moved packages out of src and set up auto version

pydra/tasks/fsl/__init__.py

@@ -0,0 +1,38 @@
+"""
+This is a basic doctest demonstrating that the package and pydra can both be successfully
+imported.
+
+>>> import pydra.engine
+>>> import pydra.tasks.fsl
+"""
+
+from warnings import warn
+from pathlib import Path
+
+pkg_path = Path(__file__).parent.parent
+
+try:
+    from ._version import __version__
+except ImportError:
+    raise RuntimeError(
+        "pydra-fsl has not been properly installed, please run "
+        f"`pip install -e {str(pkg_path)}` to install a development version"
+    )
+if "nipype" not in __version__:
+    try:
+        from .auto._version import nipype_version, nipype2pydra_version
+    except ImportError:
+        warn(
+            "Nipype interfaces haven't been automatically converted from their specs in "
+            f"`nipype-auto-conv`. Please run `{str(pkg_path / 'nipype-auto-conv' / 'generate')}` "
+            "to generated the converted Nipype interfaces in pydra.tasks.fsl.auto"
+        )
+    else:
+        n_ver = nipype_version.replace(".", "_")
+        n2p_ver = nipype2pydra_version.replace(".", "_")
+        __version__ += (
+            "_" if "+" in __version__ else "+"
+        ) + f"nipype{n_ver}_nipype2pydra{n2p_ver}"
+
+
+__all__ = ["__version__"]

pydra/tasks/fsl/latest.py

@@ -0,0 +1,3 @@
+PACKAGE_VERSION = "v6_0"
+
+from .v6_0 import *  # noqa

src/pydra/tasks/fsl/bet/bet.py → pydra/tasks/fsl/v6_0/bet/bet.py

@@ -41,9 +41,13 @@ class BETSpec(pydra.specs.ShellSpec):
         metadata={"help_string": "save brain surface outline", "argstr": "-o"}
     )
 
-    save_brain_mask: bool = attrs.field(metadata={"help_string": "save binary brain mask", "argstr": "-m"})
+    save_brain_mask: bool = attrs.field(
+        metadata={"help_string": "save binary brain mask", "argstr": "-m"}
+    )
 
-    save_skull_image: bool = attrs.field(metadata={"help_string": "save approximate skull image", "argstr": "-s"})
+    save_skull_image: bool = attrs.field(
+        metadata={"help_string": "save approximate skull image", "argstr": "-s"}
+    )
 
     save_brain_surface_mesh: bool = attrs.field(
         metadata={
@@ -74,7 +78,8 @@ class BETSpec(pydra.specs.ShellSpec):
 
     head_radius: float = attrs.field(
         metadata={
-            "help_string": "Head radius (in millimeters)." " Initial surface sphere is set to half of this value.",
+            "help_string": "Head radius (in millimeters)."
+            " Initial surface sphere is set to half of this value.",
             "argstr": "-r",
         }
     )

src/pydra/tasks/fsl/eddy/applytopup.py → pydra/tasks/fsl/v6_0/eddy/applytopup.py

@@ -58,7 +58,9 @@ def _to_input_index(field: Union[int, Sequence[int]]) -> str:
     return f"--inindex={','.join(str(index) for index in indexes)}"
 
 
-def _to_topup_basename(fieldmap_image: PathLike, field_coefficients_image: PathLike) -> str:
+def _to_topup_basename(
+    fieldmap_image: PathLike, field_coefficients_image: PathLike
+) -> str:
     if field_coefficients_image:
         path = PurePath(field_coefficients_image)
         basename = path.parent / path.name.split("_fieldcoef", 1)[0]
@@ -123,7 +125,11 @@ class ApplyTopupSpec(ShellSpec):
     )
 
     fieldmap_image: PathLike = field(
-        metadata={"help_string": "fieldmap image", "mandatory": True, "xor": {"field_coefficients_image"}}
+        metadata={
+            "help_string": "fieldmap image",
+            "mandatory": True,
+            "xor": {"field_coefficients_image"},
+        }
     )
 
     field_coefficients_image: PathLike = field(
@@ -135,10 +141,16 @@ class ApplyTopupSpec(ShellSpec):
         }
     )
 
-    movement_parameters_file: PathLike = field(metadata={"help_string": "movement parameters file computed by topup"})
+    movement_parameters_file: PathLike = field(
+        metadata={"help_string": "movement parameters file computed by topup"}
+    )
 
     output_image: PathLike = field(
-        metadata={"help_string": "output image", "argstr": "--out", "formatter": _to_output_image}
+        metadata={
+            "help_string": "output image",
+            "argstr": "--out",
+            "formatter": _to_output_image,
+        }
     )
 
     method: str = field(
@@ -168,7 +180,9 @@ class ApplyTopupSpec(ShellSpec):
         },
     )
 
-    verbose: bool = field(metadata={"help_string": "enable verbose logging", "argstr": "--verbose"})
+    verbose: bool = field(
+        metadata={"help_string": "enable verbose logging", "argstr": "--verbose"}
+    )
 
 
 class ApplyTopup(ShellCommandTask):

src/pydra/tasks/fsl/eddy/eddy.py → pydra/tasks/fsl/v6_0/eddy/eddy.py

@@ -84,7 +84,9 @@ class EddySpec(ShellSpec):
         }
     )
 
-    fieldmap_image: PathLike = field(metadata={"help_string": "fieldmap image", "argstr": "--field={fieldmap_image}"})
+    fieldmap_image: PathLike = field(
+        metadata={"help_string": "fieldmap image", "argstr": "--field={fieldmap_image}"}
+    )
 
     fieldmap_matrix: PathLike = field(
         metadata={
@@ -95,7 +97,10 @@ class EddySpec(ShellSpec):
     )
 
     no_peas: bool = field(
-        metadata={"help_string": "do not perform post-Eddy alignment of shells", "argstr": "--dont_peas"}
+        metadata={
+            "help_string": "do not perform post-Eddy alignment of shells",
+            "argstr": "--dont_peas",
+        }
     )
 
     # Parameters specifying names of output-files.
@@ -142,7 +147,9 @@ class EddySpec(ShellSpec):
         },
     )
 
-    fill_empty_planes: bool = field(metadata={"help_string": "detect and fill empty planes", "argstr": "--fep"})
+    fill_empty_planes: bool = field(
+        metadata={"help_string": "detect and fill empty planes", "argstr": "--fep"}
+    )
 
     interpolation: str = field(
         default="spline",
@@ -179,7 +186,9 @@ class EddySpec(ShellSpec):
     )
 
     # Parameters for outlier replacement (ol)
-    replace_outliers: bool = field(metadata={"help_string": "replace outliers", "argstr": "--repol"})
+    replace_outliers: bool = field(
+        metadata={"help_string": "replace outliers", "argstr": "--repol"}
+    )
 
     outlier_num_stdevs: int = field(
         metadata={
@@ -206,7 +215,12 @@ class EddySpec(ShellSpec):
         }
     )
 
-    multiband_factor: int = field(metadata={"help_string": "multiband factor", "argstr": "--mb={multiband_factor}"})
+    multiband_factor: int = field(
+        metadata={
+            "help_string": "multiband factor",
+            "argstr": "--mb={multiband_factor}",
+        }
+    )
 
     multiband_offset: int = field(
         metadata={
@@ -297,18 +311,33 @@ class EddySpec(ShellSpec):
 
     # Miscellaneous parameters.
     data_is_shelled: bool = field(
-        metadata={"help_string": "bypass checks for data shelling", "argstr": "--data_is_shelled"}
+        metadata={
+            "help_string": "bypass checks for data shelling",
+            "argstr": "--data_is_shelled",
+        }
     )
 
     random_seed: int = field(
-        metadata={"help_string": "random seed for voxel selection", "argstr": "--initrand={random_seed}"}
+        metadata={
+            "help_string": "random seed for voxel selection",
+            "argstr": "--initrand={random_seed}",
+        }
     )
 
-    save_cnr_maps: bool = field(metadata={"help_string": "save shell-wise CNR maps", "argstr": "--cnr_maps"})
+    save_cnr_maps: bool = field(
+        metadata={"help_string": "save shell-wise CNR maps", "argstr": "--cnr_maps"}
+    )
 
-    save_residuals: bool = field(metadata={"help_string": "save residuals for all scans", "argstr": "--residuals"})
+    save_residuals: bool = field(
+        metadata={
+            "help_string": "save residuals for all scans",
+            "argstr": "--residuals",
+        }
+    )
 
-    verbose: bool = field(metadata={"help_string": "enable verbose logging", "argstr": "--verbose"})
+    verbose: bool = field(
+        metadata={"help_string": "enable verbose logging", "argstr": "--verbose"}
+    )
 
 
 @define(slots=False, kw_only=True)

src/pydra/tasks/fsl/eddy/topup.py → pydra/tasks/fsl/v6_0/eddy/topup.py

@@ -48,7 +48,11 @@ class TopupSpec(ShellSpec):
     """Specifications for topup."""
 
     input_image: PathLike = field(
-        metadata={"help_string": "input image", "mandatory": True, "argstr": "--imain={input_image}"}
+        metadata={
+            "help_string": "input image",
+            "mandatory": True,
+            "argstr": "--imain={input_image}",
+        }
     )
 
     encoding_file: PathLike = field(
@@ -204,10 +208,16 @@ class TopupSpec(ShellSpec):
     )
 
     num_threads: int = field(
-        default=1, metadata={"help_string": "number of threads to use", "argstr": "--nthr={num_threads}"}
+        default=1,
+        metadata={
+            "help_string": "number of threads to use",
+            "argstr": "--nthr={num_threads}",
+        },
     )
 
-    verbose: bool = field(metadata={"help_string": "enable verbose logging", "argstr": "--verbose"})
+    verbose: bool = field(
+        metadata={"help_string": "enable verbose logging", "argstr": "--verbose"}
+    )
 
 
 @define(slots=False, kw_only=True)

src/pydra/tasks/fsl/fast.py → pydra/tasks/fsl/v6_0/fast.py

@@ -34,7 +34,9 @@ class FASTSpec(pydra.specs.ShellSpec):
             "help_string": "type of input image (T1, T2 or PD)",
             "argstr": "-t",
             "allowed_values": {"T1", "T2", "PD"},
-            "formatter": lambda image_type: "-t {:d}".format({"T1": 1, "T2": 2, "PD": 3}.get(image_type)),
+            "formatter": lambda image_type: "-t {:d}".format(
+                {"T1": 1, "T2": 2, "PD": 3}.get(image_type)
+            ),
         },
     )
 

src/pydra/tasks/fsl/flirt/convertxfm.py → pydra/tasks/fsl/v6_0/flirt/convertxfm.py

@@ -66,14 +66,19 @@ class ConvertXFMSpec(BaseSpec):
     """Specifications for convert_xfm."""
 
     fixscaleskew_matrix: os.PathLike = attrs.field(
-        metadata={"help_string": " fix scaling and skewness with this matrix", "argstr": "-fixscaleskew"}
+        metadata={
+            "help_string": " fix scaling and skewness with this matrix",
+            "argstr": "-fixscaleskew",
+        }
     )
 
     concat_matrix: os.PathLike = attrs.field(
         metadata={"help_string": "concatenate with this matrix", "argstr": "-concat"}
     )
 
-    inverse: bool = attrs.field(metadata={"help_string": "invert the resulting matrix", "argstr": "-inverse"})
+    inverse: bool = attrs.field(
+        metadata={"help_string": "invert the resulting matrix", "argstr": "-inverse"}
+    )
 
 
 class ConvertXFM(pydra.engine.ShellCommandTask):
@@ -89,7 +94,11 @@ class ConcatXFMSpec(BaseSpec):
     """Specifications for concat_xfm."""
 
     concat_matrix: os.PathLike = attrs.field(
-        metadata={"help_string": "concatenate with this matrix", "mandatory": True, "argstr": "-concat"}
+        metadata={
+            "help_string": "concatenate with this matrix",
+            "mandatory": True,
+            "argstr": "-concat",
+        }
     )
 
 
@@ -103,7 +112,10 @@ class ConcatXFM(ConvertXFM):
 class InvertXFMSpec(BaseSpec):
     """Specifications for invert_xfm."""
 
-    inverse: bool = attrs.field(default=True, metadata={"help_string": "invert the input matrix", "argstr": "-inverse"})
+    inverse: bool = attrs.field(
+        default=True,
+        metadata={"help_string": "invert the input matrix", "argstr": "-inverse"},
+    )
 
 
 class InvertXFM(ConvertXFM):

src/pydra/tasks/fsl/flirt/flirt.py → pydra/tasks/fsl/v6_0/flirt/flirt.py

@@ -74,12 +74,20 @@
 class BaseSpec(ShellSpec):
     """Common specifications for FLIRT-based tasks."""
 
-    input_image: PathLike = field(metadata={"help_string": "input image", "mandatory": True, "argstr": "-in"})
+    input_image: PathLike = field(
+        metadata={"help_string": "input image", "mandatory": True, "argstr": "-in"}
+    )
 
-    reference_image: PathLike = field(metadata={"help_string": "reference image", "mandatory": True, "argstr": "-ref"})
+    reference_image: PathLike = field(
+        metadata={"help_string": "reference image", "mandatory": True, "argstr": "-ref"}
+    )
 
     output_image: str = field(
-        metadata={"help_string": "output image", "argstr": "-out", "output_file_template": "{input_image}_flirt"}
+        metadata={
+            "help_string": "output image",
+            "argstr": "-out",
+            "output_file_template": "{input_image}_flirt",
+        }
     )
 
     output_datatype: str = field(
@@ -96,14 +104,22 @@ class FLIRTSpec(BaseSpec):
     """Specifications for FLIRT."""
 
     input_weights: PathLike = field(
-        metadata={"help_string": "voxel-wise weighting for input image", "argstr": "-inweight"}
+        metadata={
+            "help_string": "voxel-wise weighting for input image",
+            "argstr": "-inweight",
+        }
     )
 
     reference_weights: PathLike = field(
-        metadata={"help_string": "voxel-wise weighting for reference image", "argstr": "-refweight"}
+        metadata={
+            "help_string": "voxel-wise weighting for reference image",
+            "argstr": "-refweight",
+        }
     )
 
-    initial_matrix: PathLike = field(metadata={"help_string": "initial transformation matrix", "argstr": "-init"})
+    initial_matrix: PathLike = field(
+        metadata={"help_string": "initial transformation matrix", "argstr": "-init"}
+    )
 
     output_matrix: str = field(
         metadata={
@@ -155,23 +171,33 @@ class ApplyXFMSpec(BaseSpec):
     """Specifications for ApplyXFM."""
 
     initial_matrix: PathLike = field(
-        metadata={"help_string": "initial transformation matrix", "mandatory": True, "argstr": "-init"}
+        metadata={
+            "help_string": "initial transformation matrix",
+            "mandatory": True,
+            "argstr": "-init",
+        }
     )
 
     isotropic_resolution: float = field(
         default=0.0,
         metadata={
             "help_string": "force resampling to isotropic resolution",
             "formatter": lambda isotropic_resolution: (
-                f"-applyisoxfm {isotropic_resolution}" if isotropic_resolution else "-applyxfm"
+                f"-applyisoxfm {isotropic_resolution}"
+                if isotropic_resolution
+                else "-applyxfm"
             ),
         },
     )
 
-    padding_size: float = field(metadata={"help_string": "padding size in voxels", "argstr": "-paddingsize"})
+    padding_size: float = field(
+        metadata={"help_string": "padding size in voxels", "argstr": "-paddingsize"}
+    )
 
 
 class ApplyXFM(FLIRT):
     """Task definition for ApplyXFM."""
 
-    input_spec = SpecInfo(name="Input", bases=(ApplyXFMSpec, specs.InterpolationSpec, specs.VerboseSpec))
+    input_spec = SpecInfo(
+        name="Input", bases=(ApplyXFMSpec, specs.InterpolationSpec, specs.VerboseSpec)
+    )