Migrate to pip package

spinalcordtoolbox · Apr 6, 2021 · a24d1c8 · a24d1c8
1 parent b66e6b3
commit a24d1c8
Show file tree

Hide file tree

Showing 80 changed files with 6 additions and 15 deletions.
diff --git a/.distriploy.yml b/.distriploy.yml
diff --git a/setup.py b/setup.py
@@ -8,15 +8,15 @@
 import site, sys; site.ENABLE_USER_SITE = True
 
 setup(
-  name='spinalcordtoolbox-data-<dataset>',
+  name='spinalcordtoolbox-data-PAM50',
   description='Part of https://github.com/neuropoly/spinalcordtoolbox',
   long_description=(here / 'README.md').read_text(encoding='utf-8'),
   long_description_content_type='text/markdown',
   author='Neuropoly',
   author_email='[email protected]',
   url='https://spinalcordtoolbox.com/',
   project_urls={
-      'Source': 'https://github.com/sct-data/<dataset>',
+      'Source': 'https://github.com/sct-data/PAM50',
       #'Documentation': '',
   },
   #license='CC-BY-NC', ??

diff --git a/atlas/PAM50_atlas_00.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_00.nii.gz b/atlas/PAM50_atlas_00.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_00.nii.gz
diff --git a/atlas/PAM50_atlas_01.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_01.nii.gz b/atlas/PAM50_atlas_01.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_01.nii.gz
diff --git a/atlas/PAM50_atlas_02.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_02.nii.gz b/atlas/PAM50_atlas_02.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_02.nii.gz
diff --git a/atlas/PAM50_atlas_03.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_03.nii.gz b/atlas/PAM50_atlas_03.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_03.nii.gz
diff --git a/atlas/PAM50_atlas_04.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_04.nii.gz b/atlas/PAM50_atlas_04.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_04.nii.gz
diff --git a/atlas/PAM50_atlas_05.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_05.nii.gz b/atlas/PAM50_atlas_05.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_05.nii.gz
diff --git a/atlas/PAM50_atlas_06.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_06.nii.gz b/atlas/PAM50_atlas_06.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_06.nii.gz
diff --git a/atlas/PAM50_atlas_07.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_07.nii.gz b/atlas/PAM50_atlas_07.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_07.nii.gz
diff --git a/atlas/PAM50_atlas_08.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_08.nii.gz b/atlas/PAM50_atlas_08.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_08.nii.gz
diff --git a/atlas/PAM50_atlas_09.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_09.nii.gz b/atlas/PAM50_atlas_09.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_09.nii.gz
diff --git a/atlas/PAM50_atlas_10.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_10.nii.gz b/atlas/PAM50_atlas_10.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_10.nii.gz
diff --git a/atlas/PAM50_atlas_11.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_11.nii.gz b/atlas/PAM50_atlas_11.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_11.nii.gz
diff --git a/atlas/PAM50_atlas_12.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_12.nii.gz b/atlas/PAM50_atlas_12.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_12.nii.gz
diff --git a/atlas/PAM50_atlas_13.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_13.nii.gz b/atlas/PAM50_atlas_13.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_13.nii.gz
diff --git a/atlas/PAM50_atlas_14.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_14.nii.gz b/atlas/PAM50_atlas_14.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_14.nii.gz
diff --git a/atlas/PAM50_atlas_15.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_15.nii.gz b/atlas/PAM50_atlas_15.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_15.nii.gz
diff --git a/atlas/PAM50_atlas_16.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_16.nii.gz b/atlas/PAM50_atlas_16.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_16.nii.gz
diff --git a/atlas/PAM50_atlas_17.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_17.nii.gz b/atlas/PAM50_atlas_17.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_17.nii.gz
diff --git a/atlas/PAM50_atlas_18.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_18.nii.gz b/atlas/PAM50_atlas_18.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_18.nii.gz
diff --git a/atlas/PAM50_atlas_19.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_19.nii.gz b/atlas/PAM50_atlas_19.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_19.nii.gz
diff --git a/atlas/PAM50_atlas_20.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_20.nii.gz b/atlas/PAM50_atlas_20.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_20.nii.gz
diff --git a/atlas/PAM50_atlas_21.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_21.nii.gz b/atlas/PAM50_atlas_21.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_21.nii.gz
diff --git a/atlas/PAM50_atlas_22.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_22.nii.gz b/atlas/PAM50_atlas_22.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_22.nii.gz
diff --git a/atlas/PAM50_atlas_23.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_23.nii.gz b/atlas/PAM50_atlas_23.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_23.nii.gz
diff --git a/atlas/PAM50_atlas_24.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_24.nii.gz b/atlas/PAM50_atlas_24.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_24.nii.gz
diff --git a/atlas/PAM50_atlas_25.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_25.nii.gz b/atlas/PAM50_atlas_25.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_25.nii.gz
diff --git a/atlas/PAM50_atlas_26.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_26.nii.gz b/atlas/PAM50_atlas_26.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_26.nii.gz
diff --git a/atlas/PAM50_atlas_27.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_27.nii.gz b/atlas/PAM50_atlas_27.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_27.nii.gz
diff --git a/atlas/PAM50_atlas_28.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_28.nii.gz b/atlas/PAM50_atlas_28.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_28.nii.gz
diff --git a/atlas/PAM50_atlas_29.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_29.nii.gz b/atlas/PAM50_atlas_29.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_29.nii.gz
diff --git a/atlas/PAM50_atlas_30.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_30.nii.gz b/atlas/PAM50_atlas_30.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_30.nii.gz
diff --git a/atlas/PAM50_atlas_31.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_31.nii.gz b/atlas/PAM50_atlas_31.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_31.nii.gz
diff --git a/atlas/PAM50_atlas_32.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_32.nii.gz b/atlas/PAM50_atlas_32.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_32.nii.gz
diff --git a/atlas/PAM50_atlas_33.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_33.nii.gz b/atlas/PAM50_atlas_33.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_33.nii.gz
diff --git a/atlas/PAM50_atlas_34.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_34.nii.gz b/atlas/PAM50_atlas_34.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_34.nii.gz
diff --git a/atlas/PAM50_atlas_35.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_35.nii.gz b/atlas/PAM50_atlas_35.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_35.nii.gz
diff --git a/atlas/PAM50_atlas_36.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_36.nii.gz b/atlas/PAM50_atlas_36.nii.gz → ...ox/data/PAM50/atlas/PAM50_atlas_36.nii.gz
diff --git a/...pinalcordtoolbox/data/dataset/__init__.py → ...lcordtoolbox/data/PAM50/atlas/__init__.py b/...pinalcordtoolbox/data/dataset/__init__.py → ...lcordtoolbox/data/PAM50/atlas/__init__.py
diff --git a/atlas/info_label.txt → ...rdtoolbox/data/PAM50/atlas/info_label.txt b/atlas/info_label.txt → ...rdtoolbox/data/PAM50/atlas/info_label.txt
diff --git a/src/spinalcordtoolbox/data/PAM50/spinal_levels/__init__.py b/src/spinalcordtoolbox/data/PAM50/spinal_levels/__init__.py
@@ -0,0 +1,2 @@
+# empty __init__.py to enable importlib.resources
+# see < TODO >
diff --git a/spinal_levels/info_label.txt → ...x/data/PAM50/spinal_levels/info_label.txt b/spinal_levels/info_label.txt → ...x/data/PAM50/spinal_levels/info_label.txt
diff --git a/spinal_levels/spinal_level_01.nii.gz → ...AM50/spinal_levels/spinal_level_01.nii.gz b/spinal_levels/spinal_level_01.nii.gz → ...AM50/spinal_levels/spinal_level_01.nii.gz
diff --git a/spinal_levels/spinal_level_02.nii.gz → ...AM50/spinal_levels/spinal_level_02.nii.gz b/spinal_levels/spinal_level_02.nii.gz → ...AM50/spinal_levels/spinal_level_02.nii.gz
diff --git a/spinal_levels/spinal_level_03.nii.gz → ...AM50/spinal_levels/spinal_level_03.nii.gz b/spinal_levels/spinal_level_03.nii.gz → ...AM50/spinal_levels/spinal_level_03.nii.gz
diff --git a/spinal_levels/spinal_level_04.nii.gz → ...AM50/spinal_levels/spinal_level_04.nii.gz b/spinal_levels/spinal_level_04.nii.gz → ...AM50/spinal_levels/spinal_level_04.nii.gz
diff --git a/spinal_levels/spinal_level_05.nii.gz → ...AM50/spinal_levels/spinal_level_05.nii.gz b/spinal_levels/spinal_level_05.nii.gz → ...AM50/spinal_levels/spinal_level_05.nii.gz
diff --git a/spinal_levels/spinal_level_06.nii.gz → ...AM50/spinal_levels/spinal_level_06.nii.gz b/spinal_levels/spinal_level_06.nii.gz → ...AM50/spinal_levels/spinal_level_06.nii.gz
diff --git a/spinal_levels/spinal_level_07.nii.gz → ...AM50/spinal_levels/spinal_level_07.nii.gz b/spinal_levels/spinal_level_07.nii.gz → ...AM50/spinal_levels/spinal_level_07.nii.gz
diff --git a/spinal_levels/spinal_level_08.nii.gz → ...AM50/spinal_levels/spinal_level_08.nii.gz b/spinal_levels/spinal_level_08.nii.gz → ...AM50/spinal_levels/spinal_level_08.nii.gz
diff --git a/spinal_levels/spinal_level_09.nii.gz → ...AM50/spinal_levels/spinal_level_09.nii.gz b/spinal_levels/spinal_level_09.nii.gz → ...AM50/spinal_levels/spinal_level_09.nii.gz
diff --git a/spinal_levels/spinal_level_10.nii.gz → ...AM50/spinal_levels/spinal_level_10.nii.gz b/spinal_levels/spinal_level_10.nii.gz → ...AM50/spinal_levels/spinal_level_10.nii.gz
diff --git a/spinal_levels/spinal_level_11.nii.gz → ...AM50/spinal_levels/spinal_level_11.nii.gz b/spinal_levels/spinal_level_11.nii.gz → ...AM50/spinal_levels/spinal_level_11.nii.gz
diff --git a/spinal_levels/spinal_level_12.nii.gz → ...AM50/spinal_levels/spinal_level_12.nii.gz b/spinal_levels/spinal_level_12.nii.gz → ...AM50/spinal_levels/spinal_level_12.nii.gz
diff --git a/spinal_levels/spinal_level_13.nii.gz → ...AM50/spinal_levels/spinal_level_13.nii.gz b/spinal_levels/spinal_level_13.nii.gz → ...AM50/spinal_levels/spinal_level_13.nii.gz
diff --git a/spinal_levels/spinal_level_14.nii.gz → ...AM50/spinal_levels/spinal_level_14.nii.gz b/spinal_levels/spinal_level_14.nii.gz → ...AM50/spinal_levels/spinal_level_14.nii.gz
diff --git a/spinal_levels/spinal_level_15.nii.gz → ...AM50/spinal_levels/spinal_level_15.nii.gz b/spinal_levels/spinal_level_15.nii.gz → ...AM50/spinal_levels/spinal_level_15.nii.gz
diff --git a/spinal_levels/spinal_level_16.nii.gz → ...AM50/spinal_levels/spinal_level_16.nii.gz b/spinal_levels/spinal_level_16.nii.gz → ...AM50/spinal_levels/spinal_level_16.nii.gz
diff --git a/spinal_levels/spinal_level_17.nii.gz → ...AM50/spinal_levels/spinal_level_17.nii.gz b/spinal_levels/spinal_level_17.nii.gz → ...AM50/spinal_levels/spinal_level_17.nii.gz
diff --git a/spinal_levels/spinal_level_18.nii.gz → ...AM50/spinal_levels/spinal_level_18.nii.gz b/spinal_levels/spinal_level_18.nii.gz → ...AM50/spinal_levels/spinal_level_18.nii.gz
diff --git a/spinal_levels/spinal_level_19.nii.gz → ...AM50/spinal_levels/spinal_level_19.nii.gz b/spinal_levels/spinal_level_19.nii.gz → ...AM50/spinal_levels/spinal_level_19.nii.gz
diff --git a/spinal_levels/spinal_level_20.nii.gz → ...AM50/spinal_levels/spinal_level_20.nii.gz b/spinal_levels/spinal_level_20.nii.gz → ...AM50/spinal_levels/spinal_level_20.nii.gz
diff --git a/template/PAM50_centerline.nii.gz → ...ta/PAM50/template/PAM50_centerline.nii.gz b/template/PAM50_centerline.nii.gz → ...ta/PAM50/template/PAM50_centerline.nii.gz
diff --git a/template/PAM50_cord.nii.gz → ...box/data/PAM50/template/PAM50_cord.nii.gz b/template/PAM50_cord.nii.gz → ...box/data/PAM50/template/PAM50_cord.nii.gz
diff --git a/template/PAM50_csf.nii.gz → ...lbox/data/PAM50/template/PAM50_csf.nii.gz b/template/PAM50_csf.nii.gz → ...lbox/data/PAM50/template/PAM50_csf.nii.gz
diff --git a/template/PAM50_gm.nii.gz → ...olbox/data/PAM50/template/PAM50_gm.nii.gz b/template/PAM50_gm.nii.gz → ...olbox/data/PAM50/template/PAM50_gm.nii.gz
diff --git a/template/PAM50_label_body.nii.gz → ...ta/PAM50/template/PAM50_label_body.nii.gz b/template/PAM50_label_body.nii.gz → ...ta/PAM50/template/PAM50_label_body.nii.gz
diff --git a/template/PAM50_label_disc.nii.gz → ...ta/PAM50/template/PAM50_label_disc.nii.gz b/template/PAM50_label_disc.nii.gz → ...ta/PAM50/template/PAM50_label_disc.nii.gz
diff --git a/template/PAM50_label_discPosterior.nii.gz → ...template/PAM50_label_discPosterior.nii.gz b/template/PAM50_label_discPosterior.nii.gz → ...template/PAM50_label_discPosterior.nii.gz
diff --git a/template/PAM50_label_spinal_levels.nii.gz → ...template/PAM50_label_spinal_levels.nii.gz b/template/PAM50_label_spinal_levels.nii.gz → ...template/PAM50_label_spinal_levels.nii.gz
diff --git a/template/PAM50_levels.nii.gz → ...x/data/PAM50/template/PAM50_levels.nii.gz b/template/PAM50_levels.nii.gz → ...x/data/PAM50/template/PAM50_levels.nii.gz
diff --git a/template/PAM50_levels_continuous.nii.gz → ...0/template/PAM50_levels_continuous.nii.gz b/template/PAM50_levels_continuous.nii.gz → ...0/template/PAM50_levels_continuous.nii.gz
diff --git a/template/PAM50_spine.nii.gz → ...ox/data/PAM50/template/PAM50_spine.nii.gz b/template/PAM50_spine.nii.gz → ...ox/data/PAM50/template/PAM50_spine.nii.gz
diff --git a/template/PAM50_t1.nii.gz → ...olbox/data/PAM50/template/PAM50_t1.nii.gz b/template/PAM50_t1.nii.gz → ...olbox/data/PAM50/template/PAM50_t1.nii.gz
diff --git a/template/PAM50_t2.nii.gz → ...olbox/data/PAM50/template/PAM50_t2.nii.gz b/template/PAM50_t2.nii.gz → ...olbox/data/PAM50/template/PAM50_t2.nii.gz
diff --git a/template/PAM50_t2s.nii.gz → ...lbox/data/PAM50/template/PAM50_t2s.nii.gz b/template/PAM50_t2s.nii.gz → ...lbox/data/PAM50/template/PAM50_t2s.nii.gz
diff --git a/template/PAM50_wm.nii.gz → ...olbox/data/PAM50/template/PAM50_wm.nii.gz b/template/PAM50_wm.nii.gz → ...olbox/data/PAM50/template/PAM50_wm.nii.gz
diff --git a/src/spinalcordtoolbox/data/PAM50/template/__init__.py b/src/spinalcordtoolbox/data/PAM50/template/__init__.py
@@ -0,0 +1,2 @@
+# empty __init__.py to enable importlib.resources
+# see < TODO >
diff --git a/template/info_label.txt → ...oolbox/data/PAM50/template/info_label.txt b/template/info_label.txt → ...oolbox/data/PAM50/template/info_label.txt
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		# empty __init__.py to enable importlib.resources
		# see < TODO >