From a24d1c888ae581105aa96560eb748cf0be020865 Mon Sep 17 00:00:00 2001 From: Nick Guenther Date: Tue, 6 Apr 2021 11:32:16 -0400 Subject: [PATCH] Migrate to pip package --- .distriploy.yml | 13 ------------- setup.py | 4 ++-- .../data/PAM50/atlas}/PAM50_atlas_00.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_01.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_02.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_03.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_04.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_05.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_06.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_07.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_08.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_09.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_10.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_11.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_12.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_13.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_14.nii.gz | Bin 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.../data/PAM50/atlas}/PAM50_atlas_35.nii.gz | Bin .../data/PAM50/atlas}/PAM50_atlas_36.nii.gz | Bin .../data/{dataset => PAM50/atlas}/__init__.py | 0 .../data/PAM50/atlas}/info_label.txt | 0 .../data/PAM50/spinal_levels/__init__.py | 2 ++ .../data/PAM50/spinal_levels}/info_label.txt | 0 .../PAM50/spinal_levels}/spinal_level_01.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_02.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_03.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_04.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_05.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_06.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_07.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_08.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_09.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_10.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_11.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_12.nii.gz | Bin .../PAM50/spinal_levels}/spinal_level_13.nii.gz | Bin 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.../data/PAM50/template}/PAM50_t2.nii.gz | Bin .../data/PAM50/template}/PAM50_t2s.nii.gz | Bin .../data/PAM50/template}/PAM50_wm.nii.gz | Bin .../data/PAM50/template/__init__.py | 2 ++ .../data/PAM50/template}/info_label.txt | 0 80 files changed, 6 insertions(+), 15 deletions(-) delete mode 100644 .distriploy.yml rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_00.nii.gz (100%) rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_01.nii.gz (100%) rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_02.nii.gz (100%) rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_03.nii.gz (100%) rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_04.nii.gz (100%) rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_05.nii.gz (100%) rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_06.nii.gz (100%) rename {atlas => src/spinalcordtoolbox/data/PAM50/atlas}/PAM50_atlas_07.nii.gz 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src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_01.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_02.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_03.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_04.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_05.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_06.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_07.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_08.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_09.nii.gz (100%) rename {spinal_levels => src/spinalcordtoolbox/data/PAM50/spinal_levels}/spinal_level_10.nii.gz 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src/spinalcordtoolbox/data/PAM50/template}/PAM50_levels_continuous.nii.gz (100%) rename {template => src/spinalcordtoolbox/data/PAM50/template}/PAM50_spine.nii.gz (100%) rename {template => src/spinalcordtoolbox/data/PAM50/template}/PAM50_t1.nii.gz (100%) rename {template => src/spinalcordtoolbox/data/PAM50/template}/PAM50_t2.nii.gz (100%) rename {template => src/spinalcordtoolbox/data/PAM50/template}/PAM50_t2s.nii.gz (100%) rename {template => src/spinalcordtoolbox/data/PAM50/template}/PAM50_wm.nii.gz (100%) create mode 100644 src/spinalcordtoolbox/data/PAM50/template/__init__.py rename {template => src/spinalcordtoolbox/data/PAM50/template}/info_label.txt (100%) diff --git a/.distriploy.yml b/.distriploy.yml deleted file mode 100644 index 60b211b..0000000 --- a/.distriploy.yml +++ /dev/null @@ -1,13 +0,0 @@ -release: - method: github - -mirrors: - - osf: - method: osf - project: 6zbyf - folder: data - -postrelease: - add_mirror_urls: true - diff --git a/setup.py b/setup.py index 5eaee53..f4ef3af 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ import site, sys; site.ENABLE_USER_SITE = True setup( - name='spinalcordtoolbox-data-', + 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', @@ -16,7 +16,7 @@ author_email='neuropoly@googlegroups.com', url='https://spinalcordtoolbox.com/', project_urls={ - 'Source': 'https://github.com/sct-data/', + 'Source': 'https://github.com/sct-data/PAM50', #'Documentation': '', }, #license='CC-BY-NC', ?? diff --git a/atlas/PAM50_atlas_00.nii.gz b/src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz similarity index 100% rename from atlas/PAM50_atlas_00.nii.gz rename to src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_00.nii.gz diff --git a/atlas/PAM50_atlas_01.nii.gz b/src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz similarity index 100% rename from atlas/PAM50_atlas_01.nii.gz rename to src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_01.nii.gz diff --git a/atlas/PAM50_atlas_02.nii.gz b/src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz similarity index 100% rename from atlas/PAM50_atlas_02.nii.gz rename to src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_02.nii.gz diff --git a/atlas/PAM50_atlas_03.nii.gz b/src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz similarity index 100% rename from atlas/PAM50_atlas_03.nii.gz rename to src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_03.nii.gz diff --git a/atlas/PAM50_atlas_04.nii.gz b/src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz similarity index 100% rename from atlas/PAM50_atlas_04.nii.gz rename to src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_04.nii.gz diff --git a/atlas/PAM50_atlas_05.nii.gz b/src/spinalcordtoolbox/data/PAM50/atlas/PAM50_atlas_05.nii.gz similarity index 100% rename from atlas/PAM50_atlas_05.nii.gz rename to 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src/spinalcordtoolbox/data/PAM50/atlas/__init__.py diff --git a/atlas/info_label.txt b/src/spinalcordtoolbox/data/PAM50/atlas/info_label.txt similarity index 100% rename from atlas/info_label.txt rename to src/spinalcordtoolbox/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 new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ 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 b/src/spinalcordtoolbox/data/PAM50/spinal_levels/info_label.txt similarity index 100% rename from spinal_levels/info_label.txt rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/info_label.txt diff --git a/spinal_levels/spinal_level_01.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_01.nii.gz similarity index 100% rename from spinal_levels/spinal_level_01.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_01.nii.gz diff --git a/spinal_levels/spinal_level_02.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_02.nii.gz similarity index 100% rename from spinal_levels/spinal_level_02.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_02.nii.gz diff --git a/spinal_levels/spinal_level_03.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_03.nii.gz similarity index 100% rename from spinal_levels/spinal_level_03.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_03.nii.gz diff --git a/spinal_levels/spinal_level_04.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_04.nii.gz similarity index 100% rename from spinal_levels/spinal_level_04.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_04.nii.gz diff --git a/spinal_levels/spinal_level_05.nii.gz 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src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_15.nii.gz diff --git a/spinal_levels/spinal_level_16.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_16.nii.gz similarity index 100% rename from spinal_levels/spinal_level_16.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_16.nii.gz diff --git a/spinal_levels/spinal_level_17.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_17.nii.gz similarity index 100% rename from spinal_levels/spinal_level_17.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_17.nii.gz diff --git a/spinal_levels/spinal_level_18.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_18.nii.gz similarity index 100% rename from spinal_levels/spinal_level_18.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_18.nii.gz diff --git a/spinal_levels/spinal_level_19.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_19.nii.gz similarity index 100% rename from spinal_levels/spinal_level_19.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_19.nii.gz diff --git a/spinal_levels/spinal_level_20.nii.gz b/src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_20.nii.gz similarity index 100% rename from spinal_levels/spinal_level_20.nii.gz rename to src/spinalcordtoolbox/data/PAM50/spinal_levels/spinal_level_20.nii.gz diff --git a/template/PAM50_centerline.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz similarity index 100% rename from template/PAM50_centerline.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_centerline.nii.gz diff --git a/template/PAM50_cord.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz similarity index 100% rename from template/PAM50_cord.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_cord.nii.gz diff --git a/template/PAM50_csf.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz similarity index 100% rename from template/PAM50_csf.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_csf.nii.gz diff --git a/template/PAM50_gm.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz similarity index 100% rename from template/PAM50_gm.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_gm.nii.gz diff --git a/template/PAM50_label_body.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz similarity index 100% rename from template/PAM50_label_body.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_label_body.nii.gz diff --git a/template/PAM50_label_disc.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz similarity index 100% rename from template/PAM50_label_disc.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_label_disc.nii.gz diff --git a/template/PAM50_label_discPosterior.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz similarity index 100% rename from template/PAM50_label_discPosterior.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_label_discPosterior.nii.gz diff --git a/template/PAM50_label_spinal_levels.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz similarity index 100% rename from template/PAM50_label_spinal_levels.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_label_spinal_levels.nii.gz diff --git a/template/PAM50_levels.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz similarity index 100% rename from template/PAM50_levels.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_levels.nii.gz diff --git a/template/PAM50_levels_continuous.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz similarity index 100% rename from template/PAM50_levels_continuous.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_levels_continuous.nii.gz diff --git a/template/PAM50_spine.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz similarity index 100% rename from template/PAM50_spine.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_spine.nii.gz diff --git a/template/PAM50_t1.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz similarity index 100% rename from template/PAM50_t1.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_t1.nii.gz diff --git a/template/PAM50_t2.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz similarity index 100% rename from template/PAM50_t2.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_t2.nii.gz diff --git a/template/PAM50_t2s.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz similarity index 100% rename from template/PAM50_t2s.nii.gz rename to src/spinalcordtoolbox/data/PAM50/template/PAM50_t2s.nii.gz diff --git a/template/PAM50_wm.nii.gz b/src/spinalcordtoolbox/data/PAM50/template/PAM50_wm.nii.gz similarity index 100% rename from template/PAM50_wm.nii.gz rename to src/spinalcordtoolbox/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 new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ 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 b/src/spinalcordtoolbox/data/PAM50/template/info_label.txt similarity index 100% rename from template/info_label.txt rename to src/spinalcordtoolbox/data/PAM50/template/info_label.txt