clabtoolkit 0.5.2__tar.gz → 0.5.3__tar.gz

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Files changed (117) hide show
  1. clabtoolkit-0.5.3/.zenodo.json +36 -0
  2. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/CITATION.cff +1 -1
  3. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/DOCUMENTATION.md +1 -1
  4. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/HISTORY.rst +6 -0
  5. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/MANIFEST.in +1 -0
  6. {clabtoolkit-0.5.2/clabtoolkit.egg-info → clabtoolkit-0.5.3}/PKG-INFO +2 -2
  7. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/README.rst +1 -1
  8. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/__init__.py +1 -1
  9. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3/clabtoolkit.egg-info}/PKG-INFO +2 -2
  10. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit.egg-info/SOURCES.txt +1 -0
  11. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/conf.py +1 -1
  12. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/pyproject.toml +1 -1
  13. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/AUTHORS.rst +0 -0
  14. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/CONTRIBUTING.rst +0 -0
  15. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/LICENSE +0 -0
  16. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/Makefile +0 -0
  17. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/NOTICE +0 -0
  18. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/architecture_diagram.md +0 -0
  19. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/bidstools.py +0 -0
  20. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/bidstools_utils.py +0 -0
  21. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/build_visualization_layout.py +0 -0
  22. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/colorstools.py +0 -0
  23. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/config/bids.json +0 -0
  24. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/config/config.json +0 -0
  25. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/config/lobes.json +0 -0
  26. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/config/stats_mapping.json +0 -0
  27. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/config/viz_views.json +0 -0
  28. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/config/viz_views_test.json +0 -0
  29. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/connectivitytools.py +0 -0
  30. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/data/parcellationtools/sub-test2_ses-01_atlas-chimeraLFIIHISIFN_scale-1_desc-grow1mm_dseg.lut +0 -0
  31. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/data/parcellationtools/sub-test2_ses-01_atlas-chimeraLFIIHISIFN_scale-1_desc-grow1mm_dseg.nii.gz +0 -0
  32. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/dicomtools.py +0 -0
  33. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/dwitools.py +0 -0
  34. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/dwitools_utils.py +0 -0
  35. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/freesurfertools.py +0 -0
  36. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/imagetools.py +0 -0
  37. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/imagetools_utils.py +0 -0
  38. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/misctools.py +0 -0
  39. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/misctools_utils.py +0 -0
  40. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/morphometrytools.py +0 -0
  41. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/networktools.py +0 -0
  42. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/parcellationtools.py +0 -0
  43. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/pipelinetools.py +0 -0
  44. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/plottools.py +0 -0
  45. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/pointstools.py +0 -0
  46. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/qcqatools.py +0 -0
  47. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/segmentationtools.py +0 -0
  48. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/surfacetools.py +0 -0
  49. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/tracttools.py +0 -0
  50. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/tracttools_utils.py +0 -0
  51. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/visualization_utils.py +0 -0
  52. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/visualizationtools.py +0 -0
  53. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit.egg-info/dependency_links.txt +0 -0
  54. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit.egg-info/requires.txt +0 -0
  55. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit.egg-info/top_level.txt +0 -0
  56. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/Makefile +0 -0
  57. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/README.md +0 -0
  58. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/make.bat +0 -0
  59. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/_static/clabtoolkit_ecosystem.png +0 -0
  60. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/_static/clabtoolkit_favicon.ico +0 -0
  61. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/_static/clabtoolkit_favicon.png +0 -0
  62. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/_static/clabtoolkit_logo.png +0 -0
  63. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/_static/clabtoolkit_logo_notext.png +0 -0
  64. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/api.rst +0 -0
  65. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/changelog.rst +0 -0
  66. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/contributing.rst +0 -0
  67. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/examples.rst +0 -0
  68. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/index.rst +0 -0
  69. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/installation.rst +0 -0
  70. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/bidstools.rst +0 -0
  71. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/colorstools.rst +0 -0
  72. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/connectivitytools.rst +0 -0
  73. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/dicomtools.rst +0 -0
  74. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/dwitools.rst +0 -0
  75. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/freesurfertools.rst +0 -0
  76. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/imagetools.rst +0 -0
  77. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/misctools.rst +0 -0
  78. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/morphometrytools.rst +0 -0
  79. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/networktools.rst +0 -0
  80. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/parcellationtools.rst +0 -0
  81. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/pipelinetools.rst +0 -0
  82. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/plottools.rst +0 -0
  83. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/pointstools.rst +0 -0
  84. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/qcqatools.rst +0 -0
  85. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/segmentationtools.rst +0 -0
  86. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/surfacetools.rst +0 -0
  87. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/tracttools.rst +0 -0
  88. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/modules/visualizationtools.rst +0 -0
  89. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/quickstart.rst +0 -0
  90. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/environment-mac.yaml +0 -0
  91. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/environment.yaml +0 -0
  92. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/requirements-docs.txt +0 -0
  93. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/requirements.txt +0 -0
  94. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/requirements_dev.txt +0 -0
  95. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/setup.cfg +0 -0
  96. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/tox.ini +0 -0
  97. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/README.md +0 -0
  98. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/clabtoolkit_examples.ipynb +0 -0
  99. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-bidstools-methods.ipynb +0 -0
  100. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-colorstools-methods.ipynb +0 -0
  101. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-connectivitytools-methods.ipynb +0 -0
  102. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-dicomtools-methods.ipynb +0 -0
  103. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-dwitools-methods.ipynb +0 -0
  104. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-freesurfertools-methods.ipynb +0 -0
  105. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-imagetools-methods.ipynb +0 -0
  106. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-misctools-methods.ipynb +0 -0
  107. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-morphometrytools-methods.ipynb +0 -0
  108. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-networktools-methods.ipynb +0 -0
  109. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-parcellationtools-methods.ipynb +0 -0
  110. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-pipelinetools-methods.ipynb +0 -0
  111. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-plottools-methods.ipynb +0 -0
  112. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-pointstools-methods.ipynb +0 -0
  113. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-qcqatools-methods.ipynb +0 -0
  114. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-segmentationtools-methods.ipynb +0 -0
  115. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-surfacetools-methods.ipynb +0 -0
  116. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-tracttools-methods.ipynb +0 -0
  117. {clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/usage_examples/examples-visualizationtools-methods.ipynb +0 -0
clabtoolkit-0.5.3/.zenodo.json ADDED
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+ {
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+ "title": "clabtoolkit: A Python toolkit for neuroimaging data processing and analysis",
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+ "upload_type": "software",
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+ "description": "<p>clabtoolkit is a Python toolkit for neuroimaging data processing and analysis, designed for brain connectivity data, BIDS datasets and the file formats used in neuroimaging.</p><p>Documentation: <a href=\"https://clabtoolkit.readthedocs.io\">https://clabtoolkit.readthedocs.io</a></p>",
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+ "creators": [
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+ {
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+ "name": "Alemán-Gómez, Yasser",
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+ "orcid": "0000-0001-6067-8639",
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+ "affiliation": "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
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+ },
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+ {
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+ "name": "Hervé, Nino",
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+ "affiliation": "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
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+ },
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+ {
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+ "name": "Hagmann, Patric",
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+ "orcid": "0000-0002-2854-6561",
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+ "affiliation": "Connectomics Lab, Radiology Department, CHUV – Lausanne University Hospital"
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+ }
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+ ],
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+ "license": "Apache-2.0",
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+ "keywords": ["neuroimaging", "image-processing", "bids", "freesurfer", "connectivity"],
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+ "access_right": "open",
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+ "related_identifiers": [
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+ {
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+ "identifier": "https://github.com/connectomicslab/clabtoolkit",
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+ "relation": "isSupplementTo",
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+ "scheme": "url"
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+ },
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+ {
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+ "identifier": "10.48550/arXiv.2607.02638",
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+ "relation": "isDescribedBy",
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+ "scheme": "doi"
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+ }
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+ ]
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+ }
{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/CITATION.cff RENAMED
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  A Python toolkit for neuroimaging data processing and analysis, designed for
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  brain connectivity data, BIDS datasets and the file formats used in
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  neuroimaging.
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- version: 0.5.2
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  date-released: 2026-10-22
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  license: Apache-2.0
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  doi: "10.5281/zenodo.23540587" # Zenodo concept DOI: always resolves to the latest version
{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/DOCUMENTATION.md RENAMED
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  **clabtoolkit** is a comprehensive Python toolkit designed for neuroimaging data processing and analysis, with specialized focus on brain connectivity data, BIDS datasets, and various neuroimaging formats. Developed by Yasser Alemán-Gómez, this toolkit provides an end-to-end solution for connectomics research and surface-based brain analysis.
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- **Version**: 0.5.2
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+ **Version**: 0.5.3
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  **License**: Apache Software License 2.0
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  **Python Support**: 3.11+
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  **Documentation**: https://clabtoolkit.readthedocs.io
{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/HISTORY.rst RENAMED
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  History
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  =======
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+ 0.5.3 (2026-10-22)
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+ ------------------
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+
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+ * Pointed the documentation badge to app.readthedocs.org, so it renders on PyPI instead of showing its alt text
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+ * Included .zenodo.json in the source distribution (fixes the check-manifest step of the CI)
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  0.5.2 (2026-10-22)
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  ------------------
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{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/MANIFEST.in RENAMED
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  include AUTHORS.rst
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  include CITATION.cff
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{clabtoolkit-0.5.2/clabtoolkit.egg-info → clabtoolkit-0.5.3}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: clabtoolkit
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  Summary: A comprehensive toolkit for neuroimaging data processing and analysis
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  Author-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
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  Maintainer-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
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  :target: https://codecov.io/gh/connectomicslab/clabtoolkit
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  :alt: Code coverage
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{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/README.rst RENAMED
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  :target: https://codecov.io/gh/connectomicslab/clabtoolkit
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  :alt: Code coverage
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- .. image:: https://readthedocs.org/projects/clabtoolkit/badge/?version=latest
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  :alt: Documentation Status
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{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit/__init__.py RENAMED
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  __author__ = """Yasser Alemán-Gómez"""
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{clabtoolkit-0.5.2 → clabtoolkit-0.5.3/clabtoolkit.egg-info}/PKG-INFO RENAMED
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  Author-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
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  Maintainer-email: Yasser Alemán-Gómez <yasseraleman@protonmail.com>
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{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/clabtoolkit.egg-info/SOURCES.txt RENAMED
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  AUTHORS.rst
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  CONTRIBUTING.rst
{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/docs/source/conf.py RENAMED
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  project = "clabtoolkit"
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  copyright = "2024-2026, Yasser Alemán-Gómez"
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  author = "Yasser Alemán-Gómez"
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- release = "0.5.2"
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  # -- General configuration ---------------------------------------------------
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  # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/pyproject.toml RENAMED
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  authors = [
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  {name = "Yasser Alemán-Gómez", email = "yasseraleman@protonmail.com"}
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{clabtoolkit-0.5.2 → clabtoolkit-0.5.3}/LICENSE RENAMED
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