myokit 1.33.9__py3-none-any.whl → 1.35.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (229) hide show
  1. myokit/__init__.py +9 -36
  2. myokit/__main__.py +76 -142
  3. myokit/_aux.py +62 -16
  4. myokit/_bin/example.mmt +1 -2
  5. myokit/_bin/install-win/menu.json +7 -7
  6. myokit/_config.py +22 -31
  7. myokit/_datablock.py +30 -74
  8. myokit/_datalog.py +49 -72
  9. myokit/_err.py +25 -24
  10. myokit/_expressions.py +50 -68
  11. myokit/_io.py +15 -27
  12. myokit/_model_api.py +453 -249
  13. myokit/_myokit_version.py +1 -5
  14. myokit/_parsing.py +38 -44
  15. myokit/_progress.py +5 -8
  16. myokit/_protocol.py +99 -9
  17. myokit/_sim/__init__.py +7 -24
  18. myokit/_sim/cable.c +6 -8
  19. myokit/_sim/cable.py +6 -8
  20. myokit/_sim/cmodel.h +125 -70
  21. myokit/_sim/cmodel.py +12 -14
  22. myokit/_sim/compiler.py +1 -4
  23. myokit/_sim/cvodessim.c +196 -118
  24. myokit/_sim/cvodessim.py +130 -103
  25. myokit/_sim/differential.hpp +4 -4
  26. myokit/_sim/fiber_tissue.c +4 -8
  27. myokit/_sim/fiber_tissue.py +11 -13
  28. myokit/_sim/jacobian.cpp +2 -2
  29. myokit/_sim/jacobian.py +11 -8
  30. myokit/_sim/mcl.h +53 -55
  31. myokit/_sim/opencl.py +21 -27
  32. myokit/_sim/openclsim.c +3 -7
  33. myokit/_sim/openclsim.cl +3 -3
  34. myokit/_sim/openclsim.py +49 -40
  35. myokit/_sim/pacing.h +36 -16
  36. myokit/_sim/rhs.c +6 -13
  37. myokit/_sim/rhs.py +5 -14
  38. myokit/_sim/sundials.py +1 -4
  39. myokit/_system.py +10 -16
  40. myokit/_unit.py +4 -13
  41. myokit/float.py +0 -3
  42. myokit/formats/__init__.py +8 -10
  43. myokit/formats/ansic/__init__.py +0 -3
  44. myokit/formats/ansic/_ewriter.py +2 -4
  45. myokit/formats/ansic/_exporter.py +1 -4
  46. myokit/formats/ansic/template/cable.c +4 -4
  47. myokit/formats/ansic/template/euler.c +5 -5
  48. myokit/formats/ansic/template/sim.c +6 -6
  49. myokit/formats/axon/__init__.py +1 -3
  50. myokit/formats/axon/_abf.py +12 -17
  51. myokit/formats/axon/_atf.py +5 -6
  52. myokit/formats/axon/_importer.py +0 -3
  53. myokit/formats/cellml/__init__.py +0 -3
  54. myokit/formats/cellml/_ewriter.py +3 -6
  55. myokit/formats/cellml/_exporter.py +3 -6
  56. myokit/formats/cellml/_importer.py +1 -4
  57. myokit/formats/cellml/v1/__init__.py +0 -4
  58. myokit/formats/cellml/v1/_api.py +8 -11
  59. myokit/formats/cellml/v1/_parser.py +2 -5
  60. myokit/formats/cellml/v1/_writer.py +2 -11
  61. myokit/formats/cellml/v2/__init__.py +0 -3
  62. myokit/formats/cellml/v2/_api.py +8 -17
  63. myokit/formats/cellml/v2/_parser.py +2 -5
  64. myokit/formats/cellml/v2/_writer.py +1 -4
  65. myokit/formats/channelml/__init__.py +0 -3
  66. myokit/formats/channelml/_importer.py +11 -21
  67. myokit/formats/cpp/__init__.py +1 -3
  68. myokit/formats/cpp/_ewriter.py +0 -3
  69. myokit/formats/cuda/__init__.py +0 -3
  70. myokit/formats/cuda/_ewriter.py +2 -4
  71. myokit/formats/cuda/_exporter.py +0 -3
  72. myokit/formats/cuda/template/kernel.cu +8 -5
  73. myokit/formats/easyml/__init__.py +0 -3
  74. myokit/formats/easyml/_ewriter.py +9 -11
  75. myokit/formats/easyml/_exporter.py +2 -5
  76. myokit/formats/html/__init__.py +0 -3
  77. myokit/formats/html/_exporter.py +0 -3
  78. myokit/formats/html/_flatten.py +5 -21
  79. myokit/formats/latex/__init__.py +0 -3
  80. myokit/formats/latex/_ewriter.py +1 -4
  81. myokit/formats/latex/_exporter.py +4 -6
  82. myokit/formats/mathml/__init__.py +0 -3
  83. myokit/formats/mathml/_ewriter.py +2 -11
  84. myokit/formats/mathml/_parser.py +4 -6
  85. myokit/formats/matlab/__init__.py +0 -3
  86. myokit/formats/matlab/_ewriter.py +1 -4
  87. myokit/formats/matlab/_exporter.py +2 -5
  88. myokit/formats/matlab/template/main.m +3 -2
  89. myokit/formats/opencl/__init__.py +0 -3
  90. myokit/formats/opencl/_ewriter.py +2 -4
  91. myokit/formats/opencl/_exporter.py +2 -5
  92. myokit/formats/opencl/template/cable.c +10 -10
  93. myokit/formats/opencl/template/kernel.cl +1 -1
  94. myokit/formats/opencl/template/minilog.py +1 -1
  95. myokit/formats/python/__init__.py +0 -3
  96. myokit/formats/python/_ewriter.py +2 -5
  97. myokit/formats/python/_exporter.py +0 -3
  98. myokit/formats/python/template/sim.py +14 -14
  99. myokit/formats/sbml/__init__.py +0 -3
  100. myokit/formats/sbml/_api.py +50 -44
  101. myokit/formats/sbml/_importer.py +1 -4
  102. myokit/formats/sbml/_parser.py +2 -5
  103. myokit/formats/stan/__init__.py +0 -3
  104. myokit/formats/stan/_ewriter.py +2 -4
  105. myokit/formats/stan/_exporter.py +2 -5
  106. myokit/formats/stan/template/cell.stan +3 -3
  107. myokit/formats/sympy/__init__.py +0 -3
  108. myokit/formats/sympy/_ereader.py +1 -4
  109. myokit/formats/sympy/_ewriter.py +2 -5
  110. myokit/formats/wcp/__init__.py +0 -3
  111. myokit/formats/wcp/_wcp.py +2 -8
  112. myokit/formats/xml/__init__.py +0 -3
  113. myokit/formats/xml/_exporter.py +0 -3
  114. myokit/formats/xml/_split.py +0 -3
  115. myokit/gui/__init__.py +80 -246
  116. myokit/gui/datablock_viewer.py +103 -86
  117. myokit/gui/datalog_viewer.py +214 -66
  118. myokit/gui/explorer.py +15 -21
  119. myokit/gui/ide.py +171 -144
  120. myokit/gui/progress.py +9 -9
  121. myokit/gui/source.py +406 -375
  122. myokit/gui/vargrapher.py +2 -12
  123. myokit/lib/deps.py +12 -13
  124. myokit/lib/guess.py +3 -4
  125. myokit/lib/hh.py +20 -18
  126. myokit/lib/markov.py +21 -20
  127. myokit/lib/multi.py +1 -3
  128. myokit/lib/plots.py +20 -9
  129. myokit/pacing.py +0 -3
  130. myokit/pype.py +7 -18
  131. myokit/tests/__init__.py +3 -6
  132. myokit/tests/ansic_event_based_pacing.py +1 -4
  133. myokit/tests/ansic_fixed_form_pacing.py +3 -6
  134. myokit/tests/data/beeler-1977-model-compare-b.mmt +2 -2
  135. myokit/tests/data/clancy-1999-fitting.mmt +1 -0
  136. myokit/tests/test_aux.py +13 -28
  137. myokit/tests/test_cellml_v1_api.py +4 -19
  138. myokit/tests/test_cellml_v1_parser.py +0 -15
  139. myokit/tests/test_cellml_v1_writer.py +0 -9
  140. myokit/tests/test_cellml_v2_api.py +4 -19
  141. myokit/tests/test_cellml_v2_parser.py +0 -15
  142. myokit/tests/test_cellml_v2_writer.py +0 -9
  143. myokit/tests/test_cmodel.py +16 -22
  144. myokit/tests/test_compiler_detection.py +1 -11
  145. myokit/tests/test_component.py +108 -56
  146. myokit/tests/test_config.py +34 -67
  147. myokit/tests/test_datablock.py +1 -9
  148. myokit/tests/test_datalog.py +19 -24
  149. myokit/tests/test_dependency_checking.py +8 -23
  150. myokit/tests/test_expressions.py +0 -9
  151. myokit/tests/test_float.py +1 -5
  152. myokit/tests/test_formats.py +0 -9
  153. myokit/tests/test_formats_axon.py +1 -9
  154. myokit/tests/test_formats_cellml.py +0 -15
  155. myokit/tests/test_formats_channelml.py +0 -15
  156. myokit/tests/test_formats_easyml.py +0 -14
  157. myokit/tests/test_formats_exporters.py +1 -16
  158. myokit/tests/test_formats_expression_writers.py +1 -17
  159. myokit/tests/test_formats_html.py +0 -3
  160. myokit/tests/test_formats_importers.py +1 -16
  161. myokit/tests/test_formats_mathml_content.py +0 -9
  162. myokit/tests/test_formats_mathml_presentation.py +0 -9
  163. myokit/tests/test_formats_opencl.py +0 -10
  164. myokit/tests/test_formats_sbml.py +0 -15
  165. myokit/tests/test_formats_sympy.py +0 -9
  166. myokit/tests/test_formats_wcp.py +1 -3
  167. myokit/tests/test_io.py +27 -27
  168. myokit/tests/test_jacobian_calculator.py +6 -14
  169. myokit/tests/test_jacobian_tracer.py +0 -9
  170. myokit/tests/test_lib_deps.py +0 -9
  171. myokit/tests/test_lib_guess.py +0 -9
  172. myokit/tests/test_lib_hh.py +18 -12
  173. myokit/tests/test_lib_markov.py +21 -13
  174. myokit/tests/test_lib_multi.py +0 -9
  175. myokit/tests/test_lib_plots.py +13 -8
  176. myokit/tests/test_meta.py +0 -3
  177. myokit/tests/test_model.py +390 -96
  178. myokit/tests/test_model_building.py +44 -96
  179. myokit/tests/test_opencl_info.py +5 -14
  180. myokit/tests/test_pacing_factory.py +0 -3
  181. myokit/tests/test_pacing_system_c.py +1 -23
  182. myokit/tests/test_pacing_system_py.py +0 -9
  183. myokit/tests/test_parsing.py +139 -56
  184. myokit/tests/test_progress_reporters.py +0 -3
  185. myokit/tests/test_protocol.py +0 -9
  186. myokit/tests/test_protocol_floating_point.py +1 -10
  187. myokit/tests/test_protocol_time_series.py +82 -0
  188. myokit/tests/test_pype.py +0 -9
  189. myokit/tests/test_quantity.py +0 -9
  190. myokit/tests/test_rhs_benchmarker.py +1 -9
  191. myokit/tests/test_sbml_api.py +27 -42
  192. myokit/tests/test_sbml_parser.py +4 -19
  193. myokit/tests/test_simulation_1d.py +45 -25
  194. myokit/tests/test_simulation_cvodes.py +321 -55
  195. myokit/tests/test_simulation_cvodes_from_disk.py +0 -3
  196. myokit/tests/test_simulation_fiber_tissue.py +39 -12
  197. myokit/tests/test_simulation_log_interval.py +1 -431
  198. myokit/tests/test_simulation_opencl.py +69 -48
  199. myokit/tests/test_simulation_opencl_log_interval.py +1 -3
  200. myokit/tests/test_simulation_opencl_vs_cvode.py +1 -10
  201. myokit/tests/test_simulation_opencl_vs_sim1d.py +1 -10
  202. myokit/tests/test_system_info.py +1 -11
  203. myokit/tests/test_tools.py +0 -9
  204. myokit/tests/test_unit.py +1 -10
  205. myokit/tests/test_user_functions.py +0 -10
  206. myokit/tests/test_variable.py +231 -27
  207. myokit/tools.py +5 -21
  208. myokit/units.py +5 -3
  209. {myokit-1.33.9.dist-info → myokit-1.35.0.dist-info}/METADATA +12 -15
  210. myokit-1.35.0.dist-info/RECORD +391 -0
  211. {myokit-1.33.9.dist-info → myokit-1.35.0.dist-info}/WHEEL +1 -1
  212. {myokit-1.33.9.dist-info → myokit-1.35.0.dist-info}/entry_points.txt +0 -1
  213. myokit/_exec_new.py +0 -15
  214. myokit/_exec_old.py +0 -15
  215. myokit/_sim/cvodesim.c +0 -1551
  216. myokit/_sim/cvodesim.py +0 -674
  217. myokit/_sim/icsim.cpp +0 -563
  218. myokit/_sim/icsim.py +0 -363
  219. myokit/_sim/psim.cpp +0 -656
  220. myokit/_sim/psim.py +0 -493
  221. myokit/lib/common.py +0 -1094
  222. myokit/tests/test_lib_common.py +0 -130
  223. myokit/tests/test_simulation_cvode.py +0 -612
  224. myokit/tests/test_simulation_ic.py +0 -108
  225. myokit/tests/test_simulation_p.py +0 -223
  226. myokit-1.33.9.dist-info/RECORD +0 -403
  227. /myokit/formats/opencl/template/{test → test.sh} +0 -0
  228. {myokit-1.33.9.dist-info → myokit-1.35.0.dist-info}/LICENSE.txt +0 -0
  229. {myokit-1.33.9.dist-info → myokit-1.35.0.dist-info}/top_level.txt +0 -0
myokit/gui/progress.py CHANGED
@@ -4,9 +4,6 @@
4
4
  # This file is part of Myokit.
5
5
  # See http://myokit.org for copyright, sharing, and licensing details.
6
6
  #
7
- from __future__ import absolute_import, division
8
- from __future__ import print_function, unicode_literals
9
-
10
7
  import myokit
11
8
  from myokit.gui import Qt, QtCore, QtWidgets
12
9
 
@@ -22,9 +19,10 @@ class ProgressBar(QtWidgets.QProgressDialog):
22
19
  and other tasks implementing the ``ProgressReporter`` interface.
23
20
  """
24
21
  def __init__(self, parent, message):
25
- super(ProgressBar, self).__init__(
26
- message, 'Cancel', 0, N, parent=parent)
27
- self.setWindowModality(Qt.WindowModal)
22
+ super().__init__(
23
+ message, 'Cancel', 0, N, parent)
24
+ self.setWindowTitle(' ')
25
+ self.setWindowModality(Qt.WindowModality.WindowModal)
28
26
  self.setAutoClose(False)
29
27
  self.setAutoReset(False)
30
28
  self._reporter = ProgressBarReporter(self)
@@ -51,7 +49,7 @@ class ProgressBarReporter(myokit.ProgressReporter):
51
49
  """
52
50
 
53
51
  def __init__(self, pd):
54
- super(ProgressBarReporter, self).__init__()
52
+ super().__init__()
55
53
  self._pd = pd
56
54
 
57
55
  def enter(self, msg=None):
@@ -60,8 +58,9 @@ class ProgressBarReporter(myokit.ProgressReporter):
60
58
  if msg is not None:
61
59
  self._pd.setLabelText(str(msg))
62
60
  self._pd.setValue(0)
61
+ self._pd.repaint()
63
62
  QtWidgets.QApplication.processEvents(
64
- QtCore.QEventLoop.ExcludeUserInputEvents)
63
+ QtCore.QEventLoop.ProcessEventsFlag.ExcludeUserInputEvents)
65
64
 
66
65
  def exit(self):
67
66
  self._pd.setEnabled(False)
@@ -69,5 +68,6 @@ class ProgressBarReporter(myokit.ProgressReporter):
69
68
  def update(self, f):
70
69
  self._pd.setValue((int)(N * f))
71
70
  QtWidgets.QApplication.processEvents(
72
- QtCore.QEventLoop.ExcludeUserInputEvents)
71
+ QtCore.QEventLoop.ProcessEventsFlag.ExcludeUserInputEvents)
72
+ self._pd.repaint()
73
73
  return not self._pd.wasCanceled()