siibra 1.0a11__tar.gz → 1.0a19__tar.gz

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  1. {siibra-1.0a11/siibra.egg-info → siibra-1.0a19}/PKG-INFO +1 -1
  2. siibra-1.0a19/siibra/VERSION +1 -0
  3. {siibra-1.0a11 → siibra-1.0a19}/siibra/__init__.py +12 -2
  4. {siibra-1.0a11 → siibra-1.0a19}/siibra/commons.py +4 -3
  5. {siibra-1.0a11 → siibra-1.0a19}/siibra/configuration/__init__.py +1 -1
  6. {siibra-1.0a11 → siibra-1.0a19}/siibra/configuration/configuration.py +1 -1
  7. {siibra-1.0a11 → siibra-1.0a19}/siibra/configuration/factory.py +164 -117
  8. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/__init__.py +1 -1
  9. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/assignment.py +1 -1
  10. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/atlas.py +4 -3
  11. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/concept.py +18 -9
  12. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/parcellation.py +9 -3
  13. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/region.py +35 -65
  14. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/space.py +3 -1
  15. {siibra-1.0a11 → siibra-1.0a19}/siibra/core/structure.py +1 -2
  16. {siibra-1.0a11 → siibra-1.0a19}/siibra/exceptions.py +9 -1
  17. {siibra-1.0a11 → siibra-1.0a19}/siibra/explorer/__init__.py +1 -1
  18. {siibra-1.0a11 → siibra-1.0a19}/siibra/explorer/url.py +15 -0
  19. {siibra-1.0a11 → siibra-1.0a19}/siibra/explorer/util.py +1 -1
  20. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/__init__.py +1 -1
  21. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/anchor.py +1 -1
  22. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/connectivity/__init__.py +1 -1
  23. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/connectivity/functional_connectivity.py +1 -1
  24. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/connectivity/regional_connectivity.py +5 -3
  25. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/connectivity/streamline_counts.py +1 -1
  26. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/connectivity/streamline_lengths.py +1 -1
  27. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/connectivity/tracing_connectivity.py +1 -1
  28. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/dataset/__init__.py +1 -1
  29. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/dataset/ebrains.py +1 -1
  30. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/feature.py +42 -15
  31. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/image/__init__.py +1 -1
  32. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/image/image.py +18 -13
  33. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/image/sections.py +1 -1
  34. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/image/volume_of_interest.py +1 -1
  35. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/__init__.py +1 -1
  36. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/bigbrain_intensity_profile.py +1 -1
  37. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/cell_density_profile.py +5 -3
  38. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/cortical_profile.py +5 -3
  39. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/gene_expression.py +2 -2
  40. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/layerwise_bigbrain_intensities.py +1 -1
  41. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/layerwise_cell_density.py +5 -3
  42. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/receptor_density_fingerprint.py +5 -3
  43. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/receptor_density_profile.py +5 -3
  44. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/regional_timeseries_activity.py +5 -3
  45. {siibra-1.0a11 → siibra-1.0a19}/siibra/features/tabular/tabular.py +5 -3
  46. {siibra-1.0a11 → siibra-1.0a19}/siibra/livequeries/__init__.py +1 -1
  47. {siibra-1.0a11 → siibra-1.0a19}/siibra/livequeries/allen.py +9 -6
  48. {siibra-1.0a11 → siibra-1.0a19}/siibra/livequeries/bigbrain.py +1 -1
  49. {siibra-1.0a11 → siibra-1.0a19}/siibra/livequeries/ebrains.py +1 -1
  50. {siibra-1.0a11 → siibra-1.0a19}/siibra/livequeries/query.py +1 -1
  51. {siibra-1.0a11 → siibra-1.0a19}/siibra/locations/__init__.py +1 -1
  52. {siibra-1.0a11 → siibra-1.0a19}/siibra/locations/boundingbox.py +51 -17
  53. {siibra-1.0a11 → siibra-1.0a19}/siibra/locations/location.py +12 -4
  54. {siibra-1.0a11 → siibra-1.0a19}/siibra/locations/point.py +10 -5
  55. {siibra-1.0a11 → siibra-1.0a19}/siibra/locations/pointset.py +45 -11
  56. {siibra-1.0a11 → siibra-1.0a19}/siibra/retrieval/__init__.py +1 -1
  57. {siibra-1.0a11 → siibra-1.0a19}/siibra/retrieval/cache.py +1 -1
  58. {siibra-1.0a11 → siibra-1.0a19}/siibra/retrieval/datasets.py +1 -1
  59. {siibra-1.0a11 → siibra-1.0a19}/siibra/retrieval/exceptions/__init__.py +1 -1
  60. {siibra-1.0a11 → siibra-1.0a19}/siibra/retrieval/repositories.py +1 -1
  61. {siibra-1.0a11 → siibra-1.0a19}/siibra/retrieval/requests.py +1 -1
  62. {siibra-1.0a11 → siibra-1.0a19}/siibra/vocabularies/__init__.py +1 -1
  63. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/__init__.py +1 -1
  64. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/parcellationmap.py +38 -18
  65. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/providers/__init__.py +1 -1
  66. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/providers/freesurfer.py +1 -1
  67. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/providers/gifti.py +1 -1
  68. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/providers/neuroglancer.py +7 -7
  69. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/providers/nifti.py +8 -4
  70. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/providers/provider.py +2 -2
  71. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/sparsemap.py +7 -4
  72. {siibra-1.0a11 → siibra-1.0a19}/siibra/volumes/volume.py +114 -16
  73. {siibra-1.0a11 → siibra-1.0a19/siibra.egg-info}/PKG-INFO +1 -1
  74. siibra-1.0a11/siibra/VERSION +0 -1
  75. {siibra-1.0a11 → siibra-1.0a19}/LICENSE +0 -0
  76. {siibra-1.0a11 → siibra-1.0a19}/MANIFEST.in +0 -0
  77. {siibra-1.0a11 → siibra-1.0a19}/README.rst +0 -0
  78. {siibra-1.0a11 → siibra-1.0a19}/setup.cfg +0 -0
  79. {siibra-1.0a11 → siibra-1.0a19}/setup.py +0 -0
  80. {siibra-1.0a11 → siibra-1.0a19}/siibra/experimental/__init__.py +0 -0
  81. {siibra-1.0a11 → siibra-1.0a19}/siibra/experimental/contour.py +0 -0
  82. {siibra-1.0a11 → siibra-1.0a19}/siibra/experimental/cortical_profile_sampler.py +0 -0
  83. {siibra-1.0a11 → siibra-1.0a19}/siibra/experimental/patch.py +0 -0
  84. {siibra-1.0a11 → siibra-1.0a19}/siibra/experimental/plane3d.py +0 -0
  85. {siibra-1.0a11 → siibra-1.0a19}/siibra/vocabularies/gene_names.json +0 -0
  86. {siibra-1.0a11 → siibra-1.0a19}/siibra/vocabularies/receptor_symbols.json +0 -0
  87. {siibra-1.0a11 → siibra-1.0a19}/siibra/vocabularies/region_aliases.json +0 -0
  88. {siibra-1.0a11 → siibra-1.0a19}/siibra.egg-info/SOURCES.txt +0 -0
  89. {siibra-1.0a11 → siibra-1.0a19}/siibra.egg-info/dependency_links.txt +0 -0
  90. {siibra-1.0a11 → siibra-1.0a19}/siibra.egg-info/requires.txt +0 -0
  91. {siibra-1.0a11 → siibra-1.0a19}/siibra.egg-info/top_level.txt +0 -0
  92. {siibra-1.0a11 → siibra-1.0a19}/test/test_siibra.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: siibra
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- Version: 1.0a11
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+ Version: 1.0a19
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  Summary: siibra - Software interfaces for interacting with brain atlases
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  Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
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  Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)
@@ -0,0 +1 @@
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+ 1.0a19
@@ -1,4 +1,4 @@
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- # Copyright 2018-2021
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+ # Copyright 2018-2024
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  # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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  # Licensed under the Apache License, Version 2.0 (the "License");
@@ -107,6 +107,14 @@ def set_feasible_download_size(maxsize_gbyte):
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  def set_cache_size(maxsize_gbyte: int):
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+ """
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+ siibra runs maintainance on its local cache to keep it under a predetermined
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+ size of 2 gigabytes. This method changes the cache size.
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+
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+ Parameters
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+ ----------
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+ maxsize_gbyte : int
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+ """
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  assert maxsize_gbyte >= 0
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  cache.SIZE_GIB = maxsize_gbyte
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  logger.info(f"Set cache size to {maxsize_gbyte} GiB.")
@@ -150,5 +158,7 @@ def __dir__():
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  "vocabularies",
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  "__version__",
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  "cache",
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- "warm_cache"
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+ "warm_cache",
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+ "set_cache_size",
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+ "from_json",
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  ]
@@ -1,4 +1,4 @@
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- # Copyright 2018-2023
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+ # Copyright 2018-2024
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  # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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  # Licensed under the Apache License, Version 2.0 (the "License");
@@ -35,6 +35,7 @@ except ImportError:
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  # support python 3.7
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  from typing_extensions import TypedDict
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+ logging.addLevelName(21, "INFO_WO_PROGRESS_BARS")
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  logger = logging.getLogger(__name__.split(os.path.extsep)[0])
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  ch = logging.StreamHandler()
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  formatter = logging.Formatter("[{name}:{levelname}] {message}", style="{")
@@ -51,7 +52,7 @@ SIIBRA_LOG_LEVEL = os.getenv("SIIBRA_LOG_LEVEL", "INFO")
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  SIIBRA_USE_CONFIGURATION = os.getenv("SIIBRA_USE_CONFIGURATION")
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  SIIBRA_USE_LOCAL_SNAPSPOT = os.getenv("SIIBRA_USE_LOCAL_SNAPSPOT")
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  SKIP_CACHEINIT_MAINTENANCE = os.getenv("SKIP_CACHEINIT_MAINTENANCE")
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- SIIBRA_MAX_FETCH_SIZE_GIB = os.getenv("SIIBRA_MAX_FETCH_SIZE_GIB", 0.2)
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+ SIIBRA_MAX_FETCH_SIZE_GIB = float(os.getenv("SIIBRA_MAX_FETCH_SIZE_GIB", 0.2))
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  with open(os.path.join(ROOT_DIR, "VERSION"), "r") as fp:
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  __version__ = fp.read().strip()
@@ -297,7 +298,7 @@ def siibra_tqdm(iterable: Iterable[T] = None, *args, **kwargs):
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  return tqdm(
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  iterable,
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  *args,
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- disable=kwargs.pop("disable", False) or (logger.level > 20),
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+ disable=kwargs.pop("disable", False) or (logger.level > logging.INFO),
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  **kwargs
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  )
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@@ -1,4 +1,4 @@
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- # Copyright 2018-2021
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+ # Copyright 2018-2024
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  # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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  # Licensed under the Apache License, Version 2.0 (the "License");
@@ -1,4 +1,4 @@
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- # Copyright 2018-2021
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+ # Copyright 2018-2024
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  # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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  # Licensed under the Apache License, Version 2.0 (the "License");