[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.github/workflows/ci-cd.yaml

@@ -24,7 +24,7 @@ jobs:
       uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
-      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')    
+      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
     - name: Install build dependencies
@@ -53,8 +53,8 @@ jobs:
       uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
-      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')    
-    - name: Download tasks converted from Nipype 
+      run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
+    - name: Download tasks converted from Nipype
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
@@ -83,7 +83,7 @@ jobs:
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.extras.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-  
+
   fileformats-test:
     runs-on: ubuntu-latest
     strategy:
@@ -120,7 +120,7 @@ jobs:
     - name: Removed unnecessary tools to free space
       run: |
         sudo rm -rf /usr/share/dotnet
-        sudo rm -rf "$AGENT_TOOLSDIRECTORY"      
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
     - name: Get Download cache Key
       id: cache-key
       run: echo "::set-output name=key::fsl-linux-ubuntu22_amd64-7.4.1"
@@ -153,7 +153,7 @@ jobs:
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
-    - name: Download tasks converted from Nipype 
+    - name: Download tasks converted from Nipype
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
@@ -190,7 +190,7 @@ jobs:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
-        fetch-depth: 0 
+        fetch-depth: 0
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -213,7 +213,7 @@ jobs:
       with:
         user: __token__
         password: ${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}
-        packages-dir: ./related-packages/fileformats/dist 
+        packages-dir: ./related-packages/fileformats/dist
 
   deploy-fileformats-extras:
     needs: [deploy-fileformats]
@@ -222,7 +222,7 @@ jobs:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
-        fetch-depth: 0 
+        fetch-depth: 0
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -245,7 +245,7 @@ jobs:
       with:
         user: __token__
         password: ${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}
-        packages-dir: ./related-packages/fileformats-extras/dist 
+        packages-dir: ./related-packages/fileformats-extras/dist
 
   deploy:
     needs: [deploy-fileformats-extras]
@@ -255,7 +255,7 @@ jobs:
       with:
         submodules: recursive
         fetch-depth: 0
-    - name: Download tasks converted from Nipype 
+    - name: Download tasks converted from Nipype
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
@@ -268,7 +268,7 @@ jobs:
         git checkout $TAG
         git add -f pydra/tasks/fsl/auto/_version.py
         git commit -am"added auto-generated version to make new tag for package version"
-        git tag ${TAG}post${POST}    
+        git tag ${TAG}post${POST}
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -297,9 +297,9 @@ jobs:
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}   
+        password: ${{ secrets.PYPI_API_TOKEN }}
 
 # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets.
 # Secrets are not accessible in the if: condition [0], so set an output variable [1]
 # [0] https://github.community/t/16928
-# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter        
+# [1] https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#setting-an-output-parameter

README.rst

@@ -19,7 +19,7 @@ This repository aims to be the canonical set of Pydra tasks for incorporating
 
 Part of this effort is to establish a (mostly) declarative language for describing tasks that
 potentially have intricate rules for determining the availability and names from the choice of
-inputs. 
+inputs.
 
 
 Automatically-generated vs manually-curated tasks
@@ -29,7 +29,7 @@ Automatically generated tasks can be found in the `pydra.tasks.fsl.auto` package
 These packages should be treated with extreme caution as they likely do not pass testing.
 Generated tasks that have been edited and pass testing are imported into one or more of the
 `pydra.tasks.fsl.v*` packages, corresponding to the version of the fsl toolkit
-they are designed for. 
+they are designed for.
 
 Tests
 -----
@@ -160,7 +160,7 @@ in the ``inputs > types`` and ``outputs > types`` dicts of the YAML spec.
 
 If the required file-type is not found implemented within fileformats, please see the `fileformats
 docs <https://arcanaframework.github.io/fileformats/developer.html>`__ for instructions on how to define
-new fileformat types, and see 
+new fileformat types, and see
 `fileformats-medimage-extras <https://github.com/ArcanaFramework/fileformats-medimage-extras/blob/6c2dabe91e95687eebc2639bb6f034cf9595ecfc/fileformats/extras/medimage/nifti.py#L30-L48>`__
 for an example on how to implement methods to generate sample data for them.
 

nipype-auto-conv/requirements.txt

@@ -9,4 +9,4 @@ fileformats-medimage >=0.4
 fileformats-datascience >= 0.1
 fileformats-medimage-fsl
 traits
-nipype2pydra
+nipype2pydra

nipype-auto-conv/specs/apply_topup.yaml

@@ -5,18 +5,18 @@
 #
 # Docs
 # ----
-# 
+#
 #     Interface for FSL topup, a tool for estimating and correcting
 #     susceptibility induced distortions.
 #     `General reference
 #     <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ApplytopupUsersGuide>`_
 #     and `use example
 #     <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup>`_.
-# 
-# 
+#
+#
 #     Examples
 #     --------
-# 
+#
 #     >>> from nipype.interfaces.fsl import ApplyTOPUP
 #     >>> applytopup = ApplyTOPUP()
 #     >>> applytopup.inputs.in_files = ["epi.nii", "epi_rev.nii"]
@@ -27,8 +27,8 @@
 #     >>> applytopup.cmdline # doctest: +ELLIPSIS
 #     'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii --inindex=1,2 --topup=topup --out=epi_corrected.nii.gz'
 #     >>> res = applytopup.run() # doctest: +SKIP
-# 
-#     
+#
+#
 task_name: ApplyTOPUP
 nipype_name: ApplyTOPUP
 nipype_module: nipype.interfaces.fsl.epi
@@ -117,8 +117,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true
@@ -145,8 +145,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/apply_xfm.yaml

@@ -7,13 +7,13 @@
 # ----
 # Currently just a light wrapper around FLIRT,
 #     with no modifications
-# 
+#
 #     ApplyXFM is used to apply an existing transform to an image
-# 
-# 
+#
+#
 #     Examples
 #     --------
-# 
+#
 #     >>> import nipype.interfaces.fsl as fsl
 #     >>> from nipype.testing import example_data
 #     >>> applyxfm = fsl.preprocess.ApplyXFM()
@@ -23,8 +23,8 @@
 #     >>> applyxfm.inputs.reference = example_data('mni.nii')
 #     >>> applyxfm.inputs.apply_xfm = True
 #     >>> result = applyxfm.run() # doctest: +SKIP
-# 
-#     
+#
+#
 task_name: ApplyXFM
 nipype_name: ApplyXFM
 nipype_module: nipype.interfaces.fsl.preprocess
@@ -217,8 +217,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/ar1_image.yaml

@@ -7,8 +7,8 @@
 # ----
 # Use fslmaths to generate an AR1 coefficient image across a
 #     given dimension. (Should use -odt float and probably demean first)
-# 
-#     
+#
+#
 task_name: AR1Image
 nipype_name: AR1Image
 nipype_module: nipype.interfaces.fsl.maths
@@ -88,8 +88,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/av_scale.yaml

@@ -6,16 +6,16 @@
 # Docs
 # ----
 # Use FSL avscale command to extract info from mat file output of FLIRT
-# 
+#
 #     Examples
 #     --------
-# 
+#
 #     >>> avscale = AvScale()
 #     >>> avscale.inputs.mat_file = 'flirt.mat'
 #     >>> res = avscale.run()  # doctest: +SKIP
-# 
-# 
-#     
+#
+#
+#
 task_name: AvScale
 nipype_name: AvScale
 nipype_module: nipype.interfaces.fsl.utils
@@ -68,7 +68,7 @@ tests:
   # dict[str, str] - values to provide to inputs fields in the task initialisation
   # (if not specified, will try to choose a sensible value)
     all_param:
-    # type=bool|default=False: 
+    # type=bool|default=False:
     mat_file:
     # type=file|default=<undefined>: mat file to read
     ref_file:
@@ -85,8 +85,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/b0_calc.yaml

@@ -5,24 +5,24 @@
 #
 # Docs
 # ----
-# 
+#
 #     B0 inhomogeneities occur at interfaces of materials with different magnetic susceptibilities,
 #     such as tissue-air interfaces. These differences lead to distortion in the local magnetic field,
 #     as Maxwell’s equations need to be satisfied. An example of B0 inhomogneity is the first volume
 #     of the 4D volume ```$FSLDIR/data/possum/b0_ppm.nii.gz```.
-# 
+#
 #     Examples
 #     --------
-# 
+#
 #     >>> from nipype.interfaces.fsl import B0Calc
 #     >>> b0calc = B0Calc()
 #     >>> b0calc.inputs.in_file = 'tissue+air_map.nii'
 #     >>> b0calc.inputs.z_b0 = 3.0
 #     >>> b0calc.inputs.output_type = "NIFTI_GZ"
 #     >>> b0calc.cmdline
 #     'b0calc -i tissue+air_map.nii -o tissue+air_map_b0field.nii.gz --chi0=4.000000e-07 -d -9.450000e-06 --extendboundary=1.00 --b0x=0.00 --gx=0.0000 --b0y=0.00 --gy=0.0000 --b0=3.00 --gz=0.0000'
-# 
-#     
+#
+#
 task_name: B0Calc
 nipype_name: B0Calc
 nipype_module: nipype.interfaces.fsl.possum
@@ -115,8 +115,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true
@@ -139,8 +139,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true