junifer 0.0.8.dev189__tar.gz → 0.0.8.dev195__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 (550) hide show
  1. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/ci-docs.yml +1 -1
  2. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/ci.yml +2 -2
  3. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/docker-ci-publish.yml +6 -6
  4. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/docker-docs-publish.yml +6 -6
  5. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/docker-publish.yml +6 -6
  6. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/docs-preview.yml +1 -1
  7. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/docs.yml +2 -2
  8. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/lint.yml +1 -1
  9. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/publish.yml +2 -2
  10. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/PKG-INFO +1 -1
  11. junifer-0.0.8.dev195/docs/changes/newsfragments/503.enh +1 -0
  12. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/_version.py +3 -3
  13. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/gnu_parallel_local_adapter.py +16 -14
  14. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/htcondor_adapter.py +20 -16
  15. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/queue_context_adapter.py +5 -5
  16. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +8 -8
  17. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/tests/test_htcondor_adapter.py +9 -9
  18. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer.egg-info/PKG-INFO +1 -1
  19. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer.egg-info/SOURCES.txt +1 -0
  20. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer.egg-info/scm_file_list.json +1 -0
  21. junifer-0.0.8.dev195/junifer.egg-info/scm_version.json +8 -0
  22. junifer-0.0.8.dev189/junifer.egg-info/scm_version.json +0 -8
  23. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.dockerignore +0 -0
  24. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/ISSUE_TEMPLATE/bug-report.yml +0 -0
  25. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  26. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/ISSUE_TEMPLATE/dataset-request.yml +0 -0
  27. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/ISSUE_TEMPLATE/documention-request.yml +0 -0
  28. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/ISSUE_TEMPLATE/feature-request.yml +0 -0
  29. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/ISSUE_TEMPLATE/marker-request.yml +0 -0
  30. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/dependabot.yml +0 -0
  31. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/pull_request_template.md +0 -0
  32. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.github/workflows/check-stale.yml +0 -0
  33. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.gitignore +0 -0
  34. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.gitmodules +0 -0
  35. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.pre-commit-config.yaml +0 -0
  36. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/.python-version +0 -0
  37. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/AUTHORS.rst +0 -0
  38. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/Dockerfile +0 -0
  39. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/Dockerfile-ci +0 -0
  40. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/Dockerfile-docs +0 -0
  41. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/LICENSE.md +0 -0
  42. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/README.md +0 -0
  43. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/codecov.yml +0 -0
  44. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/conda-env.yml +0 -0
  45. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/Makefile +0 -0
  46. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/_static/css/custom.css +0 -0
  47. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/_static/js/custom.js +0 -0
  48. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/_templates/versions.html +0 -0
  49. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/api.rst +0 -0
  50. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/cli.rst +0 -0
  51. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/configs.rst +0 -0
  52. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/data.rst +0 -0
  53. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/datagrabbers.rst +0 -0
  54. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/datareaders.rst +0 -0
  55. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/index.rst +0 -0
  56. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/markers.rst +0 -0
  57. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/nilearn.rst +0 -0
  58. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/onthefly.rst +0 -0
  59. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/pipeline.rst +0 -0
  60. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/preprocessing.rst +0 -0
  61. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/stats.rst +0 -0
  62. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/storage.rst +0 -0
  63. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/testing.rst +0 -0
  64. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/api/utils.rst +0 -0
  65. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/builtin.rst +0 -0
  66. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/contributors.inc +0 -0
  67. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/.gitignore +0 -0
  68. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/239.enh +0 -0
  69. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/364.doc +0 -0
  70. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/364.enh +0 -0
  71. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/364.feature +0 -0
  72. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/474.misc +0 -0
  73. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/482.bugfix +0 -0
  74. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/492.bugfix +0 -0
  75. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/changes/newsfragments/502.bugfix +0 -0
  76. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/conf.py +0 -0
  77. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/contribution.rst +0 -0
  78. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/confounds_format.rst +0 -0
  79. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/coordinates.rst +0 -0
  80. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/data_dump_asset.rst +0 -0
  81. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/data_registries.rst +0 -0
  82. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/data_types.rst +0 -0
  83. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/datagrabber.rst +0 -0
  84. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/dependencies.rst +0 -0
  85. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/extension.rst +0 -0
  86. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/index.rst +0 -0
  87. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/logging.rst +0 -0
  88. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/maps.rst +0 -0
  89. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/marker.rst +0 -0
  90. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/masks.rst +0 -0
  91. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/parcellations.rst +0 -0
  92. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/plugins.rst +0 -0
  93. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/extending/preprocessor.rst +0 -0
  94. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/faq.rst +0 -0
  95. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/help.rst +0 -0
  96. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/images/junifer_logo.png +0 -0
  97. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/index.rst +0 -0
  98. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/installation.rst +0 -0
  99. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/links.inc +0 -0
  100. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/maintaining.rst +0 -0
  101. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/redirect.html +0 -0
  102. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/starting.rst +0 -0
  103. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/data.rst +0 -0
  104. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/datagrabber.rst +0 -0
  105. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/datareader.rst +0 -0
  106. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/index.rst +0 -0
  107. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/marker.rst +0 -0
  108. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/pipeline.rst +0 -0
  109. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/preprocess.rst +0 -0
  110. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/understanding/storage.rst +0 -0
  111. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/using/codeless.rst +0 -0
  112. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/using/configuring.rst +0 -0
  113. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/using/dumping.rst +0 -0
  114. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/using/index.rst +0 -0
  115. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/using/masks.rst +0 -0
  116. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/using/queueing.rst +0 -0
  117. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/using/running.rst +0 -0
  118. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/docs/whats_new.rst +0 -0
  119. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/README.rst +0 -0
  120. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/norun_hcpfc_pearson.py +0 -0
  121. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/norun_ukbvm_gmd.py +0 -0
  122. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/run_compute_parcel_mean.py +0 -0
  123. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/run_datagrabber_bids_datalad.py +0 -0
  124. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/run_ets_rss_marker.py +0 -0
  125. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/run_junifer_julearn.py +0 -0
  126. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/run_run_gmd_mean.py +0 -0
  127. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/yamls/gmd_mean.yaml +0 -0
  128. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/yamls/gmd_mean_htcondor.yaml +0 -0
  129. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/yamls/partly_cloudy_agg_mean_tian.yml +0 -0
  130. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/examples/yamls/ukb_gmd_mean.yaml +0 -0
  131. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/ignore_words.txt +0 -0
  132. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/__init__.py +0 -0
  133. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/__init__.pyi +0 -0
  134. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/__init__.py +0 -0
  135. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/__init__.pyi +0 -0
  136. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/decorators.py +0 -0
  137. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/functions.py +0 -0
  138. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/py.typed +0 -0
  139. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/__init__.py +0 -0
  140. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/__init__.pyi +0 -0
  141. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/queue_context/py.typed +0 -0
  142. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/afni/3dAFNItoNIFTI +0 -0
  143. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/afni/3dRSFC +0 -0
  144. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/afni/3dReHo +0 -0
  145. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/afni/afni +0 -0
  146. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/afni/run_afni_docker.sh +0 -0
  147. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/ants/ResampleImage +0 -0
  148. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/ants/antsApplyTransforms +0 -0
  149. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/ants/antsApplyTransformsToPoints +0 -0
  150. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/ants/run_ants_docker.sh +0 -0
  151. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/freesurfer/mri_binarize +0 -0
  152. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/freesurfer/mri_mc +0 -0
  153. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/freesurfer/mri_pretess +0 -0
  154. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/freesurfer/mris_convert +0 -0
  155. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/freesurfer/run_freesurfer_docker.sh +0 -0
  156. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/fsl/applywarp +0 -0
  157. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/fsl/flirt +0 -0
  158. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/fsl/img2imgcoord +0 -0
  159. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/res/fsl/run_fsl_docker.sh +0 -0
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  165. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/tests/test_decorators.py +0 -0
  166. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/api/tests/test_functions.py +0 -0
  167. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/__init__.py +0 -0
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  169. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/cli.py +0 -0
  170. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/parser.py +0 -0
  171. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/py.typed +0 -0
  172. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/tests/data/gmd_mean.yaml +0 -0
  173. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/tests/data/gmd_mean_htcondor.yaml +0 -0
  174. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/tests/data/partly_cloudy_agg_mean_tian.yml +0 -0
  175. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/tests/test_cli.py +0 -0
  176. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/tests/test_cli_utils.py +0 -0
  177. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/tests/test_parser.py +0 -0
  178. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/cli/utils.py +0 -0
  179. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/configs/__init__.py +0 -0
  180. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/configs/__init__.pyi +0 -0
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  507. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/datagrabbers.py +0 -0
  508. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/py.typed +0 -0
  509. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/registry.py +0 -0
  510. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py +0 -0
  511. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/tests/test_partlycloudytesting_datagrabber.py +0 -0
  512. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/tests/test_spmauditory_datagrabber.py +0 -0
  513. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/tests/test_testing_registry.py +0 -0
  514. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/testing/utils.py +0 -0
  515. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/tests/test_main.py +0 -0
  516. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/tests/test_stats.py +0 -0
  517. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/typing/__init__.py +0 -0
  518. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/typing/__init__.pyi +0 -0
  519. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/typing/_typing.py +0 -0
  520. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/typing/py.typed +0 -0
  521. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/__init__.py +0 -0
  522. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/__init__.pyi +0 -0
  523. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/_config.py +0 -0
  524. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/_yaml.py +0 -0
  525. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/fs.py +0 -0
  526. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/helpers.py +0 -0
  527. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/logging.py +0 -0
  528. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/py.typed +0 -0
  529. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/singleton.py +0 -0
  530. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/tests/test_config.py +0 -0
  531. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/tests/test_fs.py +0 -0
  532. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/tests/test_helpers.py +0 -0
  533. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer/utils/tests/test_logging.py +0 -0
  534. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer.egg-info/dependency_links.txt +0 -0
  535. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer.egg-info/entry_points.txt +0 -0
  536. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer.egg-info/requires.txt +0 -0
  537. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/junifer.egg-info/top_level.txt +0 -0
  538. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/justfile +0 -0
  539. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/pyproject.toml +0 -0
  540. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/setup.cfg +0 -0
  541. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/setup.py +0 -0
  542. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tools/create_aomic1000_example_dataset.py +0 -0
  543. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tools/create_aomicpiop1_example_dataset.py +0 -0
  544. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tools/create_aomicpiop2_example_dataset.py +0 -0
  545. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tools/create_bids_example_dataset.py +0 -0
  546. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tools/create_bids_example_dataset_sessions.py +0 -0
  547. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tools/create_dmcc13_benchmark_example_dataset.py +0 -0
  548. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tools/create_hcp1200_example_dataset.py +0 -0
  549. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/tox.ini +0 -0
  550. {junifer-0.0.8.dev189 → junifer-0.0.8.dev195}/uv.lock +0 -0
@@ -48,7 +48,7 @@ jobs:
48
48
  echo '</coverage>' >> coverage.xml
49
49
  if: matrix.python-version == 3.12
50
50
  - name: Upload mock coverage to Codecov
51
- uses: codecov/codecov-action@v5
51
+ uses: codecov/codecov-action@v7
52
52
  with:
53
53
  token: ${{ secrets.CODECOV_TOKEN }}
54
54
  # Allow coverage upload failure
@@ -57,7 +57,7 @@ jobs:
57
57
  mkdir -p $HOME/junifer_data/v7
58
58
  cp -ar /root/junifer_data/v7/. $HOME/junifer_data/v7/
59
59
  - name: Checkout repository
60
- uses: actions/checkout@v6
60
+ uses: actions/checkout@v7
61
61
  with:
62
62
  submodules: true
63
63
  - name: Set up Python ${{ matrix.python-version }}
@@ -78,7 +78,7 @@ jobs:
78
78
  git config --system --add safe.directory $(pwd)
79
79
  tox
80
80
  - name: Upload coverage to Codecov
81
- uses: codecov/codecov-action@v5
81
+ uses: codecov/codecov-action@v7
82
82
  with:
83
83
  token: ${{ secrets.CODECOV_TOKEN }}
84
84
  fail_ci_if_error: true
@@ -32,27 +32,27 @@ jobs:
32
32
  sudo docker builder prune -a
33
33
  - run: df -h
34
34
  - name: Checkout repository
35
- uses: actions/checkout@v6
35
+ uses: actions/checkout@v7
36
36
  - name: Install cosign
37
37
  if: github.event_name != 'pull_request'
38
- uses: sigstore/cosign-installer@v4.1.0
38
+ uses: sigstore/cosign-installer@v4.1.2
39
39
  - name: Set up Docker Buildx
40
- uses: docker/setup-buildx-action@v4.0.0
40
+ uses: docker/setup-buildx-action@v4.1.0
41
41
  - name: Log into registry ${{ env.REGISTRY }}
42
42
  if: github.event_name != 'pull_request'
43
- uses: docker/login-action@v4.0.0
43
+ uses: docker/login-action@v4.2.0
44
44
  with:
45
45
  registry: ${{ env.REGISTRY }}
46
46
  username: ${{ github.actor }}
47
47
  password: ${{ secrets.GITHUB_TOKEN }}
48
48
  - name: Extract Docker metadata
49
49
  id: meta
50
- uses: docker/metadata-action@v6.0.0
50
+ uses: docker/metadata-action@v6.1.0
51
51
  with:
52
52
  images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
53
53
  - name: Build and push Docker image
54
54
  id: build-and-push
55
- uses: docker/build-push-action@v7.0.0
55
+ uses: docker/build-push-action@v7.2.0
56
56
  with:
57
57
  context: .
58
58
  file: Dockerfile-ci
@@ -32,27 +32,27 @@ jobs:
32
32
  sudo docker builder prune -a
33
33
  - run: df -h
34
34
  - name: Checkout repository
35
- uses: actions/checkout@v6
35
+ uses: actions/checkout@v7
36
36
  - name: Install cosign
37
37
  if: github.event_name != 'pull_request'
38
- uses: sigstore/cosign-installer@v4.1.0
38
+ uses: sigstore/cosign-installer@v4.1.2
39
39
  - name: Set up Docker Buildx
40
- uses: docker/setup-buildx-action@v4.0.0
40
+ uses: docker/setup-buildx-action@v4.1.0
41
41
  - name: Log into registry ${{ env.REGISTRY }}
42
42
  if: github.event_name != 'pull_request'
43
- uses: docker/login-action@v4.0.0
43
+ uses: docker/login-action@v4.2.0
44
44
  with:
45
45
  registry: ${{ env.REGISTRY }}
46
46
  username: ${{ github.actor }}
47
47
  password: ${{ secrets.GITHUB_TOKEN }}
48
48
  - name: Extract Docker metadata
49
49
  id: meta
50
- uses: docker/metadata-action@v6.0.0
50
+ uses: docker/metadata-action@v6.1.0
51
51
  with:
52
52
  images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
53
53
  - name: Build and push Docker image
54
54
  id: build-and-push
55
- uses: docker/build-push-action@v7.0.0
55
+ uses: docker/build-push-action@v7.2.0
56
56
  with:
57
57
  context: .
58
58
  file: Dockerfile-docs
@@ -32,27 +32,27 @@ jobs:
32
32
  sudo docker builder prune -a
33
33
  - run: df -h
34
34
  - name: Checkout repository
35
- uses: actions/checkout@v6
35
+ uses: actions/checkout@v7
36
36
  - name: Install cosign
37
37
  if: github.event_name != 'pull_request'
38
- uses: sigstore/cosign-installer@v4.1.0
38
+ uses: sigstore/cosign-installer@v4.1.2
39
39
  - name: Set up Docker Buildx
40
- uses: docker/setup-buildx-action@v4.0.0
40
+ uses: docker/setup-buildx-action@v4.1.0
41
41
  - name: Log into registry ${{ env.REGISTRY }}
42
42
  if: github.event_name != 'pull_request'
43
- uses: docker/login-action@v4.0.0
43
+ uses: docker/login-action@v4.2.0
44
44
  with:
45
45
  registry: ${{ env.REGISTRY }}
46
46
  username: ${{ github.actor }}
47
47
  password: ${{ secrets.GITHUB_TOKEN }}
48
48
  - name: Extract Docker metadata
49
49
  id: meta
50
- uses: docker/metadata-action@v6.0.0
50
+ uses: docker/metadata-action@v6.1.0
51
51
  with:
52
52
  images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
53
53
  - name: Build and push Docker image
54
54
  id: build-and-push
55
- uses: docker/build-push-action@v7.0.0
55
+ uses: docker/build-push-action@v7.2.0
56
56
  with:
57
57
  context: .
58
58
  file: Dockerfile
@@ -43,7 +43,7 @@ jobs:
43
43
  mkdir -p $HOME/junifer_data/v7
44
44
  cp -ar /root/junifer_data/v7/. $HOME/junifer_data/v7/
45
45
  - name: Checkout repository
46
- uses: actions/checkout@v6
46
+ uses: actions/checkout@v7
47
47
  with:
48
48
  fetch-depth: 0
49
49
  submodules: true
@@ -34,7 +34,7 @@ jobs:
34
34
  mkdir -p $HOME/junifer_data/v7
35
35
  cp -ar /root/junifer_data/v7/. $HOME/junifer_data/v7/
36
36
  - name: Checkout repository
37
- uses: actions/checkout@v6
37
+ uses: actions/checkout@v7
38
38
  with:
39
39
  # require all of history to see all tagged versions' docs
40
40
  fetch-depth: 0
@@ -55,7 +55,7 @@ jobs:
55
55
  - name: Checkout gh-pages
56
56
  # As we already did a deploy of gh-pages above, it is guaranteed to be there
57
57
  # so check it out so we can selectively build docs below
58
- uses: actions/checkout@v6
58
+ uses: actions/checkout@v7
59
59
  with:
60
60
  ref: gh-pages
61
61
  path: docs/_build
@@ -8,7 +8,7 @@ jobs:
8
8
  lint:
9
9
  runs-on: ubuntu-latest
10
10
  steps:
11
- - uses: actions/checkout@v6
11
+ - uses: actions/checkout@v7
12
12
  - name: Install Python
13
13
  uses: actions/setup-python@v6
14
14
  with:
@@ -18,7 +18,7 @@ jobs:
18
18
  contents: write
19
19
  steps:
20
20
  - name: Checkout source
21
- uses: actions/checkout@v6
21
+ uses: actions/checkout@v7
22
22
  with:
23
23
  fetch-depth: 0
24
24
  submodules: true
@@ -36,7 +36,7 @@ jobs:
36
36
  - name: Publish package to PyPI
37
37
  uses: pypa/gh-action-pypi-publish@release/v1
38
38
  - name: Make release on GitHub
39
- uses: softprops/action-gh-release@v2
39
+ uses: softprops/action-gh-release@v3
40
40
  if: startsWith(github.ref, 'refs/tags/')
41
41
  with:
42
42
  files: |
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: junifer
3
- Version: 0.0.8.dev189
3
+ Version: 0.0.8.dev195
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>
@@ -0,0 +1 @@
1
+ Revert ``pre_run`` and ``pre_collect`` parameters for queue context adapters by `Synchon Mandal`_
@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
18
18
  commit_id: str | None
19
19
  __commit_id__: str | None
20
20
 
21
- __version__ = version = '0.0.8.dev189'
22
- __version_tuple__ = version_tuple = (0, 0, 8, 'dev189')
21
+ __version__ = version = '0.0.8.dev195'
22
+ __version_tuple__ = version_tuple = (0, 0, 8, 'dev195')
23
23
 
24
- __commit_id__ = commit_id = 'g5e5ce7c0b'
24
+ __commit_id__ = commit_id = 'g64d583140'
@@ -35,9 +35,9 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
35
35
  The path to the YAML config file.
36
36
  elements : ``Elements``
37
37
  Element(s) to process. Will be used to index the DataGrabber.
38
- pre_run_cmds : str or None, optional
38
+ pre_run : str or None, optional
39
39
  Extra shell commands to source before the run (default None).
40
- pre_collect_cmds : str or None, optional
40
+ pre_collect : str or None, optional
41
41
  Extra shell commands to source before the collect (default None).
42
42
  env : :class:`.QueueContextEnv` or None, optional
43
43
  The environment configuration. If None, will run without a
@@ -63,8 +63,8 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
63
63
  job_dir: Path
64
64
  yaml_config_path: Path
65
65
  elements: Elements
66
- pre_run_cmds: str | None = None
67
- pre_collect_cmds: str | None = None
66
+ pre_run: str | None = None
67
+ pre_collect: str | None = None
68
68
  env: QueueContextEnv | None = None
69
69
  verbose: str = "info"
70
70
  verbose_datalad: str | None = None
@@ -105,7 +105,7 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
105
105
 
106
106
  return "\n".join(elements_to_run)
107
107
 
108
- def pre_run(self) -> str:
108
+ def pre_run_cmds(self) -> str:
109
109
  """Return pre-run commands."""
110
110
  fixed = (
111
111
  f"#!/usr/bin/env {self.env['shell']}\n\n"
@@ -113,10 +113,10 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
113
113
  "# Force datalad to run in non-interactive mode\n"
114
114
  "DATALAD_UI_INTERACTIVE=false\n"
115
115
  )
116
- var = self.pre_run_cmds or ""
116
+ var = self.pre_run or ""
117
117
  return fixed + "\n" + var
118
118
 
119
- def run(self) -> str:
119
+ def run_cmds(self) -> str:
120
120
  """Return run commands."""
121
121
  verbose_args = f"--verbose {self.verbose}"
122
122
  if self.verbose_datalad:
@@ -141,16 +141,16 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
141
141
  f"--element"
142
142
  )
143
143
 
144
- def pre_collect(self) -> str:
144
+ def pre_collect_cmds(self) -> str:
145
145
  """Return pre-collect commands."""
146
146
  fixed = (
147
147
  f"#!/usr/bin/env {self.env['shell']}\n\n"
148
148
  "# This script is auto-generated by junifer.\n"
149
149
  )
150
- var = self.pre_collect_cmds or ""
150
+ var = self.pre_collect or ""
151
151
  return fixed + "\n" + var
152
152
 
153
- def collect(self) -> str:
153
+ def collect_cmds(self) -> str:
154
154
  """Return collect commands."""
155
155
  verbose_args = f"--verbose {self.verbose}"
156
156
  if self.verbose_datalad:
@@ -196,14 +196,14 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
196
196
  f"Writing {self._pre_run_path.name} to {self.job_dir.resolve()!s}"
197
197
  )
198
198
  self._pre_run_path.touch()
199
- self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
199
+ self._pre_run_path.write_text(textwrap.dedent(self.pre_run_cmds()))
200
200
  make_executable(self._pre_run_path)
201
201
  # Create run
202
202
  logger.info(
203
203
  f"Writing {self._run_path.name} to {self.job_dir.resolve()!s}"
204
204
  )
205
205
  self._run_path.touch()
206
- self._run_path.write_text(textwrap.dedent(self.run()))
206
+ self._run_path.write_text(textwrap.dedent(self.run_cmds()))
207
207
  make_executable(self._run_path)
208
208
  # Create pre collect
209
209
  logger.info(
@@ -211,14 +211,16 @@ class GnuParallelLocalAdapter(QueueContextAdapter):
211
211
  f"{self.job_dir.resolve()!s}"
212
212
  )
213
213
  self._pre_collect_path.touch()
214
- self._pre_collect_path.write_text(textwrap.dedent(self.pre_collect()))
214
+ self._pre_collect_path.write_text(
215
+ textwrap.dedent(self.pre_collect_cmds())
216
+ )
215
217
  make_executable(self._pre_collect_path)
216
218
  # Create collect
217
219
  logger.info(
218
220
  f"Writing {self._collect_path.name} to {self.job_dir.resolve()!s}"
219
221
  )
220
222
  self._collect_path.touch()
221
- self._collect_path.write_text(textwrap.dedent(self.collect()))
223
+ self._collect_path.write_text(textwrap.dedent(self.collect_cmds()))
222
224
  make_executable(self._collect_path)
223
225
  # Submit if required
224
226
  run_cmd = f"sh {self._run_path.resolve()!s}"
@@ -52,9 +52,9 @@ class HTCondorAdapter(QueueContextAdapter):
52
52
  The path to the YAML config file.
53
53
  elements : ``Elements``
54
54
  Element(s) to process. Will be used to index the DataGrabber.
55
- pre_run_cmds : str or None, optional
55
+ pre_run : str or None, optional
56
56
  Extra shell commands to source before the run (default None).
57
- pre_collect_cmds : str or None, optional
57
+ pre_collect : str or None, optional
58
58
  Extra shell commands to source before the collect (default None).
59
59
  env : :class:`.QueueContextEnv` or None, optional
60
60
  The environment configuration. If None, will run without a
@@ -91,8 +91,8 @@ class HTCondorAdapter(QueueContextAdapter):
91
91
  job_dir: Path
92
92
  yaml_config_path: Path
93
93
  elements: Elements
94
- pre_run_cmds: str | None = None
95
- pre_collect_cmds: str | None = None
94
+ pre_run: str | None = None
95
+ pre_collect: str | None = None
96
96
  env: QueueContextEnv | None = None
97
97
  verbose: str = "info"
98
98
  verbose_datalad: str | None = None
@@ -127,7 +127,7 @@ class HTCondorAdapter(QueueContextAdapter):
127
127
  )
128
128
  self._dag_path = self.job_dir / f"{self.job_name}.dag"
129
129
 
130
- def pre_run(self) -> str:
130
+ def pre_run_cmds(self) -> str:
131
131
  """Return pre-run commands."""
132
132
  fixed = (
133
133
  f"#!/usr/bin/env {self.env['shell']}\n\n"
@@ -135,10 +135,10 @@ class HTCondorAdapter(QueueContextAdapter):
135
135
  "# Force datalad to run in non-interactive mode\n"
136
136
  "DATALAD_UI_INTERACTIVE=false\n"
137
137
  )
138
- var = self.pre_run_cmds or ""
138
+ var = self.pre_run or ""
139
139
  return fixed + "\n" + var
140
140
 
141
- def run(self) -> str:
141
+ def run_cmds(self) -> str:
142
142
  """Return run commands."""
143
143
  verbose_args = f"--verbose {self.verbose} "
144
144
  if self.verbose_datalad is not None:
@@ -176,19 +176,19 @@ class HTCondorAdapter(QueueContextAdapter):
176
176
  var = self.extra_preamble or ""
177
177
  return fixed + "\n" + var + "\n" + "queue"
178
178
 
179
- def pre_collect(self) -> str:
179
+ def pre_collect_cmds(self) -> str:
180
180
  """Return pre-collect commands."""
181
181
  fixed = (
182
182
  f"#!/usr/bin/env {self.env['shell']}\n\n"
183
183
  "# This script is auto-generated by junifer.\n"
184
184
  )
185
- var = self.pre_collect_cmds or ""
185
+ var = self.pre_collect or ""
186
186
  # Add commands if collect="yes"
187
187
  if self.collect_task == "yes":
188
188
  var += 'if [ "${1}" == "4" ]; then\n exit 1\nfi\n'
189
189
  return fixed + "\n" + var
190
190
 
191
- def collect(self) -> str:
191
+ def collect_cmds(self) -> str:
192
192
  """Return collect commands."""
193
193
  verbose_args = f"--verbose {self.verbose} "
194
194
  if self.verbose_datalad is not None:
@@ -222,7 +222,7 @@ class HTCondorAdapter(QueueContextAdapter):
222
222
  var = self.extra_preamble or ""
223
223
  return fixed + "\n" + var + "\n" + "queue"
224
224
 
225
- def dag(self) -> str:
225
+ def dag_cmds(self) -> str:
226
226
  """Return HTCondor DAG commands."""
227
227
  fixed = ""
228
228
  for idx, element in enumerate(self.elements):
@@ -277,7 +277,7 @@ class HTCondorAdapter(QueueContextAdapter):
277
277
  f"Writing {self._pre_run_path.name} to {self.job_dir.resolve()!s}"
278
278
  )
279
279
  self._pre_run_path.touch()
280
- self._pre_run_path.write_text(textwrap.dedent(self.pre_run()))
280
+ self._pre_run_path.write_text(textwrap.dedent(self.pre_run_cmds()))
281
281
  make_executable(self._pre_run_path)
282
282
  # Create run
283
283
  logger.debug(
@@ -285,14 +285,16 @@ class HTCondorAdapter(QueueContextAdapter):
285
285
  f"{self.job_dir.resolve()!s}"
286
286
  )
287
287
  self._submit_run_path.touch()
288
- self._submit_run_path.write_text(textwrap.dedent(self.run()))
288
+ self._submit_run_path.write_text(textwrap.dedent(self.run_cmds()))
289
289
  # Create pre collect
290
290
  logger.info(
291
291
  f"Writing {self._pre_collect_path.name} to "
292
292
  f"{self.job_dir.resolve()!s}"
293
293
  )
294
294
  self._pre_collect_path.touch()
295
- self._pre_collect_path.write_text(textwrap.dedent(self.pre_collect()))
295
+ self._pre_collect_path.write_text(
296
+ textwrap.dedent(self.pre_collect_cmds())
297
+ )
296
298
  make_executable(self._pre_collect_path)
297
299
  # Create collect
298
300
  logger.debug(
@@ -300,13 +302,15 @@ class HTCondorAdapter(QueueContextAdapter):
300
302
  f"{self.job_dir.resolve()!s}"
301
303
  )
302
304
  self._submit_collect_path.touch()
303
- self._submit_collect_path.write_text(textwrap.dedent(self.collect()))
305
+ self._submit_collect_path.write_text(
306
+ textwrap.dedent(self.collect_cmds())
307
+ )
304
308
  # Create DAG
305
309
  logger.debug(
306
310
  f"Writing {self._dag_path.name} to {self.job_dir.resolve()!s}"
307
311
  )
308
312
  self._dag_path.touch()
309
- self._dag_path.write_text(textwrap.dedent(self.dag()))
313
+ self._dag_path.write_text(textwrap.dedent(self.dag_cmds()))
310
314
  # Submit if required
311
315
  condor_submit_dag_cmd = [
312
316
  "condor_submit_dag",
@@ -64,11 +64,11 @@ class QueueContextAdapter(BaseModel, ABC):
64
64
 
65
65
  model_config = ConfigDict(
66
66
  use_enum_values=True,
67
- extra="allow",
67
+ extra="forbid",
68
68
  )
69
69
 
70
70
  @abstractmethod
71
- def pre_run(self) -> str:
71
+ def pre_run_cmds(self) -> str:
72
72
  """Return pre-run commands."""
73
73
  raise_error(
74
74
  msg="Concrete classes need to implement pre_run()",
@@ -76,7 +76,7 @@ class QueueContextAdapter(BaseModel, ABC):
76
76
  )
77
77
 
78
78
  @abstractmethod
79
- def run(self) -> str:
79
+ def run_cmds(self) -> str:
80
80
  """Return run commands."""
81
81
  raise_error(
82
82
  msg="Concrete classes need to implement run()",
@@ -84,7 +84,7 @@ class QueueContextAdapter(BaseModel, ABC):
84
84
  )
85
85
 
86
86
  @abstractmethod
87
- def pre_collect(self) -> str:
87
+ def pre_collect_cmds(self) -> str:
88
88
  """Return pre-collect commands."""
89
89
  raise_error(
90
90
  msg="Concrete classes need to implement pre_collect()",
@@ -92,7 +92,7 @@ class QueueContextAdapter(BaseModel, ABC):
92
92
  )
93
93
 
94
94
  @abstractmethod
95
- def collect(self) -> str:
95
+ def collect_cmds(self) -> str:
96
96
  """Return collect commands."""
97
97
  raise_error(
98
98
  msg="Concrete classes need to implement collect()",
@@ -73,10 +73,10 @@ def test_GnuParallelLocalAdapter_pre_run(
73
73
  yaml_config_path=Path("."),
74
74
  elements=["sub01"],
75
75
  env={"kind": "conda", "name": "junifer", "shell": shell},
76
- pre_run_cmds=pre_run,
76
+ pre_run=pre_run,
77
77
  )
78
- assert shell in adapter.pre_run()
79
- assert expected_text in adapter.pre_run()
78
+ assert shell in adapter.pre_run_cmds()
79
+ assert expected_text in adapter.pre_run_cmds()
80
80
 
81
81
 
82
82
  @pytest.mark.parametrize(
@@ -111,10 +111,10 @@ def test_GnuParallelLocalAdapter_pre_collect(
111
111
  yaml_config_path=Path("."),
112
112
  elements=["sub01"],
113
113
  env={"kind": "venv", "name": "junifer", "shell": shell},
114
- pre_collect_cmds=pre_collect,
114
+ pre_collect=pre_collect,
115
115
  )
116
- assert shell in adapter.pre_collect()
117
- assert expected_text in adapter.pre_collect()
116
+ assert shell in adapter.pre_collect_cmds()
117
+ assert expected_text in adapter.pre_collect_cmds()
118
118
 
119
119
 
120
120
  def test_GnuParallelLocalAdapter_run() -> None:
@@ -125,7 +125,7 @@ def test_GnuParallelLocalAdapter_run() -> None:
125
125
  yaml_config_path=Path("."),
126
126
  elements=["sub01"],
127
127
  )
128
- assert "run" in adapter.run()
128
+ assert "run" in adapter.run_cmds()
129
129
 
130
130
 
131
131
  def test_GnuParallelLocalAdapter_collect() -> None:
@@ -136,7 +136,7 @@ def test_GnuParallelLocalAdapter_collect() -> None:
136
136
  yaml_config_path=Path("."),
137
137
  elements=["sub01"],
138
138
  )
139
- assert "collect" in adapter.collect()
139
+ assert "collect" in adapter.collect_cmds()
140
140
 
141
141
 
142
142
  @pytest.mark.parametrize(
@@ -43,10 +43,10 @@ def test_HTCondorAdapter_pre_run(
43
43
  yaml_config_path=Path("."),
44
44
  elements=["sub01"],
45
45
  env={"kind": "conda", "name": "junifer", "shell": shell},
46
- pre_run_cmds=pre_run,
46
+ pre_run=pre_run,
47
47
  )
48
- assert shell in adapter.pre_run()
49
- assert expected_text in adapter.pre_run()
48
+ assert shell in adapter.pre_run_cmds()
49
+ assert expected_text in adapter.pre_run_cmds()
50
50
 
51
51
 
52
52
  @pytest.mark.parametrize(
@@ -88,11 +88,11 @@ def test_HTCondorAdapter_pre_collect(
88
88
  yaml_config_path=Path("."),
89
89
  elements=["sub01"],
90
90
  env={"kind": "venv", "name": "junifer", "shell": shell},
91
- pre_collect_cmds=pre_collect,
91
+ pre_collect=pre_collect,
92
92
  collect_task=collect,
93
93
  )
94
- assert shell in adapter.pre_collect()
95
- assert expected_text in adapter.pre_collect()
94
+ assert shell in adapter.pre_collect_cmds()
95
+ assert expected_text in adapter.pre_collect_cmds()
96
96
 
97
97
 
98
98
  @pytest.mark.parametrize(
@@ -122,8 +122,8 @@ def test_HTCondorAdapter_run_collect(
122
122
  elements=["sub01"],
123
123
  extra_preamble=extra_preamble,
124
124
  )
125
- assert expected_text in adapter.run()
126
- assert expected_text in adapter.collect()
125
+ assert expected_text in adapter.run_cmds()
126
+ assert expected_text in adapter.collect_cmds()
127
127
 
128
128
 
129
129
  @pytest.mark.parametrize(
@@ -165,7 +165,7 @@ def test_HTCondor_dag(
165
165
  elements=elements,
166
166
  collect_task=collect,
167
167
  )
168
- assert expected_text in adapter.dag()
168
+ assert expected_text in adapter.dag_cmds()
169
169
 
170
170
 
171
171
  @pytest.mark.parametrize(
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: junifer
3
- Version: 0.0.8.dev189
3
+ Version: 0.0.8.dev195
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>
@@ -77,6 +77,7 @@ docs/changes/newsfragments/474.misc
77
77
  docs/changes/newsfragments/482.bugfix
78
78
  docs/changes/newsfragments/492.bugfix
79
79
  docs/changes/newsfragments/502.bugfix
80
+ docs/changes/newsfragments/503.enh
80
81
  docs/extending/confounds_format.rst
81
82
  docs/extending/coordinates.rst
82
83
  docs/extending/data_dump_asset.rst
@@ -531,6 +531,7 @@
531
531
  "docs/changes/newsfragments/364.feature",
532
532
  "docs/changes/newsfragments/502.bugfix",
533
533
  "docs/changes/newsfragments/474.misc",
534
+ "docs/changes/newsfragments/503.enh",
534
535
  "docs/changes/newsfragments/492.bugfix",
535
536
  "docs/changes/newsfragments/239.enh",
536
537
  "docs/changes/newsfragments/364.doc",
@@ -0,0 +1,8 @@
1
+ {
2
+ "tag": "0.0.7",
3
+ "distance": 195,
4
+ "node": "g64d583140d4faa92fa8b418a1756c2fe913fde72",
5
+ "dirty": false,
6
+ "branch": "main",
7
+ "node_date": "2026-07-21"
8
+ }
@@ -1,8 +0,0 @@
1
- {
2
- "tag": "0.0.7",
3
- "distance": 189,
4
- "node": "g5e5ce7c0b898796572d8239374720303c10900ec",
5
- "dirty": false,
6
- "branch": "main",
7
- "node_date": "2026-07-17"
8
- }