REF: Normalize all input and output spec names

ghisvail · tclose · commit b567f152b2f4 · 2024-03-25T12:49:32.000+11:00
Apply convention used upstream in Pydra:
- input_spec -&gt; Input
- output_spec -&gt; Output
diff --git a/src/pydra/tasks/fsl/bet/bet.py b/src/pydra/tasks/fsl/bet/bet.py
@@ -197,6 +197,6 @@ class BET(pydra.engine.ShellCommandTask):
 
     executable = "bet"
 
-    input_spec = pydra.specs.SpecInfo(name="BETInput", bases=(BETSpec, BETVariationsSpec))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(BETSpec, BETVariationsSpec))
 
-    output_spec = pydra.specs.SpecInfo(name="BETOutput", bases=(BETOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(BETOutSpec,))
diff --git a/src/pydra/tasks/fsl/bet/robustfov.py b/src/pydra/tasks/fsl/bet/robustfov.py
@@ -65,4 +65,4 @@ class RobustFOV(pydra.engine.ShellCommandTask):
 
     executable = "robustfov"
 
-    input_spec = pydra.specs.SpecInfo(name="RobustFOVInput", bases=(RobustFOVSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(RobustFOVSpec,))
diff --git a/src/pydra/tasks/fsl/eddy/applytopup.py b/src/pydra/tasks/fsl/eddy/applytopup.py
@@ -178,4 +178,4 @@ class ApplyTopup(ShellCommandTask):
 
     executable = "applytopup"
 
-    input_spec = SpecInfo(name="Inputs", bases=(ApplyTopupSpec,))
+    input_spec = SpecInfo(name="Input", bases=(ApplyTopupSpec,))
diff --git a/src/pydra/tasks/fsl/eddy/eddy.py b/src/pydra/tasks/fsl/eddy/eddy.py
@@ -341,6 +341,6 @@ class Eddy(ShellCommandTask):
 
     executable = "eddy"
 
-    input_spec = SpecInfo(name="Inputs", bases=(EddySpec,))
+    input_spec = SpecInfo(name="Input", bases=(EddySpec,))
 
-    output_spec = SpecInfo(name="Outputs", bases=(EddyOutSpec,))
+    output_spec = SpecInfo(name="Output", bases=(EddyOutSpec,))
diff --git a/src/pydra/tasks/fsl/eddy/topup.py b/src/pydra/tasks/fsl/eddy/topup.py
@@ -222,6 +222,6 @@ class Topup(ShellCommandTask):
 
     executable = "topup"
 
-    input_spec = SpecInfo(name="Inputs", bases=(TopupSpec,))
+    input_spec = SpecInfo(name="Input", bases=(TopupSpec,))
 
-    output_spec = SpecInfo(name="Outputs", bases=(TopupOutSpec,))
+    output_spec = SpecInfo(name="Output", bases=(TopupOutSpec,))
diff --git a/src/pydra/tasks/fsl/fast.py b/src/pydra/tasks/fsl/fast.py
@@ -207,6 +207,6 @@ class FAST(pydra.engine.ShellCommandTask):
 
     executable = "fast"
 
-    input_spec = pydra.specs.SpecInfo(name="FASTInput", bases=(FASTSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FASTSpec,))
 
-    output_spec = pydra.specs.SpecInfo(name="FASTOuput", bases=(FASTOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Ouput", bases=(FASTOutSpec,))
diff --git a/src/pydra/tasks/fsl/flirt/convertxfm.py b/src/pydra/tasks/fsl/flirt/convertxfm.py
@@ -81,7 +81,7 @@ class ConvertXFM(pydra.engine.ShellCommandTask):
 
     executable = "convert_xfm"
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(ConvertXFMSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(ConvertXFMSpec,))
 
 
 @attrs.define(slots=False, kw_only=True)
@@ -96,7 +96,7 @@ class ConcatXFMSpec(BaseSpec):
 class ConcatXFM(ConvertXFM):
     """Task definition for matrix concatenation using convert_xfm."""
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(ConcatXFMSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(ConcatXFMSpec,))
 
 
 @attrs.define(slots=False, kw_only=True)
@@ -109,7 +109,7 @@ class InvertXFMSpec(BaseSpec):
 class InvertXFM(ConvertXFM):
     """Task definition for matrix inversion using convert_xfm."""
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(InvertXFMSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(InvertXFMSpec,))
 
 
 @attrs.define(slots=False, kw_only=True)
@@ -128,4 +128,4 @@ class FixScaleSkewSpec(BaseSpec):
 class FixScaleSkew(ConvertXFM):
     """Task definition for fixing matrix scaling and skewness using convert_xfm."""
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(FixScaleSkewSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FixScaleSkewSpec,))
diff --git a/src/pydra/tasks/fsl/flirt/flirt.py b/src/pydra/tasks/fsl/flirt/flirt.py
@@ -138,7 +138,7 @@ class FLIRT(ShellCommandTask):
     executable = "flirt"
 
     input_spec = SpecInfo(
-        name="Inputs",
+        name="Input",
         bases=(
             FLIRTSpec,
             specs.SearchSpec,
@@ -174,4 +174,4 @@ class ApplyXFMSpec(BaseSpec):
 class ApplyXFM(FLIRT):
     """Task definition for ApplyXFM."""
 
-    input_spec = SpecInfo(name="Inputs", bases=(ApplyXFMSpec, specs.InterpolationSpec, specs.VerboseSpec))
+    input_spec = SpecInfo(name="Input", bases=(ApplyXFMSpec, specs.InterpolationSpec, specs.VerboseSpec))
diff --git a/src/pydra/tasks/fsl/flirt/img2imgcoord.py b/src/pydra/tasks/fsl/flirt/img2imgcoord.py
@@ -56,6 +56,6 @@ class Img2ImgCoord(pydra.engine.ShellCommandTask):
 
     executable = "img2imgcoord"
 
-    input_spec = pydra.specs.SpecInfo(name="Img2ImgCoordInput", bases=(Img2ImgCoordSpec, specs.VerboseSpec))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(Img2ImgCoordSpec, specs.VerboseSpec))
 
-    output_spec = pydra.specs.SpecInfo(name="Img2ImgCoordOutput", bases=(Img2ImgCoordOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(Img2ImgCoordOutSpec,))
diff --git a/src/pydra/tasks/fsl/flirt/img2stdcoord.py b/src/pydra/tasks/fsl/flirt/img2stdcoord.py
@@ -55,6 +55,6 @@ class Img2StdCoord(pydra.engine.ShellCommandTask):
 
     executable = "img2stdcoord"
 
-    input_spec = pydra.specs.SpecInfo(name="Img2StdCoordInput", bases=(Img2StdCoordSpec, specs.VerboseSpec))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(Img2StdCoordSpec, specs.VerboseSpec))
 
-    output_spec = pydra.specs.SpecInfo(name="Img2StdCoordOutput", bases=(Img2StdCoordOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(Img2StdCoordOutSpec,))
diff --git a/src/pydra/tasks/fsl/flirt/std2imgcoord.py b/src/pydra/tasks/fsl/flirt/std2imgcoord.py
@@ -55,6 +55,6 @@ class Std2ImgCoord(pydra.engine.ShellCommandTask):
 
     executable = "std2imgcoord"
 
-    input_spec = pydra.specs.SpecInfo(name="Std2ImgCoordSpecInput", bases=(Std2ImgCoordSpec, specs.VerboseSpec))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(Std2ImgCoordSpec, specs.VerboseSpec))
 
-    output_spec = pydra.specs.SpecInfo(name="Std2ImgCoordSpecOutput", bases=(Std2ImgCoordOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(Std2ImgCoordOutSpec,))
diff --git a/src/pydra/tasks/fsl/fnirt/applywarp.py b/src/pydra/tasks/fsl/fnirt/applywarp.py
@@ -147,7 +147,4 @@ class ApplyWarp(pydra.engine.ShellCommandTask):
 
     executable = "applywarp"
 
-    input_spec = pydra.specs.SpecInfo(
-        name="ApplyWarpInput",
-        bases=(ApplyWarpSpec, specs.VerboseSpec),
-    )
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(ApplyWarpSpec, specs.VerboseSpec))
diff --git a/src/pydra/tasks/fsl/fnirt/convertwarp.py b/src/pydra/tasks/fsl/fnirt/convertwarp.py
@@ -171,7 +171,4 @@ class ConvertWarp(pydra.engine.ShellCommandTask):
 
     executable = "convertwarp"
 
-    input_spec = pydra.specs.SpecInfo(
-        name="ConvertWarpInput",
-        bases=(ConvertWarpSpec, specs.VerboseSpec),
-    )
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(ConvertWarpSpec, specs.VerboseSpec))
diff --git a/src/pydra/tasks/fsl/fnirt/fnirt.py b/src/pydra/tasks/fsl/fnirt/fnirt.py
@@ -262,7 +262,4 @@ class FNIRT(pydra.engine.ShellCommandTask):
 
     executable = "fnirt"
 
-    input_spec = pydra.specs.SpecInfo(
-        name="FNIRTInput",
-        bases=(FNIRTSpec, specs.VerboseSpec),
-    )
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FNIRTSpec, specs.VerboseSpec))
diff --git a/src/pydra/tasks/fsl/fnirt/fnirtfileutils.py b/src/pydra/tasks/fsl/fnirt/fnirtfileutils.py
@@ -115,7 +115,4 @@ class FNIRTFileUtils(pydra.engine.ShellCommandTask):
 
     executable = "fnirtfileutils"
 
-    input_spec = pydra.specs.SpecInfo(
-        name="FNIRTFileUtilsInput",
-        bases=(FNIRTFileUtilsSpec, specs.VerboseSpec),
-    )
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FNIRTFileUtilsSpec, specs.VerboseSpec))
diff --git a/src/pydra/tasks/fsl/fnirt/invwarp.py b/src/pydra/tasks/fsl/fnirt/invwarp.py
@@ -100,7 +100,4 @@ class InvWarp(pydra.engine.ShellCommandTask):
 
     executable = "invwarp"
 
-    input_spec = pydra.specs.SpecInfo(
-        name="InvWarpInput",
-        bases=(InvWarpSpec, specs.VerboseSpec),
-    )
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(InvWarpSpec, specs.VerboseSpec))
diff --git a/src/pydra/tasks/fsl/fslmaths.py b/src/pydra/tasks/fsl/fslmaths.py
@@ -67,7 +67,7 @@ class FSLMaths(ShellCommandTask):
 
     executable = "fslmaths"
 
-    input_spec = SpecInfo(name="Inputs", bases=(FSLMathsSpec,))
+    input_spec = SpecInfo(name="Input", bases=(FSLMathsSpec,))
 
 
 @define(kw_only=True)
@@ -82,4 +82,4 @@ class MulSpec(FSLMathsSpec):
 class Mul(FSLMaths):
     """Task definition for fslmaths' mul."""
 
-    input_spec = SpecInfo(name="Inputs", bases=(MulSpec,))
+    input_spec = SpecInfo(name="Input", bases=(MulSpec,))
diff --git a/src/pydra/tasks/fsl/fugue/fsl_prepare_fieldmap.py b/src/pydra/tasks/fsl/fugue/fsl_prepare_fieldmap.py
@@ -57,4 +57,4 @@ class FSLPrepareFieldmap(pydra.engine.ShellCommandTask):
 
     executable = "fsl_prepare_fieldmap"
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(FSLPrepareFieldmapSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLPrepareFieldmapSpec,))
diff --git a/src/pydra/tasks/fsl/fugue/fugue.py b/src/pydra/tasks/fsl/fugue/fugue.py
@@ -237,6 +237,6 @@ class FUGUE(pydra.engine.ShellCommandTask):
 
     executable = "fugue"
 
-    input_spec = pydra.specs.SpecInfo(name="FUGUEInput", bases=(FUGUESpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FUGUESpec,))
 
-    output_spec = pydra.specs.SpecInfo(name="FUGUEOutput", bases=(FUGUEOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(FUGUEOutSpec,))
diff --git a/src/pydra/tasks/fsl/fugue/prelude.py b/src/pydra/tasks/fsl/fugue/prelude.py
@@ -149,4 +149,4 @@ class Prelude(pydra.engine.ShellCommandTask):
 
     executable = "prelude"
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(PreludeSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(PreludeSpec,))
diff --git a/src/pydra/tasks/fsl/fugue/sigloss.py b/src/pydra/tasks/fsl/fugue/sigloss.py
@@ -55,4 +55,4 @@ class SigLoss(pydra.engine.ShellCommandTask):
 
     executable = "sigloss"
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(SigLossSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(SigLossSpec,))
diff --git a/src/pydra/tasks/fsl/susan.py b/src/pydra/tasks/fsl/susan.py
@@ -100,4 +100,4 @@ class SUSAN(pydra.engine.ShellCommandTask):
 
     executable = "susan"
 
-    input_spec = pydra.specs.SpecInfo(name="SUSANInput", bases=(SUSANSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(SUSANSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslchfiletype.py b/src/pydra/tasks/fsl/utils/fslchfiletype.py
@@ -113,6 +113,6 @@ class FSLChFileType(pydra.engine.ShellCommandTask):
 
     executable = "fslchfiletype"
 
-    input_spec = pydra.specs.SpecInfo(name="FSLChFileTypeInput", bases=(FSLChFileTypeSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLChFileTypeSpec,))
 
-    output_spec = pydra.specs.SpecInfo(name="FSLChFileTypeOutput", bases=(FSLChFileTypeOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(FSLChFileTypeOutSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslfft.py b/src/pydra/tasks/fsl/utils/fslfft.py
@@ -53,4 +53,4 @@ class FSLFFT(pydra.engine.ShellCommandTask):
 
     executable = "fslfft"
 
-    input_spec = pydra.specs.SpecInfo(name="FSLFFTInput", bases=(FSLFFTSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLFFTSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslinfo.py b/src/pydra/tasks/fsl/utils/fslinfo.py
@@ -127,6 +127,6 @@ class FSLInfo(pydra.engine.ShellCommandTask):
 
     executable = "fslinfo"
 
-    input_spec = pydra.specs.SpecInfo(name="FSLInfoInput", bases=(FSLInfoSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLInfoSpec,))
 
-    output_spec = pydra.specs.SpecInfo(name="FSLInfoOutput", bases=(FSLInfoOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(FSLInfoOutSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslinterleave.py b/src/pydra/tasks/fsl/utils/fslinterleave.py
@@ -56,4 +56,4 @@ class FSLInterleave(pydra.engine.ShellCommandTask):
 
     executable = "fslinterleave"
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(FSLInterleaveSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLInterleaveSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslmerge.py b/src/pydra/tasks/fsl/utils/fslmerge.py
@@ -75,4 +75,4 @@ class FSLMerge(pydra.engine.ShellCommandTask):
 
     executable = "fslmerge"
 
-    input_spec = pydra.specs.SpecInfo(name="FSLMergeInput", bases=(FSLMergeSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLMergeSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslorient.py b/src/pydra/tasks/fsl/utils/fslorient.py
@@ -81,6 +81,6 @@ class FSLOrient(ShellCommandTask):
 
     executable = "fslorient"
 
-    input_spec = SpecInfo(name="Inputs", bases=(FSLOrientSpec,))
+    input_spec = SpecInfo(name="Input", bases=(FSLOrientSpec,))
 
-    output_spec = SpecInfo(name="Outputs", bases=(FSLOrientOutSpec,))
+    output_spec = SpecInfo(name="Output", bases=(FSLOrientOutSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslreorient2std.py b/src/pydra/tasks/fsl/utils/fslreorient2std.py
@@ -59,4 +59,4 @@ class FSLReorient2Std(pydra.engine.ShellCommandTask):
 
     executable = "fslreorient2std"
 
-    input_spec = pydra.specs.SpecInfo(name="FSLReorient2StdInput", bases=(FSLReorient2StdSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLReorient2StdSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslroi.py b/src/pydra/tasks/fsl/utils/fslroi.py
@@ -83,4 +83,4 @@ class FSLROI(ShellCommandTask):
 
     executable = "fslroi"
 
-    input_spec = SpecInfo(name="Inputs", bases=(FSLROISpec,))
+    input_spec = SpecInfo(name="Input", bases=(FSLROISpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslselectvols.py b/src/pydra/tasks/fsl/utils/fslselectvols.py
@@ -86,4 +86,4 @@ class FSLSelectVols(pydra.engine.ShellCommandTask):
 
     executable = "fslselectvols"
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(FSLSelectVolsSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLSelectVolsSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslsmoothfill.py b/src/pydra/tasks/fsl/utils/fslsmoothfill.py
@@ -43,4 +43,4 @@ class FSLSmoothFill(pydra.engine.ShellCommandTask):
 
     executable = "fslsmoothfill"
 
-    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(FSLSmoothFillSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLSmoothFillSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslsplit.py b/src/pydra/tasks/fsl/utils/fslsplit.py
@@ -82,9 +82,9 @@ class FSLSplit(pydra.engine.ShellCommandTask):
 
     executable = "fslsplit"
 
-    input_spec = pydra.specs.SpecInfo(name="FSLSplitInput", bases=(FSLSplitSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLSplitSpec,))
 
-    output_spec = pydra.specs.SpecInfo(name="FSLSplitOutput", bases=(FSLSplitOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(FSLSplitOutSpec,))
 
 
 @attrs.define(slots=False, kw_only=True)
@@ -108,6 +108,6 @@ class FSLSliceOutSpec(FSLSplitOutSpec):
 class FSLSlice(FSLSplit):
     """Task definition for fslslice."""
 
-    input_spec = pydra.specs.SpecInfo(name="FSLSliceInput", bases=(FSLSliceSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLSliceSpec,))
 
-    output_spec = pydra.specs.SpecInfo(name="FSLSliceOutput", bases=(FSLSliceOutSpec,))
+    output_spec = pydra.specs.SpecInfo(name="Output", bases=(FSLSliceOutSpec,))
diff --git a/src/pydra/tasks/fsl/utils/fslswapdim.py b/src/pydra/tasks/fsl/utils/fslswapdim.py
@@ -102,4 +102,4 @@ class FSLSwapDim(pydra.engine.ShellCommandTask):
 
     executable = "fslswapdim"
 
-    input_spec = pydra.specs.SpecInfo(name="FSLSwapDimInput", bases=(FSLSwapDimSpec,))
+    input_spec = pydra.specs.SpecInfo(name="Input", bases=(FSLSwapDimSpec,))

Original file line number	Diff line number	Diff line change
`@@ -65,4 +65,4 @@ class RobustFOV(pydra.engine.ShellCommandTask):`
`65`	`65`
`66`	`66`	`executable = "robustfov"`
`67`	`67`
`68`		`- input_spec = pydra.specs.SpecInfo(name="RobustFOVInput", bases=(RobustFOVSpec,))`
	`68`	`+ input_spec = pydra.specs.SpecInfo(name="Input", bases=(RobustFOVSpec,))`
Original file line number	Diff line number	Diff line change
`@@ -178,4 +178,4 @@ class ApplyTopup(ShellCommandTask):`
`178`	`178`
`179`	`179`	`executable = "applytopup"`
`180`	`180`
`181`		`- input_spec = SpecInfo(name="Inputs", bases=(ApplyTopupSpec,))`
	`181`	`+ input_spec = SpecInfo(name="Input", bases=(ApplyTopupSpec,))`