junifer 0.0.6.dev11__tar.gz → 0.0.6.dev16__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (383) hide show
  1. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/PKG-INFO +1 -1
  2. junifer-0.0.6.dev16/docs/changes/newsfragments/335.enh +1 -0
  3. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/_version.py +2 -2
  4. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/external/nilearn/junifer_connectivity_measure.py +23 -15
  5. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/external/nilearn/tests/test_junifer_connectivity_measure.py +1 -0
  6. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer.egg-info/PKG-INFO +1 -1
  7. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer.egg-info/SOURCES.txt +1 -0
  8. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/ISSUE_TEMPLATE/bug-report.yml +0 -0
  9. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  10. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/ISSUE_TEMPLATE/dataset-request.yml +0 -0
  11. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/ISSUE_TEMPLATE/documention-request.yml +0 -0
  12. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/ISSUE_TEMPLATE/feature-request.yml +0 -0
  13. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/ISSUE_TEMPLATE/marker-request.yml +0 -0
  14. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/dependabot.yml +0 -0
  15. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/pull_request_template.md +0 -0
  16. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/workflows/ci-docs.yml +0 -0
  17. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/workflows/ci.yml +0 -0
  18. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/workflows/docs-preview.yml +0 -0
  19. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/workflows/docs.yml +0 -0
  20. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/workflows/lint.yml +0 -0
  21. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.github/workflows/pypi.yml +0 -0
  22. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.gitignore +0 -0
  23. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.gitmodules +0 -0
  24. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.pre-commit-config.yaml +0 -0
  25. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/AUTHORS.rst +0 -0
  26. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/LICENSE.md +0 -0
  27. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/README.md +0 -0
  28. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/codecov.yml +0 -0
  29. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/conda-env.yml +0 -0
  30. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/Makefile +0 -0
  31. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/_static/css/custom.css +0 -0
  32. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/_static/js/custom.js +0 -0
  33. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/_templates/versions.html +0 -0
  34. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/api.rst +0 -0
  35. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/configs.rst +0 -0
  36. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/data.rst +0 -0
  37. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/datagrabbers.rst +0 -0
  38. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/datareaders.rst +0 -0
  39. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/index.rst +0 -0
  40. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/markers.rst +0 -0
  41. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/nilearn.rst +0 -0
  42. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/onthefly.rst +0 -0
  43. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/pipeline.rst +0 -0
  44. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/preprocessing.rst +0 -0
  45. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/stats.rst +0 -0
  46. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/storage.rst +0 -0
  47. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/testing.rst +0 -0
  48. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/api/utils.rst +0 -0
  49. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/builtin.rst +0 -0
  50. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/changes/contributors.inc +0 -0
  51. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/changes/newsfragments/.gitignore +0 -0
  52. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/changes/newsfragments/354.feature +0 -0
  53. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/changes/newsfragments/356.bugfix +0 -0
  54. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/changes/newsfragments/357.enh +0 -0
  55. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/conf.py +0 -0
  56. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/contribution.rst +0 -0
  57. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/coordinates.rst +0 -0
  58. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/datagrabber.rst +0 -0
  59. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/dependencies.rst +0 -0
  60. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/extension.rst +0 -0
  61. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/index.rst +0 -0
  62. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/marker.rst +0 -0
  63. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/masks.rst +0 -0
  64. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/parcellations.rst +0 -0
  65. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/extending/preprocessor.rst +0 -0
  66. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/faq.rst +0 -0
  67. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/help.rst +0 -0
  68. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/images/junifer_logo.png +0 -0
  69. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/index.rst +0 -0
  70. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/installation.rst +0 -0
  71. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/links.inc +0 -0
  72. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/maintaining.rst +0 -0
  73. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/redirect.html +0 -0
  74. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/sphinxext/gh_substitutions.py +0 -0
  75. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/starting.rst +0 -0
  76. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/data.rst +0 -0
  77. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/datagrabber.rst +0 -0
  78. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/datareader.rst +0 -0
  79. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/index.rst +0 -0
  80. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/marker.rst +0 -0
  81. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/pipeline.rst +0 -0
  82. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/preprocess.rst +0 -0
  83. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/understanding/storage.rst +0 -0
  84. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/using/codeless.rst +0 -0
  85. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/using/index.rst +0 -0
  86. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/using/masks.rst +0 -0
  87. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/using/queueing.rst +0 -0
  88. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/using/running.rst +0 -0
  89. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/docs/whats_new.rst +0 -0
  90. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/README.rst +0 -0
  91. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/norun_hcpfc_pearson.py +0 -0
  92. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/norun_ukbvm_gmd.py +0 -0
  93. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/run_compute_parcel_mean.py +0 -0
  94. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/run_datagrabber_bids_datalad.py +0 -0
  95. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/run_ets_rss_marker.py +0 -0
  96. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/run_junifer_julearn.py +0 -0
  97. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/run_run_gmd_mean.py +0 -0
  98. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/yamls/gmd_mean.yaml +0 -0
  99. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/yamls/gmd_mean_htcondor.yaml +0 -0
  100. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/yamls/partly_cloudy_agg_mean_tian.yml +0 -0
  101. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/examples/yamls/ukb_gmd_mean.yaml +0 -0
  102. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/ignore_words.txt +0 -0
  103. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/__init__.py +0 -0
  104. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/__init__.py +0 -0
  105. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/cli.py +0 -0
  106. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/decorators.py +0 -0
  107. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/functions.py +0 -0
  108. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/parser.py +0 -0
  109. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/queue_context/__init__.py +0 -0
  110. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/queue_context/gnu_parallel_local_adapter.py +0 -0
  111. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/queue_context/htcondor_adapter.py +0 -0
  112. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/queue_context/queue_context_adapter.py +0 -0
  113. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +0 -0
  114. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/queue_context/tests/test_htcondor_adapter.py +0 -0
  115. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/afni/3dAFNItoNIFTI +0 -0
  116. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/afni/3dRSFC +0 -0
  117. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/afni/3dReHo +0 -0
  118. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/afni/afni +0 -0
  119. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/afni/run_afni_docker.sh +0 -0
  120. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/ants/ResampleImage +0 -0
  121. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/ants/antsApplyTransforms +0 -0
  122. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/ants/antsApplyTransformsToPoints +0 -0
  123. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/ants/run_ants_docker.sh +0 -0
  124. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/freesurfer/mri_binarize +0 -0
  125. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/freesurfer/mri_mc +0 -0
  126. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/freesurfer/mri_pretess +0 -0
  127. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/freesurfer/mris_convert +0 -0
  128. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/freesurfer/run_freesurfer_docker.sh +0 -0
  129. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/fsl/applywarp +0 -0
  130. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/fsl/flirt +0 -0
  131. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/fsl/img2imgcoord +0 -0
  132. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/fsl/run_fsl_docker.sh +0 -0
  133. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/fsl/std2imgcoord +0 -0
  134. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/run_conda.bash +0 -0
  135. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/run_conda.zsh +0 -0
  136. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/run_venv.bash +0 -0
  137. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/res/run_venv.zsh +0 -0
  138. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/tests/data/gmd_mean.yaml +0 -0
  139. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/tests/data/gmd_mean_htcondor.yaml +0 -0
  140. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/tests/data/partly_cloudy_agg_mean_tian.yml +0 -0
  141. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/tests/test_api_utils.py +0 -0
  142. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/tests/test_cli.py +0 -0
  143. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/tests/test_functions.py +0 -0
  144. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/tests/test_parser.py +0 -0
  145. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/api/utils.py +0 -0
  146. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/__init__.py +0 -0
  147. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/__init__.py +0 -0
  148. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/__init__.py +0 -0
  149. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +0 -0
  150. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/camcan_vbm.py +0 -0
  151. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/ixi_vbm.py +0 -0
  152. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py +0 -0
  153. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/tests/test_camcan_vbm.py +0 -0
  154. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py +0 -0
  155. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/tests/test_ucla.py +0 -0
  156. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py +0 -0
  157. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/ucla.py +0 -0
  158. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/configs/juseless/datagrabbers/ukb_vbm.py +0 -0
  159. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/AutobiographicalMemory_VOIs.txt +0 -0
  160. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/CogAC_VOIs.txt +0 -0
  161. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/CogAR_VOIs.txt +0 -0
  162. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/DMNBuckner_VOIs.txt +0 -0
  163. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/Dosenbach2010_MNI_VOIs.txt +0 -0
  164. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/Empathy_VOIs.txt +0 -0
  165. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/Motor_VOIs.txt +0 -0
  166. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/MultiTask_VOIs.txt +0 -0
  167. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/PhysioStress_VOIs.txt +0 -0
  168. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/Power2011_MNI_VOIs.txt +0 -0
  169. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/Power2013_MNI_VOIs.tsv +0 -0
  170. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/Rew_VOIs.txt +0 -0
  171. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/Somatosensory_VOIs.txt +0 -0
  172. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/ToM_VOIs.txt +0 -0
  173. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/data/VOIs/meta/VigAtt_VOIs.txt +0 -0
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  336. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/preprocess/warping/_fsl_warper.py +0 -0
  337. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/preprocess/warping/space_warper.py +0 -0
  338. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/preprocess/warping/tests/test_space_warper.py +0 -0
  339. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/stats.py +0 -0
  340. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/__init__.py +0 -0
  341. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/base.py +0 -0
  342. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/hdf5.py +0 -0
  343. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/pandas_base.py +0 -0
  344. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/sqlite.py +0 -0
  345. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/tests/test_hdf5.py +0 -0
  346. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/tests/test_pandas_base.py +0 -0
  347. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/tests/test_sqlite.py +0 -0
  348. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/tests/test_storage_base.py +0 -0
  349. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/tests/test_utils.py +0 -0
  350. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/storage/utils.py +0 -0
  351. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/__init__.py +0 -0
  352. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/data/sub-0001_task-anticipation_acq-seq_desc-confounds_regressors.tsv +0 -0
  353. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/datagrabbers.py +0 -0
  354. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/registry.py +0 -0
  355. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py +0 -0
  356. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/tests/test_partlycloudytesting_datagrabber.py +0 -0
  357. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/tests/test_spmauditory_datagrabber.py +0 -0
  358. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/tests/test_testing_registry.py +0 -0
  359. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/testing/utils.py +0 -0
  360. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/tests/test_main.py +0 -0
  361. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/tests/test_stats.py +0 -0
  362. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/utils/__init__.py +0 -0
  363. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/utils/fs.py +0 -0
  364. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/utils/helpers.py +0 -0
  365. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/utils/logging.py +0 -0
  366. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/utils/tests/test_fs.py +0 -0
  367. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/utils/tests/test_helpers.py +0 -0
  368. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/utils/tests/test_logging.py +0 -0
  369. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer.egg-info/dependency_links.txt +0 -0
  370. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer.egg-info/entry_points.txt +0 -0
  371. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer.egg-info/requires.txt +0 -0
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  373. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/pyproject.toml +0 -0
  374. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/setup.cfg +0 -0
  375. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/setup.py +0 -0
  376. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tools/create_aomic1000_example_dataset.py +0 -0
  377. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tools/create_aomicpiop1_example_dataset.py +0 -0
  378. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tools/create_aomicpiop2_example_dataset.py +0 -0
  379. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tools/create_bids_example_dataset.py +0 -0
  380. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tools/create_bids_example_dataset_sessions.py +0 -0
  381. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tools/create_dmcc13_benchmark_example_dataset.py +0 -0
  382. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tools/create_hcp1200_example_dataset.py +0 -0
  383. {junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/tox.ini +0 -0
{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: junifer
3
- Version: 0.0.6.dev11
3
+ Version: 0.0.6.dev16
4
4
  Summary: JUelich NeuroImaging FEature extractoR
5
5
  Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
6
6
  Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
junifer-0.0.6.dev16/docs/changes/newsfragments/335.enh ADDED
@@ -0,0 +1 @@
1
+ Add support for Spearman's correlation in :class:`.JuniferConnectivityMeasure` by `Leonard Sasse`_
{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/_version.py RENAMED
@@ -12,5 +12,5 @@ __version__: str
12
12
  __version_tuple__: VERSION_TUPLE
13
13
  version_tuple: VERSION_TUPLE
14
14
 
15
- __version__ = version = '0.0.6.dev11'
16
- __version_tuple__ = version_tuple = (0, 0, 6, 'dev11')
15
+ __version__ = version = '0.0.6.dev16'
16
+ __version_tuple__ = version_tuple = (0, 0, 6, 'dev16')
{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/external/nilearn/junifer_connectivity_measure.py RENAMED
@@ -13,7 +13,7 @@ from nilearn.connectome import (
13
13
  prec_to_partial,
14
14
  sym_matrix_to_vec,
15
15
  )
16
- from scipy import linalg
16
+ from scipy import linalg, stats
17
17
  from sklearn.base import clone
18
18
  from sklearn.covariance import EmpiricalCovariance
19
19
 
@@ -314,15 +314,18 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
314
314
  * default ``cov_estimator`` is
315
315
  :class:`sklearn.covariance.EmpiricalCovariance`
316
316
  * default ``kind`` is ``"correlation"``
317
+ * supports Spearman's correlation via ``kind="spearman correlation"``
317
318
 
318
319
  Parameters
319
320
  ----------
320
321
  cov_estimator : estimator object, optional
321
322
  The covariance estimator
322
323
  (default ``EmpiricalCovariance(store_precision=False)``).
323
- kind : {"covariance", "correlation", "partial correlation", \
324
- "tangent", "precision"}, optional
325
- The matrix kind. For the use of ``"tangent"`` see [1]_
324
+ kind : {"covariance", "correlation", "spearman correlation", \
325
+ "partial correlation", "tangent", "precision"}, optional
326
+ The matrix kind. The default value uses Pearson's correlation.
327
+ If ``"spearman correlation"`` is used, the data will be ranked before
328
+ estimating the covariance. For the use of ``"tangent"`` see [1]_
326
329
  (default "correlation").
327
330
  vectorize : bool, optional
328
331
  If True, connectivity matrices are reshaped into 1D arrays and only
@@ -400,17 +403,22 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
400
403
  self.cov_estimator_ = clone(self.cov_estimator)
401
404
 
402
405
  # Compute all the matrices, stored in "connectivities"
403
- if self.kind == "correlation":
404
- covariances_std = [
405
- self.cov_estimator_.fit(
406
- signal.standardize_signal(
407
- x,
408
- detrend=False,
409
- standardize=self.standardize,
410
- )
411
- ).covariance_
412
- for x in X
413
- ]
406
+ if self.kind in ["correlation", "spearman correlation"]:
407
+ covariances_std = []
408
+ for x in X:
409
+ x = signal.standardize_signal(
410
+ x,
411
+ detrend=False,
412
+ standardize=self.standardize,
413
+ )
414
+
415
+ # rank data if spearman correlation
416
+ # before calculating covariance
417
+ if self.kind == "spearman correlation":
418
+ x = stats.rankdata(x, axis=0)
419
+
420
+ covariances_std.append(self.cov_estimator_.fit(x).covariance_)
421
+
414
422
  connectivities = [cov_to_corr(cov) for cov in covariances_std]
415
423
  else:
416
424
  covariances = [self.cov_estimator_.fit(x).covariance_ for x in X]
{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer/external/nilearn/tests/test_junifer_connectivity_measure.py RENAMED
@@ -71,6 +71,7 @@ CONNECTIVITY_KINDS = (
71
71
  "tangent",
72
72
  "precision",
73
73
  "partial correlation",
74
+ "spearman correlation",
74
75
  )
75
76
 
76
77
  N_FEATURES = 49
{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: junifer
3
- Version: 0.0.6.dev11
3
+ Version: 0.0.6.dev16
4
4
  Summary: JUelich NeuroImaging FEature extractoR
5
5
  Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
6
6
  Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/junifer.egg-info/SOURCES.txt RENAMED
@@ -57,6 +57,7 @@ docs/api/testing.rst
57
57
  docs/api/utils.rst
58
58
  docs/changes/contributors.inc
59
59
  docs/changes/newsfragments/.gitignore
60
+ docs/changes/newsfragments/335.enh
60
61
  docs/changes/newsfragments/354.feature
61
62
  docs/changes/newsfragments/356.bugfix
62
63
  docs/changes/newsfragments/357.enh
{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.gitignore RENAMED
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{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/.gitmodules RENAMED
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{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/AUTHORS.rst RENAMED
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{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/LICENSE.md RENAMED
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{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/README.md RENAMED
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{junifer-0.0.6.dev11 → junifer-0.0.6.dev16}/codecov.yml RENAMED
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