diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml index 43c5a35..2ba2904 100644 --- a/.github/workflows/ci-cd.yml +++ b/.github/workflows/ci-cd.yml @@ -40,8 +40,8 @@ jobs: - name: Install development Pydra and fileformats-medimage run: | pip uninstall pydra fileformats-medimage -y - pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax - pip install --no-deps git+https://github.com/arcanaframework/fileformats-medimage.git@pydra-syntax-changes + pip install --no-deps git+https://github.com/nipype/pydra.git@develop + pip install --no-deps git+https://github.com/arcanaframework/fileformats-medimage.git@updated-pydra-imports - name: Test with pytest run: | pytest -sv --cov pydra.tasks.$SUBPACKAGE --cov-report xml diff --git a/pydra/tasks/dcm2niix/utils.py b/pydra/tasks/dcm2niix/utils.py index e7afe99..7b0051e 100644 --- a/pydra/tasks/dcm2niix/utils.py +++ b/pydra/tasks/dcm2niix/utils.py @@ -1,10 +1,8 @@ from pathlib import Path import typing as ty -from pydra.engine.specs import ShellDef, ShellOutputs from fileformats.application import Json from fileformats.medimage import DicomDir, Nifti1, NiftiGz, Bvec, Bval -from pydra.design import shell - +from pydra.compose import shell FS = ty.TypeVar("FS", bound=Nifti1 | NiftiGz | Json | Bval | Bvec) @@ -98,7 +96,7 @@ def dcm2niix_out_files(out_dir: Path, filename: str) -> list[str]: @shell.define -class Dcm2Niix(ShellDef["Dcm2Niix.Outputs"]): +class Dcm2Niix(shell.Task["Dcm2Niix.Outputs"]): """ Example ------- @@ -292,7 +290,7 @@ class Dcm2Niix(ShellDef["Dcm2Niix.Outputs"]): version: bool = shell.arg(default=False, argstr="--version", help="report version") xml: bool = shell.arg(default=False, argstr="--xml", help="Slicer format features") - class Outputs(ShellOutputs): + class Outputs(shell.Outputs): out_file: Nifti1 | NiftiGz = shell.out( help=( "output NIfTI image. If multiple nifti files are created (e.g. for "