plot import generate_interactive_plot
 
     # Generate a plot for this quickly with generate_interactive_plot
     ax = generate_interactive_plot(
         [ts, ts],  # Add 2 sets of x values
         [siny, cosey],  # Add 2 sets of y values
         "Some traces",  # Title
-        labels=['sin', 'cos'],
+        labels=["sin", "cos"],
         xaxis="Time (ms)",  # x axis legend
         yaxis="Arbitrary units...",  # y axis legend
         linewidths=[1, 3],  # Thicknesses of each trace
         save_figure_to="quick.png",
     )  # Save figure
 
 else:
-
     # Generate a plot for this quickly with generate_plot
     ax = generate_plot(
         [ts, ts],  # Add 2 sets of x values
         [siny, cosey],  # Add 2 sets of y values
         "Some traces",  # Title
-        labels=['sin', 'cos'],
+        labels=["sin", "cos"],
         xaxis="Time (ms)",  # x axis legend
         yaxis="Arbitrary units...",  # y axis legend
         linewidths=[1, 3],  # Thicknesses of each trace

diff --git a/examples/record_channel_currents.py b/examples/record_channel_currents.py
@@ -15,7 +15,6 @@
 
 
 if __name__ == "__main__":
-
     root_dir = "test_data/ca1"
     cell_file = "cells/olm.cell.nml"
     cell_comp = "olmcell"

diff --git a/examples/test_data/realtime.py b/examples/test_data/realtime.py
@@ -1,8 +1,8 @@
 from pyneuroml import pynml
 
 
-command = 'python snooze.py'
-run_dir = '.'
+command = "python snooze.py"
+run_dir = "."
 
 oo = pynml.execute_command_in_dir_with_realtime_output(command, run_dir, verbose=True)
 

diff --git a/examples/tune/tunePyr.py b/examples/tune/tunePyr.py
@@ -30,7 +30,6 @@
         "cell:pyr_4_sym/channelDensity:Kdr_pyr_soma_group/mS_per_cm2": 80,
     }
     if "-tune" in sys.argv:
-
         parameters = [
             "cell:pyr_4_sym/channelDensity:Na_pyr_soma_group/mS_per_cm2",
             "cell:pyr_4_sym/channelDensity:Kdr_pyr_soma_group/mS_per_cm2",

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 1.49.3.
-.TH PYNML-ARCHIVE "1" "November 2023" "pynml-archive v1.1.9" "User Commands"
+.TH PYNML-ARCHIVE "1" "December 2023" "pynml-archive v1.1.12" "User Commands"
 .SH NAME
-pynml-archive \- manual page for pynml-archive v1.1.9
+pynml-archive \- manual page for pynml-archive v1.1.12
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-CHANNELANALYSIS "1" "November 2023" "pynml-channelanalysis v1.1.9" "User Commands"
+.TH PYNML-CHANNELANALYSIS "1" "December 2023" "pynml-channelanalysis v1.1.12" "User Commands"
 .SH NAME
-pynml-channelanalysis \- manual page for pynml-channelanalysis v1.1.9
+pynml-channelanalysis \- manual page for pynml-channelanalysis v1.1.12
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-CHANNELML2NML "1" "November 2023" "pynml-channelml2nml v1.1.9" "User Commands"
+.TH PYNML-CHANNELML2NML "1" "December 2023" "pynml-channelml2nml v1.1.12" "User Commands"
 .SH NAME
-pynml-channelml2nml \- manual page for pynml-channelml2nml v1.1.9
+pynml-channelml2nml \- manual page for pynml-channelml2nml v1.1.12
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-MODCHANANALYSIS "1" "November 2023" "pynml-modchananalysis v1.1.9" "User Commands"
+.TH PYNML-MODCHANANALYSIS "1" "December 2023" "pynml-modchananalysis v1.1.12" "User Commands"
 .SH NAME
-pynml-modchananalysis \- manual page for pynml-modchananalysis v1.1.9
+pynml-modchananalysis \- manual page for pynml-modchananalysis v1.1.12
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-plotchan.1 b/man/man1/pynml-plotchan.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTCHAN "1" "November 2023" "pynml-plotchan v1.1.9" "User Commands"
+.TH PYNML-PLOTCHAN "1" "December 2023" "pynml-plotchan v1.1.12" "User Commands"
 .SH NAME
-pynml-plotchan \- manual page for pynml-plotchan v1.1.9
+pynml-plotchan \- manual page for pynml-plotchan v1.1.12
 .SH DESCRIPTION
 usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
 .IP
@@ -25,7 +25,7 @@ Do not generate distance plots
 Do not show plots as they are generated
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .SH "SEE ALSO"
 .BR pynml (1),
 .BR pynml-channelanalysis (1),

diff --git a/man/man1/pynml-plotmorph.1 b/man/man1/pynml-plotmorph.1
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTMORPH "1" "November 2023" "pynml-plotmorph v1.1.9" "User Commands"
+.TH PYNML-PLOTMORPH "1" "December 2023" "pynml-plotmorph v1.1.12" "User Commands"
 .SH NAME
-pynml-plotmorph \- manual page for pynml-plotmorph v1.1.9
+pynml-plotmorph \- manual page for pynml-plotmorph v1.1.12
 .SH DESCRIPTION
 usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
 .TP
@@ -55,7 +55,7 @@ Scale axes so that image is approximately square, for
 2D plot
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-PLOTSPIKES "1" "November 2023" "pynml-plotspikes v1.1.9" "User Commands"
+.TH PYNML-PLOTSPIKES "1" "December 2023" "pynml-plotspikes v1.1.12" "User Commands"
 .SH NAME
-pynml-plotspikes \- manual page for pynml-plotspikes v1.1.9
+pynml-plotspikes \- manual page for pynml-plotspikes v1.1.12
 .SH DESCRIPTION
 usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
 .TP
@@ -44,7 +44,7 @@ Window for rate calculation in ms
 Number of bins for rate histogram
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-POVRAY "1" "November 2023" "pynml-povray v1.1.9" "User Commands"
+.TH PYNML-POVRAY "1" "December 2023" "pynml-povray v1.1.12" "User Commands"
 .SH NAME
-pynml-povray \- manual page for pynml-povray v1.1.9
+pynml-povray \- manual page for pynml-povray v1.1.12
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-SONATA "1" "November 2023" "pynml-sonata v1.1.9" "User Commands"
+.TH PYNML-SONATA "1" "December 2023" "pynml-sonata v1.1.12" "User Commands"
 .SH NAME
-pynml-sonata \- manual page for pynml-sonata v1.1.9
+pynml-sonata \- manual page for pynml-sonata v1.1.12
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-SUMMARY "1" "November 2023" "pynml-summary v1.1.9" "User Commands"
+.TH PYNML-SUMMARY "1" "December 2023" "pynml-summary v1.1.12" "User Commands"
 .SH NAME
-pynml-summary \- manual page for pynml-summary v1.1.9
+pynml-summary \- manual page for pynml-summary v1.1.12
 .SH DESCRIPTION
 Usage:
 .PP
@@ -19,7 +19,7 @@ enable verbose mode
 print this help text and exit
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML-TUNE "1" "November 2023" "pynml-tune v1.1.9" "User Commands"
+.TH PYNML-TUNE "1" "December 2023" "pynml-tune v1.1.12" "User Commands"
 .SH NAME
-pynml-tune \- manual page for pynml-tune v1.1.9
+pynml-tune \- manual page for pynml-tune v1.1.12
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 1.49.3.
-.TH PYNML "1" "November 2023" "pynml v1.1.9" "User Commands"
+.TH PYNML "1" "December 2023" "pynml v1.1.12" "User Commands"
 .SH NAME
-pynml \- manual page for pynml v1.1.9
+pynml \- manual page for pynml v1.1.12
 .SH DESCRIPTION
 usage: pynml [\-h|\-\-help] [<shared options>] <one of the mutually\-exclusive options>
 .PP
@@ -184,9 +184,12 @@ Validate SBML file(s), unit consistency failure generates a warning
 .TP
 \fB\-validate\-sbml\-units\fR
 Validate SBML file(s), unit consistency failure generates an error
+.TP
+\fB\-validate\-sedml\fR
+Validate SEDML file(s)
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
 .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 v1.1.9 (libNeuroML v0.5.6, jNeuroML v0.13.0)
+pyNeuroML v1.1.12 (libNeuroML v0.5.7, jNeuroML v0.13.0)
diff --git a/pyneuroml/__init__.py b/pyneuroml/__init__.py
@@ -2,9 +2,11 @@
 
 try:
     import importlib.metadata
+
     __version__ = importlib.metadata.version("pyNeuroML")
 except ImportError:
     import importlib_metadata
+
     __version__ = importlib_metadata.version("pyNeuroML")
Original file line number	Diff line number	Diff line change
Expand Up		@@ -14,7 +14,6 @@


		if __name__ == "__main__":

		############################################
		# Create a LEMS file "manually"...

Expand Down