Merge branch 'experimental' of github.com:NeuroML/pyNeuroML into experimental

* 'experimental' of github.com:NeuroML/pyNeuroML: (93 commits)
  Add plot spike support for nest 3.0 spiketime files
  Remove py2.7 in master tests
  Remove travis badge
  Test without argparse requirement
  Fix some issues with plot (was using marker='o' by default)
  chore: remove print statement
  improvement(3d-plotting): remove edge for spheres
  test: mark vispy tests to disable them on GitHub CI
  chore: format with black
  chore: format with black
  chore: complete comment
  feat(vispy): implement rotation for Turntable camera
  feat(vispy): expose theme setting to all methods
  perf(vispy-plotting): use single `Marker` object for all spheres
  improvement(vispy): remove axes from canvas
  chore(vispy): make turntable camera default
  chore: document method
  chore: format with black
  improvement(plot): tweak default scene range
  fix(plotting): fix point cell 3d plotting
  ...

Author: pgleeson

.github/workflows/ci.yml

@@ -60,7 +60,6 @@ jobs:
 
     - name: Run tests
       run: |
-        pytest --cov=pyneuroml -m "not localonly" .
         pynml -h
 
         ./test-ghactions.sh -neuron

.gitignore

@@ -153,3 +153,5 @@ examples/results/*.dat
 /tests/test_cell_analysis.cell.nml
 arm64
 *.neux
+/test_*plot*png
+/examples/plot.py

pyneuroml/__init__.py

@@ -1,6 +1,6 @@
 import logging
 
-__version__ = "0.7.6"
+__version__ = "1.0.0"
 
 JNEUROML_VERSION = "0.12.1"
 

pyneuroml/analysis/__init__.py

@@ -7,6 +7,7 @@
 from pyneuroml import pynml
 from pyneuroml.lems.LEMSSimulation import LEMSSimulation
 from pyneuroml.lems import generate_lems_file_for_neuroml
+from pyneuroml.utils.plot import get_next_hex_color
 import neuroml as nml
 from pyelectro.analysis import max_min
 from pyelectro.analysis import mean_spike_frequency
@@ -240,7 +241,7 @@ def generate_current_vs_frequency_curve(
     for i in range(number_cells):
         ref = "v_cell%i" % i
         quantity = "%s[%i]/v" % (pop.id, i)
-        ls.add_line_to_display(disp0, ref, quantity, "1mV", pynml.get_next_hex_color())
+        ls.add_line_to_display(disp0, ref, quantity, "1mV", get_next_hex_color())
         ls.add_column_to_output_file(of0, ref, quantity)
 
     lems_file_name = ls.save_to_file()

pyneuroml/lems/LEMSSimulation.py

@@ -13,7 +13,7 @@
 from neuroml import __version__ as libnml_ver
 from pyneuroml.pynml import read_neuroml2_file
 from pyneuroml.pynml import read_lems_file
-from pyneuroml.pynml import get_next_hex_color
+from pyneuroml.utils.plot import get_next_hex_color
 
 logger = logging.getLogger(__name__)
 

pyneuroml/lems/__init__.py

@@ -4,7 +4,8 @@
 import shutil
 import os
 import logging
-from pyneuroml.pynml import read_neuroml2_file, get_next_hex_color
+from pyneuroml.pynml import read_neuroml2_file
+from pyneuroml.utils.plot import get_next_hex_color
 import random
 import neuroml
 

pyneuroml/plot/Plot.py

@@ -45,7 +45,8 @@ def generate_plot(
     save_figure_to: typing.Optional[str] = None,
     title_above_plot: bool = False,
     verbose: bool = False,
-) -> matplotlib.axes.Axes:
+    close_plot: bool = False,
+) -> typing.Optional[matplotlib.axes.Axes]:
     """Utility function to generate plots using the Matplotlib library.
 
     This function can be used to generate graphs with multiple plot lines.
@@ -127,7 +128,9 @@ def generate_plot(
     :type title_above_plot: boolean
     :param verbose: enable/disable verbose logging (default: False)
     :type verbose: boolean
-    :returns: matplotlib.axes.Axes object
+    :param close_plot: call pyplot.close() to close plot after plotting
+    :type close_plot: bool
+    :returns: matplotlib.axes.Axes object if plot is not closed, else None
     """
 
     logger.info("Generating plot: %s" % (title))
@@ -174,15 +177,14 @@ def generate_plot(
         label = "" if not labels else labels[i]
         marker = None if not markers else markers[i]
         linewidth = 1 if not linewidths else linewidths[i]
-        markersize = 6 if not markersizes else markersizes[i]
+        markersize = None if not markersizes else markersizes[i]
 
         if colors:
             plt.plot(
                 xvalues[i],
                 yvalues[i],
-                "o",
-                color=colors[i],
                 marker=marker,
+                color=colors[i],
                 markersize=markersize,
                 linestyle=linestyle,
                 linewidth=linewidth,
@@ -192,7 +194,6 @@ def generate_plot(
             plt.plot(
                 xvalues[i],
                 yvalues[i],
-                "o",
                 marker=marker,
                 markersize=markersize,
                 linestyle=linestyle,
@@ -239,7 +240,13 @@ def generate_plot(
     if show_plot_already:
         plt.show()
 
-    return ax
+    if close_plot:
+        logger.info("Closing plot")
+        plt.close()
+    else:
+        return ax
+
+    return None
 
 
 def generate_interactive_plot(
@@ -376,7 +383,7 @@ def generate_interactive_plot(
         raise ValueError("labels not provided correctly")
 
     if not markersizes:
-        markersizes = len(xvalues) * [6.0]
+        markersizes = len(xvalues) * [6]
     if not markers:
         markers = len(xvalues) * [0]
     if not linestyles: