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

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Files changed (65) hide show
  1. myokit/__init__.py +6 -19
  2. myokit/_aux.py +4 -0
  3. myokit/_datablock.py +55 -65
  4. myokit/_datalog.py +42 -7
  5. myokit/_err.py +26 -3
  6. myokit/_expressions.py +241 -127
  7. myokit/_model_api.py +19 -13
  8. myokit/_myokit_version.py +1 -1
  9. myokit/_sim/jacobian.py +3 -3
  10. myokit/_sim/openclsim.py +5 -5
  11. myokit/_sim/rhs.py +1 -1
  12. myokit/formats/__init__.py +4 -9
  13. myokit/formats/ansic/_ewriter.py +4 -20
  14. myokit/formats/axon/_abf.py +11 -4
  15. myokit/formats/diffsl/__init__.py +60 -0
  16. myokit/formats/diffsl/_ewriter.py +145 -0
  17. myokit/formats/diffsl/_exporter.py +435 -0
  18. myokit/formats/heka/_patchmaster.py +345 -115
  19. myokit/formats/opencl/_ewriter.py +3 -42
  20. myokit/formats/opencl/template/minilog.py +1 -1
  21. myokit/formats/sympy/_ereader.py +2 -1
  22. myokit/formats/wcp/_wcp.py +3 -3
  23. myokit/gui/datalog_viewer.py +28 -9
  24. myokit/lib/markov.py +2 -2
  25. myokit/lib/plots.py +4 -4
  26. myokit/tests/data/formats/wcp-file-empty.wcp +0 -0
  27. myokit/tests/data/io/bad1d-2-no-header.zip +0 -0
  28. myokit/tests/data/io/bad1d-3-no-data.zip +0 -0
  29. myokit/tests/data/io/bad1d-4-not-a-zip.zip +1 -105
  30. myokit/tests/data/io/bad1d-5-bad-data-type.zip +0 -0
  31. myokit/tests/data/io/bad1d-6-time-too-short.zip +0 -0
  32. myokit/tests/data/io/bad1d-7-0d-too-short.zip +0 -0
  33. myokit/tests/data/io/bad1d-8-1d-too-short.zip +0 -0
  34. myokit/tests/data/io/bad2d-2-no-header.zip +0 -0
  35. myokit/tests/data/io/bad2d-3-no-data.zip +0 -0
  36. myokit/tests/data/io/bad2d-4-not-a-zip.zip +1 -105
  37. myokit/tests/data/io/bad2d-5-bad-data-type.zip +0 -0
  38. myokit/tests/data/io/bad2d-8-2d-too-short.zip +0 -0
  39. myokit/tests/data/io/block1d.mmt +187 -0
  40. myokit/tests/data/io/datalog-18-duplicate-keys.csv +4 -0
  41. myokit/tests/test_aux.py +4 -0
  42. myokit/tests/test_datablock.py +16 -16
  43. myokit/tests/test_datalog.py +24 -1
  44. myokit/tests/test_expressions.py +532 -251
  45. myokit/tests/test_formats_ansic.py +6 -18
  46. myokit/tests/test_formats_cpp.py +0 -5
  47. myokit/tests/test_formats_cuda.py +7 -15
  48. myokit/tests/test_formats_diffsl.py +728 -0
  49. myokit/tests/test_formats_easyml.py +4 -9
  50. myokit/tests/test_formats_exporters_run.py +3 -0
  51. myokit/tests/test_formats_latex.py +10 -11
  52. myokit/tests/test_formats_matlab.py +0 -8
  53. myokit/tests/test_formats_opencl.py +0 -29
  54. myokit/tests/test_formats_python.py +2 -19
  55. myokit/tests/test_formats_stan.py +0 -13
  56. myokit/tests/test_formats_sympy.py +3 -3
  57. myokit/tests/test_formats_wcp.py +15 -0
  58. myokit/tests/test_model.py +20 -20
  59. myokit/tests/test_parsing.py +19 -0
  60. {myokit-1.36.1.dist-info → myokit-1.37.1.dist-info}/METADATA +1 -1
  61. {myokit-1.36.1.dist-info → myokit-1.37.1.dist-info}/RECORD +65 -58
  62. {myokit-1.36.1.dist-info → myokit-1.37.1.dist-info}/LICENSE.txt +0 -0
  63. {myokit-1.36.1.dist-info → myokit-1.37.1.dist-info}/WHEEL +0 -0
  64. {myokit-1.36.1.dist-info → myokit-1.37.1.dist-info}/entry_points.txt +0 -0
  65. {myokit-1.36.1.dist-info → myokit-1.37.1.dist-info}/top_level.txt +0 -0
myokit/tests/test_formats_ansic.py CHANGED
@@ -176,11 +176,13 @@ class AnsiCExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
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177
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  def test_conditions(self):
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  a, b, c, d = self.abcd
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+ p = myokit.Equal(a, b)
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+ q = myokit.NotEqual(c, d)
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181
 
180
- self.eq(And(a, b), '(a && b)')
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- self.eq(Or(d, c), '(d || c)')
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- self.eq(Not(And(a, b)), '(!(a && b))')
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- self.eq(Not(c), '(!(c))')
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+ self.eq(And(p, q), '((a == b) && (c != d))')
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+ self.eq(Or(q, p), '((c != d) || (a == b))')
184
+ self.eq(Not(And(p, q)), '(!((a == b) && (c != d)))')
185
+ self.eq(Not(p), '(!(a == b))')
184
186
 
185
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  self.eq(Equal(a, b), '(a == b)')
186
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  self.eq(NotEqual(a, b), '(a != b)')
@@ -191,12 +193,6 @@ class AnsiCExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
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193
 
192
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  self.eq(And(Equal(a, b), NotEqual(c, d)), '((a == b) && (c != d))')
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  self.eq(Or(More(d, c), Less(b, a)), '((d > c) || (b < a))')
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- self.eq(Not(Or(Number(1), Number(2))), '(!(1.0 || 2.0))')
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- self.eq(Not(Less(Number(1), Number(2))), '(!(1.0 < 2.0))')
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- self.eq(Not(Plus(Number(1), Number(2))), '(!(1.0 + 2.0))')
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-
198
- self.eq(Equal(Equal(Number(0), Number(0)), Number(0)),
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- '((0.0 == 0.0) == 0.0)')
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201
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  def test_conditionals(self):
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198
 
@@ -206,11 +202,6 @@ class AnsiCExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
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  self.eq(Piecewise(Equal(a, b), c, Equal(a, d), Number(3), Number(4)),
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  '((a == b) ? c : ((a == d) ? 3.0 : 4.0))')
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209
- # Extra parentheses if condition is not a condition
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- self.eq(If(a, d, c), '((a) ? d : c)')
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- self.eq(Piecewise(a, b, c, d, Number(4)),
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- '((a) ? b : ((c) ? d : 4.0))')
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-
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  # Using if-then-else function
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  w = self._target()
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  w.set_lhs_function(lambda v: v.var().name())
@@ -329,9 +320,6 @@ class AnsiCExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
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  c.add(If(Not(true), a, b), 20)
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  c.add(If(Not(false), a, b), 10)
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- c.add(If(Equal(Equal(Number(0), Number(0)), Number(0)), a, b), 20)
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- c.add(If(Equal(Equal(Number(0), Number(0)), Number(1)), a, b), 10)
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-
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  c.add(Piecewise(true, Number(10), false, Number(20), Number(30)), 10)
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  c.add(Piecewise(true, Number(10), true, Number(20), Number(30)), 10)
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  c.add(Piecewise(false, Number(10), true, Number(20), Number(30)), 20)
myokit/tests/test_formats_cpp.py CHANGED
@@ -72,11 +72,6 @@ class CppExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
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  myokit.Number(4)),
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  '((a == b) ? c : ((a == d) ? 3.0 : 4.0))')
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- # Extra parentheses if condition is not a condition
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- self.eq(myokit.If(a, d, c), '((a) ? d : c)')
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- self.eq(myokit.Piecewise(a, b, c, d, myokit.Number(4)),
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- '((a) ? b : ((c) ? d : 4.0))')
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-
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  # Using if-then-else function
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  w = self._target()
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  w.set_lhs_function(lambda v: v.var().name())
myokit/tests/test_formats_cuda.py CHANGED
@@ -186,10 +186,12 @@ class CudaExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
186
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  # Inherited from c-based
187
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188
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  a, b, c, d = self.abcd
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- self.eq(And(a, b), '(a && b)')
190
- self.eq(Or(d, c), '(d || c)')
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- self.eq(Not(And(a, b)), '(!(a && b))')
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- self.eq(Not(c), '(!(c))')
189
+ p = Equal(a, b)
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+ q = NotEqual(c, d)
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+ self.eq(And(p, q), '((a == b) && (c != d))')
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+ self.eq(Or(q, p), '((c != d) || (a == b))')
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+ self.eq(Not(And(p, p)), '(!((a == b) && (a == b)))')
194
+ self.eq(Not(q), '(!(c != d))')
193
195
 
194
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  self.eq(Equal(a, b), '(a == b)')
195
197
  self.eq(NotEqual(a, b), '(a != b)')
@@ -198,14 +200,9 @@ class CudaExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
198
200
  self.eq(MoreEqual(c, a), '(c >= a)')
199
201
  self.eq(LessEqual(b, d), '(b <= d)')
200
202
 
201
- self.eq(And(Equal(a, b), NotEqual(c, d)), '((a == b) && (c != d))')
202
203
  self.eq(Or(More(d, c), Less(b, a)), '((d > c) || (b < a))')
203
- self.eq(Not(Or(Number(1), Number(2))), '(!(1.0f || 2.0f))')
204
+ self.eq(Not(Equal(Number(1), Number(2))), '(!(1.0f == 2.0f))')
204
205
  self.eq(Not(Less(Number(1), Number(2))), '(!(1.0f < 2.0f))')
205
- self.eq(Not(Plus(Number(1), Number(2))), '(!(1.0f + 2.0f))')
206
-
207
- self.eq(Equal(Equal(Number(0), Number(0)), Number(0)),
208
- '((0.0f == 0.0f) == 0.0f)')
209
206
 
210
207
  def test_conditionals(self):
211
208
  # Inherited from c-based
@@ -216,11 +213,6 @@ class CudaExpressionWriterTest(myokit.tests.ExpressionWriterTestCase):
216
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  self.eq(Piecewise(Equal(a, b), c, Equal(a, d), Number(3), Number(4)),
217
214
  '((a == b) ? c : ((a == d) ? 3.0f : 4.0f))')
218
215
 
219
- # If condition is not a condition
220
- self.eq(If(a, d, c), '((a) ? d : c)')
221
- self.eq(Piecewise(a, b, c, d, Number(4)),
222
- '((a) ? b : ((c) ? d : 4.0f))')
223
-
224
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225
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  if __name__ == '__main__':
226
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  unittest.main()