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

for more information, see https://pre-commit.ci
nipype · Mar 20, 2024 · 15a2d59 · 15a2d59
1 parent fdcf89d
commit 15a2d59
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Showing 40 changed files with 768 additions and 768 deletions.
diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
@@ -24,7 +24,7 @@ jobs:
       uses: actions/checkout@v3
     - 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@v4
     - name: Install build dependencies
@@ -53,8 +53,8 @@ jobs:
       uses: actions/checkout@v3
     - 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 $1}')
+    - name: Download tasks converted from Nipype
       uses: actions/download-artifact@v3
       with:
         name: converted-nipype
@@ -83,7 +83,7 @@ jobs:
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.medimage_ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.extras.medimage_ants as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-  
+
   fileformats-test:
     runs-on: ubuntu-latest
     strategy:
@@ -120,7 +120,7 @@ jobs:
     - name: Removed unnecessary tools to free space
       run: |
         sudo rm -rf /usr/share/dotnet
-        sudo rm -rf "$AGENT_TOOLSDIRECTORY"      
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
     - name: Get Download cache Key
       id: cache-key
       run: echo "::set-output name=key::ants-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@v3
       with:
         submodules: recursive
-        fetch-depth: 0 
+        fetch-depth: 0
     - name: Set up Python
       uses: actions/setup-python@v4
       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@v3
       with:
         submodules: recursive
-        fetch-depth: 0 
+        fetch-depth: 0
     - name: Set up Python
       uses: actions/setup-python@v4
       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/ants/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@v4
       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
diff --git a/README.rst b/README.rst
@@ -27,7 +27,7 @@ Automatically generated tasks can be found in the `pydra.tasks.ants.auto` packag
 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.ants.v*` packages, corresponding to the version of the ants toolkit
-they are designed for. 
+they are designed for.
 
 Tests
 -----
@@ -158,6 +158,6 @@ 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.
diff --git a/nipype-auto-conv/generate b/nipype-auto-conv/generate
@@ -70,7 +70,9 @@ post_release = (nipype_version + nipype2pydra_version).replace(".", "")
 """
     )
 
-auto_init += "\n\n__all__ = [\n" + "\n".join(f"    \"{i}\"," for i in all_interfaces) + "\n]\n"
+auto_init += (
+    "\n\n__all__ = [\n" + "\n".join(f'    "{i}",' for i in all_interfaces) + "\n]\n"
+)
 
 with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "__init__.py", "w") as f:
     f.write(auto_init)
diff --git a/nipype-auto-conv/requirements.txt b/nipype-auto-conv/requirements.txt
@@ -8,4 +8,4 @@ fileformats-medimage >=0.4
 fileformats-datascience >= 0.1
 fileformats-medimage-ants
 traits
-nipype2pydra
+nipype2pydra
diff --git a/nipype-auto-conv/specs/affine_initializer.yaml b/nipype-auto-conv/specs/affine_initializer.yaml
@@ -5,17 +5,17 @@
 #
 # Docs
 # ----
-# 
+#
 #     Initialize an affine transform (as in antsBrainExtraction.sh)
-# 
+#
 #     >>> from nipype.interfaces.ants import AffineInitializer
 #     >>> init = AffineInitializer()
 #     >>> init.inputs.fixed_image = 'fixed1.nii'
 #     >>> init.inputs.moving_image = 'moving1.nii'
 #     >>> init.cmdline
 #     'antsAffineInitializer 3 fixed1.nii moving1.nii transform.mat 15.000000 0.100000 0 10'
-# 
-#     
+#
+#
 task_name: AffineInitializer
 nipype_name: AffineInitializer
 nipype_module: nipype.interfaces.ants.utils
@@ -98,8 +98,8 @@ 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
@@ -120,8 +120,8 @@ 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

diff --git a/nipype-auto-conv/specs/ai.yaml b/nipype-auto-conv/specs/ai.yaml
@@ -5,9 +5,9 @@
 #
 # Docs
 # ----
-# 
+#
 #     Calculate the optimal linear transform parameters for aligning two images.
-# 
+#
 #     Examples
 #     --------
 #     >>> AI(
@@ -17,16 +17,16 @@
 #     ... ).cmdline
 #     'antsAI -c [10,1e-06,10] -d 3 -m Mattes[structural.nii,epi.nii,32,Regular,1]
 #     -o initialization.mat -p 0 -s [20,0.12] -t Affine[0.1] -v 0'
-# 
+#
 #     >>> AI(fixed_image='structural.nii',
 #     ...    moving_image='epi.nii',
 #     ...    metric=('Mattes', 32, 'Regular', 1),
 #     ...    search_grid=(12, (1, 1, 1)),
 #     ... ).cmdline
 #     'antsAI -c [10,1e-06,10] -d 3 -m Mattes[structural.nii,epi.nii,32,Regular,1]
 #     -o initialization.mat -p 0 -s [20,0.12] -g [12.0,1x1x1] -t Affine[0.1] -v 0'
-# 
-#     
+#
+#
 task_name: AI
 nipype_name: AI
 nipype_module: nipype.interfaces.ants.utils
@@ -123,8 +123,8 @@ 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