niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/quickspec_sl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QUICKSPEC_SL_METADATA = Metadata(
-    id="e5cdd0aedd96bc6df0f947244131010bf4fd383f.boutiques",
+    id="fd331c76ba98dd01a788379c9648276752fb1af2.boutiques",
     name="quickspecSL",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ QUICKSPEC_SL_METADATA = Metadata(
 
 
 QuickspecSlParameters = typing.TypedDict('QuickspecSlParameters', {
-    "__STYXTYPE__": typing.Literal["quickspecSL"],
+    "@type": typing.NotRequired[typing.Literal["afni/quickspecSL"]],
+    "surf_A": InputPathType,
+    "surf_B": InputPathType,
+    "surf_intermed_pref": typing.NotRequired[str | None],
+    "infl_surf_A": typing.NotRequired[InputPathType | None],
+    "infl_surf_B": typing.NotRequired[InputPathType | None],
+    "infl_surf_intermed_pref": typing.NotRequired[str | None],
+    "both_lr_flag": bool,
+    "out_spec": typing.NotRequired[str | None],
+})
+QuickspecSlParametersTagged = typing.TypedDict('QuickspecSlParametersTagged', {
+    "@type": typing.Literal["afni/quickspecSL"],
     "surf_A": InputPathType,
     "surf_B": InputPathType,
     "surf_intermed_pref": typing.NotRequired[str | None],
@@ -24,43 +35,11 @@ QuickspecSlParameters = typing.TypedDict('QuickspecSlParameters', {
     "both_lr_flag": bool,
     "out_spec": 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 {
-        "quickspecSL": quickspec_sl_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 {
-        "quickspecSL": quickspec_sl_outputs,
-    }.get(t)
 
 
 class QuickspecSlOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `quickspec_sl(...)`.
+    Output object returned when calling `QuickspecSlParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def quickspec_sl_params(
     infl_surf_intermed_pref: str | None = None,
     both_lr_flag: bool = False,
     out_spec: str | None = None,
-) -> QuickspecSlParameters:
+) -> QuickspecSlParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +80,7 @@ def quickspec_sl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "quickspecSL",
+        "@type": "afni/quickspecSL",
         "surf_A": surf_a,
         "surf_B": surf_b,
         "both_lr_flag": both_lr_flag,
@@ -136,38 +115,38 @@ def quickspec_sl_cargs(
     cargs.append("quickspecSL")
     cargs.extend([
         "-surf_A",
-        execution.input_file(params.get("surf_A"))
+        execution.input_file(params.get("surf_A", None))
     ])
     cargs.extend([
         "-surf_B",
-        execution.input_file(params.get("surf_B"))
+        execution.input_file(params.get("surf_B", None))
     ])
-    if params.get("surf_intermed_pref") is not None:
+    if params.get("surf_intermed_pref", None) is not None:
         cargs.extend([
             "-surf_intermed_pref",
-            params.get("surf_intermed_pref")
+            params.get("surf_intermed_pref", None)
         ])
-    if params.get("infl_surf_A") is not None:
+    if params.get("infl_surf_A", None) is not None:
         cargs.extend([
             "-infl_surf_A",
-            execution.input_file(params.get("infl_surf_A"))
+            execution.input_file(params.get("infl_surf_A", None))
         ])
-    if params.get("infl_surf_B") is not None:
+    if params.get("infl_surf_B", None) is not None:
         cargs.extend([
             "-infl_surf_B",
-            execution.input_file(params.get("infl_surf_B"))
+            execution.input_file(params.get("infl_surf_B", None))
         ])
-    if params.get("infl_surf_intermed_pref") is not None:
+    if params.get("infl_surf_intermed_pref", None) is not None:
         cargs.extend([
             "-infl_surf_intermed_pref",
-            params.get("infl_surf_intermed_pref")
+            params.get("infl_surf_intermed_pref", None)
         ])
-    if params.get("both_lr_flag"):
+    if params.get("both_lr_flag", False):
         cargs.append("-both_lr")
-    if params.get("out_spec") is not None:
+    if params.get("out_spec", None) is not None:
         cargs.extend([
             "-out_spec",
-            params.get("out_spec")
+            params.get("out_spec", None)
         ])
     return cargs
 
@@ -187,19 +166,21 @@ def quickspec_sl_outputs(
     """
     ret = QuickspecSlOutputs(
         root=execution.output_file("."),
-        output_spec_file=execution.output_file(params.get("out_spec")) if (params.get("out_spec") is not None) else None,
+        output_spec_file=execution.output_file(params.get("out_spec", None)) if (params.get("out_spec") is not None) else None,
     )
     return ret
 
 
 def quickspec_sl_execute(
     params: QuickspecSlParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QuickspecSlOutputs:
     """
-    This program makes a *.spec file after a set of intermediate surfaces have been
-    generated with SurfLayers. It can also make a *.spec file that relates inflated
-    surfaces to anatomically-correct surfaces.
+    quickspecSL
+    
+    This program makes a *.spec file after a set of intermediate surfaces have
+    been generated with SurfLayers. It can also make a *.spec file that relates
+    inflated surfaces to anatomically-correct surfaces.
     
     Author: AFNI Developers
     
@@ -207,10 +188,12 @@ def quickspec_sl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QuickspecSlOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUICKSPEC_SL_METADATA)
     params = execution.params(params)
     cargs = quickspec_sl_cargs(params, execution)
     ret = quickspec_sl_outputs(params, execution)
@@ -230,9 +213,11 @@ def quickspec_sl(
     runner: Runner | None = None,
 ) -> QuickspecSlOutputs:
     """
-    This program makes a *.spec file after a set of intermediate surfaces have been
-    generated with SurfLayers. It can also make a *.spec file that relates inflated
-    surfaces to anatomically-correct surfaces.
+    quickspecSL
+    
+    This program makes a *.spec file after a set of intermediate surfaces have
+    been generated with SurfLayers. It can also make a *.spec file that relates
+    inflated surfaces to anatomically-correct surfaces.
     
     Author: AFNI Developers
     
@@ -258,8 +243,6 @@ def quickspec_sl(
     Returns:
         NamedTuple of outputs (described in `QuickspecSlOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QUICKSPEC_SL_METADATA)
     params = quickspec_sl_params(
         surf_a=surf_a,
         surf_b=surf_b,
@@ -270,13 +253,13 @@ def quickspec_sl(
         both_lr_flag=both_lr_flag,
         out_spec=out_spec,
     )
-    return quickspec_sl_execute(params, execution)
+    return quickspec_sl_execute(params, runner)
 
 
 __all__ = [
     "QUICKSPEC_SL_METADATA",
     "QuickspecSlOutputs",
-    "QuickspecSlParameters",
     "quickspec_sl",
+    "quickspec_sl_execute",
     "quickspec_sl_params",
 ]

niwrap_afni/afni/quotize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QUOTIZE_METADATA = Metadata(
-    id="4c584c1c53b452f98fe6627b0010b0bc7d24c8a7.boutiques",
+    id="d158ee4416dbfc742de4bc2b2d90d239f3be5934.boutiques",
     name="quotize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ QUOTIZE_METADATA = Metadata(
 
 
 QuotizeParameters = typing.TypedDict('QuotizeParameters', {
-    "__STYXTYPE__": typing.Literal["quotize"],
+    "@type": typing.NotRequired[typing.Literal["afni/quotize"]],
+    "name": str,
+    "input_file": InputPathType,
+    "output_file": str,
+})
+QuotizeParametersTagged = typing.TypedDict('QuotizeParametersTagged', {
+    "@type": typing.Literal["afni/quotize"],
     "name": str,
     "input_file": InputPathType,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "quotize": quotize_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 {
-        "quotize": quotize_outputs,
-    }.get(t)
 
 
 class QuotizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `quotize(...)`.
+    Output object returned when calling `QuotizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def quotize_params(
     name: str,
     input_file: InputPathType,
     output_file: str,
-) -> QuotizeParameters:
+) -> QuotizeParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def quotize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "quotize",
+        "@type": "afni/quotize",
         "name": name,
         "input_file": input_file,
         "output_file": output_file,
@@ -102,9 +76,9 @@ def quotize_cargs(
     """
     cargs = []
     cargs.append("quotize")
-    cargs.append(params.get("name"))
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(params.get("name", None))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def quotize_outputs(
     """
     ret = QuotizeOutputs(
         root=execution.output_file("."),
-        array_output=execution.output_file(params.get("output_file")),
+        array_output=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def quotize_execute(
     params: QuotizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QuotizeOutputs:
     """
+    quotize
+    
     Turns a text file into a C array of strings initialized into an array 'char
     *name[]'.
     
@@ -142,10 +118,12 @@ def quotize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QuotizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QUOTIZE_METADATA)
     params = execution.params(params)
     cargs = quotize_cargs(params, execution)
     ret = quotize_outputs(params, execution)
@@ -160,6 +138,8 @@ def quotize(
     runner: Runner | None = None,
 ) -> QuotizeOutputs:
     """
+    quotize
+    
     Turns a text file into a C array of strings initialized into an array 'char
     *name[]'.
     
@@ -175,20 +155,18 @@ def quotize(
     Returns:
         NamedTuple of outputs (described in `QuotizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QUOTIZE_METADATA)
     params = quotize_params(
         name=name,
         input_file=input_file,
         output_file=output_file,
     )
-    return quotize_execute(params, execution)
+    return quotize_execute(params, runner)
 
 
 __all__ = [
     "QUOTIZE_METADATA",
     "QuotizeOutputs",
-    "QuotizeParameters",
     "quotize",
+    "quotize_execute",
     "quotize_params",
 ]

niwrap_afni/afni/r_pkgs_install.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 R_PKGS_INSTALL_METADATA = Metadata(
-    id="02fcafb674321d658d1a59f536c7612b3e27207f.boutiques",
+    id="21bbac9c8d45c10c34e4107732268562b9494893.boutiques",
     name="rPkgsInstall",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ R_PKGS_INSTALL_METADATA = Metadata(
 
 
 RPkgsInstallParameters = typing.TypedDict('RPkgsInstallParameters', {
-    "__STYXTYPE__": typing.Literal["rPkgsInstall"],
+    "@type": typing.NotRequired[typing.Literal["afni/rPkgsInstall"]],
+    "packages": str,
+    "download_site": typing.NotRequired[str | None],
+    "check": bool,
+    "update": bool,
+    "remove": bool,
+})
+RPkgsInstallParametersTagged = typing.TypedDict('RPkgsInstallParametersTagged', {
+    "@type": typing.Literal["afni/rPkgsInstall"],
     "packages": str,
     "download_site": typing.NotRequired[str | None],
     "check": bool,
     "update": bool,
     "remove": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "rPkgsInstall": r_pkgs_install_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 {
-        "rPkgsInstall": r_pkgs_install_outputs,
-    }.get(t)
 
 
 class RPkgsInstallOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `r_pkgs_install(...)`.
+    Output object returned when calling `RPkgsInstallParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def r_pkgs_install_params(
     check: bool = False,
     update_: bool = False,
     remove: bool = False,
-) -> RPkgsInstallParameters:
+) -> RPkgsInstallParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +65,7 @@ def r_pkgs_install_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rPkgsInstall",
+        "@type": "afni/rPkgsInstall",
         "packages": packages,
         "check": check,
         "update": update_,
@@ -117,18 +93,18 @@ def r_pkgs_install_cargs(
     cargs.append("rPkgsInstall")
     cargs.extend([
         "-pkgs",
-        params.get("packages")
+        params.get("packages", None)
     ])
-    if params.get("download_site") is not None:
+    if params.get("download_site", None) is not None:
         cargs.extend([
             "-site",
-            params.get("download_site")
+            params.get("download_site", None)
         ])
-    if params.get("check"):
+    if params.get("check", False):
         cargs.append("-check")
-    if params.get("update"):
+    if params.get("update", False):
         cargs.append("-update")
-    if params.get("remove"):
+    if params.get("remove", False):
         cargs.append("-remove")
     return cargs
 
@@ -148,16 +124,18 @@ def r_pkgs_install_outputs(
     """
     ret = RPkgsInstallOutputs(
         root=execution.output_file("."),
-        output_packages=execution.output_file(params.get("packages")),
+        output_packages=execution.output_file(params.get("packages", None)),
     )
     return ret
 
 
 def r_pkgs_install_execute(
     params: RPkgsInstallParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RPkgsInstallOutputs:
     """
+    rPkgsInstall
+    
     A tool for installing, checking, updating, or removing R packages for AFNI.
     
     Author: AFNI Developers
@@ -166,10 +144,12 @@ def r_pkgs_install_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RPkgsInstallOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(R_PKGS_INSTALL_METADATA)
     params = execution.params(params)
     cargs = r_pkgs_install_cargs(params, execution)
     ret = r_pkgs_install_outputs(params, execution)
@@ -186,6 +166,8 @@ def r_pkgs_install(
     runner: Runner | None = None,
 ) -> RPkgsInstallOutputs:
     """
+    rPkgsInstall
+    
     A tool for installing, checking, updating, or removing R packages for AFNI.
     
     Author: AFNI Developers
@@ -206,8 +188,6 @@ def r_pkgs_install(
     Returns:
         NamedTuple of outputs (described in `RPkgsInstallOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(R_PKGS_INSTALL_METADATA)
     params = r_pkgs_install_params(
         packages=packages,
         download_site=download_site,
@@ -215,13 +195,13 @@ def r_pkgs_install(
         update_=update_,
         remove=remove,
     )
-    return r_pkgs_install_execute(params, execution)
+    return r_pkgs_install_execute(params, runner)
 
 
 __all__ = [
     "RPkgsInstallOutputs",
-    "RPkgsInstallParameters",
     "R_PKGS_INSTALL_METADATA",
     "r_pkgs_install",
+    "r_pkgs_install_execute",
     "r_pkgs_install_params",
 ]