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

niwrap_freesurfer/freesurfer/fs_install_mcr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_INSTALL_MCR_METADATA = Metadata(
-    id="3368d00255c0d7e5b75947a021056a82a28657ea.boutiques",
+    id="1f9db16df19bb2b277ff35d39836ee1c013e826c.boutiques",
     name="fs_install_mcr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ FS_INSTALL_MCR_METADATA = Metadata(
 
 
 FsInstallMcrParameters = typing.TypedDict('FsInstallMcrParameters', {
-    "__STYXTYPE__": typing.Literal["fs_install_mcr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_install_mcr"]],
+    "mcr_version": str,
+})
+FsInstallMcrParametersTagged = typing.TypedDict('FsInstallMcrParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_install_mcr"],
     "mcr_version": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fs_install_mcr": fs_install_mcr_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 FsInstallMcrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_install_mcr(...)`.
+    Output object returned when calling `FsInstallMcrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class FsInstallMcrOutputs(typing.NamedTuple):
 
 def fs_install_mcr_params(
     mcr_version: str,
-) -> FsInstallMcrParameters:
+) -> FsInstallMcrParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def fs_install_mcr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_install_mcr",
+        "@type": "freesurfer/fs_install_mcr",
         "mcr_version": mcr_version,
     }
     return params
@@ -92,7 +65,7 @@ def fs_install_mcr_cargs(
     """
     cargs = []
     cargs.append("fs_install_mcr")
-    cargs.append(params.get("mcr_version"))
+    cargs.append(params.get("mcr_version", None))
     return cargs
 
 
@@ -117,9 +90,11 @@ def fs_install_mcr_outputs(
 
 def fs_install_mcr_execute(
     params: FsInstallMcrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsInstallMcrOutputs:
     """
+    fs_install_mcr
+    
     MCR installation tool for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -128,10 +103,12 @@ def fs_install_mcr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsInstallMcrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_INSTALL_MCR_METADATA)
     params = execution.params(params)
     cargs = fs_install_mcr_cargs(params, execution)
     ret = fs_install_mcr_outputs(params, execution)
@@ -144,6 +121,8 @@ def fs_install_mcr(
     runner: Runner | None = None,
 ) -> FsInstallMcrOutputs:
     """
+    fs_install_mcr
+    
     MCR installation tool for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -157,18 +136,16 @@ def fs_install_mcr(
     Returns:
         NamedTuple of outputs (described in `FsInstallMcrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_INSTALL_MCR_METADATA)
     params = fs_install_mcr_params(
         mcr_version=mcr_version,
     )
-    return fs_install_mcr_execute(params, execution)
+    return fs_install_mcr_execute(params, runner)
 
 
 __all__ = [
     "FS_INSTALL_MCR_METADATA",
     "FsInstallMcrOutputs",
-    "FsInstallMcrParameters",
     "fs_install_mcr",
+    "fs_install_mcr_execute",
     "fs_install_mcr_params",
 ]

niwrap_freesurfer/freesurfer/fs_lib_check.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_LIB_CHECK_METADATA = Metadata(
-    id="ec10aa0115c1a61f3fd66d862bbeced76be755da.boutiques",
+    id="3f837527e856251fa0e17346c777a1272fc585b1.boutiques",
     name="fs_lib_check",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ FS_LIB_CHECK_METADATA = Metadata(
 
 
 FsLibCheckParameters = typing.TypedDict('FsLibCheckParameters', {
-    "__STYXTYPE__": typing.Literal["fs_lib_check"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_lib_check"]],
+    "use_ldconfig": bool,
+    "use_rpm": bool,
+    "show_help": bool,
+    "show_version": bool,
+})
+FsLibCheckParametersTagged = typing.TypedDict('FsLibCheckParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_lib_check"],
     "use_ldconfig": bool,
     "use_rpm": bool,
     "show_help": bool,
     "show_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 {
-        "fs_lib_check": fs_lib_check_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 FsLibCheckOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_lib_check(...)`.
+    Output object returned when calling `FsLibCheckParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def fs_lib_check_params(
     use_rpm: bool = False,
     show_help: bool = False,
     show_version: bool = False,
-) -> FsLibCheckParameters:
+) -> FsLibCheckParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +60,7 @@ def fs_lib_check_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_lib_check",
+        "@type": "freesurfer/fs_lib_check",
         "use_ldconfig": use_ldconfig,
         "use_rpm": use_rpm,
         "show_help": show_help,
@@ -108,13 +84,13 @@ def fs_lib_check_cargs(
     """
     cargs = []
     cargs.append("fs_lib_check")
-    if params.get("use_ldconfig"):
+    if params.get("use_ldconfig", False):
         cargs.append("-l")
-    if params.get("use_rpm"):
+    if params.get("use_rpm", False):
         cargs.append("-r")
-    if params.get("show_help"):
+    if params.get("show_help", False):
         cargs.append("-h")
-    if params.get("show_version"):
+    if params.get("show_version", False):
         cargs.append("-v")
     return cargs
 
@@ -140,11 +116,13 @@ def fs_lib_check_outputs(
 
 def fs_lib_check_execute(
     params: FsLibCheckParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsLibCheckOutputs:
     """
-    Checks if the operating system has the necessary system libraries required to
-    run FreeSurfer.
+    fs_lib_check
+    
+    Checks if the operating system has the necessary system libraries required
+    to run FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -152,10 +130,12 @@ def fs_lib_check_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsLibCheckOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_LIB_CHECK_METADATA)
     params = execution.params(params)
     cargs = fs_lib_check_cargs(params, execution)
     ret = fs_lib_check_outputs(params, execution)
@@ -171,8 +151,10 @@ def fs_lib_check(
     runner: Runner | None = None,
 ) -> FsLibCheckOutputs:
     """
-    Checks if the operating system has the necessary system libraries required to
-    run FreeSurfer.
+    fs_lib_check
+    
+    Checks if the operating system has the necessary system libraries required
+    to run FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -192,21 +174,19 @@ def fs_lib_check(
     Returns:
         NamedTuple of outputs (described in `FsLibCheckOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_LIB_CHECK_METADATA)
     params = fs_lib_check_params(
         use_ldconfig=use_ldconfig,
         use_rpm=use_rpm,
         show_help=show_help,
         show_version=show_version,
     )
-    return fs_lib_check_execute(params, execution)
+    return fs_lib_check_execute(params, runner)
 
 
 __all__ = [
     "FS_LIB_CHECK_METADATA",
     "FsLibCheckOutputs",
-    "FsLibCheckParameters",
     "fs_lib_check",
+    "fs_lib_check_execute",
     "fs_lib_check_params",
 ]

niwrap_freesurfer/freesurfer/fs_print_help.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_PRINT_HELP_METADATA = Metadata(
-    id="1a0f96c91d8dea90a549b11726b82ded99db191b.boutiques",
+    id="364e80f34823fe82c3808e9f53e3fb55c227ffda.boutiques",
     name="fsPrintHelp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ FS_PRINT_HELP_METADATA = Metadata(
 
 
 FsPrintHelpParameters = typing.TypedDict('FsPrintHelpParameters', {
-    "__STYXTYPE__": typing.Literal["fsPrintHelp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fsPrintHelp"]],
+    "arguments": typing.NotRequired[str | None],
+})
+FsPrintHelpParametersTagged = typing.TypedDict('FsPrintHelpParametersTagged', {
+    "@type": typing.Literal["freesurfer/fsPrintHelp"],
     "arguments": 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 {
-        "fsPrintHelp": fs_print_help_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 FsPrintHelpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_print_help(...)`.
+    Output object returned when calling `FsPrintHelpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class FsPrintHelpOutputs(typing.NamedTuple):
 
 def fs_print_help_params(
     arguments: str | None = None,
-) -> FsPrintHelpParameters:
+) -> FsPrintHelpParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def fs_print_help_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fsPrintHelp",
+        "@type": "freesurfer/fsPrintHelp",
     }
     if arguments is not None:
         params["arguments"] = arguments
@@ -92,8 +65,8 @@ def fs_print_help_cargs(
     """
     cargs = []
     cargs.append("fsPrintHelp")
-    if params.get("arguments") is not None:
-        cargs.append(params.get("arguments"))
+    if params.get("arguments", None) is not None:
+        cargs.append(params.get("arguments", None))
     return cargs
 
 
@@ -118,11 +91,13 @@ def fs_print_help_outputs(
 
 def fs_print_help_execute(
     params: FsPrintHelpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsPrintHelpOutputs:
     """
-    fsPrintHelp - A tool that attempts to provide help documentation for FreeSurfer
-    commands.
+    fsPrintHelp
+    
+    fsPrintHelp - A tool that attempts to provide help documentation for
+    FreeSurfer commands.
     
     Author: FreeSurfer Developers
     
@@ -130,10 +105,12 @@ def fs_print_help_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsPrintHelpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_PRINT_HELP_METADATA)
     params = execution.params(params)
     cargs = fs_print_help_cargs(params, execution)
     ret = fs_print_help_outputs(params, execution)
@@ -146,8 +123,10 @@ def fs_print_help(
     runner: Runner | None = None,
 ) -> FsPrintHelpOutputs:
     """
-    fsPrintHelp - A tool that attempts to provide help documentation for FreeSurfer
-    commands.
+    fsPrintHelp
+    
+    fsPrintHelp - A tool that attempts to provide help documentation for
+    FreeSurfer commands.
     
     Author: FreeSurfer Developers
     
@@ -159,18 +138,16 @@ def fs_print_help(
     Returns:
         NamedTuple of outputs (described in `FsPrintHelpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_PRINT_HELP_METADATA)
     params = fs_print_help_params(
         arguments=arguments,
     )
-    return fs_print_help_execute(params, execution)
+    return fs_print_help_execute(params, runner)
 
 
 __all__ = [
     "FS_PRINT_HELP_METADATA",
     "FsPrintHelpOutputs",
-    "FsPrintHelpParameters",
     "fs_print_help",
+    "fs_print_help_execute",
     "fs_print_help_params",
 ]

niwrap_freesurfer/freesurfer/fs_run_from_mcr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_RUN_FROM_MCR_METADATA = Metadata(
-    id="912dbf3151af651160bde9f39e645669c7bf7dcb.boutiques",
+    id="b8ebcd3e7bbfa46078dc729b67efb15b249e4389.boutiques",
     name="fs_run_from_mcr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ FS_RUN_FROM_MCR_METADATA = Metadata(
 
 
 FsRunFromMcrParameters = typing.TypedDict('FsRunFromMcrParameters', {
-    "__STYXTYPE__": typing.Literal["fs_run_from_mcr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs_run_from_mcr"]],
+    "name": typing.NotRequired[str | None],
+    "command": typing.NotRequired[str | None],
+    "zeroth_flag": bool,
+    "empty_env_flag": bool,
+})
+FsRunFromMcrParametersTagged = typing.TypedDict('FsRunFromMcrParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs_run_from_mcr"],
     "name": typing.NotRequired[str | None],
     "command": typing.NotRequired[str | None],
     "zeroth_flag": bool,
     "empty_env_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fs_run_from_mcr": fs_run_from_mcr_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 FsRunFromMcrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_run_from_mcr(...)`.
+    Output object returned when calling `FsRunFromMcrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def fs_run_from_mcr_params(
     command: str | None = None,
     zeroth_flag: bool = False,
     empty_env_flag: bool = False,
-) -> FsRunFromMcrParameters:
+) -> FsRunFromMcrParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def fs_run_from_mcr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs_run_from_mcr",
+        "@type": "freesurfer/fs_run_from_mcr",
         "zeroth_flag": zeroth_flag,
         "empty_env_flag": empty_env_flag,
     }
@@ -105,16 +81,16 @@ def fs_run_from_mcr_cargs(
     """
     cargs = []
     cargs.append("fs_run_from_mcr")
-    if params.get("name") is not None:
+    if params.get("name", None) is not None:
         cargs.extend([
             "-a",
-            params.get("name")
+            params.get("name", None)
         ])
-    if params.get("command") is not None:
-        cargs.append(params.get("command"))
-    if params.get("zeroth_flag"):
+    if params.get("command", None) is not None:
+        cargs.append(params.get("command", None))
+    if params.get("zeroth_flag", False):
         cargs.append("-l")
-    if params.get("empty_env_flag"):
+    if params.get("empty_env_flag", False):
         cargs.append("-c")
     return cargs
 
@@ -140,9 +116,11 @@ def fs_run_from_mcr_outputs(
 
 def fs_run_from_mcr_execute(
     params: FsRunFromMcrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsRunFromMcrOutputs:
     """
+    fs_run_from_mcr
+    
     Replace the shell with the given command.
     
     Author: FreeSurfer Developers
@@ -151,10 +129,12 @@ def fs_run_from_mcr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsRunFromMcrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_RUN_FROM_MCR_METADATA)
     params = execution.params(params)
     cargs = fs_run_from_mcr_cargs(params, execution)
     ret = fs_run_from_mcr_outputs(params, execution)
@@ -170,6 +150,8 @@ def fs_run_from_mcr(
     runner: Runner | None = None,
 ) -> FsRunFromMcrOutputs:
     """
+    fs_run_from_mcr
+    
     Replace the shell with the given command.
     
     Author: FreeSurfer Developers
@@ -185,21 +167,19 @@ def fs_run_from_mcr(
     Returns:
         NamedTuple of outputs (described in `FsRunFromMcrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_RUN_FROM_MCR_METADATA)
     params = fs_run_from_mcr_params(
         name=name,
         command=command,
         zeroth_flag=zeroth_flag,
         empty_env_flag=empty_env_flag,
     )
-    return fs_run_from_mcr_execute(params, execution)
+    return fs_run_from_mcr_execute(params, runner)
 
 
 __all__ = [
     "FS_RUN_FROM_MCR_METADATA",
     "FsRunFromMcrOutputs",
-    "FsRunFromMcrParameters",
     "fs_run_from_mcr",
+    "fs_run_from_mcr_execute",
     "fs_run_from_mcr_params",
 ]