myokit 1.37.5__py3-none-any.whl → 1.39.0__py3-none-any.whl

myokit/tests/test_cellml_v1_api.py

@@ -410,6 +410,8 @@ class TestCellML1Model(unittest.TestCase):
         # Tests Model creation
 
         m = cellml.Model('hiya')
+        self.assertEqual(m.name(), 'hiya')
+        self.assertEqual(m.version(), '1.1')
 
         # Test bad name
         self.assertRaisesRegex(
@@ -674,6 +676,94 @@ class TestCellML1ModelConversion(unittest.TestCase):
         mm = cm.myokit_model()
         self.assertEqual(mm.get('c.y').eval(), 6.2)
 
+    def test_m2c_initial_values(self):
+        # Test conversion of initial values
+
+        m = myokit.parse_model('''
+            [[model]]
+            x.a = 1e3
+            x.b = -1       # parsed as PrefixMinus(Number(1))
+            x.c = --+-+-5  # extreme case of same
+            x.d = 1 + sqrt(4)
+            x.e = x.p
+            x.f = x.p + 3
+            x.g = y.q
+
+            [x]
+            t = 0 bind time
+            dot(a) = 0
+            dot(b) = 1
+            dot(c) = 2
+            dot(d) = 3
+            dot(e) = 4
+            dot(f) = 5
+            dot(g) = 6
+            p = 12
+            g_init = 0
+
+            [y]
+            q = 13
+        ''')
+        self.assertIsInstance(m.get('x.b').initial_value(), myokit.PrefixMinus)
+
+        # CellML 1.1
+        with WarningCollector() as w:
+            cm = cellml.Model.from_myokit_model(m, version='1.1')
+        self.assertFalse(w.has_warnings())
+        a, b, c, d, e, f, g, p = [cm['x'][i] for i in 'abcdefgp']
+        di = cm['x']['d_init']
+        fi = cm['x']['f_init']
+        gi = cm['x']['g_init_1']
+        self.assertEqual(a.initial_value(), myokit.Number(1e3))
+        self.assertEqual(b.initial_value(), myokit.Number(-1))
+        self.assertEqual(c.initial_value(), myokit.Number(5))
+        self.assertEqual(d.initial_value(), myokit.Name(di))
+        self.assertEqual(e.initial_value(), myokit.Name(p))
+        self.assertEqual(f.initial_value(), myokit.Name(fi))
+        self.assertEqual(g.initial_value(), myokit.Name(gi))
+        self.assertEqual(
+            fi.rhs(), myokit.Plus(myokit.Name(p), myokit.Number(3)))
+        # Note: ei has rhs x.q, not y.q, because connections!
+        self.assertEqual(gi.rhs(), myokit.Name(cm['x']['q']))
+        self.assertEqual(cm['x']['q'].public_interface(), 'in')
+        self.assertEqual(a.rhs(), myokit.Number(0))
+        self.assertEqual(b.rhs(), myokit.Number(1))
+        self.assertEqual(c.rhs(), myokit.Number(2))
+        self.assertEqual(d.rhs(), myokit.Number(3))
+        self.assertEqual(e.rhs(), myokit.Number(4))
+        self.assertEqual(f.rhs(), myokit.Number(5))
+        self.assertEqual(g.rhs(), myokit.Number(6))
+        cm.validate()
+        del di, fi, gi
+
+        # CellML 1.0
+        #self.assertEqual(cm['c']['x'].initial_value(), myokit.Number(2))
+
+        # Variable is OK in 1.1, but not 1.0
+        with WarningCollector() as w:
+            cm = cellml.Model.from_myokit_model(m, version='1.0')
+        self.assertEqual(w.count(), 3)
+        for warning in w.warnings():
+            self.assertIn('Incompatible expression', str(warning))
+        a, b, c, d, e, f, g, p = [cm['x'][i] for i in 'abcdefgp']
+        self.assertNotIn('f_init', cm['x'])
+        self.assertNotIn('g_init_1', cm['x'])
+        self.assertNotIn('q', cm['x'])
+        self.assertEqual(a.initial_value(), myokit.Number(1e3))
+        self.assertEqual(b.initial_value(), myokit.Number(-1))
+        self.assertEqual(c.initial_value(), myokit.Number(5))
+        self.assertEqual(d.initial_value(), myokit.Number(3))
+        self.assertEqual(e.initial_value(), myokit.Number(12))
+        self.assertEqual(f.initial_value(), myokit.Number(15))
+        self.assertEqual(g.initial_value(), myokit.Number(13))
+        self.assertEqual(a.rhs(), myokit.Number(0))
+        self.assertEqual(b.rhs(), myokit.Number(1))
+        self.assertEqual(c.rhs(), myokit.Number(2))
+        self.assertEqual(d.rhs(), myokit.Number(3))
+        self.assertEqual(e.rhs(), myokit.Number(4))
+        self.assertEqual(f.rhs(), myokit.Number(5))
+        cm.validate()
+
     def test_m2c_oxmeta(self):
         # Test that oxmeta data is passed on when creating a CellML model.
 
@@ -769,7 +859,7 @@ class TestCellML1ModelConversion(unittest.TestCase):
         self.assertEqual(mm.name(), 'm')
 
         # Check meta data is added
-        self.assertIn('author', mm.meta)
+        self.assertIn('mmt_authors', mm.meta)
 
         # Check meta data is passed on
         self.assertIn('documentation', mm.meta)
@@ -811,7 +901,7 @@ class TestCellML1ModelConversion(unittest.TestCase):
         self.assertEqual(
             mz.rhs(),
             myokit.Plus(myokit.Number(3, myokit.units.volt), myokit.Name(mx)))
-        self.assertEqual(mz2.rhs(), myokit.Number(4, myokit.units.meter))
+        self.assertEqual(mz2.rhs(), myokit.Number(4))
 
         # Check state
         self.assertTrue(mx.is_state())
@@ -820,6 +910,62 @@ class TestCellML1ModelConversion(unittest.TestCase):
         # Check binding
         self.assertEqual(mt.binding(), 'time')
 
+    def test_c2m_initial_values(self):
+        # Test conversion of initial values as variables
+
+        # Create model
+        m = cellml.Model('m')
+        a = m.add_component('a')
+        t = a.add_variable('t', 'dimensionless')
+        m.set_free_variable(t)
+        x = a.add_variable('x', 'volt')
+        x.set_initial_value(myokit.Number(1))
+        y = a.add_variable('y', 'volt')
+        y.set_initial_value(myokit.Name(x))
+        z = a.add_variable('z', 'volt')
+        z.set_is_state(True)
+        z.set_rhs(myokit.Number(2))
+        z.set_initial_value(myokit.Name(y))
+
+        # Convert and test
+        mm = m.myokit_model()
+        mx, my, mz = mm.get('a.x'), mm.get('a.y'), mm.get('a.z')
+        self.assertEqual(mx.rhs(), myokit.Number(1))
+        self.assertEqual(my.rhs(), myokit.Name(mx))
+        self.assertEqual(mz.rhs(), myokit.Number(2))
+        self.assertEqual(mz.initial_value(), myokit.Name(my))
+
+        # Initial value in other component
+        m = cellml.Model('m')
+        a = m.add_component('a')
+        t = a.add_variable('t', 'dimensionless')
+        m.set_free_variable(t)
+        ax = a.add_variable('x', 'volt', public_interface='in')
+        y = a.add_variable('y', 'volt')
+        y.set_initial_value(myokit.Name(ax))
+        y.set_is_state(True)
+        y.set_rhs(myokit.Number(12))
+        b = m.add_component('b')
+        bx = b.add_variable('x', 'volt', public_interface='out')
+        bx.set_initial_value(3)
+        m.add_connection(ax, bx)
+
+        # Convert and test
+        mm = m.myokit_model()
+        mx, my = mm.get('b.x'), mm.get('a.y')
+        self.assertEqual(mx.rhs(), myokit.Number(3))
+        self.assertEqual(my.rhs(), myokit.Number(12))
+        self.assertEqual(my.initial_value(), myokit.Name(mx))
+
+        # Missing initial values
+        y.set_initial_value(None)
+        bx.set_initial_value(None)
+        with WarningCollector() as w:
+            mm = m.myokit_model()
+        mx, my = mm.get('b.x'), mm.get('a.y')
+        self.assertEqual(my.initial_value(), myokit.Number(0))
+        self.assertEqual(mx.rhs(), myokit.Number(0, myokit.units.volt))
+
     def test_c2m_pass_through_variables(self):
         # Test support for variables used only to pass a value through a
         # hierarchical CellML structure.
@@ -1014,25 +1160,25 @@ class TestCellML1Variable(unittest.TestCase):
         self.assertIs(v.model(), m)
 
     def test_initial_value(self):
-        # Tests getting and setting intial values
+        # Tests getting and setting initial values
 
+        # Test setting and changing with numbers
         v = cellml.Model('m').add_component('c').add_variable('v', 'volt')
         self.assertIsNone(v.initial_value())
-
-        # Test setting and changing
         v.set_initial_value(4)
-        self.assertEqual(v.initial_value(), 4)
-        v.set_initial_value(-1.2e9)
-        self.assertEqual(v.initial_value(), -1.2e9)
+        self.assertEqual(v.initial_value(), myokit.Number(4))
+        e = myokit.Number(-1.2e9)
+        v.set_initial_value(e)
+        self.assertEqual(v.initial_value(), e)
+
+        # Test units are stripped
+        v.set_initial_value(myokit.Number(3, myokit.units.volt))
+        self.assertEqual(v.initial_value(), myokit.Number(3))
 
         # Test unsetting
         v.set_initial_value(None)
         self.assertIsNone(v.initial_value())
 
-        # Bad value
-        self.assertRaisesRegex(
-            cellml.CellMLError, 'real number', v.set_initial_value, 'blue')
-
         # Bad interface
         w = v.component().add_variable('w', 'volt', private_interface='in')
         self.assertRaisesRegex(
@@ -1041,7 +1187,51 @@ class TestCellML1Variable(unittest.TestCase):
         x = v.component().add_variable('x', 'volt', public_interface='in')
         self.assertRaisesRegex(
             cellml.CellMLError, 'public_interface="in"',
-            x.set_initial_value, 1)
+            x.set_initial_value, 2)
+
+        # In 1.1, can be a local variable
+        c = cellml.Model('m', version='1.1').add_component('c')
+        v = c.add_variable('v', 'volt')
+        w = c.add_variable('w', 'ampere')
+        v.set_initial_value(myokit.Name(w))
+        self.assertEqual(v.initial_value(), myokit.Name(w))
+
+        # But has to be a local variable
+        z = c.model().add_component('d').add_variable('z', 'newton')
+        self.assertRaisesRegex(
+            cellml.CellMLError, 'from the same component',
+            v.set_initial_value, myokit.Name(z))
+
+        # Can't be any other type of expression
+        self.assertRaisesRegex(
+            cellml.CellMLError, r'Initial value \(if set\)',
+            v.set_initial_value,
+            myokit.Plus(myokit.Number(1), myokit.Number(2)))
+        # or a random object type
+        self.assertRaisesRegex(
+            cellml.CellMLError, r'Initial value \(if set\)',
+            v.set_initial_value, self)
+
+        # In 1.0, can only be a number
+        c = cellml.Model('m', version='1.0').add_component('c')
+        v = c.add_variable('v', 'volt')
+        w = c.add_variable('w', 'ampere')
+        self.assertRaisesRegex(
+            cellml.CellMLError, r'In CellML 1.0, an initial value \(if set\)',
+            v.set_initial_value, myokit.Name(w))
+
+        # In 1.1, can also be a string
+        c = cellml.Model('m', version='1.1').add_component('c')
+        v = c.add_variable('v', 'volt')
+        w = c.add_variable('w', 'ampere')
+        v.set_initial_value('w')
+        self.assertEqual(v.initial_value(), myokit.Name(w))
+        c = cellml.Model('m', version='1.0').add_component('c')
+        v = c.add_variable('v', 'volt')
+        w = c.add_variable('w', 'ampere')
+        self.assertRaisesRegex(
+            cellml.CellMLError, 'In CellML 1.0, an initial value',
+            v.set_initial_value, 'w')
 
     def test_is_local_and_source(self):
         # Tests Variable.is_local() and Variable.source() and
@@ -1099,17 +1289,16 @@ class TestCellML1Variable(unittest.TestCase):
         v = cellml.Model('m').add_component('c').add_variable('bert', 'meter')
         self.assertIsNone(v.rhs_or_initial_value())
 
-        # Test initial value is returned
-        v.set_initial_value(3)
-        i = myokit.Number(3, myokit.units.meter)
-        self.assertEqual(v.rhs_or_initial_value(), i)
+        # Test initial value is returned (but with units stripped)
+        v.set_initial_value(myokit.Number(3, myokit.units.meter))
+        self.assertEqual(v.rhs_or_initial_value(), myokit.Number(3))
 
         # RHS takes precedence over initial value
         r = myokit.Number(18, myokit.units.meter)
         v.set_rhs(r)
         self.assertEqual(v.rhs_or_initial_value(), r)
         v.set_rhs(None)
-        self.assertEqual(v.rhs_or_initial_value(), i)
+        self.assertEqual(v.rhs_or_initial_value(), v.initial_value())
 
         # State never returns initial value
         v.set_is_state(True)
@@ -1126,6 +1315,11 @@ class TestCellML1Variable(unittest.TestCase):
         v.set_rhs(None)
         self.assertIsNone(v.rhs())
 
+        # Must be an expression
+        self.assertRaises(ValueError, v.set_rhs, 'a')
+        self.assertRaises(ValueError, v.set_rhs, '1 + 2')
+        self.assertRaises(ValueError, v.set_rhs, 13)
+
         # Bad interface
         w = v.component().add_variable('w', 'volt', 'in')
         self.assertRaisesRegex(
@@ -1564,21 +1758,21 @@ class TestCellML1Methods(unittest.TestCase):
         u = myokit.units.meter ** 2
         self.assertEqual(cellml.create_unit_name(u), 'm2')
 
-    def test_valid_identifier(self):
-        # Tests is_valid_identifier().
-
-        self.assertTrue(cellml.is_valid_identifier('hello'))
-        self.assertTrue(cellml.is_valid_identifier('h_e_l_l_o'))
-        self.assertTrue(cellml.is_valid_identifier('X123'))
-        self.assertTrue(cellml.is_valid_identifier('ZAa123_lo_2'))
-        self.assertTrue(cellml.is_valid_identifier('a'))
-        self.assertTrue(cellml.is_valid_identifier('_a'))
-
-        self.assertFalse(cellml.is_valid_identifier('_'))
-        self.assertFalse(cellml.is_valid_identifier('123'))
-        self.assertFalse(cellml.is_valid_identifier('1e3'))
-        self.assertFalse(cellml.is_valid_identifier('3'))
-        self.assertFalse(cellml.is_valid_identifier(''))
+    def test_is_identifier(self):
+        # Tests is_identifier().
+
+        self.assertTrue(cellml.is_identifier('hello'))
+        self.assertTrue(cellml.is_identifier('h_e_l_l_o'))
+        self.assertTrue(cellml.is_identifier('X123'))
+        self.assertTrue(cellml.is_identifier('ZAa123_lo_2'))
+        self.assertTrue(cellml.is_identifier('a'))
+        self.assertTrue(cellml.is_identifier('_a'))
+
+        self.assertFalse(cellml.is_identifier('_'))
+        self.assertFalse(cellml.is_identifier('123'))
+        self.assertFalse(cellml.is_identifier('1e3'))
+        self.assertFalse(cellml.is_identifier('3'))
+        self.assertFalse(cellml.is_identifier(''))
 
 
 if __name__ == '__main__':

myokit/tests/test_cellml_v1_parser.py

@@ -537,6 +537,52 @@ class TestCellMLParser(unittest.TestCase):
         self.assertBad(
             '<import />', 'Imports are not supported', version='1.1')
 
+    def test_initial_value(self):
+        # Test setting a variable as initial value, allowed in 1.1
+
+        x = ('<component name="a">'
+             '  <variable name="p" units="volt" initial_value="q" />'
+             '  <variable name="q" units="volt" initial_value="12.3" />'
+             '</component>')
+
+        # Not allowed in 1.0
+        self.assertBad(x, 'In CellML 1.0, an initial', version='1.0')
+
+        # But supported in 1.1
+        m = self.parse(x, version='1.1')
+        self.assertEqual(m['a']['p'].initial_value(), myokit.Name(m['a']['q']))
+        self.assertEqual(m['a']['q'].initial_value(), myokit.Number(12.3))
+
+        # Unknown variable, or non-local (API check)
+        x = ('<component name="a">'
+             '  <variable name="p" units="volt" initial_value="q" />'
+             '</component>')
+        self.assertBad(x, r'Initial value \(if set\)', version='1.1')
+        x = ('<component name="a">'
+             '  <variable name="p" units="volt" initial_value="q" />'
+             '</component>'
+             '<component name="b">'
+             '  <variable name="q" units="volt" initial_value="1" />'
+             '</component>')
+        self.assertBad(x, r'Initial value \(if set\)', version='1.1')
+
+        # Invalid attributes in either version (API check)
+        x = ('<component name="a">'
+             '  <variable name="p" units="volt" initial_value="@" />'
+             '</component>')
+        self.assertBad(x, r'Initial value \(if set\)', version='1.1')
+        x = ('<component name="a">'
+             '  <variable name="p" units="volt" initial_value="-inf" />'
+             '</component>')
+        self.assertBad(x, r'Initial value \(if set\)', version='1.1')
+
+        # Shouldn't have initial value (API check)
+        x = ('<component name="a">'
+             '  <variable name="p" units="volt" initial_value="1"'
+             '            public_interface="in" />'
+             '</component>')
+        self.assertBad(x, 'An initial value cannot be set', version='1.1')
+
     def test_math(self):
         # Tests parsing math elements
         x = ('<component name="a">'
@@ -581,7 +627,7 @@ class TestCellMLParser(unittest.TestCase):
 
         # Non-existent units
         y = '<apply><eq /><ci>x</ci><cn cellml:units="vlop">-80</cn></apply>'
-        self.assertBad(x + y + z, 'Unknown unit "vlop" referenced')
+        self.assertBad(x + y + z, 'Unknown units "vlop" referenced')
 
         # Unsupported units: Warning
         y = '<apply><eq /><ci>x</ci><cn cellml:units="celsius">2</cn></apply>'
@@ -630,21 +676,6 @@ class TestCellMLParser(unittest.TestCase):
             'Unexpected attribute mathml:name',
         )
 
-    def test_maths_1_1(self):
-        # Test setting a variable as initial value, allowed in 1.1
-
-        # Legal case in 1.1
-        x = ('<component name="a">'
-             '  <variable name="p" units="volt" initial_value="q" />'
-             '  <variable name="q" units="volt" initial_value="12.3" />'
-             '</component>')
-
-        # Not allowed in 1.0
-        self.assertBad(x, r'a real number \(3.4.3.7\)', version='1.0')
-
-        # Not supported in 1.1
-        self.assertBad(x, 'not supported', version='1.1')
-
     def test_model(self):
         # Tests parsing a model element.
 
@@ -741,7 +772,7 @@ class TestCellMLParser(unittest.TestCase):
         m = self.parse(x + a + z)
         v = m['a']['x']
         self.assertEqual(v.rhs(), myokit.Number(3))
-        self.assertEqual(v.initial_value(), 2)
+        self.assertEqual(v.initial_value(), myokit.Number(2))
 
         # Initial value and equation for a non-state
         b = ('    <apply>'

myokit/tests/test_cellml_v1_writer.py

@@ -125,7 +125,7 @@ class TestCellMLWriter(unittest.TestCase):
         self.assertIs(c.parent(), e)
         self.assertIs(b.parent(), c)
 
-    def test_initial_value_representation(self):
+    def test_initial_values(self):
         # Test the way initial values are represented in generated CellML code
 
         def find(xml):
@@ -155,6 +155,16 @@ class TestCellMLWriter(unittest.TestCase):
         x = find(cellml.write_string(m))
         self.assertEqual(x, '1.23424352342422994')
 
+        # Variables (in 1.1)
+        m = cellml.Model('m', '1.1')
+        c = m.add_component('c')
+        p = c.add_variable('p', 'mole')
+        q = c.add_variable('q', 'mole')
+        q.set_rhs(myokit.Number(1))
+        p.set_initial_value(myokit.Name(q))
+        x = find(cellml.write_string(m))
+        self.assertEqual(x, 'q')
+
     def test_maths(self):
         # Test maths is written
 
@@ -202,7 +212,7 @@ class TestCellMLWriter(unittest.TestCase):
         er2 = er1.clone(subst)
         self.assertEqual(q2.rhs(), eq2)
         self.assertEqual(r2.rhs(), er2)
-        self.assertEqual(s2.initial_value(), 1.23)
+        self.assertEqual(s2.initial_value(), myokit.Number(1.23))
         self.assertFalse(p2.is_state())
         self.assertFalse(q2.is_state())
         self.assertTrue(r2.is_state())
@@ -323,7 +333,7 @@ class TestCellMLWriter(unittest.TestCase):
         p = c.add_variable('p', 'mole')
         q = c.add_variable('q', 'kelvin', public_interface='in')
         r = c.add_variable('r', 'ampere', private_interface='out')
-        p.set_initial_value(1)
+        p.set_initial_value(myokit.Number(1, 'volt'))
 
         with WarningCollector():
             xml = cellml.write_string(m1)
@@ -339,7 +349,7 @@ class TestCellMLWriter(unittest.TestCase):
         self.assertEqual(p.private_interface(), 'none')
         self.assertEqual(q.private_interface(), 'none')
         self.assertEqual(r.private_interface(), 'out')
-        self.assertEqual(p.initial_value(), 1)
+        self.assertEqual(p.initial_value(), myokit.Number(1))
         self.assertEqual(q.initial_value(), None)
         self.assertEqual(r.initial_value(), None)