brainles-preprocessing 0.0.4__tar.gz → 0.0.5__tar.gz

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Files changed (101) hide show
  1. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/PKG-INFO +1 -1
  2. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/core.py +2 -1
  3. brainles_preprocessing-0.0.5/brainles_preprocessing/registration/__init__.py +0 -0
  4. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/pyproject.toml +2 -1
  5. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/setup.py +1 -1
  6. brainles_preprocessing-0.0.4/brainles_preprocessing/__init__.py +0 -1
  7. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/LICENSE +0 -0
  8. {brainles_preprocessing-0.0.4/brainles_preprocessing/normalization → brainles_preprocessing-0.0.5/brainles_preprocessing}/__init__.py +0 -0
  9. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brain_extraction/__init__.py +0 -0
  10. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brain_extraction/bashhdbet.py +0 -0
  11. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brain_extraction/brain_extraction.py +0 -0
  12. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brain_extraction/hdbet.py +0 -0
  13. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brain_extraction/hdbet_scripts/hd-bet_cpu-fast.sh +0 -0
  14. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brain_extraction/hdbet_scripts/hd-bet_cpu.sh +0 -0
  15. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brain_extraction/hdbet_scripts/hd-bet_gpu.sh +0 -0
  16. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brats/__init__.py +0 -0
  17. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brats/t1_centric.py +0 -0
  18. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/brats/t1c_centric.py +0 -0
  19. {brainles_preprocessing-0.0.4/brainles_preprocessing/registration → brainles_preprocessing-0.0.5/brainles_preprocessing/normalization}/__init__.py +0 -0
  20. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/normalization/normalize.py +0 -0
  21. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/atlas/copyright.md +0 -0
  22. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/atlas/t1_brats_space.nii +0 -0
  23. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/atlas/t1_skullstripped_brats_space.nii +0 -0
  24. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/functional.py +0 -0
  25. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg.py +0 -0
  26. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh +0 -0
  27. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh +0 -0
  28. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin +0 -0
  29. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average +0 -0
  30. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d +0 -0
  31. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian +0 -0
  32. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure +0 -0
  33. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample +0 -0
  34. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools +0 -0
  35. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform +0 -0
  36. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h +0 -0
  37. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h +0 -0
  38. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h +0 -0
  39. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h +0 -0
  40. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h +0 -0
  41. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h +0 -0
  42. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h +0 -0
  43. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h +0 -0
  44. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h +0 -0
  45. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h +0 -0
  46. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h +0 -0
  47. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h +0 -0
  48. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h +0 -0
  49. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h +0 -0
  50. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h +0 -0
  51. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h +0 -0
  52. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h +0 -0
  53. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp +0 -0
  54. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.h +0 -0
  55. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.cpp +0 -0
  56. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h +0 -0
  57. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h +0 -0
  58. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_blockMatching.h +0 -0
  59. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_dti.h +0 -0
  60. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h +0 -0
  61. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h +0 -0
  62. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d_sym.h +0 -0
  63. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_femTrans.h +0 -0
  64. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_globalTrans.h +0 -0
  65. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_kld.h +0 -0
  66. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_lncc.h +0 -0
  67. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans.h +0 -0
  68. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_jac.h +0 -0
  69. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_regul.h +0 -0
  70. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_macros.h +0 -0
  71. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths.h +0 -0
  72. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths_eigen.h +0 -0
  73. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_measure.h +0 -0
  74. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_mind.h +0 -0
  75. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h +0 -0
  76. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp +0 -0
  77. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.h +0 -0
  78. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_resampling.h +0 -0
  79. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_splineBasis.h +0 -0
  80. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ssd.h +0 -0
  81. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h +0 -0
  82. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h +0 -0
  83. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h +0 -0
  84. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h +0 -0
  85. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/png.h +0 -0
  86. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h +0 -0
  87. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h +0 -0
  88. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h +0 -0
  89. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h +0 -0
  90. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h +0 -0
  91. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h +0 -0
  92. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h +0 -0
  93. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h +0 -0
  94. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h +0 -0
  95. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h +0 -0
  96. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h +0 -0
  97. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/reg_aladin +0 -0
  98. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/reg_resample +0 -0
  99. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/rigid_reg.sh +0 -0
  100. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/niftyreg_scripts/transform.sh +0 -0
  101. {brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/registration/reg.py +0 -0
{brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: brainles-preprocessing
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- Version: 0.0.4
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+ Version: 0.0.5
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  Summary: TODO.
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  License: AGPL-3.0
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  Author: Florian Kofler
{brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/brainles_preprocessing/core.py RENAMED
@@ -29,6 +29,7 @@ class Modality:
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  self.normalizer = normalizer
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+ # TODO citation reminder decorator here
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  def preprocess_modality_centric_to_atlas_space(
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  center_modality: Modality,
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  moving_modalities: list[Modality],
@@ -70,7 +71,7 @@ def preprocess_modality_centric_to_atlas_space(
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  register(
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  fixed_image=cm.input_path,
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- moving_image=cm.input_path,
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+ moving_image=mm.input_path,
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  transformed_image=co_registered,
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  matrix=co_registered_matrix,
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  log_file=co_registered_log,
{brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "brainles_preprocessing"
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- version = "0.0.4"
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+ version = "0.0.5"
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  description = "TODO."
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  authors = [
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  "Florian Kofler <florian.kofler@tum.de>",
@@ -23,6 +23,7 @@ BrainLes-HD-BET = ">=0.0.5"
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  # utils
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  tqdm = ">=4.64.1"
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  auxiliary = ">=0.0.35"
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+ # TODO add citation dependency
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  [tool.poetry.dev-dependencies]
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  pytest = "^6.2"
{brainles_preprocessing-0.0.4 → brainles_preprocessing-0.0.5}/setup.py RENAMED
@@ -28,7 +28,7 @@ install_requires = \
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  setup_kwargs = {
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  'name': 'brainles-preprocessing',
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- 'version': '0.0.4',
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+ 'version': '0.0.5',
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  'description': 'TODO.',
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  'long_description': None,
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  'author': 'Florian Kofler',
brainles_preprocessing-0.0.4/brainles_preprocessing/__init__.py DELETED
@@ -1 +0,0 @@
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- from . import *