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Updated syntax to match pydra refactor #18

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Merged
merged 2 commits into from
Mar 28, 2025
Merged

Updated syntax to match pydra refactor #18

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566b243
updated syntax to match pydra refactor
tclose Mar 28, 2025
f20f267
pointed test build to development branches
tclose Mar 28, 2025
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4 changes: 2 additions & 2 deletions .github/workflows/ci-cd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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8 changes: 3 additions & 5 deletions pydra/tasks/dcm2niix/utils.py
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@@ -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)

Expand Down Expand Up @@ -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
-------
Expand Down Expand Up @@ -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 "
Expand Down