Setting up tests to use development fileformats

Author: tclose

.github/workflows/ci-cd.yml

@@ -39,12 +39,13 @@ jobs:
         pip install ".[test]"
         python -c "import pydra.tasks.$SUBPACKAGE as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-    - name: Install development Pydra
-      run: pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax
+    - name: Install development Pydra and fileformats-medimage
+      run: |
+        pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax
+        pip install --no-deps git+https://github.com/arcanaframework/fileformats-medimage.git@pydra-syntax-changes
     - name: Test with pytest
       run: |
-        pytest -sv --doctest-modules pydra/tasks/$SUBPACKAGE \
-            --cov pydra.tasks.$SUBPACKAGE --cov-report xml
+        pytest -sv --cov pydra.tasks.$SUBPACKAGE --cov-report xml
     - uses: codecov/codecov-action@v1
       if: ${{ always() }}
 

pydra/tasks/dcm2niix/tests/test_utils.py

@@ -1,12 +1,14 @@
+import os
 from pydra.tasks.dcm2niix.utils import Dcm2Niix
 from fileformats.medimage import DicomDir
 
 
 def test_dcm2niix():
     task = Dcm2Niix()
-    task.inputs.in_dir = DicomDir.mock("test-data/test_dicoms")
-    task.inputs.out_dir = "test-data"
-    task.inputs.compress = "y"
+    task.in_dir = DicomDir.mock("test-data/test_dicoms")
+    task.out_dir = "test-data"
+    task.compress = "y"
     assert (
-        task.cmdline == "dcm2niix -o test-data -f out_file -z y test-data/test_dicoms"
+        task.cmdline
+        == f"dcm2niix -b y -z y -f out_file -o test-data {os.getcwd()}/test-data/test_dicoms"
     )

pydra/tasks/dcm2niix/utils.py

@@ -1,14 +1,12 @@
-import attrs
 from pathlib import Path
 import typing as ty
 from pydra.engine.specs import ShellDef, ShellOutputs
-from fileformats.generic import File, Directory, FileSet
 from fileformats.application import Json
-from fileformats.medimage import Nifti1, NiftiGz, Bvec, Bval
+from fileformats.medimage import DicomDir, Nifti1, NiftiGz, Bvec, Bval
 from pydra.design import shell
 
 
-FS = ty.TypeVar("FS", bound=FileSet)
+FS = ty.TypeVar("FS", bound=Nifti1 | NiftiGz | Json | Bval | Bvec)
 
 
 def get_out_file(
@@ -105,16 +103,16 @@ class Dcm2Niix(ShellDef["Dcm2Niix.Outputs"]):
     Example
     -------
     >>> task = Dcm2Niix()
-    >>> task.inputs.in_dir = "test-data/test_dicoms"
-    >>> task.inputs.out_dir = "test-data"
-    >>> task.inputs.compress = "y"
+    >>> task.in_dir = "test-data/test_dicoms"
+    >>> task.out_dir = "test-data"
+    >>> task.compress = "y"
     >>> task.cmdline
-    'dcm2niix -o test-data -f out_file -z y test-data/test_dicoms'
+    'dcm2niix -b y -z y -f out_file -o test-data test-data/test_dicoms'
     """
 
     executable = "dcm2niix"
 
-    in_dir: Directory = shell.arg(
+    in_dir: DicomDir = shell.arg(
         argstr="'{in_dir}'",
         position=-1,
         help=("The directory containing the DICOMs to be converted"),
@@ -124,7 +122,7 @@ class Dcm2Niix(ShellDef["Dcm2Niix.Outputs"]):
         argstr="-o '{out_dir}'",
         help="output directory",
     )
-    filename: str = shell.arg(
+    filename: str | None = shell.arg(
         argstr="-f '{filename}'",
         help="The output name for the file",
         default="out_file",
@@ -320,7 +318,7 @@ class Outputs(ShellOutputs):
             # requires=[("bids", "y")],  # FIXME: should be either 'y' or 'o'
             callable=dcm2niix_out_bvec,
         )
-        out_files: list[File] = shell.out(
+        out_files: list[Nifti1 | NiftiGz | Json | Bval | Bvec] = shell.out(
             help=(
                 "all output files in a list, including files disambiguated "
                 "by their suffixes (e.g. echoes, phase-maps, etc... see "

pyproject.toml

@@ -7,7 +7,7 @@ name = "pydra-dcm2niix"
 description = "pydra-dcm2niix contains Pydra task specifications for the Dcm2niix converter"
 readme = "README.md"
 requires-python = ">=3.11"
-dependencies = ["pydra >=0.25"]
+dependencies = ["fileformats>=0.15a2", "pydra >=0.25"]
 license = { file = "LICENSE" }
 authors = [{ name = "Thomas G. Close", email = "[email protected]" }]
 maintainers = [{ name = "Thomas G. Close", email = "[email protected]" }]
@@ -32,7 +32,7 @@ dev = [
     "click >=8.1.3",
     "tqdm",
     "attrs >=23.1.0",
-    "fileformats-extras >= 0.12.1",
+    "fileformats-extras >= 0.15a2",
 ]
 doc = [
     "packaging",
@@ -49,7 +49,6 @@ test = [
     "pytest-xdist",
     "pytest-rerunfailures",
     "codecov",
-    "fileformats-medimage_dcm2niix-extras",
 ]
 
 [tool.hatch.version]

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+addopts = -vv