Skip to content
Permalink

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also or learn more about diff comparisons.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also . Learn more about diff comparisons here.
base repository: nipreps/smriprep
Failed to load repositories. Confirm that selected base ref is valid, then try again.
Loading
base: 0.8.0rc2
Choose a base ref
...
head repository: nipreps/smriprep
Failed to load repositories. Confirm that selected head ref is valid, then try again.
Loading
compare: master
Choose a head ref
Loading
Showing with 13,558 additions and 7,283 deletions.
  1. +241 −393 .circleci/config.yml
  2. +30 −2 .circleci/ds005_outputs.txt
  3. +3 −1 .circleci/ds005_run.sh
  4. +1 −0 .circleci/ds054_outputs.txt
  5. +3 −1 .circleci/ds054_run.sh
  6. +1 −1 .circleci/nipype.cfg
  7. +13 −0 .circleci/pytest.sh
  8. +0 −22 .dockerignore
  9. +10 −0 .git-blame-ignore-revs
  10. +4 −0 .git_archival.txt
  11. +1 −0 .gitattributes
  12. +13 −0 .github/dependabot.yml
  13. +228 −0 .github/workflows/build_test_deploy.yml
  14. +0 −98 .github/workflows/pythonpackage.yml
  15. +211 −4 .gitignore
  16. +2 −0 .maint/local_gitignore
  17. +27 −0 .maint/make_gitignore
  18. +24 −0 .pre-commit-config.yaml
  19. +18 −0 .zenodo.json
  20. +313 −2 CHANGES.rst
  21. +1 −1 CODE_OF_CONDUCT.md
  22. +2 −2 CONTRIBUTING.md
  23. +170 −135 Dockerfile
  24. +2 −1 LICENSE
  25. +0 −7 MANIFEST.in
  26. +6 −1 Makefile
  27. +18 −0 NOTICE
  28. +4 −4 README.rst
  29. +877 −0 docker/files/freesurfer7.3.2-exclude.txt
  30. +1 −0 docs/.gitignore
  31. +1 −1 docs/_static/alabaster.css
  32. +1 −1 docs/_static/basic.css
  33. +1 −1 docs/_static/documentation_options.js
  34. +4 −1 docs/_static/jquery-3.2.1.js
  35. +1 −3 docs/_static/language_data.js
  36. +1 −1 docs/_static/pygments.css
  37. +0 −1 docs/_templates/apidoc/module.rst_t
  38. +0 −1 docs/_templates/apidoc/toc.rst_t
  39. +1 −1 docs/api.rst
  40. +84 −75 docs/conf.py
  41. +6 −6 docs/installation.rst
  42. +3 −3 docs/links.rst
  43. +6 −5 docs/requirements.txt
  44. +1 −2 docs/usage.rst
  45. +36 −0 env.yml
  46. +0 −19 get_version.py
  47. +195 −1 pyproject.toml
  48. +231 −0 requirements.txt
  49. +134 −0 scripts/fetch_templates.py
  50. +0 −123 setup.cfg
  51. +0 −23 setup.py
  52. +0 −25 smriprep/__about__.py
  53. +0 −9 smriprep/__main__.py
  54. +0 −534 smriprep/_version.py
  55. +0 −636 smriprep/cli/run.py
  56. +0 −84 smriprep/data/io_spec.json
  57. +0 −171 smriprep/interfaces/freesurfer.py
  58. +0 −148 smriprep/interfaces/templateflow.py
  59. +0 −273 smriprep/utils/bids.py
  60. +0 −32 smriprep/utils/tests/test_misc.py
  61. +0 −791 smriprep/workflows/anatomical.py
  62. +0 −266 smriprep/workflows/norm.py
  63. +0 −711 smriprep/workflows/outputs.py
  64. +0 −634 smriprep/workflows/surfaces.py
  65. +41 −0 src/smriprep/__about__.py
  66. +7 −3 { → src}/smriprep/__init__.py
  67. +31 −0 src/smriprep/__main__.py
  68. 0 { → src}/smriprep/cli/__init__.py
  69. +701 −0 src/smriprep/cli/run.py
  70. +2 −1 { → src}/smriprep/conf/__init__.py
  71. +16 −0 src/smriprep/conftest.py
  72. +14 −0 src/smriprep/data/__init__.py
  73. +77 −0 src/smriprep/data/atlases/L.atlasroi.32k_fs_LR.shape.gii
  74. +85 −0 src/smriprep/data/atlases/L.atlasroi.59k_fs_LR.shape.gii
  75. +63 −0 src/smriprep/data/atlases/L.refsulc.164k_fs_LR.shape.gii
  76. +77 −0 src/smriprep/data/atlases/R.atlasroi.32k_fs_LR.shape.gii
  77. +85 −0 src/smriprep/data/atlases/R.atlasroi.59k_fs_LR.shape.gii
  78. +63 −0 src/smriprep/data/atlases/R.refsulc.164k_fs_LR.shape.gii
  79. +129 −0 src/smriprep/data/atlases/fs_L/fs_L-to-fs_LR_fsaverage.L_LR.spherical_std.164k_fs_L.surf.gii
  80. +121 −0 src/smriprep/data/atlases/fs_L/fsaverage.L.sphere.164k_fs_L.surf.gii
  81. +127 −0 src/smriprep/data/atlases/fs_R/fs_R-to-fs_LR_fsaverage.R_LR.spherical_std.164k_fs_R.surf.gii
  82. +121 −0 src/smriprep/data/atlases/fs_R/fsaverage.R.sphere.164k_fs_R.surf.gii
  83. +128 −0 src/smriprep/data/atlases/fsaverage.L_LR.spherical_std.164k_fs_LR.surf.gii
  84. +123 −0 src/smriprep/data/atlases/fsaverage.R_LR.spherical_std.164k_fs_LR.surf.gii
  85. +37 −13 { → src}/smriprep/data/boilerplate.bib
  86. +168 −0 src/smriprep/data/io_spec.json
  87. 0 { → src}/smriprep/data/itkIdentityTransform.txt
  88. +18 −0 src/smriprep/data/msm/MSMSulcStrainFinalconf
  89. +18 −0 src/smriprep/data/msm/MSMSulcStrainSloppyconf
  90. +1 −1 { → src}/smriprep/data/tests/dataset_description.json
  91. +1 −1 { → src}/smriprep/interfaces/__init__.py
  92. +192 −0 src/smriprep/interfaces/cifti.py
  93. +35 −0 src/smriprep/interfaces/conftest.py
  94. +340 −0 src/smriprep/interfaces/freesurfer.py
  95. +90 −0 src/smriprep/interfaces/gifti.py
  96. +159 −0 src/smriprep/interfaces/msm.py
  97. +56 −38 { → src}/smriprep/interfaces/reports.py
  98. +288 −0 src/smriprep/interfaces/surf.py
  99. +220 −0 src/smriprep/interfaces/templateflow.py
  100. 0 {smriprep/utils → src/smriprep/interfaces/tests}/__init__.py
  101. +3 −0 src/smriprep/interfaces/tests/data/__init__.py
  102. 0 smriprep/utils/tests/__init__.py → src/smriprep/interfaces/tests/data/lh.sphere.reg.surf.gii
  103. 0 smriprep/workflows/__init__.py → src/smriprep/interfaces/tests/data/lh.white
  104. 0 src/smriprep/interfaces/tests/data/sub-01_desc-warped_T1w.nii.gz
  105. 0 src/smriprep/interfaces/tests/data/sub-01_hemi-L_midthickness.surf.gii
  106. 0 src/smriprep/interfaces/tests/data/sub-01_hemi-L_sphere.surf.gii
  107. 0 src/smriprep/interfaces/tests/data/sub-01_hemi-L_sulc.shape.gii
  108. BIN src/smriprep/interfaces/tests/data/sub-fsaverage_res-4_desc-cropped_ribbon.nii.gz
  109. BIN src/smriprep/interfaces/tests/data/sub-fsaverage_res-4_hemi-L_desc-cropped_pialdist.nii.gz
  110. BIN src/smriprep/interfaces/tests/data/sub-fsaverage_res-4_hemi-L_desc-cropped_wmdist.nii.gz
  111. BIN src/smriprep/interfaces/tests/data/sub-fsaverage_res-4_hemi-R_desc-cropped_pialdist.nii.gz
  112. BIN src/smriprep/interfaces/tests/data/sub-fsaverage_res-4_hemi-R_desc-cropped_wmdist.nii.gz
  113. 0 src/smriprep/interfaces/tests/data/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii
  114. 0 src/smriprep/interfaces/tests/data/tpl-fsaverage_hemi-L_den-164k_desc-std_sphere.surf.gii
  115. 0 src/smriprep/interfaces/tests/data/tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii
  116. +30 −0 src/smriprep/interfaces/tests/test_surf.py
  117. +666 −0 src/smriprep/interfaces/workbench.py
  118. 0 src/smriprep/utils/__init__.py
  119. +171 −0 src/smriprep/utils/bids.py
  120. +30 −8 { → src}/smriprep/utils/misc.py
  121. +5 −0 src/smriprep/utils/tests/__init__.py
  122. +101 −0 src/smriprep/utils/tests/derivatives.yml
  123. +30 −0 src/smriprep/utils/tests/test_bids.py
  124. +54 −0 src/smriprep/utils/tests/test_misc.py
  125. 0 src/smriprep/workflows/__init__.py
  126. +1,660 −0 src/smriprep/workflows/anatomical.py
  127. +115 −66 { → src}/smriprep/workflows/base.py
  128. 0 src/smriprep/workflows/fit/__init__.py
  129. +289 −0 src/smriprep/workflows/fit/registration.py
  130. +1,336 −0 src/smriprep/workflows/outputs.py
  131. +1,713 −0 src/smriprep/workflows/surfaces.py
  132. 0 src/smriprep/workflows/tests/__init__.py
  133. +224 −0 src/smriprep/workflows/tests/test_anatomical.py
  134. +68 −0 src/smriprep/workflows/tests/test_surfaces.py
  135. +9 −0 tools/ci/activate.sh
  136. +33 −0 tools/ci/build_archive.sh
  137. +23 −0 tools/ci/check.sh
  138. +24 −0 tools/ci/create_venv.sh
  139. +6 −0 tools/ci/env.sh
  140. +38 −0 tools/ci/install.sh
  141. +24 −0 tools/ci/install_extras.sh
  142. +54 −0 tools/update_changes.sh
  143. +126 −0 tox.ini
  144. +0 −1,827 versioneer.py
  145. +27 −0 wrapper/LICENSE
  146. +3 −0 wrapper/pyproject.toml
  147. +3 −9 wrapper/setup.cfg
  148. +44 −5 wrapper/setup.py
  149. +85 −54 wrapper/smriprep_docker.py
Loading