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base repository: nipy/nibabel
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base: 5.0.1
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head repository: nipy/nibabel
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compare: master
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Showing with 6,192 additions and 4,986 deletions.
  1. +12 −3 .coveragerc
  2. +0 −9 .flake8
  3. +4 −0 .git-blame-ignore-revs
  4. +10 −0 .github/dependabot.yml
  5. +0 −70 .github/workflows/misc.yml
  6. +0 −98 .github/workflows/pre-release.yml
  7. +0 −207 .github/workflows/stable.yml
  8. +272 −0 .github/workflows/test.yml
  9. +3 −1 .gitignore
  10. +3 −0 .gitmodules
  11. +58 −48 .mailmap
  12. +0 −12 .pep8speaks.yml
  13. +16 −14 .pre-commit-config.yaml
  14. +21 −0 .readthedocs.yaml
  15. +53 −22 .zenodo.json
  16. +229 −1 Changelog
  17. +1 −20 Makefile
  18. +142 −65 README.rst
  19. +1 −2 bin/parrec2nii
  20. +3 −3 doc-requirements.txt
  21. +2 −2 doc/README.rst
  22. BIN doc/pics/logo.png
  23. +16 −3 doc/source/conf.py
  24. +1 −1 doc/source/devel/biaps/biap_0006.rst
  25. +0 −298 doc/source/devel/data_pkg_design.rst
  26. +0 −255 doc/source/devel/data_pkg_uses.rst
  27. +0 −3 doc/source/devel/devdiscuss.rst
  28. +86 −0 doc/source/devel/devguide.rst
  29. +0 −47 doc/source/devel/register_me.py
  30. +5 −5 doc/source/dicom/dicom_intro.rst
  31. +1 −1 doc/source/external/nifti1.h
  32. +1 −1 doc/source/gitwash/development_workflow.rst
  33. +14 −0 doc/source/index.rst
  34. +10 −10 doc/source/installation.rst
  35. +0 −80 doc/source/installing_data.rst
  36. +1 −0 doc/source/links_names.txt
  37. +2 −2 doc/source/nifti_images.rst
  38. +1 −1 doc/source/old/format_design.txt
  39. +1 −4 doc/tools/apigen.py
  40. +4 −2 doc/tools/build_modref_templates.py
  41. +16 −4 min-requirements.txt
  42. +1 −0 nibabel-data/dcm_qa_xa30
  43. +7 −6 nibabel/__init__.py
  44. +51 −0 nibabel/_compression.py
  45. +25 −0 nibabel/_typing.py
  46. +4 −0 nibabel/_version.pyi
  47. +5 −6 nibabel/affines.py
  48. +11 −9 nibabel/analyze.py
  49. +48 −19 nibabel/arrayproxy.py
  50. +16 −27 nibabel/arraywriters.py
  51. +1 −1 nibabel/batteryrunners.py
  52. +10 −9 nibabel/benchmarks/bench_array_to_file.py
  53. +3 −6 nibabel/benchmarks/bench_arrayproxy_slicing.py
  54. +6 −5 nibabel/benchmarks/bench_finite_range.py
  55. +8 −7 nibabel/benchmarks/bench_load_save.py
  56. +2 −3 nibabel/benchmarks/butils.py
  57. +7 −6 nibabel/brikhead.py
  58. +69 −50 nibabel/casting.py
  59. +67 −41 nibabel/cifti2/cifti2.py
  60. +12 −10 nibabel/cifti2/cifti2_axes.py
  61. +9 −14 nibabel/cifti2/parse_cifti2.py
  62. +6 −6 nibabel/cifti2/tests/test_cifti2.py
  63. +2 −3 nibabel/cifti2/tests/test_cifti2io_header.py
  64. +1 −0 nibabel/cifti2/tests/test_new_cifti2.py
  65. +1 −2 nibabel/cmdline/__init__.py
  66. +10 −12 nibabel/cmdline/dicomfs.py
  67. +9 −12 nibabel/cmdline/diff.py
  68. +9 −9 nibabel/cmdline/ls.py
  69. +19 −8 nibabel/cmdline/nifti_dx.py
  70. +2 −3 nibabel/cmdline/parrec2nii.py
  71. +1 −0 nibabel/cmdline/tck2trk.py
  72. +5 −5 nibabel/cmdline/tests/test_conform.py
  73. +11 −11 nibabel/cmdline/tests/test_convert.py
  74. +2 −2 nibabel/cmdline/tests/test_parrec2nii.py
  75. +3 −8 nibabel/cmdline/tests/test_roi.py
  76. +0 −3 nibabel/cmdline/tests/test_stats.py
  77. +40 −10 nibabel/cmdline/tests/test_utils.py
  78. +17 −38 nibabel/cmdline/utils.py
  79. +24 −1 nibabel/conftest.py
  80. +4 −6 nibabel/data.py
  81. +13 −8 nibabel/dataobj_images.py
  82. +14 −11 nibabel/deprecated.py
  83. +60 −19 nibabel/deprecator.py
  84. +7 −10 nibabel/dft.py
  85. +12 −11 nibabel/ecat.py
  86. +1 −3 nibabel/environment.py
  87. +25 −0 nibabel/externals/conftest.py
  88. +41 −39 nibabel/filebasedimages.py
  89. +20 −9 nibabel/fileholders.py
  90. +37 −33 nibabel/filename_parser.py
  91. +2 −3 nibabel/fileslice.py
  92. +1 −2 nibabel/fileutils.py
  93. +1 −2 nibabel/freesurfer/__init__.py
  94. +8 −9 nibabel/freesurfer/io.py
  95. +14 −5 nibabel/freesurfer/mghformat.py
  96. +9 −15 nibabel/freesurfer/tests/test_io.py
  97. +6 −4 nibabel/freesurfer/tests/test_mghformat.py
  98. +1 −0 nibabel/funcs.py
  99. +61 −17 nibabel/gifti/gifti.py
  100. +32 −40 nibabel/gifti/parse_gifti_fast.py
  101. +76 −0 nibabel/gifti/tests/data/ascii_flat_data.gii
  102. +114 −29 nibabel/gifti/tests/test_gifti.py
  103. +31 −11 nibabel/gifti/tests/test_parse_gifti_fast.py
  104. +1 −1 nibabel/gifti/util.py
  105. +11 −3 nibabel/imageclasses.py
  106. +1 −3 nibabel/imagestats.py
  107. +72 −58 nibabel/info.py
  108. +28 −17 nibabel/loadsave.py
  109. +4 −3 nibabel/minc1.py
  110. +12 −3 nibabel/minc2.py
  111. +1 −3 nibabel/mriutils.py
  112. +1 −0 nibabel/nicom/__init__.py
  113. +6 −10 nibabel/nicom/ascconv.py
  114. +3 −3 nibabel/nicom/csareader.py
  115. +3 −3 nibabel/nicom/dicomreaders.py
  116. +450 −135 nibabel/nicom/dicomwrappers.py
  117. +1 −0 nibabel/nicom/dwiparams.py
  118. +1 −3 nibabel/nicom/tests/test_ascconv.py
  119. +2 −3 nibabel/nicom/tests/test_csareader.py
  120. +2 −3 nibabel/nicom/tests/test_dicomreaders.py
  121. +482 −116 nibabel/nicom/tests/test_dicomwrappers.py
  122. +1 −2 nibabel/nicom/tests/test_dwiparams.py
  123. +2 −2 nibabel/nicom/tests/test_structreader.py
  124. +37 −21 nibabel/nicom/tests/test_utils.py
  125. +69 −20 nibabel/nicom/utils.py
  126. +289 −132 nibabel/nifti1.py
  127. +2 −1 nibabel/nifti2.py
  128. +30 −83 nibabel/onetime.py
  129. +107 −74 nibabel/openers.py
  130. +26 −12 nibabel/optpkg.py
  131. +2 −3 nibabel/orientations.py
  132. +7 −8 nibabel/parrec.py
  133. +14 −11 nibabel/pkg_info.py
  134. +197 −0 nibabel/pointset.py
  135. +14 −7 nibabel/processing.py
  136. +11 −2 nibabel/pydicom_compat.py
  137. +13 −11 nibabel/quaternions.py
  138. +1 −1 nibabel/rstutils.py
  139. +157 −82 nibabel/spatialimages.py
  140. +4 −2 nibabel/spm2analyze.py
  141. +7 −5 nibabel/spm99analyze.py
  142. +4 −5 nibabel/streamlines/__init__.py
  143. +5 −5 nibabel/streamlines/array_sequence.py
  144. +1 −2 nibabel/streamlines/header.py
  145. +0 −1 nibabel/streamlines/tck.py
  146. +3 −4 nibabel/streamlines/tests/test_array_sequence.py
  147. +16 −16 nibabel/streamlines/tests/test_streamlines.py
  148. +1 −2 nibabel/streamlines/tests/test_tck.py
  149. +33 −17 nibabel/streamlines/tests/test_tractogram.py
  150. +1 −3 nibabel/streamlines/tests/test_tractogram_file.py
  151. +1 −1 nibabel/streamlines/tests/test_trk.py
  152. +17 −3 nibabel/streamlines/tractogram.py
  153. +5 −5 nibabel/streamlines/tractogram_file.py
  154. +11 −11 nibabel/streamlines/trk.py
  155. +32 −22 nibabel/testing/__init__.py
  156. +4 −4 nibabel/testing/helpers.py
  157. +4 −4 nibabel/testing/np_features.py
  158. +18 −0 nibabel/tests/conftest.py
  159. +3 −2 nibabel/tests/data/check_parrec_reslice.py
  160. +1 −0 nibabel/tests/data/gen_standard.py
  161. BIN nibabel/tests/data/minc2_baddim.mnc
  162. +2 −4 nibabel/tests/nibabel_data.py
  163. +2 −2 nibabel/tests/scriptrunner.py
  164. +0 −1 nibabel/tests/test_affines.py
  165. +13 −17 nibabel/tests/test_analyze.py
  166. +6 −6 nibabel/tests/test_api_validators.py
  167. +48 −11 nibabel/tests/test_arrayproxy.py
  168. +10 −9 nibabel/tests/test_arraywriters.py
  169. +1 −2 nibabel/tests/test_batteryrunners.py
  170. +1 −1 nibabel/tests/test_brikhead.py
  171. +23 −24 nibabel/tests/test_casting.py
  172. +4 −3 nibabel/tests/test_data.py
  173. +1 −2 nibabel/tests/test_dataobj_images.py
  174. +3 −4 nibabel/tests/test_deprecated.py
  175. +12 −8 nibabel/tests/test_deprecator.py
  176. +3 −4 nibabel/tests/test_dft.py
  177. +1 −2 nibabel/tests/test_diff.py
  178. +3 −3 nibabel/tests/test_ecat.py
  179. +2 −3 nibabel/tests/test_ecat_data.py
  180. +1 −2 nibabel/tests/test_environment.py
  181. +3 −7 nibabel/tests/test_euler.py
  182. +1 −2 nibabel/tests/test_filebasedimages.py
  183. +1 −2 nibabel/tests/test_filehandles.py
  184. +1 −2 nibabel/tests/test_fileholders.py
  185. +25 −1 nibabel/tests/test_filename_parser.py
  186. +3 −4 nibabel/tests/test_files_interface.py
  187. +5 −6 nibabel/tests/test_fileslice.py
  188. +1 −3 nibabel/tests/test_fileutils.py
  189. +29 −95 nibabel/tests/test_floating.py
  190. +7 −8 nibabel/tests/test_funcs.py
  191. +28 −42 nibabel/tests/test_image_api.py
  192. +4 −4 nibabel/tests/test_image_load_save.py
  193. +1 −7 nibabel/tests/test_image_types.py
  194. +1 −5 nibabel/tests/test_imageclasses.py
  195. +2 −2 nibabel/tests/test_imageglobals.py
  196. +8 −7 nibabel/tests/test_init.py
  197. +17 −18 nibabel/tests/test_loadsave.py
  198. +1 −5 nibabel/tests/test_minc1.py
  199. +10 −0 nibabel/tests/test_minc2.py
  200. +1 −2 nibabel/tests/test_minc2_data.py
  201. +1 −3 nibabel/tests/test_mriutils.py
  202. +2 −4 nibabel/tests/test_nibabel_data.py
  203. +73 −20 nibabel/tests/test_nifti1.py
  204. +2 −1 nibabel/tests/test_nifti2.py
  205. +28 −16 nibabel/tests/test_onetime.py
  206. +36 −35 nibabel/tests/test_openers.py
  207. +1 −2 nibabel/tests/test_optpkg.py
  208. +2 −5 nibabel/tests/test_orientations.py
  209. +12 −20 nibabel/tests/test_parrec.py
  210. +2 −5 nibabel/tests/test_parrec_data.py
  211. +3 −7 nibabel/tests/test_pkg_info.py
  212. +181 −0 nibabel/tests/test_pointset.py
  213. +7 −5 nibabel/tests/test_processing.py
  214. +14 −6 nibabel/tests/test_proxy_api.py
  215. +80 −37 nibabel/tests/test_quaternions.py
  216. +4 −2 nibabel/tests/test_removalschedule.py
  217. +8 −8 nibabel/tests/test_round_trip.py
  218. +1 −2 nibabel/tests/test_rstutils.py
  219. +9 −10 nibabel/tests/test_scaling.py
  220. +8 −9 nibabel/tests/test_scripts.py
  221. +2 −3 nibabel/tests/test_spaces.py
  222. +24 −31 nibabel/tests/test_spatialimages.py
  223. +62 −51 nibabel/tests/test_spm99analyze.py
  224. +17 −15 nibabel/tests/test_testing.py
  225. +2 −7 nibabel/tests/test_tripwire.py
  226. +227 −0 nibabel/tests/test_viewers.py
  227. +31 −16 nibabel/tests/test_volumeutils.py
  228. +4 −12 nibabel/tests/test_wrapstruct.py
  229. +4 −4 nibabel/tmpdirs.py
  230. +6 −5 nibabel/tripwire.py
  231. +27 −17 nibabel/viewers.py
  232. +192 −132 nibabel/volumeutils.py
  233. +1 −0 nibabel/wrapstruct.py
  234. +16 −11 nibabel/xmlutils.py
  235. +0 −13 nisext/__init__.py
  236. +0 −38 nisext/py3builder.py
  237. +0 −285 nisext/sexts.py
  238. +0 −523 nisext/testers.py
  239. +0 −1 nisext/tests/__init__.py
  240. +0 −106 nisext/tests/test_sexts.py
  241. +0 −35 nisext/tests/test_testers.py
  242. +125 −37 pyproject.toml
  243. +4 −3 requirements.txt
  244. +0 −9 tools/ci/activate.sh
  245. +0 −31 tools/ci/build_archive.sh
  246. +0 −36 tools/ci/check.sh
  247. +0 −24 tools/ci/create_venv.sh
  248. +0 −17 tools/ci/env.sh
  249. +0 −39 tools/ci/install.sh
  250. +0 −32 tools/ci/install_dependencies.sh
  251. +0 −21 tools/ci/submit_coverage.sh
  252. +1 −1 tools/gitwash_dumper.py
  253. +1 −1 tools/make_tarball.py
  254. +140 −0 tools/markdown_release_notes.py
  255. +1 −1 tools/mpkg_wrapper.py
  256. +9 −5 tools/update_requirements.py
  257. +203 −12 tox.ini
15 changes: 12 additions & 3 deletions .coveragerc
Original file line number Diff line number Diff line change
@@ -1,9 +1,18 @@
[run]
branch = True
source = nibabel, nisext
include = */nibabel/*, */nisext/*
source = nibabel
omit =
*/externals/*
*/benchmarks/*
*/tests/*
nibabel/_version.py

[report]
exclude_also =
def __repr__
if (ty\.|typing\.)?TYPE_CHECKING:
class .*\((ty\.|typing\.)Protocol\):
@(ty\.|typing\.)overload
if 0:
if __name__ == .__main__.:
@(abc\.)?abstractmethod
raise NotImplementedError
9 changes: 0 additions & 9 deletions .flake8

This file was deleted.

4 changes: 4 additions & 0 deletions .git-blame-ignore-revs
Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
# Sun Jan 12 12:22:13 2025 -0500 - markiewicz@stanford.edu - sty: ruff format [git-blame-ignore-rev]
40e41208a0f04063b3c4e373a65da1a2a6a275b5
# Sun Jan 12 11:51:49 2025 -0500 - markiewicz@stanford.edu - STY: ruff format [git-blame-ignore-rev]
7e5d584910c67851dcfcd074ff307122689b61f5
# Sun Jan 1 12:38:02 2023 -0500 - effigies@gmail.com - STY: Run pre-commit config on all files
d14c1cf282a9c3b19189f490f10c35f5739e24d1
# Thu Dec 29 22:53:17 2022 -0500 - effigies@gmail.com - STY: Reduce array().astype() and similar constructs
10 changes: 10 additions & 0 deletions .github/dependabot.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "monthly"
groups:
actions-infrastructure:
patterns:
- "actions/*"
70 changes: 0 additions & 70 deletions .github/workflows/misc.yml

This file was deleted.

98 changes: 0 additions & 98 deletions .github/workflows/pre-release.yml

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