myokit 1.36.1__py3-none-any.whl → 1.37.1__py3-none-any.whl

myokit/formats/opencl/_ewriter.py

@@ -31,27 +31,6 @@ class OpenCLExpressionWriter(CBasedExpressionWriter):
         self._sp = (precision == myokit.SINGLE_PRECISION)
         self._nm = bool(native_math)
 
-    def _exc(self, e):
-        """Returns ``ex(e)`` if ``e`` is a Condition, else ``ex(e != 0)``."""
-        # Can be removed after https://github.com/myokit/myokit/issues/1056
-        if isinstance(e, myokit.Condition):
-            return self.ex(e)
-        return self.ex(myokit.NotEqual(e, myokit.Number(0)))
-
-    def _ex_infix_comparison(self, e, op):
-        """Handles ex() for infix condition operators (==, !=, > etc.)."""
-        # Can be removed after https://github.com/myokit/myokit/issues/1056
-        c1 = isinstance(e[0], myokit.Condition)
-        c2 = isinstance(e[1], myokit.Condition)
-        if (c1 and c2) or not (c1 or c2):
-            return f'({self.ex(e[0])} {op} {self.ex(e[1])})'
-        else:
-            return f'({self._exc(e[0])} {op} {self._exc(e[1])})'
-
-    def _ex_infix_logical(self, e, op):
-        # Can be removed after https://github.com/myokit/myokit/issues/1056
-        return f'({self._exc(e[0])} {op} {self._exc(e[1])})'
-
     #def _ex_name(self, e):
     #def _ex_derivative(self, e):
     #def _ex_initial_value(self, e):
@@ -126,25 +105,7 @@ class OpenCLExpressionWriter(CBasedExpressionWriter):
 
     #def _ex_and(self, e):
     #def _ex_or(self, e):
-
-    def _ex_not(self, e):
-        # Can be removed after https://github.com/myokit/myokit/issues/1056
-        return f'(!{self._exc(e[0])})'
-
-    def _ex_if(self, e):
-        # Can be removed after https://github.com/myokit/myokit/issues/1056
-        _if, _then, _else = self._exc(e._i), self.ex(e._t), self.ex(e._e)
-        return f'({_if} ? {_then} : {_else})'
-
-    def _ex_piecewise(self, e):
-        # Can be removed after https://github.com/myokit/myokit/issues/1056
-        _ifs = [self._exc(x) for x in e._i]
-        _thens = [self.ex(x) for x in e._e]
-        s = []
-        n = len(_ifs)
-        for _if, _then in zip(_ifs, _thens):
-            s.append(f'({_if} ? {_then} : ')
-        s.append(_thens[-1])
-        s.append(')' * len(_ifs))
-        return ''.join(s)
+    #def _ex_not(self, e):
+    #def _ex_if(self, e):
+    #def _ex_piecewise(self, e):
 

myokit/formats/opencl/template/minilog.py

@@ -177,7 +177,7 @@ class DataLog(OrderedDict):
         import numpy as np
         out = DataLog()
         for k, d in self.items():
-            out[k] = np.array(d, copy=False)
+            out[k] = np.asarray(d)
         return out
 
     def save_csv(self, filename, pad=None):

myokit/formats/sympy/_ereader.py

@@ -156,7 +156,8 @@ class SymPyExpressionReader:
     def _ex_abs(self, e):
         return myokit.Abs(self.ex(e.args[0]))
 
-    def _ex_not(self, e):
+    def _ex_not(self, e):   # pragma: no cover
+        # Sympy turns not(a == b) into a != b etc., so can't test!
         return myokit.Not(self.ex(e.args[0]))
 
     def _ex_equal(self, e):

myokit/formats/wcp/_wcp.py

@@ -241,7 +241,7 @@ class WcpFile(myokit.formats.SweepSource):
 
     def _channel_id(self, channel_id):
         """ Checks an int or str channel id and returns a valid int. """
-        if self._nr == 0:  # pragma: no cover
+        if self._nr == 0:
             raise KeyError(f'Channel {channel_id} not found (empty file).')
 
         # Handle string
@@ -314,7 +314,7 @@ class WcpFile(myokit.formats.SweepSource):
 
         # Create log
         log = myokit.DataLog()
-        if self._nr == 0:  # pragma: no cover
+        if self._nr == 0:
             return log
 
         # Get channel names
@@ -433,7 +433,7 @@ class WcpFile(myokit.formats.SweepSource):
         return self._nr
 
     def records(self):
-        """ Deprecated alias of :meth:`sweep_count`. """
+        """ Deprecated alias of :meth:`record_count`. """
         # Deprecated since 2023-06-22
         import warnings
         warnings.warn(

myokit/gui/datalog_viewer.py

@@ -641,13 +641,18 @@ class SweepSourceTab(GraphTabWidget):
     def __init__(self, parent, source):
         super().__init__(parent)
 
-        # Add A/D
-        for i in range(source.channel_count()):
-            self._add_graph_tab(source, i)
+        if source.sweep_count() > 0:
+            # Must have this condition to avoid getting exceptions with e.g.
+            # the empty WCP file in the test data set.
+            # myokit log myokit/tests/data/formats/wcp-file-empty.wcp
 
-        # Add D/A
-        for i in range(source.da_count()):
-            self._add_graph_tab(source, i, True)
+            # Add A/D
+            for i in range(source.channel_count()):
+                self._add_graph_tab(source, i)
+
+            # Add D/A
+            for i in range(source.da_count()):
+                self._add_graph_tab(source, i, True)
 
         # Add meta data
         self._add_meta_tab(source)
@@ -846,6 +851,10 @@ class CsvTab(GraphTabWidget):
         for k in keys:
             self.addTab(self.create_graph_tab(k, groups.get(k)), k)
 
+        # Add meta data tab
+        if log.meta:
+            self.addTab(self.create_meta_tab(log.meta), 'info')
+
     def create_graph_tab(self, key, indices=None):
         """ Creates a widget displaying the data stored under ``key``. """
         widget = QtWidgets.QWidget(self)
@@ -875,6 +884,18 @@ class CsvTab(GraphTabWidget):
         self._axes.append(axes)
         return widget
 
+    def create_meta_tab(self, meta):
+        """
+        Returns a tab showing information from a DataLog meta data object.
+        """
+        widget = QtWidgets.QTextEdit(self)
+        lines = []
+        for k, v in meta.items():
+            lines.append(f'{k}: {v}')
+        widget.setText('\n'.join(lines))
+        widget.setReadOnly(True)
+        return widget
+
 
 class MatTab(GraphTabWidget):
     """ A widget displaying a .mat file. """
@@ -992,9 +1013,7 @@ class TxtTab(GraphTabWidget):
             return
 
     def create_graph_tab(self, time, data):
-        """
-        Creates a widget displaying a time series.
-        """
+        """ Creates a widget displaying a time series. """
         widget = QtWidgets.QWidget(self)
         # Create figure
         figure = matplotlib.figure.Figure()

myokit/lib/markov.py

@@ -1077,7 +1077,7 @@ class AnalyticalSimulation:
         y0 = PI.dot(self._state.reshape((n, 1)))
 
         # Reshape times array
-        times = np.array(times, copy=False).reshape((len(times),))
+        times = np.asarray(times).reshape((len(times),))
 
         # Calculate state
         x = P.dot(y0 * np.exp(times * E))
@@ -1223,7 +1223,7 @@ class DiscreteSimulation:
 
         Returns a discretized state ``y`` where ``sum(y) = nchannels``.
         """
-        x = np.array(x, copy=False, dtype=float)
+        x = np.asarray(x, dtype=float)
         if (np.abs(1 - np.sum(x))) > 1e-6:
             raise ValueError(
                 'The sum of fractions in the state to be discretized must'

myokit/lib/plots.py

@@ -62,28 +62,28 @@ def simulation_times(
     def stair(ax, time, realtime, evaluations):
         if time is None:
             raise ValueError('This plotting mode requires "time" to be set.')
-        time = np.array(time, copy=False)
+        time = np.asarray(time)
         step = np.arange(0, len(time))
         ax.step(time, step, label=label)
 
     def stair_inverse(ax, time, realtime, evaluations):
         if time is None:
             raise ValueError('This plotting mode requires "time" to be set.')
-        time = np.array(time, copy=False)
+        time = np.asarray(time)
         step = np.arange(0, len(time))
         ax.step(step, time, label=label)
 
     def load(ax, time, realtime, evaluations):
         if time is None:
             raise ValueError('This plotting mode requires "time" to be set.')
-        time = np.array(time, copy=False)
+        time = np.asarray(time)
         size = np.log(1 / (time[1:] - time[:-1]))
         ax.step(time[1:], size, label=label)
 
     def histo(ax, time, realtime, evaluations):
         if time is None:
             raise ValueError('This plotting mode requires "time" to be set.')
-        time = np.array(time, copy=False)
+        time = np.asarray(time)
         zero = float(time[0])
         bucket_w = (time[-1] - zero) / nbuckets
         bucket_x = np.zeros(nbuckets)

myokit/tests/data/io/bad1d-4-not-a-zip.zip

@@ -1,105 +1 @@
-[[model]]
-name: beeler-1977
-author: Michael Clerx
-desc: """
-    The 1997 Beeler Reuter model of the AP in ventricular myocytes
-
-    Reference:
-
-    Beeler, Reuter (1976) Reconstruction of the action potential of ventricular
-    myocardial fibres
-    """
-f(x) = 4 * x
-# Initial values:
-membrane.V  = -84.622
-calcium.Cai = 2e-7
-ina.m       = 0.01
-ina.h       = 0.99
-ina.j       = 0.98
-isi.d       = 0.003
-isi.f       = 0.99
-ix1.x1      = 0.0004
-
-
-[engine]
-time = 0 in [ms] bind time
-pace = 0 bind pace
-
-[membrane]
-C = 1 [uF/cm^2] : The membrane capacitance
-dot(V) = -(1/C) * (i_ion + i_stim)
-    in [mV]
-    label membrane_potential
-    desc: Membrane potential    
-i_ion = ik1.IK1 + ix1.Ix1 + ina.INa + isi.Isi
-    label cellular_current
-    in [uA/cm^2]
-i_stim = engine.pace * amplitude
-    amplitude = -25 [uA/cm^2]
-
-[ina]
-use membrane.V as V
-gNaBar = 4 [mS/cm^2]
-gNaC = 0.003 [mS/cm^2]
-ENa = 50 [mV]
-INa = (gNaBar * m^3 * h * j + gNaC) * (V - ENa)
-    in [uA/cm^2]
-    desc: The excitatory inward sodium current
-dot(m) =  alpha * (1 - m) - beta * m
-    alpha = (V + 47) / (1 - exp(-0.1 * (V + 47)))
-    beta  = 40 * exp(-0.056 * (V + 72))
-    desc: The activation parameter
-dot(h) =  alpha * (1 - h) - beta * h
-    alpha = 0.126 * exp(-0.25 * (V + 77))
-    beta  = 1.7 / (1 + exp(-0.082 * (V + 22.5)))
-    desc: An inactivation parameter
-dot(j) =  alpha * (1 - j) - beta * j
-    alpha = 0.055 * exp(-0.25 * (V + 78)) / (1 + exp(-0.2 * (V + 78)))
-    beta  = 0.3 / (1 + exp(-0.1 * (V + 32)))
-    desc: An inactivation parameter
-
-[isi]
-use membrane.V as V
-gsBar = 0.09
-Es = -82.3 - 13.0287 * log(calcium.Cai)
-    in [mV]
-Isi = gsBar * d * f * (V - Es)
-    in [uA/cm^2]
-    desc: """
-    The slow inward current, primarily carried by calcium ions. Called either
-    "iCa" or "is" in the paper.
-    """
-dot(d) =  alpha * (1 - d) - beta * d
-    alpha = 0.095 * exp(-0.01 * (V + -5)) / (exp(-0.072 * (V + -5)) + 1)
-    beta  = 0.07 * exp(-0.017 * (V + 44)) / (exp(0.05 * (V + 44)) + 1)
-dot(f) = alpha * (1 - f) - beta * f
-    alpha = 0.012 * exp(-0.008 * (V + 28)) / (exp(0.15 * (V + 28)) + 1)
-    beta  = 0.0065 * exp(-0.02 * (V + 30)) / (exp(-0.2 * (V + 30)) + 1)
-
-[calcium]
-dot(Cai) = -1e-7 * isi.Isi + 0.07 * (1e-7 - Cai)
-    desc: The intracellular Calcium concentration
-    in [mol/L]
-
-[ik1]
-use membrane.V as V
-IK1 = 0.35 * (
-        4 * (exp(0.04 * (V + 85)) - 1)
-        / (exp(0.08 * (V + 53)) + exp(0.04 * (V + 53)))
-        + 0.2 * (V + 23)
-        / (1 - exp(-0.04 * (V + 23)))
-    )
-    in [uA/cm^2]
-    desc: """A time-independent outward potassium current exhibiting
-          inward-going rectification"""
-
-[ix1]
-use membrane.V as V
-Ix1 = x1 * 0.8 * (exp(0.04 * (V + 77)) - 1) / exp(0.04 * (V + 35))
-    in [uA/cm^2]
-    desc: """A voltage- and time-dependent outward current, primarily carried
-          by potassium ions"""
-dot(x1) = alpha * (1 - x1) - beta * x1
-    alpha = 0.0005 * exp(0.083 * (V + 50)) / (exp(0.057 * (V + 50)) + 1)
-    beta  = 0.0013 * exp(-0.06 * (V + 20)) / (exp(-0.04 * (V + 333)) + 1)
-
+;

myokit/tests/data/io/bad2d-4-not-a-zip.zip

@@ -1,105 +1 @@
-[[model]]
-name: beeler-1977
-author: Michael Clerx
-desc: """
-    The 1997 Beeler Reuter model of the AP in ventricular myocytes
-
-    Reference:
-
-    Beeler, Reuter (1976) Reconstruction of the action potential of ventricular
-    myocardial fibres
-    """
-f(x) = 4 * x
-# Initial values:
-membrane.V  = -84.622
-calcium.Cai = 2e-7
-ina.m       = 0.01
-ina.h       = 0.99
-ina.j       = 0.98
-isi.d       = 0.003
-isi.f       = 0.99
-ix1.x1      = 0.0004
-
-
-[engine]
-time = 0 in [ms] bind time
-pace = 0 bind pace
-
-[membrane]
-C = 1 [uF/cm^2] : The membrane capacitance
-dot(V) = -(1/C) * (i_ion + i_stim)
-    in [mV]
-    label membrane_potential
-    desc: Membrane potential    
-i_ion = ik1.IK1 + ix1.Ix1 + ina.INa + isi.Isi
-    label cellular_current
-    in [uA/cm^2]
-i_stim = engine.pace * amplitude
-    amplitude = -25 [uA/cm^2]
-
-[ina]
-use membrane.V as V
-gNaBar = 4 [mS/cm^2]
-gNaC = 0.003 [mS/cm^2]
-ENa = 50 [mV]
-INa = (gNaBar * m^3 * h * j + gNaC) * (V - ENa)
-    in [uA/cm^2]
-    desc: The excitatory inward sodium current
-dot(m) =  alpha * (1 - m) - beta * m
-    alpha = (V + 47) / (1 - exp(-0.1 * (V + 47)))
-    beta  = 40 * exp(-0.056 * (V + 72))
-    desc: The activation parameter
-dot(h) =  alpha * (1 - h) - beta * h
-    alpha = 0.126 * exp(-0.25 * (V + 77))
-    beta  = 1.7 / (1 + exp(-0.082 * (V + 22.5)))
-    desc: An inactivation parameter
-dot(j) =  alpha * (1 - j) - beta * j
-    alpha = 0.055 * exp(-0.25 * (V + 78)) / (1 + exp(-0.2 * (V + 78)))
-    beta  = 0.3 / (1 + exp(-0.1 * (V + 32)))
-    desc: An inactivation parameter
-
-[isi]
-use membrane.V as V
-gsBar = 0.09
-Es = -82.3 - 13.0287 * log(calcium.Cai)
-    in [mV]
-Isi = gsBar * d * f * (V - Es)
-    in [uA/cm^2]
-    desc: """
-    The slow inward current, primarily carried by calcium ions. Called either
-    "iCa" or "is" in the paper.
-    """
-dot(d) =  alpha * (1 - d) - beta * d
-    alpha = 0.095 * exp(-0.01 * (V + -5)) / (exp(-0.072 * (V + -5)) + 1)
-    beta  = 0.07 * exp(-0.017 * (V + 44)) / (exp(0.05 * (V + 44)) + 1)
-dot(f) = alpha * (1 - f) - beta * f
-    alpha = 0.012 * exp(-0.008 * (V + 28)) / (exp(0.15 * (V + 28)) + 1)
-    beta  = 0.0065 * exp(-0.02 * (V + 30)) / (exp(-0.2 * (V + 30)) + 1)
-
-[calcium]
-dot(Cai) = -1e-7 * isi.Isi + 0.07 * (1e-7 - Cai)
-    desc: The intracellular Calcium concentration
-    in [mol/L]
-
-[ik1]
-use membrane.V as V
-IK1 = 0.35 * (
-        4 * (exp(0.04 * (V + 85)) - 1)
-        / (exp(0.08 * (V + 53)) + exp(0.04 * (V + 53)))
-        + 0.2 * (V + 23)
-        / (1 - exp(-0.04 * (V + 23)))
-    )
-    in [uA/cm^2]
-    desc: """A time-independent outward potassium current exhibiting
-          inward-going rectification"""
-
-[ix1]
-use membrane.V as V
-Ix1 = x1 * 0.8 * (exp(0.04 * (V + 77)) - 1) / exp(0.04 * (V + 35))
-    in [uA/cm^2]
-    desc: """A voltage- and time-dependent outward current, primarily carried
-          by potassium ions"""
-dot(x1) = alpha * (1 - x1) - beta * x1
-    alpha = 0.0005 * exp(0.083 * (V + 50)) / (exp(0.057 * (V + 50)) + 1)
-    beta  = 0.0013 * exp(-0.06 * (V + 20)) / (exp(-0.04 * (V + 333)) + 1)
-
+;

myokit/tests/data/io/block1d.mmt

@@ -0,0 +1,187 @@
+[[model]]
+author: Michael Clerx
+desc: """
+Implementation of the Luo-Rudy model I for the ventricular myocyte.
+Based on an updated formulation downloaded from http://rudylab.wustl.edu
+
+Original copyright notice:
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+Copyright (C) 2006 by Leonid Livshitz and Yoram Rudy
+Email rudy@wustl.edu
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the
+Free Software Foundation, Inc.,
+59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+"""
+name: Luo-Rudy model (1991)
+# Initial conditions
+membrane.V = -84.5286
+ina.m      = 0.0017
+ina.h      = 0.9832
+ina.j      = 0.995484
+ica.d      = 0.000003
+ica.f      = 1
+ik.x       = 0.0057
+ica.Ca_i   = 0.0002
+
+# Engine variables
+[engine]
+time = 0 bind time
+pace = 1 bind pace  # Set to 1 to test if it becomes 0 without a protocol
+
+# Membrane potential and stimulus
+[membrane]
+dot(V) = -(i_ion + i_stim + i_diff)
+    label membrane_potential
+    in [mV]
+    desc: The membrane potential
+i_ion = ina.INa + ik.IK + ib.Ib + ikp.IKp + ik1.IK1 + ica.ICa
+i_stim = engine.pace * stim_amplitude
+    stim_amplitude = -80 [uA/cm^2]
+        desc: """
+        Stimulus amplitude.
+        The online matlab implementation features this 80 uA/cm^2, 0.5 millisecond
+        pulse. The cellml version uses a 2 millisecond 25.5 uA/cm^2 pulse.
+        """
+i_diff = 0 bind diffusion_current
+    in [uA/cm^2]
+
+# Fast Sodium current
+[ina]
+use membrane.V as V
+ENa = cell.RTF * log(cell.Na_o / cell.Na_i)
+    desc: Nernst potential of Na
+    in [mV]
+a = 1 - 1 / (1 + exp(-(V + 40) / 0.24))
+    desc: Used instead of if statement.
+dot(m) =  alpha * (1 - m) - beta * m
+    alpha = if(V == -47.13, -3.2,
+            0.32 * (V + 47.13) / (1 - exp(-0.1 * (V + 47.13))))
+    beta  = 0.08 * exp(-V / 11)
+    desc: """
+    Activation parameter of the fast sodium channel, based on Ebihara-Johnson
+    (E-J) model of cardiac cells (chicken embryo)
+    """
+dot(h) = alpha * (1 - h) - beta * h
+    alpha = a * 0.135 * exp((80 + V) / -6.8)
+    beta  = a * (3.56 * exp(0.079 * V) + 3.1e5 * exp(0.35 * V)) \
+          + (1 - a) / (0.13 * (1 + exp((V + 10.66) / -11.1)))
+    desc: """
+    (Fast) Inactivation parameter of the fast sodium channel, based on
+    Ebihara-Johnson (E-J) model of cardiac cells (chicken embryo)
+    """
+dot(j) =  alpha * (1 - j) - beta * j
+    alpha = a * ( -127140 * exp(0.2444 * V) - 3.474e-5 * exp(-0.04391 * V)) \
+              * (V + 37.78) / (1 + exp(0.311 * (V + 79.23)))
+    beta  = a * (0.1212 * exp(-0.01052 * V) / (1 + exp(-0.1378 * (V + 40.14)))) \
+          + (1 - a) * (0.3 * exp(-2.535e-7 * V) / (1 + exp(-0.1 * (V + 32))))
+    desc: """
+    Slow inactivation gate. Inspired by Beeler-Reuter and Haas. Steady-state
+    value (j_inf) is set to value from h gate (h_inf). Time constant obtained
+    from Beeler-Reuter model.
+    """
+gNa = 16
+INa = gNa * m^3 * h * j * (V - ENa)
+    desc: Fast sodium current
+    in [uA/cm^2]
+
+# Time-dependent Potassium current
+[ik]
+use membrane.V as V
+PNa_K = 0.01833 : Permability ratio of Na to K
+gK = 0.282 * sqrt(cell.K_o / 5.4)
+    in [mS/uF]
+E = cell.RTF * log((cell.K_o + PNa_K * cell.Na_o) / (cell.K_i + PNa_K * cell.Na_i))
+    in [mV]
+xi = if(V < -100,
+    1,
+    if(V == -77,
+        2.837 * 0.04 / exp(0.04 * (V + 35)),
+        2.837 * (exp(0.04 * (V + 77)) - 1) / ((V + 77) * exp(0.04 * (V + 35)))
+        ))
+dot(x) = alpha * (1 - x) - beta * x
+    alpha = 0.0005 * exp(0.083 * (V + 50)) / (1 + exp(0.057 * (V + 50)))
+    beta  = 0.0013 * exp(-0.06 * (V + 20)) / (1 + exp(-0.04 * (V + 20)))
+IK = gK * xi * x * (V - E)
+    desc: Time-dependent Potassium current
+
+# Plateau Potassium current
+[ikp]
+use membrane.V as V
+gKp = 0.0183
+IKp = gKp * (V + 87.8789) / (1 + exp((7.488 - V) / 5.98))
+    desc: Plateau Potassium current
+
+# Slow inward Calcium current
+[ica]
+use membrane.V as V
+dot(Ca_i) =  -1e-4 * ICa + 0.07 * (1e-4 - Ca_i)
+    desc: Intracellular Calcium concentration
+E = 7.7 - 13.0287 * log(Ca_i / cell.Ca_o)
+    desc: Nernst potential
+    in [mV]
+dot(d) =  alpha * (1 - d) - beta * d
+    alpha = 0.095 * exp(-0.01 * (V - 5)) / (1 + exp(-0.072 * (V - 5)))
+    beta  = 0.07 * exp(-0.017 * (V + 44)) / (1 + exp(0.05 * (V + 44)))
+dot(f) =  alpha * (1-f) - beta * f
+    alpha = 0.012 * exp(-0.008 * (V + 28)) / (1 + exp(0.15 * (V + 28)))
+    beta  = 0.0065 * exp(-0.02 * (V + 30)) / (1 + exp(-0.2 * (V + 30)))
+gCa = 0.09
+ICa = gCa * d * f * (V - E)
+
+# Time-independent potassium current
+[ik1]
+use membrane.V as V
+E = cell.RTF * log(cell.K_o / cell.K_i)
+gK1 = 0.6047 * sqrt(cell.K_o / 5.4) * alpha / (alpha + beta)
+    alpha = 1.02 / (1 + exp(0.2385 * (V - E - 59.215)))
+    beta  = (0.49124 * exp(0.08032 * (V - E + 5.476)) + exp(0.06175 * (V - E - 594.31)))  \
+          / (1 + exp(-0.5143 * (V - E + 4.753)))
+IK1 = gK1 * (V - E)
+
+# Background current
+[ib]
+gb = 0.03921
+Ib = gb * (membrane.V + 59.87) : Background current
+
+# Cell parameters (ventricular mammalian cell)
+[cell]
+K_o = 5.4 [mM]
+K_i = 145 [mM]
+Na_o = 140 [mM]
+Na_i = 10 [mM]
+Ca_o = 1.8 [mM]
+RTF = R*T/F
+    R = 8.314 [J/K] : Gas constant
+    T = 273 + 37 [K] : Absolute temperature
+    F = 96.5 [C/mol] : Faraday constant
+
+[[protocol]]
+# Level Start Length Period Multiplier
+1.0     1     0.5    1000   0
+
+[[script]]
+import matplotlib.pyplot as pl
+import myokit
+
+# Create simulation
+m = get_model()
+p = get_protocol()
+s = myokit.SimulationOpenCL(m, p, 16)
+
+# Run
+d = s.run(5, log=['engine.time', 'membrane.V', 'engine.pace'])
+b = d.block1d()
+b.save('block1d.zip')
+

myokit/tests/data/io/datalog-18-duplicate-keys.csv

@@ -0,0 +1,4 @@
+"time","x","x","ys-2","x","ys-2","x-2"
+1, 0, 2, 4, 6, 8, 5
+2, 1, 3, 5, 7, 9, 4
+

myokit/tests/test_aux.py

@@ -526,6 +526,10 @@ class AuxTest(unittest.TestCase):
             self.assertEqual(a, b)
         self.assertEqual(len(x), len(y))
 
+        # No issues when passing initial state from a model
+        # See https://github.com/myokit/myokit/pull/1083
+        myokit.step(m1, reference=m2, initial=m1.initial_values())
+
     def test_strfloat(self):
         # Deprecated alias of myokit.float.str
         args = ['-1.234', True, myokit.SINGLE_PRECISION]