junifer 0.0.5.dev240__tar.gz → 0.0.5.dev242__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.
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  1. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/PKG-INFO +1 -1
  2. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/whats_new.rst +121 -0
  3. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/_version.py +2 -2
  4. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer.egg-info/PKG-INFO +1 -1
  5. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer.egg-info/SOURCES.txt +0 -33
  6. junifer-0.0.5.dev240/docs/changes/newsfragments/115.doc +0 -1
  7. junifer-0.0.5.dev240/docs/changes/newsfragments/136.enh +0 -1
  8. junifer-0.0.5.dev240/docs/changes/newsfragments/161.feature +0 -1
  9. junifer-0.0.5.dev240/docs/changes/newsfragments/273.feature +0 -1
  10. junifer-0.0.5.dev240/docs/changes/newsfragments/318.misc +0 -1
  11. junifer-0.0.5.dev240/docs/changes/newsfragments/323.feature +0 -1
  12. junifer-0.0.5.dev240/docs/changes/newsfragments/324.bugfix +0 -1
  13. junifer-0.0.5.dev240/docs/changes/newsfragments/327.doc +0 -1
  14. junifer-0.0.5.dev240/docs/changes/newsfragments/330.doc +0 -1
  15. junifer-0.0.5.dev240/docs/changes/newsfragments/331.bugfix +0 -1
  16. junifer-0.0.5.dev240/docs/changes/newsfragments/332.bugfix +0 -1
  17. junifer-0.0.5.dev240/docs/changes/newsfragments/336.removal +0 -1
  18. junifer-0.0.5.dev240/docs/changes/newsfragments/337.misc +0 -1
  19. junifer-0.0.5.dev240/docs/changes/newsfragments/339.bugfix +0 -1
  20. junifer-0.0.5.dev240/docs/changes/newsfragments/340.bugfix +0 -1
  21. junifer-0.0.5.dev240/docs/changes/newsfragments/341.enh +0 -1
  22. junifer-0.0.5.dev240/docs/changes/newsfragments/342.misc +0 -1
  23. junifer-0.0.5.dev240/docs/changes/newsfragments/343.feature +0 -1
  24. junifer-0.0.5.dev240/docs/changes/newsfragments/344.feature +0 -1
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  26. junifer-0.0.5.dev240/docs/changes/newsfragments/346.enh +0 -1
  27. junifer-0.0.5.dev240/docs/changes/newsfragments/346.feature +0 -1
  28. junifer-0.0.5.dev240/docs/changes/newsfragments/347.misc +0 -1
  29. junifer-0.0.5.dev240/docs/changes/newsfragments/348.change +0 -1
  30. junifer-0.0.5.dev240/docs/changes/newsfragments/348.enh +0 -1
  31. junifer-0.0.5.dev240/docs/changes/newsfragments/348.feature +0 -1
  32. junifer-0.0.5.dev240/docs/changes/newsfragments/349.change +0 -1
  33. junifer-0.0.5.dev240/docs/changes/newsfragments/349.enh +0 -1
  34. junifer-0.0.5.dev240/docs/changes/newsfragments/350.enh +0 -1
  35. junifer-0.0.5.dev240/docs/changes/newsfragments/351.change +0 -1
  36. junifer-0.0.5.dev240/docs/changes/newsfragments/351.enh +0 -1
  37. junifer-0.0.5.dev240/docs/changes/newsfragments/351.feature +0 -1
  38. junifer-0.0.5.dev240/docs/changes/newsfragments/351.misc +0 -1
  39. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/ISSUE_TEMPLATE/bug-report.yml +0 -0
  40. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  41. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/ISSUE_TEMPLATE/dataset-request.yml +0 -0
  42. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/ISSUE_TEMPLATE/documention-request.yml +0 -0
  43. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/ISSUE_TEMPLATE/feature-request.yml +0 -0
  44. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/ISSUE_TEMPLATE/marker-request.yml +0 -0
  45. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/dependabot.yml +0 -0
  46. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/pull_request_template.md +0 -0
  47. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/workflows/ci-docs.yml +0 -0
  48. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/workflows/ci.yml +0 -0
  49. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/workflows/docs-preview.yml +0 -0
  50. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/workflows/docs.yml +0 -0
  51. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/workflows/lint.yml +0 -0
  52. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.github/workflows/pypi.yml +0 -0
  53. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.gitignore +0 -0
  54. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.gitmodules +0 -0
  55. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/.pre-commit-config.yaml +0 -0
  56. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/AUTHORS.rst +0 -0
  57. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/LICENSE.md +0 -0
  58. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/README.md +0 -0
  59. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/codecov.yml +0 -0
  60. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/conda-env.yml +0 -0
  61. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/Makefile +0 -0
  62. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/_static/css/custom.css +0 -0
  63. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/_static/js/custom.js +0 -0
  64. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/_templates/versions.html +0 -0
  65. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/api.rst +0 -0
  66. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/configs.rst +0 -0
  67. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/data.rst +0 -0
  68. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/datagrabbers.rst +0 -0
  69. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/datareaders.rst +0 -0
  70. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/index.rst +0 -0
  71. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/markers.rst +0 -0
  72. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/nilearn.rst +0 -0
  73. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/onthefly.rst +0 -0
  74. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/pipeline.rst +0 -0
  75. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/preprocessing.rst +0 -0
  76. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/stats.rst +0 -0
  77. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/storage.rst +0 -0
  78. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/testing.rst +0 -0
  79. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/api/utils.rst +0 -0
  80. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/builtin.rst +0 -0
  81. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/changes/contributors.inc +0 -0
  82. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/changes/newsfragments/.gitignore +0 -0
  83. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/conf.py +0 -0
  84. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/contribution.rst +0 -0
  85. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/coordinates.rst +0 -0
  86. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/datagrabber.rst +0 -0
  87. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/dependencies.rst +0 -0
  88. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/extension.rst +0 -0
  89. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/index.rst +0 -0
  90. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/marker.rst +0 -0
  91. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/masks.rst +0 -0
  92. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/parcellations.rst +0 -0
  93. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/extending/preprocessor.rst +0 -0
  94. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/faq.rst +0 -0
  95. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/help.rst +0 -0
  96. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/images/junifer_logo.png +0 -0
  97. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/index.rst +0 -0
  98. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/installation.rst +0 -0
  99. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/links.inc +0 -0
  100. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/maintaining.rst +0 -0
  101. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/redirect.html +0 -0
  102. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/sphinxext/gh_substitutions.py +0 -0
  103. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/starting.rst +0 -0
  104. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/data.rst +0 -0
  105. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/datagrabber.rst +0 -0
  106. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/datareader.rst +0 -0
  107. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/index.rst +0 -0
  108. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/marker.rst +0 -0
  109. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/pipeline.rst +0 -0
  110. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/preprocess.rst +0 -0
  111. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/understanding/storage.rst +0 -0
  112. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/using/codeless.rst +0 -0
  113. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/using/index.rst +0 -0
  114. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/using/masks.rst +0 -0
  115. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/using/queueing.rst +0 -0
  116. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/using/running.rst +0 -0
  117. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/README.rst +0 -0
  118. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/norun_hcpfc_pearson.py +0 -0
  119. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/norun_ukbvm_gmd.py +0 -0
  120. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/run_compute_parcel_mean.py +0 -0
  121. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/run_datagrabber_bids_datalad.py +0 -0
  122. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/run_ets_rss_marker.py +0 -0
  123. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/run_junifer_julearn.py +0 -0
  124. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/run_run_gmd_mean.py +0 -0
  125. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/yamls/gmd_mean.yaml +0 -0
  126. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/yamls/gmd_mean_htcondor.yaml +0 -0
  127. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/yamls/partly_cloudy_agg_mean_tian.yml +0 -0
  128. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/examples/yamls/ukb_gmd_mean.yaml +0 -0
  129. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/ignore_words.txt +0 -0
  130. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/__init__.py +0 -0
  131. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/__init__.py +0 -0
  132. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/cli.py +0 -0
  133. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/decorators.py +0 -0
  134. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/functions.py +0 -0
  135. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/parser.py +0 -0
  136. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/queue_context/__init__.py +0 -0
  137. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/queue_context/gnu_parallel_local_adapter.py +0 -0
  138. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/queue_context/htcondor_adapter.py +0 -0
  139. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/queue_context/queue_context_adapter.py +0 -0
  140. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +0 -0
  141. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/queue_context/tests/test_htcondor_adapter.py +0 -0
  142. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/afni/3dAFNItoNIFTI +0 -0
  143. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/afni/3dRSFC +0 -0
  144. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/afni/3dReHo +0 -0
  145. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/afni/afni +0 -0
  146. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/afni/run_afni_docker.sh +0 -0
  147. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/ants/ResampleImage +0 -0
  148. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/ants/antsApplyTransforms +0 -0
  149. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/ants/antsApplyTransformsToPoints +0 -0
  150. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/ants/run_ants_docker.sh +0 -0
  151. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/freesurfer/mri_binarize +0 -0
  152. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/freesurfer/mri_mc +0 -0
  153. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/freesurfer/mri_pretess +0 -0
  154. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/freesurfer/mris_convert +0 -0
  155. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/freesurfer/run_freesurfer_docker.sh +0 -0
  156. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/fsl/applywarp +0 -0
  157. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/fsl/flirt +0 -0
  158. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/res/fsl/img2imgcoord +0 -0
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  168. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/tests/test_api_utils.py +0 -0
  169. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/tests/test_cli.py +0 -0
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  172. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/api/utils.py +0 -0
  173. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/__init__.py +0 -0
  174. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/__init__.py +0 -0
  175. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/__init__.py +0 -0
  176. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +0 -0
  177. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/camcan_vbm.py +0 -0
  178. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/ixi_vbm.py +0 -0
  179. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py +0 -0
  180. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/tests/test_camcan_vbm.py +0 -0
  181. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py +0 -0
  182. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/tests/test_ucla.py +0 -0
  183. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py +0 -0
  184. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/ucla.py +0 -0
  185. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/configs/juseless/datagrabbers/ukb_vbm.py +0 -0
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  346. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/pipeline/tests/test_workdir_manager.py +0 -0
  347. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/pipeline/update_meta_mixin.py +0 -0
  348. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/pipeline/utils.py +0 -0
  349. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/pipeline/workdir_manager.py +0 -0
  350. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/__init__.py +0 -0
  351. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/base.py +0 -0
  352. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/confounds/__init__.py +0 -0
  353. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/confounds/fmriprep_confound_remover.py +0 -0
  354. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +0 -0
  355. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/smoothing/__init__.py +0 -0
  356. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/smoothing/_afni_smoothing.py +0 -0
  357. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/smoothing/_fsl_smoothing.py +0 -0
  358. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/smoothing/_nilearn_smoothing.py +0 -0
  359. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/smoothing/smoothing.py +0 -0
  360. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/smoothing/tests/test_smoothing.py +0 -0
  361. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/tests/test_preprocess_base.py +0 -0
  362. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/warping/__init__.py +0 -0
  363. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/warping/_ants_warper.py +0 -0
  364. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/warping/_fsl_warper.py +0 -0
  365. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/warping/space_warper.py +0 -0
  366. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/preprocess/warping/tests/test_space_warper.py +0 -0
  367. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/stats.py +0 -0
  368. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/__init__.py +0 -0
  369. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/base.py +0 -0
  370. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/hdf5.py +0 -0
  371. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/pandas_base.py +0 -0
  372. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/sqlite.py +0 -0
  373. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/tests/test_hdf5.py +0 -0
  374. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/tests/test_pandas_base.py +0 -0
  375. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/tests/test_sqlite.py +0 -0
  376. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/tests/test_storage_base.py +0 -0
  377. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/tests/test_utils.py +0 -0
  378. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/storage/utils.py +0 -0
  379. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/__init__.py +0 -0
  380. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/data/sub-0001_task-anticipation_acq-seq_desc-confounds_regressors.tsv +0 -0
  381. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/datagrabbers.py +0 -0
  382. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/registry.py +0 -0
  383. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py +0 -0
  384. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/tests/test_partlycloudytesting_datagrabber.py +0 -0
  385. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/tests/test_spmauditory_datagrabber.py +0 -0
  386. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/tests/test_testing_registry.py +0 -0
  387. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/testing/utils.py +0 -0
  388. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/tests/test_main.py +0 -0
  389. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/tests/test_stats.py +0 -0
  390. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/utils/__init__.py +0 -0
  391. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/utils/fs.py +0 -0
  392. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/utils/helpers.py +0 -0
  393. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/utils/logging.py +0 -0
  394. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/utils/tests/test_fs.py +0 -0
  395. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/utils/tests/test_helpers.py +0 -0
  396. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/utils/tests/test_logging.py +0 -0
  397. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer.egg-info/dependency_links.txt +0 -0
  398. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer.egg-info/entry_points.txt +0 -0
  399. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer.egg-info/requires.txt +0 -0
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  403. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/setup.py +0 -0
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  405. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/tools/create_aomicpiop1_example_dataset.py +0 -0
  406. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/tools/create_aomicpiop2_example_dataset.py +0 -0
  407. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/tools/create_bids_example_dataset.py +0 -0
  408. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/tools/create_bids_example_dataset_sessions.py +0 -0
  409. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/tools/create_dmcc13_benchmark_example_dataset.py +0 -0
  410. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/tools/create_hcp1200_example_dataset.py +0 -0
  411. {junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/tox.ini +0 -0
{junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: junifer
3
- Version: 0.0.5.dev240
3
+ Version: 0.0.5.dev242
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-0.0.5.dev240 → junifer-0.0.5.dev242}/docs/whats_new.rst RENAMED
@@ -8,6 +8,127 @@ What's new
8
8
 
9
9
  .. towncrier release notes start
10
10
 
11
+ Junifer 0.0.5 (2024-07-22)
12
+ --------------------------
13
+
14
+ Bugfixes
15
+ ^^^^^^^^
16
+
17
+ - Remove extra dimension from parcellations warped via ANTs to other template
18
+ spaces by `Synchon Mandal`_ (:gh:`324`)
19
+ - Remove extra dimension from parcellations warped via ANTs when merging
20
+ parcellations by `Synchon Mandal`_ (:gh:`331`)
21
+ - Fix ``junifer reset`` to properly delete storage directory and handle
22
+ ``junifer_jobs`` deletion if not empty by `Synchon Mandal`_ (:gh:`332`)
23
+ - Fix validation failure of multiple Preprocessors with different input data
24
+ types requirement by `Synchon Mandal`_ (:gh:`339`)
25
+ - Remove extra dimension from masks warped via ANTs by `Synchon Mandal`_
26
+ (:gh:`340`)
27
+
28
+
29
+ API Changes
30
+ ^^^^^^^^^^^
31
+
32
+ - For :class:`.CrossParcellationFC`, ``aggregation_method`` and
33
+ ``correlation_method`` have been renamed to ``agg_method`` and
34
+ ``corr_method`` respectively and ``agg_method_params`` has been added; for
35
+ ``FunctionalConnectivityBase``, :class:`.FunctionalConnectivityParcels`,
36
+ :class:`.FunctionalConnectivitySpheres`, :class:`.EdgeCentricFCParcels` and
37
+ :class:`.EdgeCentricFCSpheres`, ``cor_method`` and ``cor_method_params`` have
38
+ been renamed to ``conn_method`` and ``conn_method_params`` by `Synchon
39
+ Mandal`_ (:gh:`348`)
40
+ - ``fractional`` parameter for ``ALFFBase``, :class:`.ALFFParcels` and
41
+ :class:`.ALFFSpheres` have been removed in favour of returning both ALFF and
42
+ fALFF by `Synchon Mandal`_ (:gh:`349`)
43
+ - Add ``partial_pattern_ok`` argument to :class:`.PatternDataGrabber` to not
44
+ raise error on missing mandatory key checks for data types by `Synchon
45
+ Mandal`_ (:gh:`351`)
46
+
47
+
48
+ Improved Documentation
49
+ ^^^^^^^^^^^^^^^^^^^^^^
50
+
51
+ - Improve sub-package level docstrings to better reflect their purposes by
52
+ `Synchon Mandal`_ (:gh:`115`)
53
+ - Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_ (:gh:`327`)
54
+ - Add missing DataGrabber ``types`` options in respective docstrings of
55
+ :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`,
56
+ :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` by `Synchon
57
+ Mandal`_ (:gh:`330`)
58
+
59
+
60
+ Enhancements
61
+ ^^^^^^^^^^^^
62
+
63
+ - Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean
64
+ aggregation function behaves exactly as
65
+ :class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_ (:gh:`136`)
66
+ - Refactor DataGrabber ``patterns`` to make helper types like ``*_mask`` as
67
+ "nested types" of the actual data type by `Synchon Mandal`_ (:gh:`341`)
68
+ - Adapt :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and
69
+ :class:`.DataladAOMICPIOP2` to support ``FreeSurfer`` data type by `Synchon
70
+ Mandal`_ (:gh:`346`)
71
+ - ``FunctionalConnectivity``-family Markers now use
72
+ :class:`sklearn.covariance.EmpiricalCovariance` as the default covariance
73
+ estimator and ``correlation`` as the default connecivity matrix kind by
74
+ `Synchon Mandal`_ (:gh:`348`)
75
+ - Enable Markers to output multiple features by `Synchon Mandal`_ (:gh:`349`)
76
+ - Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_ (:gh:`350`)
77
+ - Adapt :class:`.MultipleDataGrabber` to handle "nested types" introduced in
78
+ :gh:`341` by `Synchon Mandal`_ (:gh:`351`)
79
+
80
+
81
+ Features
82
+ ^^^^^^^^
83
+
84
+ - Introduce :class:`.Smoothing` for smoothing / blurring images as a
85
+ preprocessing step by `Synchon Mandal`_ (:gh:`161`)
86
+ - Add support for choosing between ``bash`` and ``zsh`` shells when queueing by
87
+ `Synchon Mandal`_ (:gh:`273`)
88
+ - Add ``junifer list-elements`` to list out available elements for a
89
+ DataGrabber based on filtering via ``--element`` by `Synchon Mandal`_
90
+ (:gh:`323`)
91
+ - Introduce new storage type ``scalar_table`` and adapt
92
+ :class:`.HDF5FeatureStorage` to support it by `Synchon Mandal`_ (:gh:`343`)
93
+ - Add support for `BrainPrint
94
+ <https://github.com/Deep-MI/BrainPrint?tab=readme-ov-file>`_ marker by
95
+ `Synchon Mandal`_ (:gh:`344`)
96
+ - Allow Unix path expansion directives to be used in
97
+ :class:`.PatternDataGrabber` ``patterns`` by `Synchon Mandal`_ (:gh:`345`)
98
+ - Add support for ``FreeSurfer`` data type for :class:`.PatternDataGrabber` by
99
+ `Synchon Mandal`_ (:gh:`346`)
100
+ - Introduce :class:`.JuniferConnectivityMeasure` for customising functional
101
+ connectivity matrix kinds and measurements by `Synchon Mandal`_ (:gh:`348`)
102
+ - Introduce :class:`.PatternValidationMixin` to simplify validation for
103
+ pattern-based DataGrabbers and :func:`.deep_update` for updating dictionary
104
+ with varying width and depth by `Synchon Mandal`_ (:gh:`351`)
105
+
106
+
107
+ Miscellaneous
108
+ ^^^^^^^^^^^^^
109
+
110
+ - Improve CI to allow external tool installation to fail gracefully and update
111
+ necessary dependency version and conditional checks by `Synchon Mandal`_
112
+ (:gh:`318`)
113
+ - Update ``pre-commit`` dependency versions, add ``blacken-docs`` to
114
+ ``pre-commit``, add ``__all__`` for modules, sub-packages and package, update
115
+ ``ruff`` and ``pytest`` configs in ``pyproject.toml`` by `Synchon Mandal`_
116
+ (:gh:`337`)
117
+ - Add support for accessing FreeSurfer via Docker wrapper along with
118
+ ``mri_binarize``, ``mri_pretess``, ``mri_mc`` and ``mris_convert`` by
119
+ `Synchon Mandal`_ (:gh:`342`)
120
+ - Update core and docs dependencies by `Synchon Mandal`_ (:gh:`347`)
121
+ - Integrate ``warnings`` with ``logging`` respecting filters by `Fede
122
+ Raimondo`_ (:gh:`351`)
123
+
124
+
125
+ Deprecations and Removals
126
+ ^^^^^^^^^^^^^^^^^^^^^^^^^
127
+
128
+ - Remove ``Power`` coordinates, ``fetch_icbm152_brain_gm_mask`` mask,
129
+ ``BOLDWarper`` Preprocessor by `Synchon Mandal`_ (:gh:`336`)
130
+
131
+
11
132
  Junifer 0.0.4 (2024-04-05)
12
133
  --------------------------
13
134
 
{junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer/_version.py RENAMED
@@ -12,5 +12,5 @@ __version__: str
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13
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14
14
 
15
- __version__ = version = '0.0.5.dev240'
16
- __version_tuple__ = version_tuple = (0, 0, 5, 'dev240')
15
+ __version__ = version = '0.0.5.dev242'
16
+ __version_tuple__ = version_tuple = (0, 0, 5, 'dev242')
{junifer-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: junifer
3
- Version: 0.0.5.dev240
3
+ Version: 0.0.5.dev242
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-0.0.5.dev240 → junifer-0.0.5.dev242}/junifer.egg-info/SOURCES.txt RENAMED
@@ -57,39 +57,6 @@ 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/115.doc
61
- docs/changes/newsfragments/136.enh
62
- docs/changes/newsfragments/161.feature
63
- docs/changes/newsfragments/273.feature
64
- docs/changes/newsfragments/318.misc
65
- docs/changes/newsfragments/323.feature
66
- docs/changes/newsfragments/324.bugfix
67
- docs/changes/newsfragments/327.doc
68
- docs/changes/newsfragments/330.doc
69
- docs/changes/newsfragments/331.bugfix
70
- docs/changes/newsfragments/332.bugfix
71
- docs/changes/newsfragments/336.removal
72
- docs/changes/newsfragments/337.misc
73
- docs/changes/newsfragments/339.bugfix
74
- docs/changes/newsfragments/340.bugfix
75
- docs/changes/newsfragments/341.enh
76
- docs/changes/newsfragments/342.misc
77
- docs/changes/newsfragments/343.feature
78
- docs/changes/newsfragments/344.feature
79
- docs/changes/newsfragments/345.feature
80
- docs/changes/newsfragments/346.enh
81
- docs/changes/newsfragments/346.feature
82
- docs/changes/newsfragments/347.misc
83
- docs/changes/newsfragments/348.change
84
- docs/changes/newsfragments/348.enh
85
- docs/changes/newsfragments/348.feature
86
- docs/changes/newsfragments/349.change
87
- docs/changes/newsfragments/349.enh
88
- docs/changes/newsfragments/350.enh
89
- docs/changes/newsfragments/351.change
90
- docs/changes/newsfragments/351.enh
91
- docs/changes/newsfragments/351.feature
92
- docs/changes/newsfragments/351.misc
93
60
  docs/extending/coordinates.rst
94
61
  docs/extending/datagrabber.rst
95
62
  docs/extending/dependencies.rst
junifer-0.0.5.dev240/docs/changes/newsfragments/115.doc DELETED
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junifer-0.0.5.dev240/docs/changes/newsfragments/136.enh DELETED
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- Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean aggregation function behaves exactly as :class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/161.feature DELETED
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junifer-0.0.5.dev240/docs/changes/newsfragments/273.feature DELETED
@@ -1 +0,0 @@
1
- Add support for choosing between ``bash`` and ``zsh`` shells when queueing by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/318.misc DELETED
@@ -1 +0,0 @@
1
- Improve CI to allow external tool installation to fail gracefully and update necessary dependency version and conditional checks by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/323.feature DELETED
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1
- Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/330.doc DELETED
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1
- Add missing DataGrabber ``types`` options in respective docstrings of :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/331.bugfix DELETED
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- Remove extra dimension from parcellations warped via ANTs when merging parcellations by `Synchon Mandal`_
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- Update ``pre-commit`` dependency versions, add ``blacken-docs`` to ``pre-commit``, add ``__all__`` for modules, sub-packages and package, update ``ruff`` and ``pytest`` configs in ``pyproject.toml`` by `Synchon Mandal`_
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junifer-0.0.5.dev240/docs/changes/newsfragments/340.bugfix DELETED
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- Remove extra dimension from masks warped via ANTs by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/341.enh DELETED
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- Refactor DataGrabber ``patterns`` to make helper types like ``*_mask`` as "nested types" of the actual data type by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/342.misc DELETED
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- Add support for accessing FreeSurfer via Docker wrapper along with ``mri_binarize``, ``mri_pretess``, ``mri_mc`` and ``mris_convert`` by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/343.feature DELETED
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- Introduce new storage type ``scalar_table`` and adapt :class:`.HDF5FeatureStorage` to support it by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/344.feature DELETED
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- Add support for `BrainPrint <https://github.com/Deep-MI/BrainPrint?tab=readme-ov-file>`_ marker by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/345.feature DELETED
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- Allow Unix path expansion directives to be used in :class:`.PatternDataGrabber` ``patterns`` by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/346.enh DELETED
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- Adapt :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2` to support ``FreeSurfer`` data type by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/346.feature DELETED
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- Add support for ``FreeSurfer`` data type for :class:`.PatternDataGrabber` by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/347.misc DELETED
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- Update core and docs dependencies by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/348.change DELETED
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- For :class:`.CrossParcellationFC`, ``aggregation_method`` and ``correlation_method`` have been renamed to ``agg_method`` and ``corr_method`` respectively and ``agg_method_params`` has been added; for ``FunctionalConnectivityBase``, :class:`.FunctionalConnectivityParcels`, :class:`.FunctionalConnectivitySpheres`, :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres`, ``cor_method`` and ``cor_method_params`` have been renamed to ``conn_method`` and ``conn_method_params`` by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/348.enh DELETED
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- ``FunctionalConnectivity``-family Markers now use :class:`sklearn.covariance.EmpiricalCovariance` as the default covariance estimator and ``correlation`` as the default connecivity matrix kind by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/348.feature DELETED
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- Introduce :class:`.JuniferConnectivityMeasure` for customising functional connectivity matrix kinds and measurements by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/349.change DELETED
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- ``fractional`` parameter for ``ALFFBase``, :class:`.ALFFParcels` and :class:`.ALFFSpheres` have been removed in favour of returning both ALFF and fALFF by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/349.enh DELETED
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- Enable Markers to output multiple features by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/350.enh DELETED
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- Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/351.change DELETED
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- Add ``partial_pattern_ok`` argument to :class:`.PatternDataGrabber` to not raise error on missing mandatory key checks for data types by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/351.enh DELETED
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- Adapt :class:`.MultipleDataGrabber` to handle "nested types" introduced in :gh:`341` by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/351.feature DELETED
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- Introduce :class:`.PatternValidationMixin` to simplify validation for pattern-based DataGrabbers and :func:`.deep_update` for updating dictionary with varying width and depth by `Synchon Mandal`_
junifer-0.0.5.dev240/docs/changes/newsfragments/351.misc DELETED
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- Integrate ``warnings`` with ``logging`` respecting filters by `Fede Raimondo`_
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