niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/init_user_dotfiles_py.py

@@ -0,0 +1,353 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+INIT_USER_DOTFILES_PY_METADATA = Metadata(
+    id="8d4c58837ffe3486d2bbcb23d32442b108816c2b.boutiques",
+    name="init_user_dotfiles.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+InitUserDotfilesPyParameters = typing.TypedDict('InitUserDotfilesPyParameters', {
+    "__STYX_TYPE__": typing.Literal["init_user_dotfiles.py"],
+    "help": bool,
+    "help_dotfiles_all": bool,
+    "help_dotfiles_mod": bool,
+    "help_shells": bool,
+    "hist": bool,
+    "show_valid_opts": bool,
+    "ver": bool,
+    "dot_files_list": typing.NotRequired[list[str] | None],
+    "dir_bin": typing.NotRequired[str | None],
+    "dir_dot": typing.NotRequired[str | None],
+    "do_updates": typing.NotRequired[list[str] | None],
+    "dry_run": bool,
+    "force": bool,
+    "make_backup": typing.NotRequired[str | None],
+    "shell_list": typing.NotRequired[list[str] | None],
+    "test": bool,
+    "verbosity_level": typing.NotRequired[int | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "init_user_dotfiles.py": init_user_dotfiles_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 InitUserDotfilesPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `init_user_dotfiles_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def init_user_dotfiles_py_params(
+    help_: bool = False,
+    help_dotfiles_all: bool = False,
+    help_dotfiles_mod: bool = False,
+    help_shells: bool = False,
+    hist: bool = False,
+    show_valid_opts: bool = False,
+    ver: bool = False,
+    dot_files_list: list[str] | None = None,
+    dir_bin: str | None = None,
+    dir_dot: str | None = None,
+    do_updates: list[str] | None = None,
+    dry_run: bool = False,
+    force: bool = False,
+    make_backup: str | None = None,
+    shell_list: list[str] | None = None,
+    test: bool = False,
+    verbosity_level: int | None = None,
+) -> InitUserDotfilesPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        help_: Show this help.
+        help_dotfiles_all: Display dot files known by the program.
+        help_dotfiles_mod: Display modifiable dot files.
+        help_shells: Display shells known by the program.
+        hist: Show module history.
+        show_valid_opts: List valid options.
+        ver: Show current version.
+        dot_files_list: Specify dot files to focus on (default from\
+            -help_dotfiles_mod).
+        dir_bin: Specify bin directory to add to PATH (default comes from\
+            `which afni_proc.py`).
+        dir_dot: Specify directory containing dot files.
+        do_updates: Specify which updates to make (default is nothing).
+        dry_run: Do not modify files, but see what would happen.
+        force: Force edits, whether they seem needed or not.
+        make_backup: Specify whether to make backups of originals (default is\
+            yes).
+        shell_list: Specify shells instead of using -dflist.
+        test: Just test the files for potential changes.
+        verbosity_level: Set the verbosity level (default 1).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "init_user_dotfiles.py",
+        "help": help_,
+        "help_dotfiles_all": help_dotfiles_all,
+        "help_dotfiles_mod": help_dotfiles_mod,
+        "help_shells": help_shells,
+        "hist": hist,
+        "show_valid_opts": show_valid_opts,
+        "ver": ver,
+        "dry_run": dry_run,
+        "force": force,
+        "test": test,
+    }
+    if dot_files_list is not None:
+        params["dot_files_list"] = dot_files_list
+    if dir_bin is not None:
+        params["dir_bin"] = dir_bin
+    if dir_dot is not None:
+        params["dir_dot"] = dir_dot
+    if do_updates is not None:
+        params["do_updates"] = do_updates
+    if make_backup is not None:
+        params["make_backup"] = make_backup
+    if shell_list is not None:
+        params["shell_list"] = shell_list
+    if verbosity_level is not None:
+        params["verbosity_level"] = verbosity_level
+    return params
+
+
+def init_user_dotfiles_py_cargs(
+    params: InitUserDotfilesPyParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("init_user_dotfiles.py")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("help_dotfiles_all"):
+        cargs.append("-help_dotfiles_all")
+    if params.get("help_dotfiles_mod"):
+        cargs.append("-help_dotfiles_mod")
+    if params.get("help_shells"):
+        cargs.append("-help_shells")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("show_valid_opts"):
+        cargs.append("-show_valid_opts")
+    if params.get("ver"):
+        cargs.append("-ver")
+    if params.get("dot_files_list") is not None:
+        cargs.extend([
+            "-dflist",
+            *params.get("dot_files_list")
+        ])
+    if params.get("dir_bin") is not None:
+        cargs.extend([
+            "-dir_bin",
+            params.get("dir_bin")
+        ])
+    if params.get("dir_dot") is not None:
+        cargs.extend([
+            "-dir_dot",
+            params.get("dir_dot")
+        ])
+    if params.get("do_updates") is not None:
+        cargs.extend([
+            "-do_updates",
+            *params.get("do_updates")
+        ])
+    if params.get("dry_run"):
+        cargs.append("-dry_run")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("make_backup") is not None:
+        cargs.extend([
+            "-make_backup",
+            params.get("make_backup")
+        ])
+    if params.get("shell_list") is not None:
+        cargs.extend([
+            "-shell_list",
+            *params.get("shell_list")
+        ])
+    if params.get("test"):
+        cargs.append("-test")
+    if params.get("verbosity_level") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity_level"))
+        ])
+    return cargs
+
+
+def init_user_dotfiles_py_outputs(
+    params: InitUserDotfilesPyParameters,
+    execution: Execution,
+) -> InitUserDotfilesPyOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = InitUserDotfilesPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def init_user_dotfiles_py_execute(
+    params: InitUserDotfilesPyParameters,
+    execution: Execution,
+) -> InitUserDotfilesPyOutputs:
+    """
+    Initialize or evaluate user dot files (.cshrc, .bashrc, ...) for system
+    settings.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `InitUserDotfilesPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = init_user_dotfiles_py_cargs(params, execution)
+    ret = init_user_dotfiles_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def init_user_dotfiles_py(
+    help_: bool = False,
+    help_dotfiles_all: bool = False,
+    help_dotfiles_mod: bool = False,
+    help_shells: bool = False,
+    hist: bool = False,
+    show_valid_opts: bool = False,
+    ver: bool = False,
+    dot_files_list: list[str] | None = None,
+    dir_bin: str | None = None,
+    dir_dot: str | None = None,
+    do_updates: list[str] | None = None,
+    dry_run: bool = False,
+    force: bool = False,
+    make_backup: str | None = None,
+    shell_list: list[str] | None = None,
+    test: bool = False,
+    verbosity_level: int | None = None,
+    runner: Runner | None = None,
+) -> InitUserDotfilesPyOutputs:
+    """
+    Initialize or evaluate user dot files (.cshrc, .bashrc, ...) for system
+    settings.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        help_: Show this help.
+        help_dotfiles_all: Display dot files known by the program.
+        help_dotfiles_mod: Display modifiable dot files.
+        help_shells: Display shells known by the program.
+        hist: Show module history.
+        show_valid_opts: List valid options.
+        ver: Show current version.
+        dot_files_list: Specify dot files to focus on (default from\
+            -help_dotfiles_mod).
+        dir_bin: Specify bin directory to add to PATH (default comes from\
+            `which afni_proc.py`).
+        dir_dot: Specify directory containing dot files.
+        do_updates: Specify which updates to make (default is nothing).
+        dry_run: Do not modify files, but see what would happen.
+        force: Force edits, whether they seem needed or not.
+        make_backup: Specify whether to make backups of originals (default is\
+            yes).
+        shell_list: Specify shells instead of using -dflist.
+        test: Just test the files for potential changes.
+        verbosity_level: Set the verbosity level (default 1).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `InitUserDotfilesPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INIT_USER_DOTFILES_PY_METADATA)
+    params = init_user_dotfiles_py_params(
+        help_=help_,
+        help_dotfiles_all=help_dotfiles_all,
+        help_dotfiles_mod=help_dotfiles_mod,
+        help_shells=help_shells,
+        hist=hist,
+        show_valid_opts=show_valid_opts,
+        ver=ver,
+        dot_files_list=dot_files_list,
+        dir_bin=dir_bin,
+        dir_dot=dir_dot,
+        do_updates=do_updates,
+        dry_run=dry_run,
+        force=force,
+        make_backup=make_backup,
+        shell_list=shell_list,
+        test=test,
+        verbosity_level=verbosity_level,
+    )
+    return init_user_dotfiles_py_execute(params, execution)
+
+
+__all__ = [
+    "INIT_USER_DOTFILES_PY_METADATA",
+    "InitUserDotfilesPyOutputs",
+    "InitUserDotfilesPyParameters",
+    "init_user_dotfiles_py",
+    "init_user_dotfiles_py_params",
+]

niwrap_afni/afni/inspec.py

@@ -0,0 +1,255 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+INSPEC_METADATA = Metadata(
+    id="6a13b0f30f764b4a293786927f7b9ec71eacbd6c.boutiques",
+    name="inspec",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+InspecParameters = typing.TypedDict('InspecParameters', {
+    "__STYX_TYPE__": typing.Literal["inspec"],
+    "specfile": InputPathType,
+    "newspecname": typing.NotRequired[str | None],
+    "detail": typing.NotRequired[float | None],
+    "leftspec": typing.NotRequired[InputPathType | None],
+    "rightspec": typing.NotRequired[InputPathType | None],
+    "state_rm": typing.NotRequired[str | None],
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "inspec": inspec_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 InspecOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `inspec(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def inspec_params(
+    specfile: InputPathType,
+    newspecname: str | None = None,
+    detail: float | None = None,
+    leftspec: InputPathType | None = None,
+    rightspec: InputPathType | None = None,
+    state_rm: str | None = None,
+    help_: bool = False,
+) -> InspecParameters:
+    """
+    Build parameters.
+    
+    Args:
+        specfile: Spec file to be read.
+        newspecname: Rewrite spec file.
+        detail: Level of output detail. Default is 1 in general, 0 with\
+            -LRmerge. Available levels are 0, 1, 2, and 3.
+        leftspec: Merge two spec files in a way that makes sense for viewing in\
+            SUMA.
+        rightspec: Merge two spec files in a way that makes sense for viewing\
+            in SUMA.
+        state_rm: Get rid of state STATE_RM from the specfile.
+        help_: Display help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "inspec",
+        "specfile": specfile,
+        "help": help_,
+    }
+    if newspecname is not None:
+        params["newspecname"] = newspecname
+    if detail is not None:
+        params["detail"] = detail
+    if leftspec is not None:
+        params["leftspec"] = leftspec
+    if rightspec is not None:
+        params["rightspec"] = rightspec
+    if state_rm is not None:
+        params["state_rm"] = state_rm
+    return params
+
+
+def inspec_cargs(
+    params: InspecParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("inspec")
+    cargs.extend([
+        "-spec",
+        execution.input_file(params.get("specfile"))
+    ])
+    if params.get("newspecname") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("newspecname")
+        ])
+    if params.get("detail") is not None:
+        cargs.extend([
+            "-detail",
+            str(params.get("detail"))
+        ])
+    if params.get("leftspec") is not None:
+        cargs.extend([
+            "-LRmerge",
+            execution.input_file(params.get("leftspec"))
+        ])
+    if params.get("rightspec") is not None:
+        cargs.extend([
+            "-LRmerge",
+            execution.input_file(params.get("rightspec"))
+        ])
+    if params.get("state_rm") is not None:
+        cargs.extend([
+            "-remove_state",
+            params.get("state_rm")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def inspec_outputs(
+    params: InspecParameters,
+    execution: Execution,
+) -> InspecOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = InspecOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def inspec_execute(
+    params: InspecParameters,
+    execution: Execution,
+) -> InspecOutputs:
+    """
+    Outputs information found from specfile.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `InspecOutputs`).
+    """
+    params = execution.params(params)
+    cargs = inspec_cargs(params, execution)
+    ret = inspec_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def inspec(
+    specfile: InputPathType,
+    newspecname: str | None = None,
+    detail: float | None = None,
+    leftspec: InputPathType | None = None,
+    rightspec: InputPathType | None = None,
+    state_rm: str | None = None,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> InspecOutputs:
+    """
+    Outputs information found from specfile.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        specfile: Spec file to be read.
+        newspecname: Rewrite spec file.
+        detail: Level of output detail. Default is 1 in general, 0 with\
+            -LRmerge. Available levels are 0, 1, 2, and 3.
+        leftspec: Merge two spec files in a way that makes sense for viewing in\
+            SUMA.
+        rightspec: Merge two spec files in a way that makes sense for viewing\
+            in SUMA.
+        state_rm: Get rid of state STATE_RM from the specfile.
+        help_: Display help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `InspecOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INSPEC_METADATA)
+    params = inspec_params(
+        specfile=specfile,
+        newspecname=newspecname,
+        detail=detail,
+        leftspec=leftspec,
+        rightspec=rightspec,
+        state_rm=state_rm,
+        help_=help_,
+    )
+    return inspec_execute(params, execution)
+
+
+__all__ = [
+    "INSPEC_METADATA",
+    "InspecOutputs",
+    "InspecParameters",
+    "inspec",
+    "inspec_params",
+]