From 4b8e242bd1cf43ccbf8373a9bd90de6383eac8c0 Mon Sep 17 00:00:00 2001 From: Nick Guenther Date: Mon, 5 Apr 2021 21:45:52 -0400 Subject: [PATCH 1/2] Template for packaging spinalcordtoolbox datasets in pip. --- .github/workflows/build.yml | 24 ++++++++++ .github/workflows/release.yml | 44 +++++++++++++++++++ .gitignore | 6 +++ pyproject.toml | 3 ++ setup.py | 44 +++++++++++++++++++ .../data/dataset/__init__.py | 2 + 6 files changed, 123 insertions(+) create mode 100644 .github/workflows/build.yml create mode 100644 .github/workflows/release.yml create mode 100644 .gitignore create mode 100644 pyproject.toml create mode 100644 setup.py create mode 100644 src/spinalcordtoolbox/data/dataset/__init__.py diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..93e519a --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,24 @@ +name: Test the Build + +on: + # test on PRs and double-test on merges to master, or manually. + pull_request: + push: + branches: + - master + workflow_dispatch: + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python + uses: actions/setup-python@v1 + - name: Build tools + run: | + python -m pip install --upgrade pip + pip install build + - name: Build + run: | + python -m build --wheel --sdist diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..e6b1fa3 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,44 @@ +name: Publish + +on: + # publish from the Releases page: + release: + types: [published] + # publish from the Actions page: + workflow_dispatch: + inputs: + version: + description: 'Version (e.g. 2.0.3)' + required: true + +jobs: + publish: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set up Python + uses: actions/setup-python@v1 + - name: Build tools + run: | + python -m pip install --upgrade pip + pip install build + - name: Build + run: | + python -m build --wheel --sdist + ### TODO: can the uploads be parallelized? + - name: Publish to Github + uses: softprops/action-gh-release@v1 + with: + files: 'dist/*' + fail_on_unmatched_files: true + tag_name: ${{ github.event.inputs.version }} # in the workflow_dispatch case, make a new tag from the given input; in the published release case, this will be empty and will fall back to updating that release. + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + #password: ${{ secrets.PYPI_PASSWORD }} + # DEBUG: + password: ${{ secrets.TEST_PYPI_API_TOKEN }} + repository_url: https://test.pypi.org/legacy/ diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..92148bd --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +dist/ +build/ + +*.whl +*.egg-info +__pycache__ diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..1ce1d64 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,3 @@ +# this ensures builds are done reliably +[build-system] +requires = ["setuptools>=40.8.0", "setuptools_scm[toml]", "wheel"] diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..5eaee53 --- /dev/null +++ b/setup.py @@ -0,0 +1,44 @@ +from setuptools import setup, find_packages, find_namespace_packages +import pathlib + +here = pathlib.Path(__file__).parent.resolve() + +# workaround a bug introduced by pyproject.toml +# https://github.com/pypa/pip/issues/7953#issuecomment-645133255 +import site, sys; site.ENABLE_USER_SITE = True + +setup( + name='spinalcordtoolbox-data-', + 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='neuropoly@googlegroups.com', + url='https://spinalcordtoolbox.com/', + project_urls={ + 'Source': 'https://github.com/sct-data/', + #'Documentation': '', + }, + #license='CC-BY-NC', ?? + #license_files=[ ... ] # TODO? + + packages=find_namespace_packages('src/'), + package_dir={"":"src/"}, + + # with setuptools_scm, means it includes non-python files if they're under git + include_package_data=True, + + # with setuptools_scm, get the version out of the most recent git tag. + # the tags must be formatted as semver. + use_scm_version=True, + + # pyproject.toml::build-system.requires is supposed to supersede this, but it's still very new so we duplicate it. + setup_requires=[ + 'setuptools', + 'setuptools_scm[toml]', + 'wheel', + ], + + zip_safe=False, # guarantees that importlib.resources.path() is safe +) + diff --git a/src/spinalcordtoolbox/data/dataset/__init__.py b/src/spinalcordtoolbox/data/dataset/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/data/dataset/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > From d672cabfd6bfb3ecd99fcb2a5ec8ba331a56d60d Mon Sep 17 00:00:00 2001 From: Nick Guenther Date: Tue, 6 Apr 2021 11:48:33 -0400 Subject: [PATCH 2/2] Migrate to pip --- .distriploy.yml | 13 ------------- README.md | 8 ++------ setup.py | 7 +++---- .../{data/dataset => testing/data}/__init__.py | 0 .../testing/data/dmri/__init__.py | 2 ++ .../spinalcordtoolbox/testing/data/dmri}/bvals.txt | 0 .../spinalcordtoolbox/testing/data/dmri}/bvecs.txt | 0 .../testing/data/dmri}/dmri.nii.gz | Bin .../testing/data/dmri}/dmri_T0000.nii.gz | Bin .../testing/data/dmri}/dmri_T0001.nii.gz | Bin .../testing/data/dmri}/dmri_T0002.nii.gz | Bin .../testing/data/dmri}/dmri_T0003.nii.gz | Bin .../testing/data/dmri}/dmri_T0004.nii.gz | Bin .../testing/data/dmri}/dmri_T0005.nii.gz | Bin .../testing/data/dmri}/dmri_T0006.nii.gz | Bin .../testing/data/dmri}/dwi.nii.gz | Bin .../testing/data/dmri}/dwi_mean.nii.gz | Bin .../data/dmri}/dwi_mean_centerline-optic.csv | 0 .../data/dmri}/dwi_mean_centerline-optic.nii.gz | 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=> src/spinalcordtoolbox/testing/data/template}/template/PAM50_small_cord.nii.gz (100%) rename {template => src/spinalcordtoolbox/testing/data/template}/template/PAM50_small_label_disc.nii.gz (100%) rename {template => src/spinalcordtoolbox/testing/data/template}/template/PAM50_small_label_discPosterior.nii.gz (100%) rename {template => src/spinalcordtoolbox/testing/data/template}/template/PAM50_small_levels.nii.gz (100%) rename {template => src/spinalcordtoolbox/testing/data/template}/template/PAM50_small_t2.nii.gz (100%) rename {template => src/spinalcordtoolbox/testing/data/template}/template/PAM50_small_t2_pmj_manual.nii.gz (100%) create mode 100644 src/spinalcordtoolbox/testing/data/template/template/__init__.py rename {template => src/spinalcordtoolbox/testing/data/template}/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/README.md b/README.md index e114123..e06eaa5 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,5 @@ -sct_example_data +sct_testing_data ================ -Example data for the Spinal Cord Toolbox (errsm_30). +Testing data for the [`spinalcordtoolbox`](https://github.com/neuropoly/spinalcordtoolbox). -To release after changes, use [distriploy](https://github.com/neuropoly/distriploy/): -```bash -distriploy --revision rYYYYMMDD release -``` diff --git a/setup.py b/setup.py index 5eaee53..91a59e8 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-testing', description='Part of https://github.com/neuropoly/spinalcordtoolbox', long_description=(here / 'README.md').read_text(encoding='utf-8'), long_description_content_type='text/markdown', @@ -16,11 +16,10 @@ author_email='neuropoly@googlegroups.com', url='https://spinalcordtoolbox.com/', project_urls={ - 'Source': 'https://github.com/sct-data/', + 'Source': 'https://github.com/sct-data/sct_testing_data', #'Documentation': '', }, - #license='CC-BY-NC', ?? - #license_files=[ ... ] # TODO? + license_files=[ 'LICENSE' ], packages=find_namespace_packages('src/'), package_dir={"":"src/"}, diff --git a/src/spinalcordtoolbox/data/dataset/__init__.py b/src/spinalcordtoolbox/testing/data/__init__.py similarity index 100% rename from src/spinalcordtoolbox/data/dataset/__init__.py rename to src/spinalcordtoolbox/testing/data/__init__.py diff --git a/src/spinalcordtoolbox/testing/data/dmri/__init__.py b/src/spinalcordtoolbox/testing/data/dmri/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/dmri/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/dmri/bvals.txt b/src/spinalcordtoolbox/testing/data/dmri/bvals.txt similarity index 100% rename from dmri/bvals.txt rename to src/spinalcordtoolbox/testing/data/dmri/bvals.txt diff --git a/dmri/bvecs.txt b/src/spinalcordtoolbox/testing/data/dmri/bvecs.txt similarity index 100% rename from dmri/bvecs.txt rename to src/spinalcordtoolbox/testing/data/dmri/bvecs.txt diff --git a/dmri/dmri.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri.nii.gz similarity index 100% rename from dmri/dmri.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri.nii.gz diff --git a/dmri/dmri_T0000.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri_T0000.nii.gz similarity index 100% rename from dmri/dmri_T0000.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri_T0000.nii.gz diff --git a/dmri/dmri_T0001.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri_T0001.nii.gz similarity index 100% rename from dmri/dmri_T0001.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri_T0001.nii.gz diff --git a/dmri/dmri_T0002.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri_T0002.nii.gz similarity index 100% rename from dmri/dmri_T0002.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri_T0002.nii.gz diff --git a/dmri/dmri_T0003.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri_T0003.nii.gz similarity index 100% rename from dmri/dmri_T0003.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri_T0003.nii.gz diff --git a/dmri/dmri_T0004.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri_T0004.nii.gz similarity index 100% rename from dmri/dmri_T0004.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri_T0004.nii.gz diff --git a/dmri/dmri_T0005.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri_T0005.nii.gz similarity index 100% rename from dmri/dmri_T0005.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri_T0005.nii.gz diff --git a/dmri/dmri_T0006.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dmri_T0006.nii.gz similarity index 100% rename from dmri/dmri_T0006.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dmri_T0006.nii.gz diff --git a/dmri/dwi.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dwi.nii.gz similarity index 100% rename from dmri/dwi.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dwi.nii.gz diff --git a/dmri/dwi_mean.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dwi_mean.nii.gz similarity index 100% rename from dmri/dwi_mean.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dwi_mean.nii.gz diff --git a/dmri/dwi_mean_centerline-optic.csv b/src/spinalcordtoolbox/testing/data/dmri/dwi_mean_centerline-optic.csv similarity index 100% rename from dmri/dwi_mean_centerline-optic.csv rename to src/spinalcordtoolbox/testing/data/dmri/dwi_mean_centerline-optic.csv diff --git a/dmri/dwi_mean_centerline-optic.nii.gz b/src/spinalcordtoolbox/testing/data/dmri/dwi_mean_centerline-optic.nii.gz similarity index 100% rename from dmri/dwi_mean_centerline-optic.nii.gz rename to src/spinalcordtoolbox/testing/data/dmri/dwi_mean_centerline-optic.nii.gz diff --git a/dmribvecs.txt b/src/spinalcordtoolbox/testing/data/dmribvecs.txt similarity index 100% rename from dmribvecs.txt rename to src/spinalcordtoolbox/testing/data/dmribvecs.txt diff --git a/src/spinalcordtoolbox/testing/data/fmri/__init__.py b/src/spinalcordtoolbox/testing/data/fmri/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/fmri/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/fmri/fmri.nii.gz b/src/spinalcordtoolbox/testing/data/fmri/fmri.nii.gz similarity index 100% rename from fmri/fmri.nii.gz rename to src/spinalcordtoolbox/testing/data/fmri/fmri.nii.gz diff --git a/fmri/fmri_r.nii.gz b/src/spinalcordtoolbox/testing/data/fmri/fmri_r.nii.gz similarity index 100% rename from fmri/fmri_r.nii.gz rename to src/spinalcordtoolbox/testing/data/fmri/fmri_r.nii.gz diff --git a/fmri/fmri_tsnr.nii.gz b/src/spinalcordtoolbox/testing/data/fmri/fmri_tsnr.nii.gz similarity index 100% rename from fmri/fmri_tsnr.nii.gz rename to src/spinalcordtoolbox/testing/data/fmri/fmri_tsnr.nii.gz diff --git a/mt/README.md b/src/spinalcordtoolbox/testing/data/mt/README.md similarity index 100% rename from mt/README.md rename to src/spinalcordtoolbox/testing/data/mt/README.md diff --git a/src/spinalcordtoolbox/testing/data/mt/__init__.py b/src/spinalcordtoolbox/testing/data/mt/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/mt/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/src/spinalcordtoolbox/testing/data/mt/label/__init__.py b/src/spinalcordtoolbox/testing/data/mt/label/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/mt/label/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/mt/label/atlas/PAM50_atlas_00.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_00.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_00.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_00.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_01.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_01.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_01.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_01.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_02.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_02.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_02.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_02.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_03.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_03.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_03.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_03.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_04.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_04.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_04.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_04.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_05.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_05.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_05.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_05.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_06.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_06.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_06.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_06.nii.gz diff --git 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mt/label/atlas/PAM50_atlas_10.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_10.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_11.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_11.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_11.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_11.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_12.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_12.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_12.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_12.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_13.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_13.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_13.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_13.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_14.nii.gz 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src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_31.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_32.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_32.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_32.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_32.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_33.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_33.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_33.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_33.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_34.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_34.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_34.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_34.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_35.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_35.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_35.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_35.nii.gz diff --git a/mt/label/atlas/PAM50_atlas_36.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_36.nii.gz similarity index 100% rename from mt/label/atlas/PAM50_atlas_36.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/PAM50_atlas_36.nii.gz diff --git a/src/spinalcordtoolbox/testing/data/mt/label/atlas/__init__.py b/src/spinalcordtoolbox/testing/data/mt/label/atlas/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/mt/label/atlas/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/mt/label/atlas/info_label.txt b/src/spinalcordtoolbox/testing/data/mt/label/atlas/info_label.txt similarity index 100% rename from mt/label/atlas/info_label.txt rename to src/spinalcordtoolbox/testing/data/mt/label/atlas/info_label.txt diff --git a/mt/label/template/PAM50_cord.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_cord.nii.gz similarity index 100% rename from mt/label/template/PAM50_cord.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_cord.nii.gz diff --git a/mt/label/template/PAM50_csf.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_csf.nii.gz similarity index 100% rename from mt/label/template/PAM50_csf.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_csf.nii.gz diff --git a/mt/label/template/PAM50_gm.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_gm.nii.gz similarity index 100% rename from mt/label/template/PAM50_gm.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_gm.nii.gz diff --git a/mt/label/template/PAM50_levels.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_levels.nii.gz similarity index 100% rename from mt/label/template/PAM50_levels.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_levels.nii.gz diff --git a/mt/label/template/PAM50_t1.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_t1.nii.gz similarity index 100% rename from mt/label/template/PAM50_t1.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_t1.nii.gz diff --git a/mt/label/template/PAM50_t2.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_t2.nii.gz similarity index 100% rename from mt/label/template/PAM50_t2.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_t2.nii.gz diff --git a/mt/label/template/PAM50_t2s.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_t2s.nii.gz similarity index 100% rename from mt/label/template/PAM50_t2s.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_t2s.nii.gz diff --git a/mt/label/template/PAM50_wm.nii.gz b/src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_wm.nii.gz similarity index 100% rename from mt/label/template/PAM50_wm.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/label/template/PAM50_wm.nii.gz diff --git a/src/spinalcordtoolbox/testing/data/mt/label/template/__init__.py b/src/spinalcordtoolbox/testing/data/mt/label/template/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/mt/label/template/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/mt/label/template/info_label.txt b/src/spinalcordtoolbox/testing/data/mt/label/template/info_label.txt similarity index 100% rename from mt/label/template/info_label.txt rename to src/spinalcordtoolbox/testing/data/mt/label/template/info_label.txt diff --git a/mt/mt0.json b/src/spinalcordtoolbox/testing/data/mt/mt0.json similarity index 100% rename from mt/mt0.json rename to src/spinalcordtoolbox/testing/data/mt/mt0.json diff --git a/mt/mt0.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt0.nii.gz similarity index 100% rename from mt/mt0.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt0.nii.gz diff --git a/mt/mt0_mask_viewer.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt0_mask_viewer.nii.gz similarity index 100% rename from mt/mt0_mask_viewer.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt0_mask_viewer.nii.gz diff --git a/mt/mt0_reg_slicereg_goldstandard.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt0_reg_slicereg_goldstandard.nii.gz similarity index 100% rename from mt/mt0_reg_slicereg_goldstandard.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt0_reg_slicereg_goldstandard.nii.gz diff --git a/mt/mt0_reg_syn_goldstandard.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt0_reg_syn_goldstandard.nii.gz similarity index 100% rename from mt/mt0_reg_syn_goldstandard.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt0_reg_syn_goldstandard.nii.gz diff --git a/mt/mt0_seg.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt0_seg.nii.gz similarity index 100% rename from mt/mt0_seg.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt0_seg.nii.gz diff --git a/mt/mt1.json b/src/spinalcordtoolbox/testing/data/mt/mt1.json similarity index 100% rename from mt/mt1.json rename to src/spinalcordtoolbox/testing/data/mt/mt1.json diff --git a/mt/mt1.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt1.nii.gz similarity index 100% rename from mt/mt1.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt1.nii.gz diff --git a/mt/mt1_gmseg.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt1_gmseg.nii.gz similarity index 100% rename from mt/mt1_gmseg.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt1_gmseg.nii.gz diff --git a/mt/mt1_gmseg_goldstandard.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt1_gmseg_goldstandard.nii.gz similarity index 100% rename from mt/mt1_gmseg_goldstandard.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt1_gmseg_goldstandard.nii.gz diff --git a/mt/mt1_point.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt1_point.nii.gz similarity index 100% rename from mt/mt1_point.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt1_point.nii.gz diff --git a/mt/mt1_seg.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt1_seg.nii.gz similarity index 100% rename from mt/mt1_seg.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt1_seg.nii.gz diff --git a/mt/mt1_wmseg.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mt1_wmseg.nii.gz similarity index 100% rename from mt/mt1_wmseg.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mt1_wmseg.nii.gz diff --git a/mt/mtr.nii.gz b/src/spinalcordtoolbox/testing/data/mt/mtr.nii.gz similarity index 100% rename from mt/mtr.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/mtr.nii.gz diff --git a/mt/step1TxTy_poly_groundtruth.csv b/src/spinalcordtoolbox/testing/data/mt/step1TxTy_poly_groundtruth.csv similarity index 100% rename from mt/step1TxTy_poly_groundtruth.csv rename to src/spinalcordtoolbox/testing/data/mt/step1TxTy_poly_groundtruth.csv diff --git a/mt/t1w.json b/src/spinalcordtoolbox/testing/data/mt/t1w.json similarity index 100% rename from mt/t1w.json rename to src/spinalcordtoolbox/testing/data/mt/t1w.json diff --git a/mt/t1w.nii.gz b/src/spinalcordtoolbox/testing/data/mt/t1w.nii.gz similarity index 100% rename from mt/t1w.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/t1w.nii.gz diff --git a/mt/warp_t22mt1.nii.gz b/src/spinalcordtoolbox/testing/data/mt/warp_t22mt1.nii.gz similarity index 100% rename from mt/warp_t22mt1.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/warp_t22mt1.nii.gz diff --git a/mt/warp_template2mt.nii.gz b/src/spinalcordtoolbox/testing/data/mt/warp_template2mt.nii.gz similarity index 100% rename from mt/warp_template2mt.nii.gz rename to src/spinalcordtoolbox/testing/data/mt/warp_template2mt.nii.gz diff --git a/src/spinalcordtoolbox/testing/data/t1/__init__.py b/src/spinalcordtoolbox/testing/data/t1/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/t1/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/t1/init_label_vertebrae.txt b/src/spinalcordtoolbox/testing/data/t1/init_label_vertebrae.txt similarity index 100% rename from t1/init_label_vertebrae.txt rename to src/spinalcordtoolbox/testing/data/t1/init_label_vertebrae.txt diff --git a/t1/t1w.nii.gz b/src/spinalcordtoolbox/testing/data/t1/t1w.nii.gz similarity index 100% rename from t1/t1w.nii.gz rename to src/spinalcordtoolbox/testing/data/t1/t1w.nii.gz diff --git a/t1/t1w_seg-manual.nii.gz b/src/spinalcordtoolbox/testing/data/t1/t1w_seg-manual.nii.gz similarity index 100% rename from t1/t1w_seg-manual.nii.gz rename to src/spinalcordtoolbox/testing/data/t1/t1w_seg-manual.nii.gz diff --git a/t2/README.md b/src/spinalcordtoolbox/testing/data/t2/README.md similarity index 100% rename from t2/README.md rename to src/spinalcordtoolbox/testing/data/t2/README.md diff --git a/src/spinalcordtoolbox/testing/data/t2/__init__.py b/src/spinalcordtoolbox/testing/data/t2/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/t2/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/t2/init_label_vertebrae.txt b/src/spinalcordtoolbox/testing/data/t2/init_label_vertebrae.txt similarity index 100% rename from t2/init_label_vertebrae.txt rename to src/spinalcordtoolbox/testing/data/t2/init_label_vertebrae.txt diff --git a/t2/labels.nii.gz b/src/spinalcordtoolbox/testing/data/t2/labels.nii.gz similarity index 100% rename from t2/labels.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/labels.nii.gz diff --git a/t2/t2.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2.nii.gz similarity index 100% rename from t2/t2.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2.nii.gz diff --git a/t2/t2_centerline-manual.csv b/src/spinalcordtoolbox/testing/data/t2/t2_centerline-manual.csv similarity index 100% rename from t2/t2_centerline-manual.csv rename to src/spinalcordtoolbox/testing/data/t2/t2_centerline-manual.csv diff --git a/t2/t2_centerline-manual.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2_centerline-manual.nii.gz similarity index 100% rename from t2/t2_centerline-manual.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2_centerline-manual.nii.gz diff --git a/t2/t2_centerline-optic.csv b/src/spinalcordtoolbox/testing/data/t2/t2_centerline-optic.csv similarity index 100% rename from t2/t2_centerline-optic.csv rename to src/spinalcordtoolbox/testing/data/t2/t2_centerline-optic.csv diff --git a/t2/t2_centerline-optic.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2_centerline-optic.nii.gz similarity index 100% rename from t2/t2_centerline-optic.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2_centerline-optic.nii.gz diff --git a/t2/t2_contrast_1_mean_ref.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2_contrast_1_mean_ref.nii.gz similarity index 100% rename from t2/t2_contrast_1_mean_ref.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2_contrast_1_mean_ref.nii.gz diff --git a/t2/t2_labeled_center_manual.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2_labeled_center_manual.nii.gz similarity index 100% rename from t2/t2_labeled_center_manual.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2_labeled_center_manual.nii.gz diff --git a/t2/t2_seg-deepseg_sc-2d.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2_seg-deepseg_sc-2d.nii.gz similarity index 100% rename from t2/t2_seg-deepseg_sc-2d.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2_seg-deepseg_sc-2d.nii.gz diff --git a/t2/t2_seg-deepseg_sc-3d.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2_seg-deepseg_sc-3d.nii.gz similarity index 100% rename from t2/t2_seg-deepseg_sc-3d.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2_seg-deepseg_sc-3d.nii.gz diff --git a/t2/t2_seg-manual.nii.gz b/src/spinalcordtoolbox/testing/data/t2/t2_seg-manual.nii.gz similarity index 100% rename from t2/t2_seg-manual.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/t2_seg-manual.nii.gz diff --git a/t2/warp_template2anat.nii.gz b/src/spinalcordtoolbox/testing/data/t2/warp_template2anat.nii.gz similarity index 100% rename from t2/warp_template2anat.nii.gz rename to src/spinalcordtoolbox/testing/data/t2/warp_template2anat.nii.gz diff --git a/t2s/MNI-Poly-AMU_level_crop.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/MNI-Poly-AMU_level_crop.nii.gz similarity index 100% rename from t2s/MNI-Poly-AMU_level_crop.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/MNI-Poly-AMU_level_crop.nii.gz diff --git a/src/spinalcordtoolbox/testing/data/t2s/__init__.py b/src/spinalcordtoolbox/testing/data/t2s/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/t2s/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/t2s/t2s.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/t2s.nii.gz similarity index 100% rename from t2s/t2s.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/t2s.nii.gz diff --git a/t2s/t2s_centerline-optic.csv b/src/spinalcordtoolbox/testing/data/t2s/t2s_centerline-optic.csv similarity index 100% rename from t2s/t2s_centerline-optic.csv rename to src/spinalcordtoolbox/testing/data/t2s/t2s_centerline-optic.csv diff --git a/t2s/t2s_centerline-optic.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/t2s_centerline-optic.nii.gz similarity index 100% rename from t2s/t2s_centerline-optic.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/t2s_centerline-optic.nii.gz diff --git a/t2s/t2s_gmseg_manual.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/t2s_gmseg_manual.nii.gz similarity index 100% rename from t2s/t2s_gmseg_manual.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/t2s_gmseg_manual.nii.gz diff --git a/t2s/t2s_seg-deepseg.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/t2s_seg-deepseg.nii.gz similarity index 100% rename from t2s/t2s_seg-deepseg.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/t2s_seg-deepseg.nii.gz diff --git a/t2s/t2s_seg.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/t2s_seg.nii.gz similarity index 100% rename from t2s/t2s_seg.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/t2s_seg.nii.gz diff --git a/t2s/t2s_uncropped.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/t2s_uncropped.nii.gz similarity index 100% rename from t2s/t2s_uncropped.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/t2s_uncropped.nii.gz diff --git a/t2s/t2s_uncropped_gmseg_manual.nii.gz b/src/spinalcordtoolbox/testing/data/t2s/t2s_uncropped_gmseg_manual.nii.gz similarity index 100% rename from t2s/t2s_uncropped_gmseg_manual.nii.gz rename to src/spinalcordtoolbox/testing/data/t2s/t2s_uncropped_gmseg_manual.nii.gz diff --git a/template/README.md b/src/spinalcordtoolbox/testing/data/template/README.md similarity index 100% rename from template/README.md rename to src/spinalcordtoolbox/testing/data/template/README.md diff --git a/src/spinalcordtoolbox/testing/data/template/__init__.py b/src/spinalcordtoolbox/testing/data/template/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/template/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/template/template/PAM50_small_cord.nii.gz b/src/spinalcordtoolbox/testing/data/template/template/PAM50_small_cord.nii.gz similarity index 100% rename from template/template/PAM50_small_cord.nii.gz rename to src/spinalcordtoolbox/testing/data/template/template/PAM50_small_cord.nii.gz diff --git a/template/template/PAM50_small_label_disc.nii.gz b/src/spinalcordtoolbox/testing/data/template/template/PAM50_small_label_disc.nii.gz similarity index 100% rename from template/template/PAM50_small_label_disc.nii.gz rename to src/spinalcordtoolbox/testing/data/template/template/PAM50_small_label_disc.nii.gz diff --git a/template/template/PAM50_small_label_discPosterior.nii.gz b/src/spinalcordtoolbox/testing/data/template/template/PAM50_small_label_discPosterior.nii.gz similarity index 100% rename from template/template/PAM50_small_label_discPosterior.nii.gz rename to src/spinalcordtoolbox/testing/data/template/template/PAM50_small_label_discPosterior.nii.gz diff --git a/template/template/PAM50_small_levels.nii.gz b/src/spinalcordtoolbox/testing/data/template/template/PAM50_small_levels.nii.gz similarity index 100% rename from template/template/PAM50_small_levels.nii.gz rename to src/spinalcordtoolbox/testing/data/template/template/PAM50_small_levels.nii.gz diff --git a/template/template/PAM50_small_t2.nii.gz b/src/spinalcordtoolbox/testing/data/template/template/PAM50_small_t2.nii.gz similarity index 100% rename from template/template/PAM50_small_t2.nii.gz rename to src/spinalcordtoolbox/testing/data/template/template/PAM50_small_t2.nii.gz diff --git a/template/template/PAM50_small_t2_pmj_manual.nii.gz b/src/spinalcordtoolbox/testing/data/template/template/PAM50_small_t2_pmj_manual.nii.gz similarity index 100% rename from template/template/PAM50_small_t2_pmj_manual.nii.gz rename to src/spinalcordtoolbox/testing/data/template/template/PAM50_small_t2_pmj_manual.nii.gz diff --git a/src/spinalcordtoolbox/testing/data/template/template/__init__.py b/src/spinalcordtoolbox/testing/data/template/template/__init__.py new file mode 100644 index 0000000..ead4c67 --- /dev/null +++ b/src/spinalcordtoolbox/testing/data/template/template/__init__.py @@ -0,0 +1,2 @@ +# empty __init__.py to enable importlib.resources +# see < TODO > diff --git a/template/template/info_label.txt b/src/spinalcordtoolbox/testing/data/template/template/info_label.txt similarity index 100% rename from template/template/info_label.txt rename to src/spinalcordtoolbox/testing/data/template/template/info_label.txt