junifer 0.0.5.dev242__py3-none-any.whl → 0.0.6__py3-none-any.whl

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 (279) hide show
  1. junifer/__init__.py +2 -31
  2. junifer/__init__.pyi +37 -0
  3. junifer/_version.py +9 -4
  4. junifer/api/__init__.py +3 -5
  5. junifer/api/__init__.pyi +4 -0
  6. junifer/api/decorators.py +14 -19
  7. junifer/api/functions.py +165 -109
  8. junifer/api/py.typed +0 -0
  9. junifer/api/queue_context/__init__.py +2 -4
  10. junifer/api/queue_context/__init__.pyi +5 -0
  11. junifer/api/queue_context/gnu_parallel_local_adapter.py +22 -6
  12. junifer/api/queue_context/htcondor_adapter.py +23 -6
  13. junifer/api/queue_context/py.typed +0 -0
  14. junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +3 -3
  15. junifer/api/queue_context/tests/test_htcondor_adapter.py +3 -3
  16. junifer/api/tests/test_functions.py +168 -74
  17. junifer/cli/__init__.py +24 -0
  18. junifer/cli/__init__.pyi +3 -0
  19. junifer/{api → cli}/cli.py +141 -125
  20. junifer/cli/parser.py +235 -0
  21. junifer/cli/py.typed +0 -0
  22. junifer/{api → cli}/tests/test_cli.py +8 -8
  23. junifer/{api/tests/test_api_utils.py → cli/tests/test_cli_utils.py} +5 -4
  24. junifer/{api → cli}/tests/test_parser.py +2 -2
  25. junifer/{api → cli}/utils.py +6 -16
  26. junifer/configs/juseless/__init__.py +2 -2
  27. junifer/configs/juseless/__init__.pyi +3 -0
  28. junifer/configs/juseless/datagrabbers/__init__.py +2 -12
  29. junifer/configs/juseless/datagrabbers/__init__.pyi +13 -0
  30. junifer/configs/juseless/datagrabbers/ixi_vbm.py +2 -2
  31. junifer/configs/juseless/datagrabbers/py.typed +0 -0
  32. junifer/configs/juseless/datagrabbers/tests/test_ucla.py +2 -2
  33. junifer/configs/juseless/datagrabbers/ucla.py +4 -4
  34. junifer/configs/juseless/py.typed +0 -0
  35. junifer/conftest.py +25 -0
  36. junifer/data/__init__.py +2 -42
  37. junifer/data/__init__.pyi +29 -0
  38. junifer/data/_dispatch.py +248 -0
  39. junifer/data/coordinates/__init__.py +9 -0
  40. junifer/data/coordinates/__init__.pyi +5 -0
  41. junifer/data/coordinates/_ants_coordinates_warper.py +104 -0
  42. junifer/data/coordinates/_coordinates.py +385 -0
  43. junifer/data/coordinates/_fsl_coordinates_warper.py +81 -0
  44. junifer/data/{tests → coordinates/tests}/test_coordinates.py +26 -33
  45. junifer/data/masks/__init__.py +9 -0
  46. junifer/data/masks/__init__.pyi +6 -0
  47. junifer/data/masks/_ants_mask_warper.py +177 -0
  48. junifer/data/masks/_fsl_mask_warper.py +106 -0
  49. junifer/data/masks/_masks.py +802 -0
  50. junifer/data/{tests → masks/tests}/test_masks.py +67 -63
  51. junifer/data/parcellations/__init__.py +9 -0
  52. junifer/data/parcellations/__init__.pyi +6 -0
  53. junifer/data/parcellations/_ants_parcellation_warper.py +166 -0
  54. junifer/data/parcellations/_fsl_parcellation_warper.py +89 -0
  55. junifer/data/parcellations/_parcellations.py +1388 -0
  56. junifer/data/{tests → parcellations/tests}/test_parcellations.py +165 -295
  57. junifer/data/pipeline_data_registry_base.py +76 -0
  58. junifer/data/py.typed +0 -0
  59. junifer/data/template_spaces.py +44 -79
  60. junifer/data/tests/test_data_utils.py +1 -2
  61. junifer/data/tests/test_template_spaces.py +8 -4
  62. junifer/data/utils.py +109 -4
  63. junifer/datagrabber/__init__.py +2 -26
  64. junifer/datagrabber/__init__.pyi +27 -0
  65. junifer/datagrabber/aomic/__init__.py +2 -4
  66. junifer/datagrabber/aomic/__init__.pyi +5 -0
  67. junifer/datagrabber/aomic/id1000.py +81 -52
  68. junifer/datagrabber/aomic/piop1.py +83 -55
  69. junifer/datagrabber/aomic/piop2.py +85 -56
  70. junifer/datagrabber/aomic/py.typed +0 -0
  71. junifer/datagrabber/aomic/tests/test_id1000.py +19 -12
  72. junifer/datagrabber/aomic/tests/test_piop1.py +52 -18
  73. junifer/datagrabber/aomic/tests/test_piop2.py +50 -17
  74. junifer/datagrabber/base.py +22 -18
  75. junifer/datagrabber/datalad_base.py +71 -34
  76. junifer/datagrabber/dmcc13_benchmark.py +31 -18
  77. junifer/datagrabber/hcp1200/__init__.py +2 -3
  78. junifer/datagrabber/hcp1200/__init__.pyi +4 -0
  79. junifer/datagrabber/hcp1200/datalad_hcp1200.py +3 -3
  80. junifer/datagrabber/hcp1200/hcp1200.py +26 -15
  81. junifer/datagrabber/hcp1200/py.typed +0 -0
  82. junifer/datagrabber/hcp1200/tests/test_hcp1200.py +8 -2
  83. junifer/datagrabber/multiple.py +14 -9
  84. junifer/datagrabber/pattern.py +132 -96
  85. junifer/datagrabber/pattern_validation_mixin.py +206 -94
  86. junifer/datagrabber/py.typed +0 -0
  87. junifer/datagrabber/tests/test_datalad_base.py +27 -12
  88. junifer/datagrabber/tests/test_dmcc13_benchmark.py +28 -11
  89. junifer/datagrabber/tests/test_multiple.py +48 -2
  90. junifer/datagrabber/tests/test_pattern_datalad.py +1 -1
  91. junifer/datagrabber/tests/test_pattern_validation_mixin.py +6 -6
  92. junifer/datareader/__init__.py +2 -2
  93. junifer/datareader/__init__.pyi +3 -0
  94. junifer/datareader/default.py +6 -6
  95. junifer/datareader/py.typed +0 -0
  96. junifer/external/nilearn/__init__.py +2 -3
  97. junifer/external/nilearn/__init__.pyi +4 -0
  98. junifer/external/nilearn/junifer_connectivity_measure.py +25 -17
  99. junifer/external/nilearn/junifer_nifti_spheres_masker.py +4 -4
  100. junifer/external/nilearn/py.typed +0 -0
  101. junifer/external/nilearn/tests/test_junifer_connectivity_measure.py +17 -16
  102. junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py +2 -3
  103. junifer/markers/__init__.py +2 -38
  104. junifer/markers/__init__.pyi +37 -0
  105. junifer/markers/base.py +11 -14
  106. junifer/markers/brainprint.py +12 -14
  107. junifer/markers/complexity/__init__.py +2 -18
  108. junifer/markers/complexity/__init__.pyi +17 -0
  109. junifer/markers/complexity/complexity_base.py +9 -11
  110. junifer/markers/complexity/hurst_exponent.py +7 -7
  111. junifer/markers/complexity/multiscale_entropy_auc.py +7 -7
  112. junifer/markers/complexity/perm_entropy.py +7 -7
  113. junifer/markers/complexity/py.typed +0 -0
  114. junifer/markers/complexity/range_entropy.py +7 -7
  115. junifer/markers/complexity/range_entropy_auc.py +7 -7
  116. junifer/markers/complexity/sample_entropy.py +7 -7
  117. junifer/markers/complexity/tests/test_complexity_base.py +1 -1
  118. junifer/markers/complexity/tests/test_hurst_exponent.py +5 -5
  119. junifer/markers/complexity/tests/test_multiscale_entropy_auc.py +5 -5
  120. junifer/markers/complexity/tests/test_perm_entropy.py +5 -5
  121. junifer/markers/complexity/tests/test_range_entropy.py +5 -5
  122. junifer/markers/complexity/tests/test_range_entropy_auc.py +5 -5
  123. junifer/markers/complexity/tests/test_sample_entropy.py +5 -5
  124. junifer/markers/complexity/tests/test_weighted_perm_entropy.py +5 -5
  125. junifer/markers/complexity/weighted_perm_entropy.py +7 -7
  126. junifer/markers/ets_rss.py +12 -11
  127. junifer/markers/falff/__init__.py +2 -3
  128. junifer/markers/falff/__init__.pyi +4 -0
  129. junifer/markers/falff/_afni_falff.py +38 -45
  130. junifer/markers/falff/_junifer_falff.py +16 -19
  131. junifer/markers/falff/falff_base.py +7 -11
  132. junifer/markers/falff/falff_parcels.py +9 -9
  133. junifer/markers/falff/falff_spheres.py +8 -8
  134. junifer/markers/falff/py.typed +0 -0
  135. junifer/markers/falff/tests/test_falff_spheres.py +3 -1
  136. junifer/markers/functional_connectivity/__init__.py +2 -12
  137. junifer/markers/functional_connectivity/__init__.pyi +13 -0
  138. junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py +9 -8
  139. junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py +8 -8
  140. junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py +7 -7
  141. junifer/markers/functional_connectivity/functional_connectivity_base.py +13 -12
  142. junifer/markers/functional_connectivity/functional_connectivity_parcels.py +8 -8
  143. junifer/markers/functional_connectivity/functional_connectivity_spheres.py +7 -7
  144. junifer/markers/functional_connectivity/py.typed +0 -0
  145. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py +1 -2
  146. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py +1 -2
  147. junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py +6 -6
  148. junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py +5 -5
  149. junifer/markers/parcel_aggregation.py +22 -17
  150. junifer/markers/py.typed +0 -0
  151. junifer/markers/reho/__init__.py +2 -3
  152. junifer/markers/reho/__init__.pyi +4 -0
  153. junifer/markers/reho/_afni_reho.py +29 -35
  154. junifer/markers/reho/_junifer_reho.py +13 -14
  155. junifer/markers/reho/py.typed +0 -0
  156. junifer/markers/reho/reho_base.py +7 -11
  157. junifer/markers/reho/reho_parcels.py +10 -10
  158. junifer/markers/reho/reho_spheres.py +9 -9
  159. junifer/markers/sphere_aggregation.py +22 -17
  160. junifer/markers/temporal_snr/__init__.py +2 -3
  161. junifer/markers/temporal_snr/__init__.pyi +4 -0
  162. junifer/markers/temporal_snr/py.typed +0 -0
  163. junifer/markers/temporal_snr/temporal_snr_base.py +11 -10
  164. junifer/markers/temporal_snr/temporal_snr_parcels.py +8 -8
  165. junifer/markers/temporal_snr/temporal_snr_spheres.py +7 -7
  166. junifer/markers/tests/test_ets_rss.py +3 -3
  167. junifer/markers/tests/test_parcel_aggregation.py +24 -24
  168. junifer/markers/tests/test_sphere_aggregation.py +6 -6
  169. junifer/markers/utils.py +3 -3
  170. junifer/onthefly/__init__.py +2 -1
  171. junifer/onthefly/_brainprint.py +138 -0
  172. junifer/onthefly/read_transform.py +5 -8
  173. junifer/pipeline/__init__.py +2 -10
  174. junifer/pipeline/__init__.pyi +13 -0
  175. junifer/{markers/collection.py → pipeline/marker_collection.py} +8 -14
  176. junifer/pipeline/pipeline_component_registry.py +294 -0
  177. junifer/pipeline/pipeline_step_mixin.py +15 -11
  178. junifer/pipeline/py.typed +0 -0
  179. junifer/{markers/tests/test_collection.py → pipeline/tests/test_marker_collection.py} +2 -3
  180. junifer/pipeline/tests/test_pipeline_component_registry.py +200 -0
  181. junifer/pipeline/tests/test_pipeline_step_mixin.py +36 -37
  182. junifer/pipeline/tests/test_update_meta_mixin.py +4 -4
  183. junifer/pipeline/tests/test_workdir_manager.py +43 -0
  184. junifer/pipeline/update_meta_mixin.py +21 -17
  185. junifer/pipeline/utils.py +6 -6
  186. junifer/pipeline/workdir_manager.py +19 -5
  187. junifer/preprocess/__init__.py +2 -10
  188. junifer/preprocess/__init__.pyi +11 -0
  189. junifer/preprocess/base.py +10 -10
  190. junifer/preprocess/confounds/__init__.py +2 -2
  191. junifer/preprocess/confounds/__init__.pyi +3 -0
  192. junifer/preprocess/confounds/fmriprep_confound_remover.py +243 -64
  193. junifer/preprocess/confounds/py.typed +0 -0
  194. junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +121 -14
  195. junifer/preprocess/py.typed +0 -0
  196. junifer/preprocess/smoothing/__init__.py +2 -2
  197. junifer/preprocess/smoothing/__init__.pyi +3 -0
  198. junifer/preprocess/smoothing/_afni_smoothing.py +40 -40
  199. junifer/preprocess/smoothing/_fsl_smoothing.py +22 -32
  200. junifer/preprocess/smoothing/_nilearn_smoothing.py +35 -14
  201. junifer/preprocess/smoothing/py.typed +0 -0
  202. junifer/preprocess/smoothing/smoothing.py +11 -13
  203. junifer/preprocess/warping/__init__.py +2 -2
  204. junifer/preprocess/warping/__init__.pyi +3 -0
  205. junifer/preprocess/warping/_ants_warper.py +136 -32
  206. junifer/preprocess/warping/_fsl_warper.py +73 -22
  207. junifer/preprocess/warping/py.typed +0 -0
  208. junifer/preprocess/warping/space_warper.py +39 -11
  209. junifer/preprocess/warping/tests/test_space_warper.py +5 -9
  210. junifer/py.typed +0 -0
  211. junifer/stats.py +5 -5
  212. junifer/storage/__init__.py +2 -10
  213. junifer/storage/__init__.pyi +11 -0
  214. junifer/storage/base.py +47 -13
  215. junifer/storage/hdf5.py +95 -33
  216. junifer/storage/pandas_base.py +12 -11
  217. junifer/storage/py.typed +0 -0
  218. junifer/storage/sqlite.py +11 -11
  219. junifer/storage/tests/test_hdf5.py +86 -4
  220. junifer/storage/tests/test_sqlite.py +2 -2
  221. junifer/storage/tests/test_storage_base.py +5 -2
  222. junifer/storage/tests/test_utils.py +33 -7
  223. junifer/storage/utils.py +95 -9
  224. junifer/testing/__init__.py +2 -3
  225. junifer/testing/__init__.pyi +4 -0
  226. junifer/testing/datagrabbers.py +10 -11
  227. junifer/testing/py.typed +0 -0
  228. junifer/testing/registry.py +4 -7
  229. junifer/testing/tests/test_testing_registry.py +9 -17
  230. junifer/tests/test_stats.py +2 -2
  231. junifer/typing/__init__.py +9 -0
  232. junifer/typing/__init__.pyi +31 -0
  233. junifer/typing/_typing.py +68 -0
  234. junifer/utils/__init__.py +2 -12
  235. junifer/utils/__init__.pyi +18 -0
  236. junifer/utils/_config.py +110 -0
  237. junifer/utils/_yaml.py +16 -0
  238. junifer/utils/helpers.py +6 -6
  239. junifer/utils/logging.py +117 -8
  240. junifer/utils/py.typed +0 -0
  241. junifer/{pipeline → utils}/singleton.py +19 -14
  242. junifer/utils/tests/test_config.py +59 -0
  243. {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/METADATA +43 -38
  244. junifer-0.0.6.dist-info/RECORD +350 -0
  245. {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/WHEEL +1 -1
  246. junifer-0.0.6.dist-info/entry_points.txt +2 -0
  247. junifer/api/parser.py +0 -118
  248. junifer/data/coordinates.py +0 -408
  249. junifer/data/masks.py +0 -670
  250. junifer/data/parcellations.py +0 -1828
  251. junifer/pipeline/registry.py +0 -177
  252. junifer/pipeline/tests/test_registry.py +0 -150
  253. junifer-0.0.5.dev242.dist-info/RECORD +0 -275
  254. junifer-0.0.5.dev242.dist-info/entry_points.txt +0 -2
  255. /junifer/{api → cli}/tests/data/gmd_mean.yaml +0 -0
  256. /junifer/{api → cli}/tests/data/gmd_mean_htcondor.yaml +0 -0
  257. /junifer/{api → cli}/tests/data/partly_cloudy_agg_mean_tian.yml +0 -0
  258. /junifer/data/{VOIs → coordinates/VOIs}/meta/AutobiographicalMemory_VOIs.txt +0 -0
  259. /junifer/data/{VOIs → coordinates/VOIs}/meta/CogAC_VOIs.txt +0 -0
  260. /junifer/data/{VOIs → coordinates/VOIs}/meta/CogAR_VOIs.txt +0 -0
  261. /junifer/data/{VOIs → coordinates/VOIs}/meta/DMNBuckner_VOIs.txt +0 -0
  262. /junifer/data/{VOIs → coordinates/VOIs}/meta/Dosenbach2010_MNI_VOIs.txt +0 -0
  263. /junifer/data/{VOIs → coordinates/VOIs}/meta/Empathy_VOIs.txt +0 -0
  264. /junifer/data/{VOIs → coordinates/VOIs}/meta/Motor_VOIs.txt +0 -0
  265. /junifer/data/{VOIs → coordinates/VOIs}/meta/MultiTask_VOIs.txt +0 -0
  266. /junifer/data/{VOIs → coordinates/VOIs}/meta/PhysioStress_VOIs.txt +0 -0
  267. /junifer/data/{VOIs → coordinates/VOIs}/meta/Power2011_MNI_VOIs.txt +0 -0
  268. /junifer/data/{VOIs → coordinates/VOIs}/meta/Power2013_MNI_VOIs.tsv +0 -0
  269. /junifer/data/{VOIs → coordinates/VOIs}/meta/Rew_VOIs.txt +0 -0
  270. /junifer/data/{VOIs → coordinates/VOIs}/meta/Somatosensory_VOIs.txt +0 -0
  271. /junifer/data/{VOIs → coordinates/VOIs}/meta/ToM_VOIs.txt +0 -0
  272. /junifer/data/{VOIs → coordinates/VOIs}/meta/VigAtt_VOIs.txt +0 -0
  273. /junifer/data/{VOIs → coordinates/VOIs}/meta/WM_VOIs.txt +0 -0
  274. /junifer/data/{VOIs → coordinates/VOIs}/meta/eMDN_VOIs.txt +0 -0
  275. /junifer/data/{VOIs → coordinates/VOIs}/meta/eSAD_VOIs.txt +0 -0
  276. /junifer/data/{VOIs → coordinates/VOIs}/meta/extDMN_VOIs.txt +0 -0
  277. {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info/licenses}/AUTHORS.rst +0 -0
  278. {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info/licenses}/LICENSE.md +0 -0
  279. {junifer-0.0.5.dev242.dist-info → junifer-0.0.6.dist-info}/top_level.txt +0 -0
@@ -1,177 +0,0 @@
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- """Provide functions for registry."""
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-
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- # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
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- # Leonard Sasse <l.sasse@fz-juelich.de>
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- # Synchon Mandal <s.mandal@fz-juelich.de>
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- # License: AGPL
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-
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- from typing import TYPE_CHECKING, Dict, List, Optional, Union
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-
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- from ..utils.logging import logger, raise_error
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-
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-
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- if TYPE_CHECKING:
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- from ..datagrabber import BaseDataGrabber
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- from ..storage import BaseFeatureStorage
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- from .pipeline_step_mixin import PipelineStepMixin
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-
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-
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- __all__ = ["register", "get_step_names", "get_class", "build"]
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-
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-
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- # Define valid steps for operation
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- _VALID_STEPS: List[str] = [
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- "datagrabber",
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- "datareader",
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- "preprocessing",
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- "marker",
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- "storage",
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- ]
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-
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- # Define registry for valid steps
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- _REGISTRY: Dict[str, Dict[str, type]] = {x: {} for x in _VALID_STEPS}
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-
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-
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- def register(step: str, name: str, klass: type) -> None:
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- """Register a function to be used in a pipeline step.
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-
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- Parameters
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- ----------
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- step : str
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- Name of the step.
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- name : str
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- Name of the function.
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- klass : class
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- Class to be registered.
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-
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- Raises
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- ------
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- ValueError
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- If the ``step`` is invalid.
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-
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- """
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- # Verify step
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- if step not in _VALID_STEPS:
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- raise_error(msg=f"Invalid step: {step}", klass=ValueError)
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-
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- logger.info(f"Registering {name} in {step}")
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- _REGISTRY[step][name] = klass
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-
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-
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- def get_step_names(step: str) -> List[str]:
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- """Get the names of the registered functions for a given step.
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-
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- Parameters
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- ----------
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- step : str
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- Name of the step.
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-
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- Returns
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- -------
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- list
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- List of registered function names.
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-
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- Raises
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- ------
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- ValueError
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- If the ``step`` is invalid.
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-
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- """
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- # Verify step
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- if step not in _VALID_STEPS:
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- raise_error(msg=f"Invalid step: {step}", klass=ValueError)
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-
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- return list(_REGISTRY[step].keys())
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-
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-
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- def get_class(step: str, name: str) -> type:
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- """Get the class of the registered function for a given step.
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-
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- Parameters
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- ----------
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- step : str
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- Name of the step.
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- name : str
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- Name of the function.
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-
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- Returns
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- -------
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- class
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- Registered function class.
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-
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- Raises
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- ------
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- ValueError
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- If the ``step`` or ``name`` is invalid.
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-
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- """
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- # Verify step
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- if step not in _VALID_STEPS:
110
- raise_error(msg=f"Invalid step: {step}", klass=ValueError)
111
- # Verify step name
112
- if name not in _REGISTRY[step]:
113
- raise_error(msg=f"Invalid name: {name}", klass=ValueError)
114
-
115
- return _REGISTRY[step][name]
116
-
117
-
118
- def build(
119
- step: str,
120
- name: str,
121
- baseclass: type,
122
- init_params: Optional[Dict] = None,
123
- ) -> Union["BaseDataGrabber", "PipelineStepMixin", "BaseFeatureStorage"]:
124
- """Ensure that the given object is an instance of the given class.
125
-
126
- Parameters
127
- ----------
128
- step : str
129
- Name of the step.
130
- name : str
131
- Name of the function.
132
- baseclass : class
133
- Class to be checked against.
134
- init_params : dict or None, optional
135
- Parameters to pass to the base class constructor (default None).
136
-
137
- Returns
138
- -------
139
- object
140
- An instance of the given base class.
141
-
142
- Raises
143
- ------
144
- RuntimeError
145
- If there is a problem creating the instance.
146
- ValueError
147
- If the created object with the given name is not an instance of the
148
- base class.
149
-
150
- """
151
- # Set default init parameters
152
- if init_params is None:
153
- init_params = {}
154
- # Get class of the registered function
155
- logger.debug(f"Building {step}/{name}")
156
- klass = get_class(step=step, name=name)
157
- logger.debug(f"\tClass: {klass.__name__}")
158
- logger.debug(f"\tInit params: {init_params}")
159
- try:
160
- # Create instance of the class
161
- object_ = klass(**init_params)
162
- except (ValueError, TypeError) as e:
163
- raise_error(
164
- msg=f"Failed to create {step} ({name}). Error: {e}",
165
- klass=RuntimeError,
166
- exception=e,
167
- )
168
- # Verify created instance belongs to the base class
169
- if not isinstance(object_, baseclass):
170
- raise_error(
171
- msg=(
172
- f"Invalid {step} ({object_.__class__.__name__}). "
173
- f"Must inherit from {baseclass.__name__}"
174
- ),
175
- klass=ValueError,
176
- )
177
- return object_
@@ -1,150 +0,0 @@
1
- """Provide tests for registry."""
2
-
3
- # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
4
- # Leonard Sasse <l.sasse@fz-juelich.de>
5
- # Synchon Mandal <s.mandal@fz-juelich.de>
6
- # License: AGPL
7
- import logging
8
- from abc import ABC
9
- from typing import Type
10
-
11
- import pytest
12
-
13
- from junifer.datagrabber import PatternDataGrabber
14
- from junifer.pipeline.registry import (
15
- build,
16
- get_class,
17
- get_step_names,
18
- register,
19
- )
20
- from junifer.storage import SQLiteFeatureStorage
21
-
22
-
23
- def test_register_invalid_step():
24
- """Test register invalid step name."""
25
- with pytest.raises(ValueError, match="Invalid step:"):
26
- register(step="foo", name="bar", klass=str)
27
-
28
-
29
- # TODO: improve parametrization
30
- @pytest.mark.parametrize(
31
- "step, name, klass",
32
- [
33
- ("datagrabber", "pattern-dg", PatternDataGrabber),
34
- ("storage", "sqlite-storage", SQLiteFeatureStorage),
35
- ],
36
- )
37
- def test_register(
38
- caplog: pytest.LogCaptureFixture, step: str, name: str, klass: Type
39
- ) -> None:
40
- """Test register.
41
-
42
- Parameters
43
- ----------
44
- caplog : pytest.LogCaptureFixture
45
- The pytest.LogCaptureFixture object.
46
- step : str
47
- The parametrized name of the step.
48
- name : str
49
- The parametrized name of the function.
50
- klass : str
51
- The parametrized name of the base class.
52
-
53
- """
54
- with caplog.at_level(logging.INFO):
55
- # Register
56
- register(step=step, name=name, klass=klass)
57
- # Check logging message
58
- assert "Registering" in caplog.text
59
-
60
-
61
- def test_get_step_names_invalid_step() -> None:
62
- """Test get step name invalid step name."""
63
- with pytest.raises(ValueError, match="Invalid step:"):
64
- get_step_names(step="foo")
65
-
66
-
67
- def test_get_step_names_absent() -> None:
68
- """Test get step names for absent name."""
69
- # Get step names for datagrabber
70
- datagrabbers = get_step_names(step="datagrabber")
71
- # Check for datagrabber step name
72
- assert "bar" not in datagrabbers
73
-
74
-
75
- def test_get_step_names() -> None:
76
- """Test get step names."""
77
- # Register datagrabber
78
- register(step="datagrabber", name="bar", klass=str)
79
- # Get step names for datagrabber
80
- datagrabbers = get_step_names(step="datagrabber")
81
- # Check for datagrabber step name
82
- assert "bar" in datagrabbers
83
-
84
-
85
- def test_get_class_invalid_step() -> None:
86
- """Test get class invalid step name."""
87
- with pytest.raises(ValueError, match="Invalid step:"):
88
- get_class(step="foo", name="bar")
89
-
90
-
91
- def test_get_class_invalid_name() -> None:
92
- """Test get class invalid function name."""
93
- with pytest.raises(ValueError, match="Invalid name:"):
94
- get_class(step="datagrabber", name="foo")
95
-
96
-
97
- # TODO: enable parametrization
98
- def test_get_class():
99
- """Test get class."""
100
- # Register datagrabber
101
- register(step="datagrabber", name="bar", klass=str)
102
- # Get class
103
- obj = get_class(step="datagrabber", name="bar")
104
- assert isinstance(obj, type(str))
105
-
106
-
107
- # TODO: possible parametrization?
108
- def test_build():
109
- """Test building objects from names."""
110
- import numpy as np
111
-
112
- # Define abstract base class
113
- class SuperClass(ABC):
114
- pass
115
-
116
- # Define concrete class
117
- class ConcreteClass(SuperClass):
118
- def __init__(self, value=1):
119
- self.value = value
120
-
121
- # Register
122
- register(step="datagrabber", name="concrete", klass=ConcreteClass)
123
-
124
- # Build
125
- obj = build(step="datagrabber", name="concrete", baseclass=SuperClass)
126
- assert isinstance(obj, ConcreteClass)
127
- assert obj.value == 1
128
-
129
- # Build
130
- obj = build(
131
- step="datagrabber",
132
- name="concrete",
133
- baseclass=SuperClass,
134
- init_params={"value": 2},
135
- )
136
- assert isinstance(obj, ConcreteClass)
137
- assert obj.value == 2
138
-
139
- # Check error
140
- with pytest.raises(ValueError, match="Must inherit"):
141
- build(step="datagrabber", name="concrete", baseclass=np.ndarray)
142
-
143
- # Check error
144
- with pytest.raises(RuntimeError, match="Failed to create"):
145
- build(
146
- step="datagrabber",
147
- name="concrete",
148
- baseclass=SuperClass,
149
- init_params={"wrong": 2},
150
- )
@@ -1,275 +0,0 @@
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54
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66
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67
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68
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69
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70
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71
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72
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73
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74
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75
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76
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80
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82
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84
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86
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@@ -1,2 +0,0 @@
1
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2
- junifer = junifer.api.cli:cli
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