ENH: Drop FSL prefix from maths (#60)

Author: ghisvail

README.md

@@ -26,17 +26,17 @@ for FMRI, MRI and DTI brain imaging data.
 
 ## Available tasks
 
-| Module   | Tasks                                                                                                              |
-|----------|--------------------------------------------------------------------------------------------------------------------|
-| bet      | BET, RobustFOV                                                                                                     |
-| eddy     | Eddy, ApplyTopup, Topup                                                                                            |
-| fast     | FAST                                                                                                               |
-| flirt    | FLIRT, ApplyXFM, ConcatXFM, ConvertXFM, InvertXFM, FixScaleSkew, Img2ImgCoord, Img2StdCoord, Std2ImgCoord          |
-| fnirt    | FNIRT, FNIRTFileUtils, ApplyWarp, ConvertWarp, InvWarp                                                             |
-| fugue    | FUGUE, PrepareFieldmap, Prelude, SigLoss                                                                           |
-| fslmaths | (**experimental**) FSLMaths, Mul                                                                                   |
-| susan    | SUSAN                                                                                                              |
-| utils    | ChFileType, FFT, Info, Interleave, Merge, Orient, Reorient2Std, ROI, SelectVols, Slice, SmoothFill, Split, SwapDim |
+| Module | Tasks                                                                                                              |
+|--------|--------------------------------------------------------------------------------------------------------------------|
+| bet    | BET, RobustFOV                                                                                                     |
+| eddy   | Eddy, ApplyTopup, Topup                                                                                            |
+| fast   | FAST                                                                                                               |
+| flirt  | FLIRT, ApplyXFM, ConcatXFM, ConvertXFM, InvertXFM, FixScaleSkew, Img2ImgCoord, Img2StdCoord, Std2ImgCoord          |
+| fnirt  | FNIRT, FNIRTFileUtils, ApplyWarp, ConvertWarp, InvWarp                                                             |
+| fugue  | FUGUE, PrepareFieldmap, Prelude, SigLoss                                                                           |
+| maths  | (**experimental**) Maths, Mul                                                                                      |
+| susan  | SUSAN                                                                                                              |
+| utils  | ChFileType, FFT, Info, Interleave, Merge, Orient, Reorient2Std, ROI, SelectVols, Slice, SmoothFill, Split, SwapDim |
 
 ## Installation
 

src/pydra/tasks/fsl/__init__.py

@@ -17,7 +17,7 @@
 .. automodule:: pydra.tasks.fsl.utils
 """
 
-from . import fslmaths
+from . import maths
 from .bet import BET, RobustFOV
 from .eddy import ApplyTopup, Eddy, Topup
 from .fast import FAST
@@ -66,3 +66,4 @@
 FSLSmoothFill = SmoothFill
 FSLSplit = Split
 FSLSwapDim = SwapDim
+fslmaths = maths

src/pydra/tasks/fsl/fslmaths.py renamed to src/pydra/tasks/fsl/maths.py

@@ -9,22 +9,18 @@
 
 Convert input image to float:
 
->>> task = FSLMaths(input_image="input.nii")
->>> task.cmdline  # doctest: +ELLIPSIS
-'fslmaths input.nii .../input_fslmaths.nii -odt float'
+>>> task = Maths(input_image="input.nii")
+>>> task.cmdline    # doctest: +ELLIPSIS
+'fslmaths input.nii .../input_fslmaths.nii'
 
-Apply mask to input image:
+Multiply input image with a binary mask:
 
->>> task = Mul(
-...     input_image="input.nii",
-...     other_image="mask.nii",
-...     output_image="output.nii",
-... )
+>>> task = Mul(input_image="input.nii", other_image="mask.nii", output_image="output.nii")
 >>> task.cmdline
-'fslmaths input.nii -mul mask.nii output.nii -odt float'
+'fslmaths input.nii -mul mask.nii output.nii'
 """
 
-__all__ = ["FSLMaths", "Mul"]
+__all__ = ["Maths", "MathsSpec", "Mul"]
 
 from os import PathLike
 
@@ -33,8 +29,8 @@
 from pydra.engine.task import ShellCommandTask
 
 
-@define(slots=False, kw_only=True)
-class FSLMathsSpec(ShellSpec):
+@define(kw_only=True)
+class MathsSpec(ShellSpec):
     """Specifications for fslmaths."""
 
     _datatypes = {"char", "short", "int", "float", "double", "input"}
@@ -57,29 +53,34 @@ class FSLMathsSpec(ShellSpec):
     )
 
     output_datatype: str = field(
-        default="float",
-        metadata={"help_string": "output datatype", "argstr": "-odt", "position": -1, "allowed_values": _datatypes},
+        metadata={"help_string": "output datatype", "argstr": "-odt", "position": -1, "allowed_values": _datatypes}
     )
 
 
-class FSLMaths(ShellCommandTask):
+class Maths(ShellCommandTask):
     """Task definition for fslmaths."""
 
     executable = "fslmaths"
 
-    input_spec = SpecInfo(name="Input", bases=(FSLMathsSpec,))
+    input_spec = SpecInfo(name="Input", bases=(MathsSpec,))
 
 
 @define(kw_only=True)
-class MulSpec(FSLMathsSpec):
+class MulSpec(MathsSpec):
     """Specifications for fslmaths' mul."""
 
     other_image: PathLike = field(
         metadata={"help_string": "multiply input with other image", "mandatory": True, "argstr": "-mul"}
     )
 
 
-class Mul(FSLMaths):
+class Mul(Maths):
     """Task definition for fslmaths' mul."""
 
     input_spec = SpecInfo(name="Input", bases=(MulSpec,))
+
+
+# TODO: Drop compatibility alias for 0.x
+FSLMaths = Maths
+FSLMathsSpec = MathsSpec
+__all__ += ["FSLMaths", "FSLMathsSpec"]