diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 26ec90516..a435b535c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -17,7 +17,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, macos-latest] - python-version: ['3.9', '3.10', '3.11', '3.12'] + python-version: ['3.10', '3.11', '3.12', '3.13'] steps: - uses: actions/checkout@v6 - uses: snok/install-poetry@v1 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 180fbe64f..c0c04ac53 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -13,7 +13,6 @@ repos: rev: v2.3.0 hooks: - id: codespell - args: ["--ignore-words-list=ALS"] additional_dependencies: - tomli - repo: https://github.com/python-poetry/poetry diff --git a/clinica/pipelines/statistics_surface/_utils.py b/clinica/pipelines/statistics_surface/_utils.py index 3cc78d3a6..134ecb457 100644 --- a/clinica/pipelines/statistics_surface/_utils.py +++ b/clinica/pipelines/statistics_surface/_utils.py @@ -158,12 +158,12 @@ def build_design_matrix(contrast: str, covariates: Optional[str] = None) -> str: Example ------- - >>> from clinica.pipelines.statistics_surface.statistics_surface_utils import _build_design_matrix - >>> _build_design_matrix('group', 'age sex group') + >>> from clinica.pipelines.statistics_surface._utils import build_design_matrix + >>> build_design_matrix('group', 'age sex group') 1 + group + age + sex - >>> _build_design_matrix('group', 'age') + >>> build_design_matrix('group', 'age') 1 + group + age - >>> _build_design_matrix('group', None) + >>> build_design_matrix('group', None) 1 + group """ if covariates: diff --git a/clinica/utils/image.py b/clinica/utils/image.py index e0d83210b..7df314527 100644 --- a/clinica/utils/image.py +++ b/clinica/utils/image.py @@ -16,7 +16,6 @@ "compute_aggregated_volume", "get_new_image_like", "merge_nifti_images_in_time_dimension", - "remove_dummy_dimension_from_image", "crop_nifti", "clip_nifti", "crop_nifti_using_t1_mni_template", @@ -220,31 +219,6 @@ def _check_volumes_from_images(images: Tuple[Path, ...]) -> Tuple[np.ndarray, .. return tuple(four_dimensional_volumes) -def remove_dummy_dimension_from_image(image: str, output: str) -> str: - """Remove all dummy dimensions (i.e. equal to 1) from an image. - - Parameters - ---------- - image : str - Path to the input image. - - output : str - Path to the desired output image. - - Returns - ------- - str : - The path to the output image. - """ - import nibabel as nib - from nilearn.image import new_img_like - - img = new_img_like(image, nib.load(image).get_fdata().squeeze()) - nib.save(img, output) - - return output - - @dataclass class Slice: """Interval composed of a starting point and ending point.""" diff --git a/ignore_words.txt b/ignore_words.txt index ffa73ac8c..bab4eba63 100644 --- a/ignore_words.txt +++ b/ignore_words.txt @@ -6,3 +6,4 @@ nd siz te vox +ALS diff --git a/poetry.lock b/poetry.lock index 142627484..7fe9ecb73 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. 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b/pyproject.toml index 04e4173f8..d9edda84a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ maintainers = [ { name = "Clinica developers", email = "clinica.run@gmail.com>" }, ] readme = "README.md" -requires-python = ">=3.9,<3.13" +requires-python = ">=3.10,<3.14" keywords = [ "bids", "image processing", @@ -33,7 +33,7 @@ classifiers = [ ] dependencies = [ "nibabel (>=5)", - "nipype (>=1.8.6)", + "nipype (>=1.10.0)", "argcomplete (>=1.9.4,<2)", "pandas (>=2,<3)", "jinja2 (>=3,<4)", @@ -43,7 +43,7 @@ dependencies = [ "nilearn (>=0.10.3,<1.0)", "colorlog (>=5,<6)", "xgboost", - "scipy (>=1.12,<2)", + "scipy (>=1.14,<2)", "matplotlib", "scikit-image", "pydicom", @@ -63,8 +63,9 @@ dependencies = [ "pydra-freesurfer (>=0.0.9)", "pydra-petpvc (>=0.0.4)", "pydra-fsl (>=0.0.22)", - "antspyx (>=0.4.2)", + "antspyx (>=0.5.4)", "rich (>=13.8.0)", + "brainstat (>=0.5.2)", ] [project.urls] @@ -90,9 +91,6 @@ mkdocs = "^1.1" mkdocs-material = ">=7.1.8" pymdown-extensions = "*" 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"output_image.nii.gz") - assert_array_equal(result_image.affine, np.eye(4)) - assert_array_equal(result_image.get_fdata(), input_data) - - def test_slice_error(): from clinica.utils.image import Slice # noqa