musica 0.12.0__cp310-cp310-win_amd64.whl → 0.12.2__cp310-cp310-win_amd64.whl

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Files changed (76) hide show
  1. musica/CMakeLists.txt +28 -2
  2. musica/__init__.py +9 -49
  3. musica/_musica.cp310-win_amd64.pyd +0 -0
  4. musica/_version.py +1 -1
  5. musica/backend.py +41 -0
  6. musica/binding_common.cpp +23 -6
  7. musica/carma.cpp +911 -0
  8. musica/carma.py +1729 -0
  9. musica/constants.py +1 -1
  10. musica/cpu_binding.cpp +2 -1
  11. musica/cuda.py +4 -1
  12. musica/examples/__init__.py +1 -0
  13. musica/examples/carma_aluminum.py +124 -0
  14. musica/examples/carma_sulfate.py +246 -0
  15. musica/examples/examples.py +165 -0
  16. musica/examples/sulfate_box_model.py +439 -0
  17. musica/examples/ts1_latin_hypercube.py +245 -0
  18. musica/gpu_binding.cpp +2 -1
  19. musica/main.py +89 -0
  20. musica/mechanism_configuration/__init__.py +1 -1
  21. musica/mechanism_configuration/aqueous_equilibrium.py +227 -54
  22. musica/mechanism_configuration/arrhenius.py +228 -42
  23. musica/mechanism_configuration/branched.py +249 -66
  24. musica/mechanism_configuration/condensed_phase_arrhenius.py +243 -50
  25. musica/mechanism_configuration/condensed_phase_photolysis.py +16 -19
  26. musica/mechanism_configuration/emission.py +10 -6
  27. musica/mechanism_configuration/first_order_loss.py +133 -26
  28. musica/mechanism_configuration/henrys_law.py +7 -48
  29. musica/mechanism_configuration/mechanism_configuration.py +114 -41
  30. musica/mechanism_configuration/phase.py +6 -2
  31. musica/mechanism_configuration/photolysis.py +12 -7
  32. musica/mechanism_configuration/reactions.py +20 -8
  33. musica/mechanism_configuration/simpol_phase_transfer.py +180 -51
  34. musica/mechanism_configuration/species.py +23 -4
  35. musica/mechanism_configuration/surface.py +14 -9
  36. musica/mechanism_configuration/ternary_chemical_activation.py +352 -0
  37. musica/mechanism_configuration/troe.py +259 -44
  38. musica/mechanism_configuration/tunneling.py +196 -49
  39. musica/mechanism_configuration/user_defined.py +9 -4
  40. musica/mechanism_configuration/wet_deposition.py +11 -8
  41. musica/mechanism_configuration.cpp +184 -95
  42. musica/musica.cpp +48 -61
  43. musica/test/examples/v1/full_configuration/full_configuration.json +39 -22
  44. musica/test/examples/v1/full_configuration/full_configuration.yaml +29 -20
  45. musica/test/{test_analytical.py → integration/test_analytical.py} +0 -1
  46. musica/test/integration/test_carma.py +227 -0
  47. musica/test/integration/test_carma_aluminum.py +12 -0
  48. musica/test/integration/test_carma_sulfate.py +17 -0
  49. musica/test/integration/test_sulfate_box_model.py +34 -0
  50. musica/test/integration/test_tuvx.py +62 -0
  51. musica/test/unit/test_parser.py +64 -0
  52. musica/test/{test_serializer.py → unit/test_serializer.py} +2 -2
  53. musica/test/unit/test_state.py +325 -0
  54. musica/test/{test_util_full_mechanism.py → unit/test_util_full_mechanism.py} +152 -122
  55. musica/tools/prepare_build_environment_linux.sh +23 -34
  56. musica/tools/prepare_build_environment_macos.sh +1 -0
  57. musica/tuvx.cpp +93 -0
  58. musica/tuvx.py +199 -0
  59. musica/types.py +120 -73
  60. {musica-0.12.0.dist-info → musica-0.12.2.dist-info}/METADATA +41 -39
  61. musica-0.12.2.dist-info/RECORD +70 -0
  62. {musica-0.12.0.dist-info → musica-0.12.2.dist-info}/WHEEL +1 -1
  63. musica-0.12.2.dist-info/entry_points.txt +3 -0
  64. musica/test/examples/v0/config.json +0 -7
  65. musica/test/examples/v0/config.yaml +0 -3
  66. musica/test/examples/v0/reactions.json +0 -193
  67. musica/test/examples/v0/reactions.yaml +0 -142
  68. musica/test/examples/v0/species.json +0 -40
  69. musica/test/examples/v0/species.yaml +0 -19
  70. musica/test/test_parser.py +0 -57
  71. musica/test/tuvx.py +0 -10
  72. musica/tools/prepare_build_environment_windows.sh +0 -22
  73. musica-0.12.0.dist-info/RECORD +0 -57
  74. /musica/test/{test_chapman.py → integration/test_chapman.py} +0 -0
  75. {musica-0.12.0.dist-info → musica-0.12.2.dist-info}/licenses/AUTHORS.md +0 -0
  76. {musica-0.12.0.dist-info → musica-0.12.2.dist-info}/licenses/LICENSE +0 -0
@@ -1,57 +0,0 @@
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- import pytest
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- from musica.mechanism_configuration import *
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- from test_util_full_mechanism import get_fully_defined_mechanism, validate_full_v1_mechanism
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-
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-
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- def test_parsed_full_v1_configuration():
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- parser = Parser()
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- extensions = [".yaml", ".json"]
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- for extension in extensions:
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- path = f"musica/test/examples/v1/full_configuration/full_configuration{extension}"
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- mechanism = parser.parse(path)
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- validate_full_v1_mechanism(mechanism)
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-
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-
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- def test_parser_reports_bad_files():
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- parser = Parser()
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- extensions = [".yaml", ".json"]
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- for extension in extensions:
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- path = f"musica/test/examples/_missing_configuration{extension}"
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- with pytest.raises(Exception):
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- parser.parse(path)
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-
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-
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- def test_hard_coded_full_v1_configuration():
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- MECHANISM_FULLY_DEFINED = get_fully_defined_mechanism()
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- validate_full_v1_mechanism(MECHANISM_FULLY_DEFINED)
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-
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-
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- def test_hard_coded_default_constructed_types():
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- arrhenius = Arrhenius()
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- assert arrhenius.type == ReactionType.Arrhenius
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- condensed_phase_arrhenius = CondensedPhaseArrhenius()
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- assert condensed_phase_arrhenius.type == ReactionType.CondensedPhaseArrhenius
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- condensed_phase_photolysis = CondensedPhasePhotolysis()
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- assert condensed_phase_photolysis.type == ReactionType.CondensedPhasePhotolysis
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- emission = Emission()
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- assert emission.type == ReactionType.Emission
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- first_order_loss = FirstOrderLoss()
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- assert first_order_loss.type == ReactionType.FirstOrderLoss
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- henrys_law = HenrysLaw()
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- assert henrys_law.type == ReactionType.HenrysLaw
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- photolysis = Photolysis()
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- assert photolysis.type == ReactionType.Photolysis
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- simpol_phase_transfer = SimpolPhaseTransfer()
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- assert simpol_phase_transfer.type == ReactionType.SimpolPhaseTransfer
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- surface = Surface()
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- assert surface.type == ReactionType.Surface
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- troe = Troe()
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- assert troe.type == ReactionType.Troe
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- tunneling = Tunneling()
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- assert tunneling.type == ReactionType.Tunneling
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- wet_deposition = WetDeposition()
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- assert wet_deposition.type == ReactionType.WetDeposition
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- branched = Branched()
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- assert branched.type == ReactionType.Branched
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- user_defined = UserDefined()
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- assert user_defined.type == ReactionType.UserDefined
musica/test/tuvx.py DELETED
@@ -1,10 +0,0 @@
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- import pytest
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- import musica
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-
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-
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- def test_tuvx_run():
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- assert 1 != 0
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-
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-
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- if __name__ == '__main__':
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- pytest.main()
@@ -1,22 +0,0 @@
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- #! /bin/bash
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-
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- set -e
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- set -x
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-
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- CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8"
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- # curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.2.2/local_installers/cuda_12.2.2_537.13_windows.exe
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- curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_572.61_windows.exe
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- ./cuda.exe -s nvcc_12.8 cudart_12.8 cublas_dev_12.8 curand_dev_12.8
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- rm cuda.exe
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-
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- export CUDA_PATH="/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8"
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- export PATH="$CUDA_PATH/bin:$PATH"
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-
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- ls "c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8/extras/visual_studio_integration/MSBuildExtensions"
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- ls "c/Program Files (x86)/Microsoft Visual Studio/"
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-
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- # choco install cuda
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-
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- ls "$CUDA_PATH"
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- ls "$CUDA_PATH/bin"
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- which nvcc.exe
@@ -1,57 +0,0 @@
1
- musica/__init__.py,sha256=-TtiqPge1QqHDQHJLZb1S13378oCvioqxveGFsTG1K4,1799
2
- musica/_musica.cp310-win_amd64.pyd,sha256=rDdpqOsRdGVBMF-aJu61lPL6PMfVrc0Scamn5QOxJPE,1371648
3
- musica/_version.py,sha256=9e9mHDi2fUgxlhglOE73A-PATsMwCeXLJ4vRvu3ZC2A,20
4
- musica/binding_common.cpp,sha256=A1Y5LxGjWXi09Eczv06H5iJC-9i0R9eya2ehz2jnD9U,575
5
- musica/binding_common.hpp,sha256=YAcb9WnfXL7Ps-rR-iMBSwUgBQZfZZdCQQod5CTMEZA,108
6
- musica/CMakeLists.txt,sha256=qRSE9QuzRR1go16-ujVBHpkdHf-5dCuPZLbCrP7ygHc,1092
7
- musica/constants.py,sha256=o0PjiiTyGMdCPWmBewiQKaX-JBOR6vkz1n0pAacuZNU,124
8
- musica/cpu_binding.cpp,sha256=J-9SfvuXeWYvOAwX5luG6f5DieV0pchkutRAJ3xoN2Y,234
9
- musica/cuda.cpp,sha256=oTG2ZnL-SiW2kx9eL4XJOQGJeIiGuy8tJ5BEoLRWL4M,358
10
- musica/cuda.py,sha256=6Qe6cBbPN9K5Uqu7wBt18zTUjRIgvnQKBJZr6tHJrs8,234
11
- musica/gpu_binding.cpp,sha256=sv1_exUAhGRXY0kzT_q-f0Yl_GYgkYRKwmqWGSi0Qx8,238
12
- musica/mechanism_configuration/__init__.py,sha256=WVIbDCgpAd-jH9TBPou-5tyrdxb5Vbm9Zl2h7xmNiQ8,38
13
- musica/mechanism_configuration/aqueous_equilibrium.py,sha256=O0QuSk-kwc4DKslOeiqgR0E2YrrJhl_BKI-CwNRQzlM,4861
14
- musica/mechanism_configuration/arrhenius.py,sha256=oEVg7_5XXpiiSeVEOW3_567gHVekvr8kADOBTSqFokM,5268
15
- musica/mechanism_configuration/branched.py,sha256=MjWJl86BbhJj7M85QRqhiFIyGwzI9u8R2z_oeOIvYLg,5331
16
- musica/mechanism_configuration/condensed_phase_arrhenius.py,sha256=rUluAt0z_Q79apJKnpC20Ng9Jk1wk5YPn8tvtzXv0wo,5477
17
- musica/mechanism_configuration/condensed_phase_photolysis.py,sha256=KTebLSs6Hakd4p4oqkGftHgC9QBIExIrMBS7qi0zk-Y,4483
18
- musica/mechanism_configuration/emission.py,sha256=ak45GY1NswB3P4BwDxRwIky73krz2vxds9t_rP8PxMI,3013
19
- musica/mechanism_configuration/first_order_loss.py,sha256=Ign87rhDSOiIWV0fSKhHBP1dNvjwBVoXkZ8_H17pE8g,3115
20
- musica/mechanism_configuration/henrys_law.py,sha256=tbyKP0p_wI7KzmQHaBnjIbdeObu9LzG9fwMDxJBgWZA,4266
21
- musica/mechanism_configuration/mechanism_configuration.py,sha256=pfDOUxZyyYNYrBzl-Lg_CoWtvQ4Dst5NMubalFVpkdY,7028
22
- musica/mechanism_configuration/phase.py,sha256=fN8sicZTRVAcFE4djXaj5Pu_pnb-cjA-BymSx38R16Y,1582
23
- musica/mechanism_configuration/photolysis.py,sha256=nh_0VXWeIqaBugox-anTbbVpqKikKrLQZzhLmaJJk_A,3827
24
- musica/mechanism_configuration/reactions.py,sha256=jLGo1ZfD_k3EVRBjIvn6LNGZ-oELLittgAB1tdDB0po,1735
25
- musica/mechanism_configuration/simpol_phase_transfer.py,sha256=AkKgMyCnLmF3n4ueLi470me8jj2Khd0bOuqj7bbJG68,4335
26
- musica/mechanism_configuration/species.py,sha256=-Rzfyg5Kg5DzLVoAF5exxAuygilvp2HILu-1iZJFXXM,3995
27
- musica/mechanism_configuration/surface.py,sha256=nYMdIPtgo3XwPG4zht-BNEY7MOf5rWQ15GMpH0HUo0E,4274
28
- musica/mechanism_configuration/troe.py,sha256=mtVAJcjF9jX3_3q8Z8rG47DvOIrEMB2e6BtSDImOJQA,6713
29
- musica/mechanism_configuration/tunneling.py,sha256=KVJD7Ej7PecdP0Q4orm8PzMQtgFyHJhSQnFh17qjmgo,4408
30
- musica/mechanism_configuration/user_defined.py,sha256=7p7xGbAous_3Ef2qfNnc8d63g0G86GpPOGl-GmGRvrs,3835
31
- musica/mechanism_configuration/utils.py,sha256=dhMFrydNchhdRrfeJw35oJB8Y5oQJa6p65Z7I127P-8,356
32
- musica/mechanism_configuration/wet_deposition.py,sha256=_9xKNyHFZpfKPBbpi0L_Hi2dilBZIPAMw1rXY2VmUcs,2232
33
- musica/mechanism_configuration.cpp,sha256=OI1Ua3xypbSe7dPfL50J9qCyHY1b809bRv1DdXu31Iw,27552
34
- musica/musica.cpp,sha256=w6kI-mrUqNbJPeYuuPzzsDrb7GsHy2bKNoOt0b8tJTY,8614
35
- musica/test/examples/v0/config.json,sha256=JDQdrDNRmRXGYlytX1uiSDV1lkYIAneLwlodHKFw-os,85
36
- musica/test/examples/v0/config.yaml,sha256=r31QbiFE2YDudGxLGpTKnpyveTnlfXeLgJ2qSrQddDY,47
37
- musica/test/examples/v0/reactions.json,sha256=SmRUE5XOAv0h3HOWg4Fb1swBiZvZ-1hsIrmMCJqEVIk,4380
38
- musica/test/examples/v0/reactions.yaml,sha256=5QeEkhjeAL_rXxNYCLOuqDUudTmgwLW3NERDupKpj6s,2408
39
- musica/test/examples/v0/species.json,sha256=klFuYb2vAtWdHfHJVYuIuPe_6LHRTuB0Aw29YhwfCFc,604
40
- musica/test/examples/v0/species.yaml,sha256=ECT9DDa2GMwhSRaRLxjOiCATTKkTRTPwugRsUjHSytY,302
41
- musica/test/examples/v1/full_configuration/full_configuration.json,sha256=QgCno36VZANP1FcH25ogeYuBtnesdFcc7Mj6CztK4Ds,9660
42
- musica/test/examples/v1/full_configuration/full_configuration.yaml,sha256=I-eMC2jSCRQ8AvV2WQeF2y96A6ouNDLrvPjvRZV-AXc,5820
43
- musica/test/test_analytical.py,sha256=domkY4O00RplSdnFvssqUGtPyoXQiV0cfRaLH3gsQ2c,14131
44
- musica/test/test_chapman.py,sha256=t6p0CadUy-B4OP7A-EZ9Wz52diuYs5yc9LKiFUS9T6A,3651
45
- musica/test/test_parser.py,sha256=1lL2DZ7ZT1IBGKG3aAc1P_z5GW3u8oBgP6vn3tGr150,2316
46
- musica/test/test_serializer.py,sha256=mVOXgUFiN5OmCK-8ramsd4hLAYjgvunqBElRbs6nzyM,2535
47
- musica/test/test_util_full_mechanism.py,sha256=pDWZhJWdP1Q8iCab9AV7GMNIlNdMdgNuAJRqqRccDuw,24730
48
- musica/test/tuvx.py,sha256=L8X7rJ09HiRlrhLK6fjircI8tGHnFCZJzVow8He5YOE,126
49
- musica/tools/prepare_build_environment_linux.sh,sha256=kdcBj9qELh811OzY8o5tQDAnLXJFXqzwIkZmkRAcLFY,1500
50
- musica/tools/prepare_build_environment_windows.sh,sha256=sBBWhJQaS2zWDVFLIDMNBMOMPw8auXwnwz7nhuB5Q_k,847
51
- musica/tools/repair_wheel_gpu.sh,sha256=nQueyGNC2qWcBAicjVdAfB6JH4m_51dFOG83vVxke54,1525
52
- musica/types.py,sha256=aBDIOOF9I3u7_drTJebln0O88z0z9dfRNGWhAhP8_7o,15148
53
- musica-0.12.0.dist-info/METADATA,sha256=ecoVy_lRUnvTA_JTGQRg8SB3EtlnFMr2Lq_8Ke8X1gs,25995
54
- musica-0.12.0.dist-info/WHEEL,sha256=Bg3xfVZCdvCQkqUyMs2y8LOfK6ua4a-d4Njc-PtQZvk,106
55
- musica-0.12.0.dist-info/licenses/AUTHORS.md,sha256=1ssAXR4WOMdfl5Or1raPu_2nxHbkwCpxfwJwzpF_cJM,2691
56
- musica-0.12.0.dist-info/licenses/LICENSE,sha256=HrhfyXIkWY2tGFK11kg7vPCqhgh5DcxleloqdhrpyMY,11558
57
- musica-0.12.0.dist-info/RECORD,,