pyNeuroML 1.2.2__tar.gz → 1.2.4__tar.gz

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 (315) hide show
  1. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/CONTRIBUTING.md +22 -0
  2. {pyNeuroML-1.2.2/pyNeuroML.egg-info → pyNeuroML-1.2.4}/PKG-INFO +1 -1
  3. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-archive.1 +3 -3
  4. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-channelanalysis.1 +3 -3
  5. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-channelml2nml.1 +3 -3
  6. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-modchananalysis.1 +3 -3
  7. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plotchan.1 +3 -3
  8. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plotmorph.1 +3 -3
  9. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plotspikes.1 +3 -3
  10. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plottimeseries.1 +3 -3
  11. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-povray.1 +3 -3
  12. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-sonata.1 +3 -3
  13. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-summary.1 +3 -3
  14. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-tune.1 +3 -3
  15. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml.1 +3 -3
  16. pyNeuroML-1.2.4/man/man1/version.h2m +3 -0
  17. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4/pyNeuroML.egg-info}/PKG-INFO +1 -1
  18. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/lems/LEMSSimulation.py +11 -3
  19. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/pynml.py +1 -0
  20. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/setup.cfg +1 -1
  21. pyNeuroML-1.2.2/man/man1/version.h2m +0 -3
  22. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/LICENSE.lesser +0 -0
  23. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/MANIFEST.in +0 -0
  24. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/README.md +0 -0
  25. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/Makefile +0 -0
  26. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/extras/Readme.md +0 -0
  27. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/extras/pyneuroml.neuron.analysis.rst +0 -0
  28. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/extras/pyneuroml.neuron.rst +0 -0
  29. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/make.bat +0 -0
  30. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/_static/neuroml_logo.png +0 -0
  31. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/_static/pynml_jnml.svg +0 -0
  32. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/conf.py +0 -0
  33. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/index.rst +0 -0
  34. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/introduction.rst +0 -0
  35. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.analysis.rst +0 -0
  36. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.annotations.rst +0 -0
  37. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.archive.rst +0 -0
  38. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.channelml.rst +0 -0
  39. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.io.rst +0 -0
  40. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.lems.rst +0 -0
  41. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.modelgraphs.rst +0 -0
  42. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.neuron.rst +0 -0
  43. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.nsgr.rst +0 -0
  44. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.plot.rst +0 -0
  45. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.povray.rst +0 -0
  46. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.pynml.rst +0 -0
  47. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.rst +0 -0
  48. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.runners.rst +0 -0
  49. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.sbml.rst +0 -0
  50. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.swc.rst +0 -0
  51. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.tune.rst +0 -0
  52. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/pyneuroml.utils.rst +0 -0
  53. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/refs.bib +0 -0
  54. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/IM.channel.nml +0 -0
  55. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/KConductance.channel.nml +0 -0
  56. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/Kd.channel.nml +0 -0
  57. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/LEMS_NML2_Ex5_DetCell.xml +0 -0
  58. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/LEMS_NML2_Ex9_FN.xml +0 -0
  59. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/LeakConductance.channel.nml +0 -0
  60. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/LeakConductance.mod +0 -0
  61. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/NML2_SingleCompHHCell.nml +0 -0
  62. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/NaConductance.channel.nml +0 -0
  63. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/NaConductance2.mod +0 -0
  64. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/README.md +0 -0
  65. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/Vm_plot.py +0 -0
  66. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/analyseNaMod.sh +0 -0
  67. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/analyseNaNml2.sh +0 -0
  68. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/analyseNaNml2_iv.sh +0 -0
  69. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/component_evaluation.py +0 -0
  70. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/create_new_lems_file.py +0 -0
  71. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/dt_dependence.py +0 -0
  72. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/export_neuroml1.py +0 -0
  73. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/export_neuroml2.py +0 -0
  74. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/generate_if_curve.py +0 -0
  75. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/generate_povray.py +0 -0
  76. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/quick_plot.py +0 -0
  77. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/readAnnots.py +0 -0
  78. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/record_channel_currents.py +0 -0
  79. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/reload_data.py +0 -0
  80. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/results/README.md +0 -0
  81. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/run_jneuroml_plot_matplotlib.py +0 -0
  82. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test/hinf_NaConductance.dat +0 -0
  83. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test/htau_NaConductance.dat +0 -0
  84. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test/minf_NaConductance.dat +0 -0
  85. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test/mtau_NaConductance.dat +0 -0
  86. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test/ninf_Gran_H_98.dat +0 -0
  87. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test/ntau_Gran_H_98.dat +0 -0
  88. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test.hoc +0 -0
  89. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Ca_conc.nml +0 -0
  90. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Ca_pyr.channel.nml +0 -0
  91. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/EGL-36.channel.nml +0 -0
  92. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/HHCellNetwork.net.nml +0 -0
  93. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Kahp_pyr.channel.nml +0 -0
  94. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Kdr_bask.channel.nml +0 -0
  95. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Kdr_pyr.channel.nml +0 -0
  96. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/LEMS_HH_Simulation.xml +0 -0
  97. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/LeakConductance_bask.channel.nml +0 -0
  98. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/LeakConductance_pyr.channel.nml +0 -0
  99. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/NML2_FullCell.nml +0 -0
  100. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/NML2_SimpleIonChannel.nml +0 -0
  101. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Na_bask.channel.nml +0 -0
  102. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Na_pyr.channel.nml +0 -0
  103. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/Purk2M9s.nml +0 -0
  104. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/TwoCell.net.nml +0 -0
  105. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/bask.cell.nml +0 -0
  106. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/LEMS_SimTestOLMChannels.xml +0 -0
  107. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/TestOLMChannels.net.nml +0 -0
  108. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/TestOLMNet.net.nml +0 -0
  109. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/cells/olm.cell.nml +0 -0
  110. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/channels/HCNolm.channel.nml +0 -0
  111. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/channels/Kdrfast.channel.nml +0 -0
  112. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/channels/KvAolm.channel.nml +0 -0
  113. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/channels/Nav.channel.nml +0 -0
  114. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/ca1/channels/leak_chan.channel.nml +0 -0
  115. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/complex_cell.cell.nml +0 -0
  116. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/hhcell.cell.nml +0 -0
  117. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/kChan.channel.nml +0 -0
  118. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/naChan.channel.nml +0 -0
  119. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/passiveChan.channel.nml +0 -0
  120. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/pyr_4_sym.cell.nml +0 -0
  121. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/realtime.py +0 -0
  122. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/simple_cell.cell.nml +0 -0
  123. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/simplenet.nml +0 -0
  124. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/simplenet.py +0 -0
  125. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/snooze.py +0 -0
  126. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/snooze.sh +0 -0
  127. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/valid_doc.sbml +0 -0
  128. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/valid_doc_sedml.sbml +0 -0
  129. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test_data/valid_doc_sedml.sedml +0 -0
  130. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/Ca_conc.nml +0 -0
  131. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/Ca_pyr.channel.nml +0 -0
  132. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/Kahp_pyr.channel.nml +0 -0
  133. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/Kdr_pyr.channel.nml +0 -0
  134. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/LEMS_OnePyr.xml +0 -0
  135. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/LeakConductance_pyr.channel.nml +0 -0
  136. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/Na_pyr.channel.nml +0 -0
  137. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/OnePyr.net.nml +0 -0
  138. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/README.md +0 -0
  139. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/Selection_817.jpg +0 -0
  140. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/pyr_4_sym.cell.nml +0 -0
  141. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/temp/README.md +0 -0
  142. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tune/tunePyr.py +0 -0
  143. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tuneHHCell.py +0 -0
  144. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/tuneHHCell.sh +0 -0
  145. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/units.py +0 -0
  146. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/install_local_java.sh +0 -0
  147. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/README.md +0 -0
  148. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/common.h2m +0 -0
  149. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/generate-man-pages.sh +0 -0
  150. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyNeuroML.egg-info/SOURCES.txt +0 -0
  151. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyNeuroML.egg-info/dependency_links.txt +0 -0
  152. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyNeuroML.egg-info/entry_points.txt +0 -0
  153. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyNeuroML.egg-info/requires.txt +0 -0
  154. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyNeuroML.egg-info/top_level.txt +0 -0
  155. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/__init__.py +0 -0
  156. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/analysis/ChannelDensityPlot.py +0 -0
  157. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/analysis/ChannelHelper.py +0 -0
  158. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/analysis/ChannelInfo_TEMPLATE.html +0 -0
  159. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/analysis/ChannelInfo_TEMPLATE.md +0 -0
  160. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/analysis/LEMS_Test_TEMPLATE.xml +0 -0
  161. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/analysis/NML2ChannelAnalysis.py +0 -0
  162. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/analysis/__init__.py +0 -0
  163. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/annotations.py +0 -0
  164. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/archive/__init__.py +0 -0
  165. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/channelml/ChannelML2NeuroML2.xsl +0 -0
  166. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/channelml/ChannelML2NeuroML2beta.xsl +0 -0
  167. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/channelml/__init__.py +0 -0
  168. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/errors.py +0 -0
  169. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/io.py +0 -0
  170. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/lems/LEMS_TEMPLATE.xml +0 -0
  171. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/lems/__init__.py +0 -0
  172. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/lib/jNeuroML-0.13.0-jar-with-dependencies.jar +0 -0
  173. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/modelgraphs.py +0 -0
  174. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/TEMPLATE.channel.nml +0 -0
  175. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/__init__.py +0 -0
  176. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/analysis/HHanalyse.py +0 -0
  177. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/analysis/__init__.py +0 -0
  178. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/mview_neuroml1.hoc +0 -0
  179. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/mview_neuroml2.hoc +0 -0
  180. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/nrn_export_utils.py +0 -0
  181. {pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/neuron/utils.hoc +0 -0
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{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/CONTRIBUTING.md RENAMED
@@ -3,6 +3,14 @@
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3
  Please open issues to discuss enhancements and bugs that you may encounter with
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4
  pyNeuroML. Pull requests with enhancements and bug fixes are welcome.
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5
 
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+ ## Virtual environments and editable installs
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+
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+ It is best to use [virtual environments](https://docs.python.org/3/tutorial/venv.html) when developing Python packages.
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+ This ensures that one uses a clean environment that includes the necessary
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+ dependencies and does not affect the overall system installation.
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+
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+ For quick development, consider using [editable installs](https://setuptools.pypa.io/en/latest/userguide/development_mode.html).
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+
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  ## Code style
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15
 
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  1. We use [flake8](https://pypi.org/project/flake8/) to ensure that the code
@@ -15,6 +23,12 @@ pyNeuroML. Pull requests with enhancements and bug fixes are welcome.
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  format](https://stackoverflow.com/a/24385103/375067) for Python docstrings.
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  Please document your code when opening pull requests.
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25
 
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+ ## Tests
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+
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+ Bug fixes and new features should include unit tests to test for correctness.
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+ One can base new tests off the current ones included in the `tests/` directory.
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+ To see how tests are run, please see the [GitHub Actions configuration file](https://github.com/NeuroML/pyNeuroML/blob/development/.github/workflows/ci.yml).
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+
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  ## Pull Request Process
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  1. Please contribute pull requests against the `development` branch.
@@ -28,3 +42,11 @@ A number of [pre-commit](https://pre-commit.com/) hooks are used to improve code
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  Please run the following code to set up the pre-commit hooks:
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  $ pre-commit install
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+
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+ ## Commit messages
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+
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+ Writing good commit messages makes things easy to follow.
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+ Please see these posts:
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+
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+ - [How to write a Git commit message](https://cbea.ms/git-commit/)
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+ - While not compulsory, we prefer [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/)
{pyNeuroML-1.2.2/pyNeuroML.egg-info → pyNeuroML-1.2.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: pyNeuroML
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- Version: 1.2.2
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+ Version: 1.2.4
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  Summary: Python utilities for NeuroML
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  Home-page: https://github.com/NeuroML/pyNeuroML
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  Author: Padraig Gleeson
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-archive.1 RENAMED
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  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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- .TH PYNML-ARCHIVE "1" "February 2024" "pynml-archive v1.2.2" "User Commands"
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+ .TH PYNML-ARCHIVE "1" "March 2024" "pynml-archive v1.2.4" "User Commands"
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  .SH NAME
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- pynml-archive \- manual page for pynml-archive v1.2.2
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+ pynml-archive \- manual page for pynml-archive v1.2.4
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  .SH DESCRIPTION
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  usage: pynml\-archive [\-h] [\-zipfileName <zip file name>]
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  .TP
@@ -45,4 +45,4 @@ Explicit list of files to create archive of.
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  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
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  .SH ENVIRONMENT
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  .PP
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- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
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+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-channelanalysis.1 RENAMED
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  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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- .TH PYNML-CHANNELANALYSIS "1" "February 2024" "pynml-channelanalysis v1.2.2" "User Commands"
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+ .TH PYNML-CHANNELANALYSIS "1" "March 2024" "pynml-channelanalysis v1.2.4" "User Commands"
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  .SH NAME
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- pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.2
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+ pynml-channelanalysis \- manual page for pynml-channelanalysis v1.2.4
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  .SH DESCRIPTION
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  usage: pynml\-channelanalysis [\-h] [\-v] [\-minV <min v>] [\-maxV <max v>]
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  .TP
@@ -110,4 +110,4 @@ plot current vs voltage for ion channel
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  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
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  .SH ENVIRONMENT
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  .PP
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- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
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+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-channelml2nml.1 RENAMED
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  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
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- .TH PYNML-CHANNELML2NML "1" "February 2024" "pynml-channelml2nml v1.2.2" "User Commands"
2
+ .TH PYNML-CHANNELML2NML "1" "March 2024" "pynml-channelml2nml v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.2
4
+ pynml-channelml2nml \- manual page for pynml-channelml2nml v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-channelml2nml [\-h] [\-xsltfile <XSLT file>]
7
7
  .TP
@@ -41,4 +41,4 @@ Name of the outputfile file
41
41
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
42
42
  .SH ENVIRONMENT
43
43
  .PP
44
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
44
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-modchananalysis.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-MODCHANANALYSIS "1" "February 2024" "pynml-modchananalysis v1.2.2" "User Commands"
2
+ .TH PYNML-MODCHANANALYSIS "1" "March 2024" "pynml-modchananalysis v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.2
4
+ pynml-modchananalysis \- manual page for pynml-modchananalysis v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-modchananalysis [\-h] [\-v] [\-nogui] [\-minV <min v>]
7
7
  .TP
@@ -72,4 +72,4 @@ Name of the mod file containing the channel
72
72
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
73
73
  .SH ENVIRONMENT
74
74
  .PP
75
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
75
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plotchan.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-PLOTCHAN "1" "February 2024" "pynml-plotchan v1.2.2" "User Commands"
2
+ .TH PYNML-PLOTCHAN "1" "March 2024" "pynml-plotchan v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-plotchan \- manual page for pynml-plotchan v1.2.2
4
+ pynml-plotchan \- manual page for pynml-plotchan v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-plotchan [\-h] [\-noDistancePlots] [\-nogui]
7
7
  .IP
@@ -41,4 +41,4 @@ Do not show plots as they are generated
41
41
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
42
42
  .SH ENVIRONMENT
43
43
  .PP
44
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
44
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plotmorph.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-PLOTMORPH "1" "February 2024" "pynml-plotmorph v1.2.2" "User Commands"
2
+ .TH PYNML-PLOTMORPH "1" "March 2024" "pynml-plotmorph v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-plotmorph \- manual page for pynml-plotmorph v1.2.2
4
+ pynml-plotmorph \- manual page for pynml-plotmorph v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-plotmorph [\-h] [\-v] [\-nogui] [\-plane2d <plane, e.g. xy, yz, zx>]
7
7
  .TP
@@ -71,4 +71,4 @@ Scale axes so that image is approximately square, for
71
71
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
72
72
  .SH ENVIRONMENT
73
73
  .PP
74
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
74
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plotspikes.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-PLOTSPIKES "1" "February 2024" "pynml-plotspikes v1.2.2" "User Commands"
2
+ .TH PYNML-PLOTSPIKES "1" "March 2024" "pynml-plotspikes v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-plotspikes \- manual page for pynml-plotspikes v1.2.2
4
+ pynml-plotspikes \- manual page for pynml-plotspikes v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-plotspikes [\-h] [\-format <format>] [\-rates] [\-showPlotsAlready]
7
7
  .TP
@@ -60,4 +60,4 @@ Number of bins for rate histogram
60
60
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
61
61
  .SH ENVIRONMENT
62
62
  .PP
63
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
63
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-plottimeseries.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-PLOTTIMESERIES "1" "February 2024" "pynml-plottimeseries v1.2.2" "User Commands"
2
+ .TH PYNML-PLOTTIMESERIES "1" "March 2024" "pynml-plottimeseries v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-plottimeseries \- manual page for pynml-plottimeseries v1.2.2
4
+ pynml-plottimeseries \- manual page for pynml-plottimeseries v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-plottimeseries [\-h] [\-offset] [<a LEMS file or data files> ...]
7
7
  .PP
@@ -36,4 +36,4 @@ Toggle whether plots are overlaid or offset
36
36
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
37
37
  .SH ENVIRONMENT
38
38
  .PP
39
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
39
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-povray.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-POVRAY "1" "February 2024" "pynml-povray v1.2.2" "User Commands"
2
+ .TH PYNML-POVRAY "1" "March 2024" "pynml-povray v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-povray \- manual page for pynml-povray v1.2.2
4
+ pynml-povray \- manual page for pynml-povray v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-povray [\-h] [\-split] [\-background <background colour>] [\-movie]
7
7
  .TP
@@ -112,4 +112,4 @@ Show segment ids
112
112
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
113
113
  .SH ENVIRONMENT
114
114
  .PP
115
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
115
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-sonata.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-SONATA "1" "February 2024" "pynml-sonata v1.2.2" "User Commands"
2
+ .TH PYNML-SONATA "1" "March 2024" "pynml-sonata v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-sonata \- manual page for pynml-sonata v1.2.2
4
+ pynml-sonata \- manual page for pynml-sonata v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-sonata [\-h] [\-h5] [\-jnml] [\-neuron]
7
7
  .IP
@@ -50,4 +50,4 @@ jNeuroML_NEURON
50
50
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
51
51
  .SH ENVIRONMENT
52
52
  .PP
53
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
53
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-summary.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-SUMMARY "1" "February 2024" "pynml-summary v1.2.2" "User Commands"
2
+ .TH PYNML-SUMMARY "1" "March 2024" "pynml-summary v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-summary \- manual page for pynml-summary v1.2.2
4
+ pynml-summary \- manual page for pynml-summary v1.2.4
5
5
  .SH DESCRIPTION
6
6
  Usage:
7
7
  .PP
@@ -35,4 +35,4 @@ print this help text and exit
35
35
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
36
36
  .SH ENVIRONMENT
37
37
  .PP
38
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
38
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml-tune.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML-TUNE "1" "February 2024" "pynml-tune v1.2.2" "User Commands"
2
+ .TH PYNML-TUNE "1" "March 2024" "pynml-tune v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml-tune \- manual page for pynml-tune v1.2.2
4
+ pynml-tune \- manual page for pynml-tune v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml\-tune [\-h] [\-simTime <simTime>] [\-dt <dt>]
7
7
  .IP
@@ -148,4 +148,4 @@ as optimisation progresses?
148
148
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
149
149
  .SH ENVIRONMENT
150
150
  .PP
151
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
151
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/man/man1/pynml.1 RENAMED
@@ -1,7 +1,7 @@
1
1
  .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3.
2
- .TH PYNML "1" "February 2024" "pynml v1.2.2" "User Commands"
2
+ .TH PYNML "1" "March 2024" "pynml v1.2.4" "User Commands"
3
3
  .SH NAME
4
- pynml \- manual page for pynml v1.2.2
4
+ pynml \- manual page for pynml v1.2.4
5
5
  .SH DESCRIPTION
6
6
  usage: pynml [\-h|\-\-help] [<shared options>] <one of the mutually\-exclusive options>
7
7
  .PP
@@ -221,4 +221,4 @@ Validate SEDML file(s)
221
221
  Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
222
222
  .SH ENVIRONMENT
223
223
  .PP
224
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
224
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
pyNeuroML-1.2.4/man/man1/version.h2m ADDED
@@ -0,0 +1,3 @@
1
+ [environment]
2
+ .PP
3
+ pyNeuroML v1.2.4 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4/pyNeuroML.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: pyNeuroML
3
- Version: 1.2.2
3
+ Version: 1.2.4
4
4
  Summary: Python utilities for NeuroML
5
5
  Home-page: https://github.com/NeuroML/pyNeuroML
6
6
  Author: Padraig Gleeson
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/lems/LEMSSimulation.py RENAMED
@@ -7,6 +7,7 @@ import os.path
7
7
  import logging
8
8
  import typing
9
9
  import random
10
+ import os
10
11
 
11
12
  import airspeed
12
13
  from pyneuroml import __version__ as pynml_ver
@@ -389,12 +390,19 @@ class LEMSSimulation:
389
390
  :returns: name of file
390
391
  :rtype: str
391
392
  """
393
+
392
394
  if file_name is None:
393
395
  file_name = "LEMS_%s.xml" % self.lems_info["sim_id"]
394
396
 
395
- lems_file = open(file_name, "w")
396
- lems_file.write(self.to_xml())
397
- lems_file.close()
397
+ logger.info(
398
+ "Writing LEMS Simulation %s to file: %s..."
399
+ % (self.lems_info["sim_id"], file_name)
400
+ )
401
+ with open(file_name, "w") as lems_file:
402
+ lems_file.write(self.to_xml())
403
+ lems_file.flush()
404
+ os.fsync(lems_file.fileno())
405
+
398
406
  logger.info(
399
407
  "Written LEMS Simulation %s to file: %s"
400
408
  % (self.lems_info["sim_id"], file_name)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/pyneuroml/pynml.py RENAMED
@@ -36,6 +36,7 @@ from pyneuroml.validators import *
36
36
  from pyneuroml.annotations import *
37
37
  from pyneuroml.io import *
38
38
  from pyneuroml.utils.info import *
39
+ from pyneuroml.utils.misc import *
39
40
 
40
41
  logger = logging.getLogger(__name__)
41
42
  logger.setLevel(logging.INFO)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
1
1
  [metadata]
2
2
  name = pyNeuroML
3
- version = 1.2.2
3
+ version = 1.2.4
4
4
  author = Padraig Gleeson
5
5
  author_email = p.gleeson@gmail.com
6
6
  url = https://github.com/NeuroML/pyNeuroML
pyNeuroML-1.2.2/man/man1/version.h2m DELETED
@@ -1,3 +0,0 @@
1
- [environment]
2
- .PP
3
- pyNeuroML v1.2.2 (libNeuroML v0.5.8, jNeuroML v0.13.0)
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/LICENSE.lesser RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/MANIFEST.in RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/README.md RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/Makefile RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/make.bat RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/docs/source/conf.py RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/README.md RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/Vm_plot.py RENAMED
File without changes
{pyNeuroML-1.2.2 → pyNeuroML-1.2.4}/examples/test.hoc RENAMED
File without changes