updated nipype converter specs

nipype-auto-conv/generate

@@ -8,7 +8,7 @@ from importlib import import_module
 import yaml
 import nipype
 import nipype2pydra.utils
-from nipype2pydra.task import TaskConverter
+from nipype2pydra.task import get_converter
 
 
 SPECS_DIR = Path(__file__).parent / "specs"
@@ -49,7 +49,7 @@ for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
 
     module_name = nipype2pydra.utils.to_snake_case(spec["task_name"])
 
-    converter = TaskConverter(
+    converter = get_converter(
         output_module=f"pydra.tasks.{PKG_NAME}.auto.{module_name}",
         callables_module=callables,  # type: ignore
         **spec,

nipype-auto-conv/specs/eddy.yaml

@@ -66,9 +66,9 @@ inputs:
     # type=file|default=<undefined>: File containing indices for all volumes in --imain into --acqp and --topup
     in_acqp: generic/file
     # type=file|default=<undefined>: File containing acquisition parameters
-    in_bvec: generic/file
+    in_bvec: medimage/bvec
     # type=file|default=<undefined>: File containing the b-vectors for all volumes in --imain
-    in_bval: generic/file
+    in_bval: medimage/bval
     # type=file|default=<undefined>: File containing the b-values for all volumes in --imain
     session: generic/file
     # type=file|default=<undefined>: File containing session indices for all volumes in --imain
@@ -82,7 +82,7 @@ inputs:
     # type=file|default=<undefined>: Matrix specifying the relative positions of the fieldmap, --field, and the first volume of the input file, --imain
     slice_order: text/text-file
     # type=file|default='': Name of text file completely specifying slice/group acquisition
-    json: generic/file
+    json: application/json
     # type=file|default='': Name of .json text file with information about slice timing
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)

nipype-auto-conv/specs/eddy_quad.yaml

@@ -49,9 +49,9 @@ inputs:
     # type=file|default=<undefined>: File containing acquisition parameters
     mask_file: generic/file
     # type=file|default=<undefined>: Binary mask file
-    bval_file: generic/file
+    bval_file: medimage/bval
     # type=file|default=<undefined>: b-values file
-    bvec_file: generic/file
+    bvec_file: medimage/bvec
     # type=file|default=<undefined>: b-vectors file - only used when <base_name>.eddy_residuals file is present
     field: generic/file
     # type=file|default=<undefined>: TOPUP estimated field (in Hz)

nipype-auto-conv/specs/smm.yaml

@@ -42,7 +42,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-   _p_map: generic/file
+    null_p_map: generic/file
     activation_p_map: generic/file
     # type=file: 
     deactivation_p_map: generic/file

nipype-auto-conv/specs/topup.yaml

@@ -58,7 +58,19 @@ inputs:
     out_logfile: generic/file
     # type=file: name of log-file
     # type=file|default=<undefined>: name of log-file
+    warp_res: typing.List[float]
+    subsamp: typing.List[int]
+    fwhm: typing.List[float]
+    reg_lambda: typing.List[float]
+    regmod: str
+    estmov: typing.List[int]
+    minmet: typing.List[int]
+    splineorder: int
+    interp: str
+    scale: bool
   metadata:
+    scale:
+      argstr: "--scale {int(scale)}"
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)
 outputs:
   omit: