OSBModelValidation 0.2.22__tar.gz → 0.3.2__tar.gz

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Files changed (130) hide show
  1. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2/OSBModelValidation.egg-info}/PKG-INFO +2 -2
  2. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/OSBModelValidation.egg-info/requires.txt +1 -1
  3. {osbmodelvalidation-0.2.22/OSBModelValidation.egg-info → osbmodelvalidation-0.3.2}/PKG-INFO +2 -2
  4. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getjnml.py +1 -1
  5. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getnest.py +1 -1
  6. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getnrn.py +1 -1
  7. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getpynn.py +5 -1
  8. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/setup.cfg +2 -2
  9. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/LICENSE.lesser +0 -0
  10. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/MANIFEST.in +0 -0
  11. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/OSBModelValidation.egg-info/SOURCES.txt +0 -0
  12. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/OSBModelValidation.egg-info/dependency_links.txt +0 -0
  13. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/OSBModelValidation.egg-info/entry_points.txt +0 -0
  14. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/OSBModelValidation.egg-info/top_level.txt +0 -0
  15. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/README.md +0 -0
  16. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/__init__.py +0 -0
  17. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/__init__.py +0 -0
  18. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/activation.py +0 -0
  19. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/analyzer.py +0 -0
  20. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/dryrun.py +0 -0
  21. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/input_resistance.py +0 -0
  22. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/morphology.py +0 -0
  23. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/rates.py +0 -0
  24. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/resting.py +0 -0
  25. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/spikes.py +0 -0
  26. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/temperature.py +0 -0
  27. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/timeseries.py +0 -0
  28. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/utils/__init__.py +0 -0
  29. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/utils/filenode.py +0 -0
  30. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/analyzers/utils/timeseries.py +0 -0
  31. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/autogen.py +0 -0
  32. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/common/__init__.py +0 -0
  33. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/common/inout.py +0 -0
  34. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/__init__.py +0 -0
  35. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/arbor_.py +0 -0
  36. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/brian1.py +0 -0
  37. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/brian2_.py +0 -0
  38. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/eden_.py +0 -0
  39. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/engine.py +0 -0
  40. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/genesis.py +0 -0
  41. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getarbor.py +0 -0
  42. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getbrian1.py +0 -0
  43. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getbrian2.py +0 -0
  44. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/geteden.py +0 -0
  45. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getgenesis.py +0 -0
  46. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getjlems.py +0 -0
  47. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getlibsbml.py +0 -0
  48. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getmoose.py +0 -0
  49. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getnetpyne.py +0 -0
  50. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getneuroconstruct.py +0 -0
  51. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getnml2.py +0 -0
  52. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getoctave.py +0 -0
  53. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getpylems.py +0 -0
  54. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getpyneuroml.py +0 -0
  55. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getxpp.py +0 -0
  56. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jlems.py +0 -0
  57. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuroml.py +0 -0
  58. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlbrian.py +0 -0
  59. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlbrian2.py +0 -0
  60. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromleden.py +0 -0
  61. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlmoose.py +0 -0
  62. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlnetpyne.py +0 -0
  63. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlnetpyne_np2.py +0 -0
  64. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlnetpyne_np4.py +0 -0
  65. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlnrn.py +0 -0
  66. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlpynnnrn.py +0 -0
  67. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlvalidate.py +0 -0
  68. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlvalidatev1.py +0 -0
  69. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/jneuromlxpp.py +0 -0
  70. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/moose_.py +0 -0
  71. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/nestsli.py +0 -0
  72. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/netpyne_.py +0 -0
  73. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/netpyne__np2.py +0 -0
  74. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/netpyne__np4.py +0 -0
  75. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/neuron_.py +0 -0
  76. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/octave.py +0 -0
  77. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pylems.py +0 -0
  78. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pylemsnml2.py +0 -0
  79. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pynest.py +0 -0
  80. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pyneuroconstruct.py +0 -0
  81. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pyneuroml_.py +0 -0
  82. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pyneuromlvalidatesbml.py +0 -0
  83. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pyneuromlxpp.py +0 -0
  84. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pyneuron.py +0 -0
  85. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pynn.py +0 -0
  86. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pynnbrian1.py +0 -0
  87. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pynnbrian2.py +0 -0
  88. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pynnnest.py +0 -0
  89. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pynnneuroml.py +0 -0
  90. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/pynnneuron.py +0 -0
  91. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/utils/__init__.py +0 -0
  92. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/utils/genesis_utils.g +0 -0
  93. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/utils/wdir.py +0 -0
  94. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/xpp.py +0 -0
  95. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/experiment.py +0 -0
  96. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/find_tests.py +0 -0
  97. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/omt_mep_parser.py +0 -0
  98. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/omv_util.py +0 -0
  99. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/parse_omt.py +0 -0
  100. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/mep.yaml +0 -0
  101. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/base/observable_datafile.yaml +0 -0
  102. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/base/observable_literal.yaml +0 -0
  103. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/base/observables.yaml +0 -0
  104. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/base/test/observable_datafile.yaml +0 -0
  105. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/base/test/observable_literal.1.yaml +0 -0
  106. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/base/test/observable_literal.3.yaml +0 -0
  107. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/expected.yaml +0 -0
  108. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/experiment.yaml +0 -0
  109. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/observable.yaml +0 -0
  110. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/protocol.yaml +0 -0
  111. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/protocol_properties.yaml +0 -0
  112. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/expected.1.yaml +0 -0
  113. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/expected.2.yaml +0 -0
  114. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/expected.3.yaml +0 -0
  115. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/expected.4.yaml +0 -0
  116. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/experiment.1.yaml +0 -0
  117. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/experiment.2.yaml +0 -0
  118. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/observable.yaml +0 -0
  119. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/protocol.1.yaml +0 -0
  120. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/schemata/types/test/protocol.2.yaml +0 -0
  121. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/tally.py +0 -0
  122. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/test/__init__.py +0 -0
  123. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/test/test_rates.py +0 -0
  124. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/test/test_types.py +0 -0
  125. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/validation/__init__.py +0 -0
  126. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/validation/rx_validator.py +0 -0
  127. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/validation/utils.py +0 -0
  128. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/validation/validate.py +0 -0
  129. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/validation/validate_mep.py +0 -0
  130. {osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/pyproject.toml +0 -0
{osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2/OSBModelValidation.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: OSBModelValidation
3
- Version: 0.2.22
3
+ Version: 0.3.2
4
4
  Summary: Open Source Brain Model validation
5
5
  Home-page: https://github.com/OpenSourceBrain/osb-model-validation
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  Author: Boris Marin, Padraig Gleeson
@@ -20,7 +20,7 @@ Classifier: Topic :: Scientific/Engineering
20
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  Description-Content-Type: text/markdown
21
21
  License-File: LICENSE.lesser
22
22
  Requires-Dist: PyYAML
23
- Requires-Dist: numpy
23
+ Requires-Dist: numpy<2.0.0
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24
  Requires-Dist: pyrx
25
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  Requires-Dist: pathlib; python_version < "3.4"
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  Requires-Dist: docopt
{osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/OSBModelValidation.egg-info/requires.txt RENAMED
@@ -1,5 +1,5 @@
1
1
  PyYAML
2
- numpy
2
+ numpy<2.0.0
3
3
  pyrx
4
4
  docopt
5
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  setuptools
{osbmodelvalidation-0.2.22/OSBModelValidation.egg-info → osbmodelvalidation-0.3.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: OSBModelValidation
3
- Version: 0.2.22
3
+ Version: 0.3.2
4
4
  Summary: Open Source Brain Model validation
5
5
  Home-page: https://github.com/OpenSourceBrain/osb-model-validation
6
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  Author: Boris Marin, Padraig Gleeson
@@ -20,7 +20,7 @@ Classifier: Topic :: Scientific/Engineering
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  Description-Content-Type: text/markdown
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  License-File: LICENSE.lesser
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  Requires-Dist: PyYAML
23
- Requires-Dist: numpy
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+ Requires-Dist: numpy<2.0.0
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  Requires-Dist: pyrx
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  Requires-Dist: pathlib; python_version < "3.4"
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  Requires-Dist: docopt
{osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getjnml.py RENAMED
@@ -10,7 +10,7 @@ from omv.common.inout import inform
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  def install_jnml(version):
11
11
 
12
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  if not version:
13
- version = "v0.13.1"
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+ version = "v0.13.2"
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15
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  try:
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  jnmlhome = os.environ["JNML_HOME"]
{osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getnest.py RENAMED
@@ -8,7 +8,7 @@ import sys
8
8
 
9
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  def install_nest(version):
10
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  if not version:
11
- version = "3.3"
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+ version = "3.5"
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13
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  inform("Installing NEST", indent=2, verbosity=1)
14
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  nestpath = os.path.join(os.environ["HOME"], "nest")
{osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getnrn.py RENAMED
@@ -11,7 +11,7 @@ from omv.engines.utils.wdir import working_dir
11
11
  def install_neuron(version):
12
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  if not version:
13
13
  if sys.version_info.major == 3:
14
- version = "8.1" # 8.1 works with pynn 0.10.1
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+ version = "8.2.2" # for pynn 0.11.0
15
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  else:
16
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  version = "7.6"
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{osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/omv/engines/getpynn.py RENAMED
@@ -7,12 +7,15 @@ from omv.engines.utils.wdir import working_dir
7
7
 
8
8
  def install_pynn(version=None):
9
9
  if not version:
10
- version = "0.10.1"
10
+ version = "0.11.0"
11
11
 
12
12
  try:
13
13
  # pip_install('lazyarray') # This should ideally be automatically installed with PyNN...
14
14
  # pip_install('neo>=0.11.0') # This should ideally be automatically installed with PyNN...
15
15
 
16
+ pip_install("pynn", version)
17
+ import pyNN
18
+ '''
16
19
  install_root = os.environ["HOME"]
17
20
 
18
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  pyNN_src = "PyNN_src"
@@ -33,6 +36,7 @@ def install_pynn(version=None):
33
36
  print(check_output(["pwd"]))
34
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  print("Finished attempting to install PyNN")
35
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  # import pyNN
39
+ '''
36
40
  m = "Successfully installed pyNN..."
37
41
  except Exception as e:
38
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  m = "ERROR during install_pynn: %s" % e
{osbmodelvalidation-0.2.22 → osbmodelvalidation-0.3.2}/setup.cfg RENAMED
@@ -1,6 +1,6 @@
1
1
  [metadata]
2
2
  name = OSBModelValidation
3
- version = 0.2.22
3
+ version = 0.3.2
4
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  author = Boris Marin, Padraig Gleeson
5
5
  author_email = borismarin@gmail.com
6
6
  url = https://github.com/OpenSourceBrain/osb-model-validation
@@ -24,7 +24,7 @@ classifiers =
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  [options]
25
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  install_requires =
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  PyYAML
27
- numpy
27
+ numpy<2.0.0 # Due to other packages (e.g. tables) not working yet with numpy v2
28
28
  pyrx
29
29
  pathlib; python_version<'3.4'
30
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  docopt