Merge branch 'test_travis' into development

Author: pgleeson

.github/workflows/non-omv.yml

@@ -2,9 +2,9 @@ name: Non OMV tests
 
 on:
   push:
-    branches: [ master, development, experimental ]
+    branches: [ master, development, experimental, test* ]
   pull_request:
-    branches: [ master, development, experimental ]
+    branches: [ master, development, experimental, test* ]
 
 jobs:
   build:
@@ -16,14 +16,14 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    
+
     - name: Set up Python  ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version:  ${{ matrix.python-version }}
-        
+
     - name: Test python HH
       run: |
         pip install scipy matplotlib
         cd Tutorial/Source
-        python HodgkinHuxley.py 
+        python HodgkinHuxley.py

.github/workflows/omv-ci.yml

@@ -3,9 +3,9 @@ name: Continuous build using OMV
 
 on:
   push:
-    branches: [ master, development, experimental ]
+    branches: [ master, development, experimental, test* ]
   pull_request:
-    branches: [ master, development, experimental ]
+    branches: [ master, development, experimental, test* ]
 
 jobs:
   build:

Tutorial/Source/HodgkinHuxley.py

@@ -120,13 +120,8 @@ def I_inj(self, t):
             return 10*(t>100) - 10*(t>200) + 35*(t>300) - 35*(t>400)
 
         #""" running jupyterLab notebook """
-        #advanced input (if checkbox selected)
-        elif self.I_inj_width>0:              
-            return self.I_inj_max*(t>self.I_inj_trans) - self.I_inj_max*(t>self.I_inj_trans+self.I_inj_width)
-        
-        #basic input
         else:
-            return 10*(t>100) - 10*(t>200) + 35*(t>300) - 35*(t>400)
+            return self.I_inj_max*(t>self.I_inj_trans) - self.I_inj_max*(t>self.I_inj_trans+self.I_inj_width)
 
     @staticmethod
     def dALLdt(X, t, self):
@@ -164,6 +159,7 @@ def Main(self):
             plt.rcParams['figure.figsize'] = [12, 8]
             plt.rcParams['font.size'] = 15
             plt.rcParams['legend.fontsize'] = 12
+            plt.rcParams['legend.loc'] = "upper right"
 
         fig=plt.figure()
 
@@ -189,7 +185,6 @@ def Main(self):
         plt.legend()
 
         plt.subplot(4,1,4, sharex = ax1)
-       
         plt.plot(self.t, V, 'k')
         plt.ylabel('V (mV)')
         plt.xlabel('t (ms)')

Tutorial/_media/figure_1.png

@@ -48,7 +48,7 @@ This variable from `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 8-9
+   :lines: 12-15
 
 Is used in this line in `hhcell.cell.nml <hhcell.html>`_:
 
@@ -65,11 +65,11 @@ These variables from `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 11-12
+   :lines: 12-13,17-18
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 20-21
+   :lines: 26-27
 
 Are used in this line in `hhcell.cell.nml <hhcell.html>`_:
 
@@ -87,11 +87,11 @@ These variables from `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 14-15
+   :lines: 12-13,20-21
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 23-24
+   :lines: 29-30
 
 Are used in this line in `hhcell.cell.nml <hhcell.html>`_:
 
@@ -108,11 +108,11 @@ These variables from `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 17-18
+   :lines: 12-13,23-24
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 26-27
+   :lines: 32-33
 
 Are used in this line in `hhcell.cell.nml <hhcell.html>`_:
 
@@ -129,7 +129,7 @@ This variable from `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 29-30
+   :lines: 12-13,35-36
 
 Is used in this line in `LEMS_HH_Simulation.xml <LEMS_HH_Simulation.html>`_:
 
@@ -266,7 +266,7 @@ This line from `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 124
+   :lines: 153
 
 Is used to define the initial values for the model in `hhcell.cell.nml <hhcell.html>`_:
 
@@ -294,7 +294,7 @@ This line in `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 135-138
+   :lines: 191-194
 
 Is used in these lines in `LEMS_HH_Simulation.xml <LEMS_HH_Simulation.html>`_:
 
@@ -306,7 +306,7 @@ This line in `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 140-145
+   :lines: 177-182
 
 Is used in these lines in `LEMS_HH_Simulation.xml <LEMS_HH_Simulation.html>`_:
 
@@ -318,7 +318,7 @@ This line in `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 147-152
+   :lines: 184-189
 
 Is used in these lines in `LEMS_HH_Simulation.xml <LEMS_HH_Simulation.html>`_:
 
@@ -330,7 +330,7 @@ This line in `HodgkinHuxley.py <Hodgkin%20Huxley.html>`_:
 
 .. literalinclude:: ../Source/HodgkinHuxley.py
    :language: python
-   :lines: 154-158
+   :lines: 170-175
 
 Is used in these lines in `LEMS_HH_Simulation.xml <LEMS_HH_Simulation.html>`_:
 

Tutorial/_toc/Tutorial.rst

@@ -270,4 +270,3 @@
     import sphinx_rtd_theme
     html_theme = 'sphinx_rtd_theme'
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-

Tutorial/conf.py

@@ -48,13 +48,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a4fcb2202ee348999f01df623a6598e9",
+       "model_id": "1d3c73d3138d47af8f717354d52f302c",
        "version_major": 2,
        "version_minor": 0
       },
@@ -68,7 +68,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "af43f6c641d140c0a0a4459b17e39637",
+       "model_id": "814554308e89435dac419867021cf088",
        "version_major": 2,
        "version_minor": 0
       },
@@ -121,8 +121,15 @@
     "1) Starting from the bottom, the first (bottom-most) plot shows neural membrane voltage activity. The spikes here are called \"action potentials\" and correspond directly to the current/time plot. Outflux of *Na* directly followed by influx of *K* causes the spiking activity observed in the plot.\n",
     "2) The second plot from the bottom shows the activation/inactivation parameters of the ion channels in the neuron. \n",
     "3) Third plot from the bottom (the current/time plot) makes this more concrete, showing the influx (negative y-axis) and outflux (positive y-axis) of ions passing through each type of ion channel being modeled.\n",
-    "4) The top-most plot, shows two currents injected into the cell membrane at times 100ms and 300ms for default values. If injection current is changed from above slider then it will be a single rectangular pulse based on user input."
+    "4) The top-most plot, shows current injected into the cell membrane at times 150ms for default values. The injection current can be changed from above slider for amplitude, duration and delay."
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

notebook/notebook.ipynb

@@ -12,11 +12,11 @@
 default_pot_K        = -77
 default_pot_L        = -54.387
 default_t0           = 0
-default_tn           = 450
+default_tn           = 150
 default_deltat       = 0.01
-default_amplitude    = 50
-default_width        = 0
-default_translation  = 50
+default_amplitude    = 10
+default_width        = 100
+default_translation  = 25
 
 #function to reset input values to default on button click
 def resetTodefault(_):
@@ -42,13 +42,14 @@ def showDefault(response):
 
 #function to change slider handle colour when move from default
 def highlight_slider():
-    inputList    = [slider_capacitance, slider_cond_Na, slider_cond_K, slider_cond_L, slider_pot_Na, slider_pot_K, slider_pot_L]
-    inputDefault = [default_capacitance, default_cond_Na, default_cond_K, default_cond_L, default_pot_Na, default_pot_K, default_pot_L]
+    inputList    = [slider_capacitance, slider_cond_Na, slider_cond_K, slider_cond_L, slider_pot_Na, slider_pot_K, slider_pot_L, slider_amplitude, slider_width, slider_translation]
+    inputDefault = [default_capacitance, default_cond_Na, default_cond_K, default_cond_L, default_pot_Na, default_pot_K, default_pot_L, default_amplitude, default_width, default_translation]
     for l, d in zip(inputList,inputDefault):
         if l.value == d:
             l.style.handle_color = 'white'
         else:
             l.style.handle_color = 'orange'
+    """
     if slider_width.value == default_width:
         slider_amplitude.style.handle_color = 'white'
         slider_width.style.handle_color = 'white'
@@ -57,6 +58,7 @@ def highlight_slider():
         slider_amplitude.style.handle_color = 'orange'
         slider_width.style.handle_color = 'orange'
         slider_translation.style.handle_color = 'orange'
+    """
 
 #defining the widgets
 #Header or texts as HTMLMath to include symbols
@@ -65,7 +67,7 @@ def highlight_slider():
 header_potential   = ipywidgets.HTMLMath(value=r"<b> Nernst Reverasal Potentials, \(mV\)</b>")
 header_simTime     = ipywidgets.HTMLMath(value=r"<b> Simulation Time, \(ms\)</b>")
 header_injCurrent  = ipywidgets.HTMLMath(value=r"<b> Injection Current, \(\mu{A}/cm^2\)</b>")
-injCurrent_note    = ipywidgets.HTML(value=f"<i>*For injection current width = 0, the model uses default two pulse signal from tutorial</i>")
+injCurrent_note    = ipywidgets.HTML(value=f"<i>*For injection current duration = 0, the model uses default pulse signal from tutorial</i>")
 
 #slider widgets
 slider_capacitance = ipywidgets.FloatSlider(value=default_capacitance,min=0,max=3,step=0.1,description='Capacitance',readout=False,continuous_update=False)
@@ -76,13 +78,13 @@ def highlight_slider():
 slider_pot_K       = ipywidgets.FloatSlider(value=default_pot_K,min=-100,max=100,step=0.1,description='Potassium',readout=False,continuous_update=False)
 slider_pot_L       = ipywidgets.FloatSlider(value=default_pot_L,min=-100,max=100,step=0.1,description='Leak',readout=False,continuous_update=False)
 slider_amplitude   = ipywidgets.FloatSlider(value=default_amplitude,min=-20,max=200,step=0.1,description='Amplitude',readout=False,continuous_update=False)
-slider_width       = ipywidgets.FloatSlider(value=default_width,min=0,max=500,step=0.1,description='Width',readout=False,continuous_update=False)
-slider_translation = ipywidgets.FloatSlider(value=default_translation,min=0,max=250,step=0.1,description='Start at',readout=False,continuous_update=False)
+slider_width       = ipywidgets.FloatSlider(value=default_width,min=0,max=500,step=0.1,description='Duration',readout=False,continuous_update=False)
+slider_translation = ipywidgets.FloatSlider(value=default_translation,min=0,max=250,step=0.1,description='Time Delay',readout=False,continuous_update=False)
 
 #text box widgets
-time_start         = ipywidgets.FloatText(value=0,description='Start Time',disabled=True)
-time_end           = ipywidgets.FloatText(value=450,description='Total Time',disabled=False)
-time_step          = ipywidgets.FloatText(value=0.01,description='Time Step',disabled=False)
+time_start         = ipywidgets.FloatText(value=default_t0,description='Start Time',disabled=True)
+time_end           = ipywidgets.FloatText(value=default_tn,description='Total Time',disabled=False)
+time_step          = ipywidgets.FloatText(value=default_deltat,description='Time Step',disabled=False)
 
 #text box widgets to link with sliders (included to type in values for slider inputs also)
 textBox_capacitance = ipywidgets.FloatText(value=default_capacitance,step=0.1,layout=ipywidgets.Layout(width='5%'))