niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v__update_afni_binaries.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__UPDATE_AFNI_BINARIES_METADATA = Metadata(
-    id="e0b835db0cb53555b172344e21f8897821de7ba7.boutiques",
+    id="deec96bb732968f11c7b74728a2a3574bd4352bf.boutiques",
     name="@update.afni.binaries",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,34 @@ V__UPDATE_AFNI_BINARIES_METADATA = Metadata(
 
 
 VUpdateAfniBinariesParameters = typing.TypedDict('VUpdateAfniBinariesParameters', {
-    "__STYXTYPE__": typing.Literal["@update.afni.binaries"],
+    "@type": typing.NotRequired[typing.Literal["afni/@update.afni.binaries"]],
+    "defaults_flag": bool,
+    "help_flag": bool,
+    "help_sys_progs_flag": bool,
+    "apsearch": typing.NotRequired[str | None],
+    "bindir": typing.NotRequired[str | None],
+    "curl_flag": bool,
+    "do_dotfiles_flag": bool,
+    "do_extras_flag": bool,
+    "echo_flag": bool,
+    "make_backup": typing.NotRequired[str | None],
+    "no_cert_verify_flag": bool,
+    "no_recur_flag": bool,
+    "proto": typing.NotRequired[str | None],
+    "quick_flag": bool,
+    "show_obsoletes_flag": bool,
+    "show_obsoletes_grep_flag": bool,
+    "show_system_progs_flag": bool,
+    "sys_ok_flag": bool,
+    "test_flag": bool,
+    "test_protos_flag": bool,
+    "revert_flag": bool,
+    "local_package": typing.NotRequired[str | None],
+    "prog_list": typing.NotRequired[list[str] | None],
+    "package": typing.NotRequired[str | None],
+})
+VUpdateAfniBinariesParametersTagged = typing.TypedDict('VUpdateAfniBinariesParametersTagged', {
+    "@type": typing.Literal["afni/@update.afni.binaries"],
     "defaults_flag": bool,
     "help_flag": bool,
     "help_sys_progs_flag": bool,
@@ -40,42 +67,11 @@ VUpdateAfniBinariesParameters = typing.TypedDict('VUpdateAfniBinariesParameters'
     "prog_list": typing.NotRequired[list[str] | None],
     "package": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@update.afni.binaries": v__update_afni_binaries_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class VUpdateAfniBinariesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__update_afni_binaries(...)`.
+    Output object returned when calling `VUpdateAfniBinariesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -106,7 +102,7 @@ def v__update_afni_binaries_params(
     local_package: str | None = None,
     prog_list: list[str] | None = None,
     package: str | None = None,
-) -> VUpdateAfniBinariesParameters:
+) -> VUpdateAfniBinariesParametersTagged:
     """
     Build parameters.
     
@@ -140,7 +136,7 @@ def v__update_afni_binaries_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@update.afni.binaries",
+        "@type": "afni/@update.afni.binaries",
         "defaults_flag": defaults_flag,
         "help_flag": help_flag,
         "help_sys_progs_flag": help_sys_progs_flag,
@@ -191,74 +187,74 @@ def v__update_afni_binaries_cargs(
     """
     cargs = []
     cargs.append("@update.afni.binaries")
-    if params.get("defaults_flag"):
+    if params.get("defaults_flag", False):
         cargs.append("-defaults")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
-    if params.get("help_sys_progs_flag"):
+    if params.get("help_sys_progs_flag", False):
         cargs.append("-help_sys_progs")
-    if params.get("apsearch") is not None:
+    if params.get("apsearch", None) is not None:
         cargs.extend([
             "-apsearch",
-            params.get("apsearch")
+            params.get("apsearch", None)
         ])
-    if params.get("bindir") is not None:
+    if params.get("bindir", None) is not None:
         cargs.extend([
             "-bindir",
-            params.get("bindir")
+            params.get("bindir", None)
         ])
-    if params.get("curl_flag"):
+    if params.get("curl_flag", False):
         cargs.append("-curl")
-    if params.get("do_dotfiles_flag"):
+    if params.get("do_dotfiles_flag", False):
         cargs.append("-do_dotfiles")
-    if params.get("do_extras_flag"):
+    if params.get("do_extras_flag", False):
         cargs.append("-do_extras")
-    if params.get("echo_flag"):
+    if params.get("echo_flag", False):
         cargs.append("-echo")
-    if params.get("make_backup") is not None:
+    if params.get("make_backup", None) is not None:
         cargs.extend([
             "-make_backup",
-            params.get("make_backup")
+            params.get("make_backup", None)
         ])
-    if params.get("no_cert_verify_flag"):
+    if params.get("no_cert_verify_flag", False):
         cargs.append("-no_cert_verify")
-    if params.get("no_recur_flag"):
+    if params.get("no_recur_flag", False):
         cargs.append("-no_recur")
-    if params.get("proto") is not None:
+    if params.get("proto", None) is not None:
         cargs.extend([
             "-proto",
-            params.get("proto")
+            params.get("proto", None)
         ])
-    if params.get("quick_flag"):
+    if params.get("quick_flag", False):
         cargs.append("-quick")
-    if params.get("show_obsoletes_flag"):
+    if params.get("show_obsoletes_flag", False):
         cargs.append("-show_obsoletes")
-    if params.get("show_obsoletes_grep_flag"):
+    if params.get("show_obsoletes_grep_flag", False):
         cargs.append("-show_obsoletes_grep")
-    if params.get("show_system_progs_flag"):
+    if params.get("show_system_progs_flag", False):
         cargs.append("-show_system_progs")
-    if params.get("sys_ok_flag"):
+    if params.get("sys_ok_flag", False):
         cargs.append("-sys_ok")
-    if params.get("test_flag"):
+    if params.get("test_flag", False):
         cargs.append("-test")
-    if params.get("test_protos_flag"):
+    if params.get("test_protos_flag", False):
         cargs.append("-test_protos")
-    if params.get("revert_flag"):
+    if params.get("revert_flag", False):
         cargs.append("-revert")
-    if params.get("local_package") is not None:
+    if params.get("local_package", None) is not None:
         cargs.extend([
             "-local_package",
-            params.get("local_package")
+            params.get("local_package", None)
         ])
-    if params.get("prog_list") is not None:
+    if params.get("prog_list", None) is not None:
         cargs.extend([
             "-prog_list",
-            *params.get("prog_list")
+            *params.get("prog_list", None)
         ])
-    if params.get("package") is not None:
+    if params.get("package", None) is not None:
         cargs.extend([
             "-package",
-            params.get("package")
+            params.get("package", None)
         ])
     return cargs
 
@@ -284,9 +280,11 @@ def v__update_afni_binaries_outputs(
 
 def v__update_afni_binaries_execute(
     params: VUpdateAfniBinariesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VUpdateAfniBinariesOutputs:
     """
+    @update.afni.binaries
+    
     Install or update AFNI binaries.
     
     Author: AFNI Developers
@@ -295,10 +293,12 @@ def v__update_afni_binaries_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VUpdateAfniBinariesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__UPDATE_AFNI_BINARIES_METADATA)
     params = execution.params(params)
     cargs = v__update_afni_binaries_cargs(params, execution)
     ret = v__update_afni_binaries_outputs(params, execution)
@@ -334,6 +334,8 @@ def v__update_afni_binaries(
     runner: Runner | None = None,
 ) -> VUpdateAfniBinariesOutputs:
     """
+    @update.afni.binaries
+    
     Install or update AFNI binaries.
     
     Author: AFNI Developers
@@ -370,8 +372,6 @@ def v__update_afni_binaries(
     Returns:
         NamedTuple of outputs (described in `VUpdateAfniBinariesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__UPDATE_AFNI_BINARIES_METADATA)
     params = v__update_afni_binaries_params(
         defaults_flag=defaults_flag,
         help_flag=help_flag,
@@ -398,13 +398,13 @@ def v__update_afni_binaries(
         prog_list=prog_list,
         package=package,
     )
-    return v__update_afni_binaries_execute(params, execution)
+    return v__update_afni_binaries_execute(params, runner)
 
 
 __all__ = [
     "VUpdateAfniBinariesOutputs",
-    "VUpdateAfniBinariesParameters",
     "V__UPDATE_AFNI_BINARIES_METADATA",
     "v__update_afni_binaries",
+    "v__update_afni_binaries_execute",
     "v__update_afni_binaries_params",
 ]

niwrap_afni/afni/v__vol_center.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__VOL_CENTER_METADATA = Metadata(
-    id="4ce13662130110b3fd50b4a405a5d296faf47380.boutiques",
+    id="6057d3213d321732bc8f15f10b6aef3f38c82e7d.boutiques",
     name="@VolCenter",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ V__VOL_CENTER_METADATA = Metadata(
 
 
 VVolCenterParameters = typing.TypedDict('VVolCenterParameters', {
-    "__STYXTYPE__": typing.Literal["@VolCenter"],
+    "@type": typing.NotRequired[typing.Literal["afni/@VolCenter"]],
+    "dset": InputPathType,
+    "orient": typing.NotRequired[str | None],
+})
+VVolCenterParametersTagged = typing.TypedDict('VVolCenterParametersTagged', {
+    "@type": typing.Literal["afni/@VolCenter"],
     "dset": InputPathType,
     "orient": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@VolCenter": v__vol_center_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class VVolCenterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__vol_center(...)`.
+    Output object returned when calling `VVolCenterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class VVolCenterOutputs(typing.NamedTuple):
 def v__vol_center_params(
     dset: InputPathType,
     orient: str | None = None,
-) -> VVolCenterParameters:
+) -> VVolCenterParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def v__vol_center_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@VolCenter",
+        "@type": "afni/@VolCenter",
         "dset": dset,
     }
     if orient is not None:
@@ -98,12 +72,12 @@ def v__vol_center_cargs(
     cargs.append("@VolCenter")
     cargs.extend([
         "-dset",
-        execution.input_file(params.get("dset"))
+        execution.input_file(params.get("dset", None))
     ])
-    if params.get("orient") is not None:
+    if params.get("orient", None) is not None:
         cargs.extend([
             "-or",
-            params.get("orient")
+            params.get("orient", None)
         ])
     return cargs
 
@@ -129,9 +103,11 @@ def v__vol_center_outputs(
 
 def v__vol_center_execute(
     params: VVolCenterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VVolCenterOutputs:
     """
+    @VolCenter
+    
     Tool to return the center of volume for a given dataset.
     
     Author: AFNI Developers
@@ -140,10 +116,12 @@ def v__vol_center_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VVolCenterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__VOL_CENTER_METADATA)
     params = execution.params(params)
     cargs = v__vol_center_cargs(params, execution)
     ret = v__vol_center_outputs(params, execution)
@@ -157,6 +135,8 @@ def v__vol_center(
     runner: Runner | None = None,
 ) -> VVolCenterOutputs:
     """
+    @VolCenter
+    
     Tool to return the center of volume for a given dataset.
     
     Author: AFNI Developers
@@ -170,19 +150,17 @@ def v__vol_center(
     Returns:
         NamedTuple of outputs (described in `VVolCenterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__VOL_CENTER_METADATA)
     params = v__vol_center_params(
         dset=dset,
         orient=orient,
     )
-    return v__vol_center_execute(params, execution)
+    return v__vol_center_execute(params, runner)
 
 
 __all__ = [
     "VVolCenterOutputs",
-    "VVolCenterParameters",
     "V__VOL_CENTER_METADATA",
     "v__vol_center",
+    "v__vol_center_execute",
     "v__vol_center_params",
 ]

niwrap_afni/afni/v__xyz_to_ijk.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__XYZ_TO_IJK_METADATA = Metadata(
-    id="c2f8c6ad40a232de3a6ff1e49118e8e23fa42606.boutiques",
+    id="bff15d1cd48403683f15642cc72a7a49d29fbb18.boutiques",
     name="@xyz_to_ijk",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V__XYZ_TO_IJK_METADATA = Metadata(
 
 
 VXyzToIjkParameters = typing.TypedDict('VXyzToIjkParameters', {
-    "__STYXTYPE__": typing.Literal["@xyz_to_ijk"],
+    "@type": typing.NotRequired[typing.Literal["afni/@xyz_to_ijk"]],
+    "inset": InputPathType,
+    "x_coord": float,
+    "y_coord": float,
+    "z_coord": float,
+    "prefix": typing.NotRequired[str | None],
+})
+VXyzToIjkParametersTagged = typing.TypedDict('VXyzToIjkParametersTagged', {
+    "@type": typing.Literal["afni/@xyz_to_ijk"],
     "inset": InputPathType,
     "x_coord": float,
     "y_coord": float,
     "z_coord": float,
     "prefix": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@xyz_to_ijk": v__xyz_to_ijk_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "@xyz_to_ijk": v__xyz_to_ijk_outputs,
-    }.get(t)
 
 
 class VXyzToIjkOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__xyz_to_ijk(...)`.
+    Output object returned when calling `VXyzToIjkParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def v__xyz_to_ijk_params(
     y_coord: float,
     z_coord: float,
     prefix: str | None = None,
-) -> VXyzToIjkParameters:
+) -> VXyzToIjkParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def v__xyz_to_ijk_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@xyz_to_ijk",
+        "@type": "afni/@xyz_to_ijk",
         "inset": inset,
         "x_coord": x_coord,
         "y_coord": y_coord,
@@ -113,18 +89,18 @@ def v__xyz_to_ijk_cargs(
     cargs.append("@xyz_to_ijk")
     cargs.extend([
         "-inset",
-        execution.input_file(params.get("inset"))
+        execution.input_file(params.get("inset", None))
     ])
     cargs.extend([
         "-xyz",
-        str(params.get("x_coord"))
+        str(params.get("x_coord", None))
     ])
-    cargs.append(str(params.get("y_coord")))
-    cargs.append(str(params.get("z_coord")))
-    if params.get("prefix") is not None:
+    cargs.append(str(params.get("y_coord", None)))
+    cargs.append(str(params.get("z_coord", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
     return cargs
 
@@ -144,16 +120,18 @@ def v__xyz_to_ijk_outputs(
     """
     ret = VXyzToIjkOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v__xyz_to_ijk_execute(
     params: VXyzToIjkParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VXyzToIjkOutputs:
     """
+    @xyz_to_ijk
+    
     Helper script to convert (x, y, z) coordinates to (i, j, k) indices for a
     volumetric dataset.
     
@@ -163,10 +141,12 @@ def v__xyz_to_ijk_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VXyzToIjkOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__XYZ_TO_IJK_METADATA)
     params = execution.params(params)
     cargs = v__xyz_to_ijk_cargs(params, execution)
     ret = v__xyz_to_ijk_outputs(params, execution)
@@ -183,6 +163,8 @@ def v__xyz_to_ijk(
     runner: Runner | None = None,
 ) -> VXyzToIjkOutputs:
     """
+    @xyz_to_ijk
+    
     Helper script to convert (x, y, z) coordinates to (i, j, k) indices for a
     volumetric dataset.
     
@@ -200,8 +182,6 @@ def v__xyz_to_ijk(
     Returns:
         NamedTuple of outputs (described in `VXyzToIjkOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__XYZ_TO_IJK_METADATA)
     params = v__xyz_to_ijk_params(
         inset=inset,
         x_coord=x_coord,
@@ -209,13 +189,13 @@ def v__xyz_to_ijk(
         z_coord=z_coord,
         prefix=prefix,
     )
-    return v__xyz_to_ijk_execute(params, execution)
+    return v__xyz_to_ijk_execute(params, runner)
 
 
 __all__ = [
     "VXyzToIjkOutputs",
-    "VXyzToIjkParameters",
     "V__XYZ_TO_IJK_METADATA",
     "v__xyz_to_ijk",
+    "v__xyz_to_ijk_execute",
     "v__xyz_to_ijk_params",
 ]