Update __init__.py to catch attempts to plot species instead of speci…

.github/workflows/coverage.yml

@@ -92,6 +92,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
+          python -m pip install --upgrade -r ci_requirements.txt
 
       - name: Set up Python@${{ env.PY_MID_VERSION }}
         uses: actions/setup-python@v4
@@ -108,6 +109,8 @@ jobs:
         run: |
           python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
+          python -m pip install --upgrade -r ci_requirements.txt
+
 
       - name: Build & Test
         id: build-test

.github/workflows/neuron-ci.yml

@@ -144,6 +144,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
+          python -m pip install --upgrade -r ci_requirements.txt
 
       - name: Set up Python@${{ env.PY_MAX_VERSION }}
         uses: actions/setup-python@v4
@@ -155,6 +156,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip -r nrn_requirements.txt
           python -m pip install --upgrade -r external/nmodl/requirements.txt
+          python -m pip install --upgrade -r ci_requirements.txt
 
       - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
         if: matrix.config.music == 'ON'

ci_requirements.txt

@@ -0,0 +1,2 @@
+plotly
+ipywidgets>=7.0.0

share/lib/python/neuron/__init__.py

@@ -1021,6 +1021,7 @@ def __call__(self, graph, *args, **kwargs):
 
         def _get_pyplot_axis3d(fig):
             """requires matplotlib"""
+            from . import rxd
             from matplotlib.pyplot import cm
             import matplotlib.pyplot as plt
             from mpl_toolkits.mplot3d import Axes3D
@@ -1087,6 +1088,11 @@ def _do_plot(
                     lines = {}
                     lines_list = []
                     vals = []
+
+                    if isinstance(variable, rxd.species.Species):
+                        if len(variable.regions) > 1:
+                            raise Exception("Please specify region for the species.")
+
                     for sec in sections:
                         all_seg_pts = _segment_3d_pts(sec)
                         for seg, (xs, ys, zs, _, _) in zip(sec, all_seg_pts):
@@ -1227,6 +1233,7 @@ def color_to_hex(col):
         def _do_plot_on_plotly(width=2, color=None, cmap=None):
             """requires matplotlib for colormaps if not specified explicitly"""
             import ctypes
+            from . import rxd
             import plotly.graph_objects as go
 
             class FigureWidgetWithNEURON(go.FigureWidget):
@@ -1307,6 +1314,11 @@ def mark(self, segment, marker="or", **kwargs):
                 val_range = hi - lo
 
                 data = []
+
+                if isinstance(variable, rxd.species.Species):
+                    if len(variable.regions) > 1:
+                        raise Exception("Please specify region for the species.")
+
                 for sec in secs:
                     all_seg_pts = _segment_3d_pts(sec)
                     for seg, (xs, ys, zs, _, _) in zip(sec, all_seg_pts):

test/rxd/test_pltvar.py

@@ -0,0 +1,67 @@
+import pytest
+import plotly
+from neuron import units
+from matplotlib import pyplot
+
+
+def test_plt_variable(neuron_instance):
+    """Test to make sure species with multiple regions is not plotted"""
+
+    h, rxd, _, _ = neuron_instance
+
+    dend1 = h.Section("dend1")
+    dend2 = h.Section("dend2")
+    dend2.connect(dend1(1))
+
+    dend1.nseg = dend1.L = dend2.nseg = dend2.L = 11
+    dend1.diam = dend2.diam = 2 * units.µm
+
+    cyt = rxd.Region(dend1.wholetree(), nrn_region="i")
+    cyt2 = rxd.Region(dend2.wholetree(), nrn_region="i")
+
+    ca = rxd.Species(
+        [cyt, cyt2],
+        name="ca",
+        charge=2,
+        initial=0 * units.mM,
+        d=1 * units.µm**2 / units.ms,
+    )
+
+    ca.nodes(dend1(0.5))[0].include_flux(1e-13, units="mmol/ms")
+
+    h.finitialize(-65 * units.mV)
+    h.fadvance()
+
+    ps = h.PlotShape(False)
+
+    # Expecting an error for matplotlib
+    with pytest.raises(Exception, match="Please specify region for the species."):
+        ps.variable(ca)
+        ps.plot(pyplot)
+
+    # Expecting an error for plotly
+    with pytest.raises(Exception, match="Please specify region for the species."):
+        ps.variable(ca)
+        ps.plot(plotly)
+
+    cb = rxd.Species(
+        [cyt],
+        name="cb",
+        charge=2,
+        initial=0 * units.mM,
+        d=1 * units.µm**2 / units.ms,
+    )
+
+    # Scenarios that should work
+    ps.variable(ca[cyt])
+    ps.plot(plotly)  # No error expected here
+
+    ps.variable(ca[cyt])
+    ps.plot(pyplot)  # No error expected here
+
+    # Test plotting with only one region
+    ps.variable(cb)
+    ps.plot(plotly)  # No Error expected here
+
+    ps.variable(cb)
+    ps.plot(pyplot)  # No Error expected here