Merge pull request #291 from NeuroML/experimental

pgleeson · web-flow · commit 789f43a91fd4 · 2023-12-14T10:48:02.000Z
To v1.1.10 &amp; black formatting
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/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")
 
 
diff --git a/pyneuroml/lems/__init__.py b/pyneuroml/lems/__init__.py
@@ -41,7 +41,6 @@ def generate_lems_file_for_neuroml(
     verbose=False,
     simulation_seed=12345,
 ):
-
     my_random = random.Random()
     if lems_file_generate_seed:
         my_random.seed(
@@ -117,7 +116,6 @@ def generate_lems_file_for_neuroml(
         )
 
         for include in nml_doc_inc_not_included.includes:
-
             if nml_dir == "." and os.path.isfile(include.href):
                 incl_curr = include.href
             else:
@@ -167,7 +165,6 @@ def generate_lems_file_for_neuroml(
                         if not os.path.isfile(
                             "%s/%s" % (target_dir, os.path.basename(incl_curr))
                         ) and not os.path.isfile("%s/%s" % (target_dir, incl_curr)):
-
                             shutil.copy(incl_curr, target_dir)
                             ls.include_neuroml2_file(
                                 include.href, include_included=False
@@ -186,10 +183,8 @@ def generate_lems_file_for_neuroml(
         or gen_spike_saves_for_all_somas
         or len(gen_spike_saves_for_only_populations) > 0
     ):
-
         for network in nml_doc.networks:
             for population in network.populations:
-
                 variable = "v"
                 quantity_template_e = "%s[%i]"
 
@@ -322,7 +317,6 @@ def generate_lems_file_for_neuroml(
                         quantities_saved.append(quantity)
 
     for display in sorted(gen_plots_for_quantities.keys()):
-
         quantities = gen_plots_for_quantities[display]
         max_ = "1"
         min_ = "-1"
@@ -349,7 +343,6 @@ def generate_lems_file_for_neuroml(
             quantities_saved.append(q)
 
     for file_name in sorted(gen_spike_saves_for_cells.keys()):
-
         quantities = gen_spike_saves_for_cells[file_name]
         of_id = safe_variable(file_name)
         ls.create_event_output_file(of_id, file_name)
diff --git a/pyneuroml/neuron/__init__.py b/pyneuroml/neuron/__init__.py
@@ -135,7 +135,6 @@ def export_to_neuroml1(hoc_file, nml1_file_name, level=1, validate=True):
     h.mvnml1.exportNeuroML(nml1_file_name, level)
 
     if validate:
-
         validate_neuroml1(nml1_file_name)
 
 
diff --git a/pyneuroml/neuron/analysis/HHanalyse.py b/pyneuroml/neuron/analysis/HHanalyse.py
@@ -137,7 +137,6 @@ def get_suffix(txt):
 
 
 def main():
-
     args = process_args()
     verbose = args.v
 
@@ -203,19 +202,20 @@ def main():
     try:
         sec.insert(str(chanToTest))
     except ValueError:
-        print(f"{chanToTest} mechanism has not been compiled yet. Trying to run `nrnivmodl`.")
+        print(
+            f"{chanToTest} mechanism has not been compiled yet. Trying to run `nrnivmodl`."
+        )
         try:
             subprocess.run("nrnivmodl", check=True, capture_output=True)
         except subprocess.CalledProcessError as e:
             print(f"Could not compile {modFileName}. nrivmodl returned {e.returncode}.")
-            #print(e.stderr.decode())
+            # print(e.stderr.decode())
             print("Try running nrnivmodl manually and checking its output.")
             print("Exiting...")
             return 1
         h.nrn_load_dll("x86_64/.libs/libnrnmech.so")
         sec.insert(str(chanToTest))
 
-
     for temperature in temperatures:
         h.celsius = temperature
         print("Set temperature for simulation to: %s" % h.celsius)
@@ -363,7 +363,6 @@ def main():
                                             % (s, slope, rateVal, timeToCheckTau)
                                         )
                                 elif initSlopeVal[s] != 1e9:
-
                                     if fractOfInit < 0.367879441:
                                         tau = (
                                             h.t - timeToCheckTau
@@ -404,7 +403,11 @@ def main():
                         val = eval("sec(0.5)." + s + "_" + chanToTest)
 
                         if s not in foundInf:
-                            rel_dif = (lastCheckVal[s] - val) / val if val > sys.float_info.epsilon else lastCheckVal[s]
+                            rel_dif = (
+                                (lastCheckVal[s] - val) / val
+                                if val > sys.float_info.epsilon
+                                else lastCheckVal[s]
+                            )
                             if abs(rel_dif) > tolerance:
                                 if verbose:
                                     print(
diff --git a/pyneuroml/plot/PlotMorphologyPlotly.py b/pyneuroml/plot/PlotMorphologyPlotly.py
@@ -76,7 +76,9 @@ def plot_3D_cell_morphology_plotly(
     elif isinstance(nml_file, NeuroMLDocument):
         nml_model = nml_file
     else:
-        raise TypeError("Passed model is not a NeuroML file path, nor a neuroml.Cell, nor a neuroml.NeuroMLDocument")
+        raise TypeError(
+            "Passed model is not a NeuroML file path, nor a neuroml.Cell, nor a neuroml.NeuroMLDocument"
+        )
 
     fig = go.Figure()
     for cell in nml_model.cells:
diff --git a/pyneuroml/povray/MakeMovie.py b/pyneuroml/povray/MakeMovie.py
@@ -134,7 +134,6 @@ def main(argv):
     pref = args.prefix
 
     if gen_images:
-
         for i in range(args.frames):
             index = str(i + 1)
             while len(index) < (len(str(args.frames))):
diff --git a/pyneuroml/swc/ExportSWC.py b/pyneuroml/swc/ExportSWC.py
@@ -13,7 +13,6 @@
 
 
 def _get_lines_for_seg_group(cell, sg, type):
-
     global line_count
     global line_index_vs_distals
     global line_index_vs_proximals
@@ -126,7 +125,6 @@ def convert_to_swc(nml_file_name, add_comments=False, target_dir=None):
     comment_lines = []
 
     for cell in nml_doc.cells:
-
         swc_file_name = "%s/%s.swc" % (target_dir, cell.id)
         swc_file = open(swc_file_name, "w")
 
diff --git a/pyneuroml/tune/NeuroMLController.py b/pyneuroml/tune/NeuroMLController.py
@@ -125,9 +125,7 @@ def run(self, candidates, parameters):
         start_time = time.time()
 
         if self.num_parallel_evaluations == 1:
-
             for candidate_i in range(len(candidates)):
-
                 candidate = candidates[candidate_i]
                 sim_var = dict(zip(parameters, candidate))
                 print_v(
@@ -296,7 +294,6 @@ def run_individual(
         nml_doc = neuroml.loaders.read_neuroml2_string(nml_doc)
 
     for var_name in sim_var.keys():
-
         individual_var_names = var_name.split("+")
 
         for individual_var_name in individual_var_names:
diff --git a/pyneuroml/tune/NeuroMLSimulation.py b/pyneuroml/tune/NeuroMLSimulation.py
@@ -51,9 +51,7 @@ def show(self):
         from matplotlib import pyplot as plt
 
         if self.already_run:
-
             for ref in self.volts.keys():
-
                 plt.plot(self.t, self.volts[ref], label=ref)
                 plt.title("Simulation voltage vs time")
                 plt.legend()
@@ -130,7 +128,6 @@ def go(self):
     dt = 0.05
 
     if len(sys.argv) == 2 and sys.argv[1] == "-net":
-
         sim = NeuroMLSimulation(
             "TestNet",
             "../../examples/test_data/simplenet.nml",
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = pyNeuroML
-version = 1.1.9
+version = 1.1.10
 author = Padraig Gleeson
 author_email = p.gleeson@gmail.com
 url = https://github.com/NeuroML/pyNeuroML
diff --git a/tests/analysis/test_cell_analysis.py b/tests/analysis/test_cell_analysis.py
@@ -22,8 +22,7 @@ class TestCellAnalysis(unittest.TestCase):
 
     def test_cell_analysis(self):
         """Test analyse_point_neuron"""
-        doc = neuroml.Izhikevich2007Cell.component_factory("NeuroMLDocument",
-                                                           id="test")
+        doc = neuroml.Izhikevich2007Cell.component_factory("NeuroMLDocument", id="test")
         doc.add(
             "Izhikevich2007Cell",
             id="izh2007RS0",
@@ -38,16 +37,21 @@ def test_cell_analysis(self):
             c="-50.0mV",
             d="100pA",
         )
-        neuroml.writers.NeuroMLWriter.write(doc, "tests/analysis/test_cell_analysis.cell.nml")
-        generate_current_vs_frequency_curve("tests/analysis/test_cell_analysis.cell.nml",
-                                            "izh2007RS0",
-                                            plot_voltage_traces=True,
-                                            plot_iv=True,
-                                            show_plot_already=False,
-                                            save_voltage_traces_to="tests/analysis/test_analysis_traces.png",
-                                            save_if_figure_to="tests/analysis/test_analysis_if.png",
-                                            save_iv_figure_to="tests/analysis/test_analysis_iv.png"
-                                            )
-        self.assertTrue(pathlib.Path("tests/analysis/test_analysis_traces.png").is_file())
+        neuroml.writers.NeuroMLWriter.write(
+            doc, "tests/analysis/test_cell_analysis.cell.nml"
+        )
+        generate_current_vs_frequency_curve(
+            "tests/analysis/test_cell_analysis.cell.nml",
+            "izh2007RS0",
+            plot_voltage_traces=True,
+            plot_iv=True,
+            show_plot_already=False,
+            save_voltage_traces_to="tests/analysis/test_analysis_traces.png",
+            save_if_figure_to="tests/analysis/test_analysis_if.png",
+            save_iv_figure_to="tests/analysis/test_analysis_iv.png",
+        )
+        self.assertTrue(
+            pathlib.Path("tests/analysis/test_analysis_traces.png").is_file()
+        )
         self.assertTrue(pathlib.Path("tests/analysis/test_analysis_if.png").is_file())
         self.assertTrue(pathlib.Path("tests/analysis/test_analysis_iv.png").is_file())
diff --git a/tests/analysis/test_channel_density_plots.py b/tests/analysis/test_channel_density_plots.py
@@ -75,13 +75,20 @@ def test_plot_channel_densities(self):
             channel_density_ids=["Ih_apical", "Ih_somatic", "Ih_basal", "Ih"],
             distance_plots=True,
             show_plots_already=False,
-            target_directory='tests/analysis'
+            target_directory="tests/analysis",
         )
         plot_channel_densities(
-            cell, ion_channels=["Ih"], distance_plots=True, show_plots_already=False,
-            target_directory='tests/analysis'
+            cell,
+            ion_channels=["Ih"],
+            distance_plots=True,
+            show_plots_already=False,
+            target_directory="tests/analysis",
         )
         # no channel densities or ion channels, so generate for all ion
         # channels
-        plot_channel_densities(cell, distance_plots=True, show_plots_already=False,
-            target_directory='tests/analysis')
+        plot_channel_densities(
+            cell,
+            distance_plots=True,
+            show_plots_already=False,
+            target_directory="tests/analysis",
+        )
diff --git a/tests/neuron/__init__.py b/tests/neuron/__init__.py
@@ -16,7 +16,7 @@
 
 
 def load_olm_cell():
-    """Setup for all tests """
+    """Setup for all tests"""
     thispath = pathlib.Path(__file__)
     dirname = str(thispath.parent / pathlib.Path("test_data"))
     subprocess.run(["nrnivmodl", dirname + "/mods"])
diff --git a/tests/neuron/test_neuron_utils.py b/tests/neuron/test_neuron_utils.py

Original file line number	Diff line number	Diff line change
`@@ -16,5 +16,5 @@`
`16`	`16`	`plot_voltage_traces=not nogui,`
`17`	`17`	`plot_if=not nogui,`
`18`	`18`	`plot_iv=not nogui,`
`19`		`- save_if_data_to="if_data.dat"`
	`19`	`+ save_if_data_to="if_data.dat",`
`20`	`20`	`)`
Original file line number	Diff line number	Diff line change
`@@ -30,7 +30,6 @@`
`30`	`30`	`"cell:pyr_4_sym/channelDensity:Kdr_pyr_soma_group/mS_per_cm2": 80,`
`31`	`31`	`}`
`32`	`32`	`if "-tune" in sys.argv:`
`33`		`-`
`34`	`33`	`parameters = [`
`35`	`34`	`"cell:pyr_4_sym/channelDensity:Na_pyr_soma_group/mS_per_cm2",`
`36`	`35`	`"cell:pyr_4_sym/channelDensity:Kdr_pyr_soma_group/mS_per_cm2",`