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

niwrap_afni/afni/trr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TRR_METADATA = Metadata(
-    id="bd682eac2506d81d16a0fea9c2fa13b1b23a36c9.boutiques",
+    id="c435bab7378f5e16dad1fc03144f5b28d0a7cf22.boutiques",
     name="TRR",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ TRR_METADATA = Metadata(
 
 
 TrrParameters = typing.TypedDict('TrrParameters', {
-    "__STYXTYPE__": typing.Literal["TRR"],
+    "@type": typing.NotRequired[typing.Literal["afni/TRR"]],
+    "prefix": str,
+    "chains": typing.NotRequired[float | None],
+    "iterations": typing.NotRequired[float | None],
+    "response_var": str,
+    "subject_var": str,
+    "repetition_var": typing.NotRequired[str | None],
+    "condition_var": typing.NotRequired[str | None],
+    "data_table": InputPathType,
+    "categorical_vars": typing.NotRequired[str | None],
+    "quantitative_vars": typing.NotRequired[str | None],
+    "response_dist": typing.NotRequired[str | None],
+    "model": typing.NotRequired[str | None],
+    "plot_size": typing.NotRequired[list[float] | None],
+    "standard_error": typing.NotRequired[str | None],
+    "t_stat": typing.NotRequired[str | None],
+    "within_chain_parallelization": typing.NotRequired[float | None],
+    "debug": bool,
+    "verbose": typing.NotRequired[float | None],
+})
+TrrParametersTagged = typing.TypedDict('TrrParametersTagged', {
+    "@type": typing.Literal["afni/TRR"],
     "prefix": str,
     "chains": typing.NotRequired[float | None],
     "iterations": typing.NotRequired[float | None],
@@ -34,43 +55,11 @@ TrrParameters = typing.TypedDict('TrrParameters', {
     "debug": bool,
     "verbose": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "TRR": trr_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 {
-        "TRR": trr_outputs,
-    }.get(t)
 
 
 class TrrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `trr(...)`.
+    Output object returned when calling `TrrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -102,7 +91,7 @@ def trr_params(
     within_chain_parallelization: float | None = None,
     debug: bool = False,
     verbose: float | None = None,
-) -> TrrParameters:
+) -> TrrParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +122,7 @@ def trr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "TRR",
+        "@type": "afni/TRR",
         "prefix": prefix,
         "response_var": response_var,
         "subject_var": subject_var,
@@ -186,86 +175,86 @@ def trr_cargs(
     cargs.append("TRR")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("chains") is not None:
+    if params.get("chains", None) is not None:
         cargs.extend([
             "-chains",
-            str(params.get("chains"))
+            str(params.get("chains", None))
         ])
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "-iterations",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
     cargs.extend([
         "-Y",
-        params.get("response_var")
+        params.get("response_var", None)
     ])
     cargs.extend([
         "-subject",
-        params.get("subject_var")
+        params.get("subject_var", None)
     ])
-    if params.get("repetition_var") is not None:
+    if params.get("repetition_var", None) is not None:
         cargs.extend([
             "-repetition",
-            params.get("repetition_var")
+            params.get("repetition_var", None)
         ])
-    if params.get("condition_var") is not None:
+    if params.get("condition_var", None) is not None:
         cargs.extend([
             "-condition",
-            params.get("condition_var")
+            params.get("condition_var", None)
         ])
     cargs.extend([
         "-dataTable",
-        execution.input_file(params.get("data_table"))
+        execution.input_file(params.get("data_table", None))
     ])
-    if params.get("categorical_vars") is not None:
+    if params.get("categorical_vars", None) is not None:
         cargs.extend([
             "-cVars",
-            params.get("categorical_vars")
+            params.get("categorical_vars", None)
         ])
-    if params.get("quantitative_vars") is not None:
+    if params.get("quantitative_vars", None) is not None:
         cargs.extend([
             "-qVars",
-            params.get("quantitative_vars")
+            params.get("quantitative_vars", None)
         ])
-    if params.get("response_dist") is not None:
+    if params.get("response_dist", None) is not None:
         cargs.extend([
             "-distY",
-            params.get("response_dist")
+            params.get("response_dist", None)
         ])
-    if params.get("model") is not None:
+    if params.get("model", None) is not None:
         cargs.extend([
             "-model",
-            params.get("model")
+            params.get("model", None)
         ])
-    if params.get("plot_size") is not None:
+    if params.get("plot_size", None) is not None:
         cargs.extend([
             "-PDP",
-            *map(str, params.get("plot_size"))
+            *map(str, params.get("plot_size", None))
         ])
-    if params.get("standard_error") is not None:
+    if params.get("standard_error", None) is not None:
         cargs.extend([
             "-se",
-            params.get("standard_error")
+            params.get("standard_error", None)
         ])
-    if params.get("t_stat") is not None:
+    if params.get("t_stat", None) is not None:
         cargs.extend([
             "-tstat",
-            params.get("t_stat")
+            params.get("t_stat", None)
         ])
-    if params.get("within_chain_parallelization") is not None:
+    if params.get("within_chain_parallelization", None) is not None:
         cargs.extend([
             "-WCP",
-            str(params.get("within_chain_parallelization"))
+            str(params.get("within_chain_parallelization", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-dbgArgs")
-    if params.get("verbose") is not None:
+    if params.get("verbose", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbose"))
+            str(params.get("verbose", None))
         ])
     return cargs
 
@@ -285,18 +274,20 @@ def trr_outputs(
     """
     ret = TrrOutputs(
         root=execution.output_file("."),
-        output_file_txt=execution.output_file(params.get("prefix") + ".txt"),
-        output_file_pdf=execution.output_file(params.get("prefix") + ".pdf"),
-        output_file_rdata=execution.output_file(params.get("prefix") + ".RData"),
+        output_file_txt=execution.output_file(params.get("prefix", None) + ".txt"),
+        output_file_pdf=execution.output_file(params.get("prefix", None) + ".pdf"),
+        output_file_rdata=execution.output_file(params.get("prefix", None) + ".RData"),
     )
     return ret
 
 
 def trr_execute(
     params: TrrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TrrOutputs:
     """
+    TRR
+    
     Test-Retest Reliability Program through Bayesian Multilevel Modeling.
     
     Author: AFNI Developers
@@ -305,10 +296,12 @@ def trr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TrrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRR_METADATA)
     params = execution.params(params)
     cargs = trr_cargs(params, execution)
     ret = trr_outputs(params, execution)
@@ -338,6 +331,8 @@ def trr(
     runner: Runner | None = None,
 ) -> TrrOutputs:
     """
+    TRR
+    
     Test-Retest Reliability Program through Bayesian Multilevel Modeling.
     
     Author: AFNI Developers
@@ -371,8 +366,6 @@ def trr(
     Returns:
         NamedTuple of outputs (described in `TrrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TRR_METADATA)
     params = trr_params(
         prefix=prefix,
         chains=chains,
@@ -393,13 +386,13 @@ def trr(
         debug=debug,
         verbose=verbose,
     )
-    return trr_execute(params, execution)
+    return trr_execute(params, runner)
 
 
 __all__ = [
     "TRR_METADATA",
     "TrrOutputs",
-    "TrrParameters",
     "trr",
+    "trr_execute",
     "trr_params",
 ]

niwrap_afni/afni/uber_align_test_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UBER_ALIGN_TEST_PY_METADATA = Metadata(
-    id="20699d437f455f9157d451d23c5cf085923ab9b5.boutiques",
+    id="8db49cffc0b0ffff63d0de6633fa5778cf55d4ab.boutiques",
     name="uber_align_test.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ UBER_ALIGN_TEST_PY_METADATA = Metadata(
 
 
 UberAlignTestPyParameters = typing.TypedDict('UberAlignTestPyParameters', {
-    "__STYXTYPE__": typing.Literal["uber_align_test.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/uber_align_test.py"]],
+    "no_gui": bool,
+    "print_script": bool,
+    "save_script": typing.NotRequired[str | None],
+    "user_variable": typing.NotRequired[list[str] | None],
+    "qt_opts": typing.NotRequired[str | None],
+    "help": bool,
+    "help_gui": bool,
+    "history": bool,
+    "show_valid_opts": bool,
+    "version": bool,
+})
+UberAlignTestPyParametersTagged = typing.TypedDict('UberAlignTestPyParametersTagged', {
+    "@type": typing.Literal["afni/uber_align_test.py"],
     "no_gui": bool,
     "print_script": bool,
     "save_script": typing.NotRequired[str | None],
@@ -26,42 +39,11 @@ UberAlignTestPyParameters = typing.TypedDict('UberAlignTestPyParameters', {
     "show_valid_opts": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "uber_align_test.py": uber_align_test_py_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 UberAlignTestPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `uber_align_test_py(...)`.
+    Output object returned when calling `UberAlignTestPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def uber_align_test_py_params(
     history: bool = False,
     show_valid_opts: bool = False,
     version: bool = False,
-) -> UberAlignTestPyParameters:
+) -> UberAlignTestPyParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +79,7 @@ def uber_align_test_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "uber_align_test.py",
+        "@type": "afni/uber_align_test.py",
         "no_gui": no_gui,
         "print_script": print_script,
         "help": help_,
@@ -130,34 +112,34 @@ def uber_align_test_py_cargs(
     """
     cargs = []
     cargs.append("uber_align_test.py")
-    if params.get("no_gui"):
+    if params.get("no_gui", False):
         cargs.append("-no_gui")
-    if params.get("print_script"):
+    if params.get("print_script", False):
         cargs.append("-print_script")
-    if params.get("save_script") is not None:
+    if params.get("save_script", None) is not None:
         cargs.extend([
             "-save_script",
-            params.get("save_script")
+            params.get("save_script", None)
         ])
-    if params.get("user_variable") is not None:
+    if params.get("user_variable", None) is not None:
         cargs.extend([
             "-uvar",
-            *params.get("user_variable")
+            *params.get("user_variable", None)
         ])
-    if params.get("qt_opts") is not None:
+    if params.get("qt_opts", None) is not None:
         cargs.extend([
             "-qt_opts",
-            params.get("qt_opts")
+            params.get("qt_opts", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("help_gui"):
+    if params.get("help_gui", False):
         cargs.append("-help_gui")
-    if params.get("history"):
+    if params.get("history", False):
         cargs.append("-hist")
-    if params.get("show_valid_opts"):
+    if params.get("show_valid_opts", False):
         cargs.append("-show_valid_opts")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-ver")
     return cargs
 
@@ -183,9 +165,11 @@ def uber_align_test_py_outputs(
 
 def uber_align_test_py_execute(
     params: UberAlignTestPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UberAlignTestPyOutputs:
     """
+    uber_align_test.py
+    
     Generate script to test anatomical/EPI alignment.
     
     Author: AFNI Developers
@@ -194,10 +178,12 @@ def uber_align_test_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UberAlignTestPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UBER_ALIGN_TEST_PY_METADATA)
     params = execution.params(params)
     cargs = uber_align_test_py_cargs(params, execution)
     ret = uber_align_test_py_outputs(params, execution)
@@ -219,6 +205,8 @@ def uber_align_test_py(
     runner: Runner | None = None,
 ) -> UberAlignTestPyOutputs:
     """
+    uber_align_test.py
+    
     Generate script to test anatomical/EPI alignment.
     
     Author: AFNI Developers
@@ -240,8 +228,6 @@ def uber_align_test_py(
     Returns:
         NamedTuple of outputs (described in `UberAlignTestPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UBER_ALIGN_TEST_PY_METADATA)
     params = uber_align_test_py_params(
         no_gui=no_gui,
         print_script=print_script,
@@ -254,13 +240,13 @@ def uber_align_test_py(
         show_valid_opts=show_valid_opts,
         version=version,
     )
-    return uber_align_test_py_execute(params, execution)
+    return uber_align_test_py_execute(params, runner)
 
 
 __all__ = [
     "UBER_ALIGN_TEST_PY_METADATA",
     "UberAlignTestPyOutputs",
-    "UberAlignTestPyParameters",
     "uber_align_test_py",
+    "uber_align_test_py_execute",
     "uber_align_test_py_params",
 ]

niwrap_afni/afni/uber_proc_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 UBER_PROC_PY_METADATA = Metadata(
-    id="810164b90b5470d8a01aa9ff880068dc2dfc8cc0.boutiques",
+    id="8b5bcd3ef76584ffc1c5ae37a1caf9d140efdf4b.boutiques",
     name="uber_proc.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,45 +14,18 @@ UBER_PROC_PY_METADATA = Metadata(
 
 
 UberProcPyParameters = typing.TypedDict('UberProcPyParameters', {
-    "__STYXTYPE__": typing.Literal["uber_proc.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/uber_proc.py"]],
+    "results_dir": typing.NotRequired[str | None],
+})
+UberProcPyParametersTagged = typing.TypedDict('UberProcPyParametersTagged', {
+    "@type": typing.Literal["afni/uber_proc.py"],
     "results_dir": 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 {
-        "uber_proc.py": uber_proc_py_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 UberProcPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `uber_proc_py(...)`.
+    Output object returned when calling `UberProcPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class UberProcPyOutputs(typing.NamedTuple):
 
 def uber_proc_py_params(
     results_dir: str | None = None,
-) -> UberProcPyParameters:
+) -> UberProcPyParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def uber_proc_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "uber_proc.py",
+        "@type": "afni/uber_proc.py",
     }
     if results_dir is not None:
         params["results_dir"] = results_dir
@@ -93,8 +66,8 @@ def uber_proc_py_cargs(
     """
     cargs = []
     cargs.append("uber_proc.py")
-    if params.get("results_dir") is not None:
-        cargs.append(params.get("results_dir"))
+    if params.get("results_dir", None) is not None:
+        cargs.append(params.get("results_dir", None))
     return cargs
 
 
@@ -119,9 +92,11 @@ def uber_proc_py_outputs(
 
 def uber_proc_py_execute(
     params: UberProcPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> UberProcPyOutputs:
     """
+    uber_proc.py
+    
     Uber processing tool - work in progress.
     
     Author: AFNI Developers
@@ -130,10 +105,12 @@ def uber_proc_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `UberProcPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UBER_PROC_PY_METADATA)
     params = execution.params(params)
     cargs = uber_proc_py_cargs(params, execution)
     ret = uber_proc_py_outputs(params, execution)
@@ -146,6 +123,8 @@ def uber_proc_py(
     runner: Runner | None = None,
 ) -> UberProcPyOutputs:
     """
+    uber_proc.py
+    
     Uber processing tool - work in progress.
     
     Author: AFNI Developers
@@ -159,18 +138,16 @@ def uber_proc_py(
     Returns:
         NamedTuple of outputs (described in `UberProcPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(UBER_PROC_PY_METADATA)
     params = uber_proc_py_params(
         results_dir=results_dir,
     )
-    return uber_proc_py_execute(params, execution)
+    return uber_proc_py_execute(params, runner)
 
 
 __all__ = [
     "UBER_PROC_PY_METADATA",
     "UberProcPyOutputs",
-    "UberProcPyParameters",
     "uber_proc_py",
+    "uber_proc_py_execute",
     "uber_proc_py_params",
 ]