niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__update_afni_binaries.py

@@ -0,0 +1,410 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__UPDATE_AFNI_BINARIES_METADATA = Metadata(
+    id="893694dbbccc046a97eb3b039a42a123a05bfc8f.boutiques",
+    name="@update.afni.binaries",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VUpdateAfniBinariesParameters = typing.TypedDict('VUpdateAfniBinariesParameters', {
+    "__STYX_TYPE__": typing.Literal["@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],
+})
+
+
+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(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__update_afni_binaries_params(
+    defaults_flag: bool = False,
+    help_flag: bool = False,
+    help_sys_progs_flag: bool = False,
+    apsearch: str | None = None,
+    bindir: str | None = None,
+    curl_flag: bool = False,
+    do_dotfiles_flag: bool = False,
+    do_extras_flag: bool = False,
+    echo_flag: bool = False,
+    make_backup: str | None = None,
+    no_cert_verify_flag: bool = False,
+    no_recur_flag: bool = False,
+    proto: str | None = None,
+    quick_flag: bool = False,
+    show_obsoletes_flag: bool = False,
+    show_obsoletes_grep_flag: bool = False,
+    show_system_progs_flag: bool = False,
+    sys_ok_flag: bool = False,
+    test_flag: bool = False,
+    test_protos_flag: bool = False,
+    revert_flag: bool = False,
+    local_package: str | None = None,
+    prog_list: list[str] | None = None,
+    package: str | None = None,
+) -> VUpdateAfniBinariesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        defaults_flag: Install current package into abin.
+        help_flag: Show this help.
+        help_sys_progs_flag: List system programs that block update.
+        apsearch: Specify getting apsearch updates.
+        bindir: Set AFNI binary directory to ABIN.
+        curl_flag: Default to curl instead of wget.
+        do_dotfiles_flag: Try to initialize dot files if needed.
+        do_extras_flag: Do extra niceties (beyond simple install).
+        echo_flag: Turn on shell command echo.
+        make_backup: Make a backup of binaries before replacing.
+        no_cert_verify_flag: Do not verify the server CA certificate.
+        no_recur_flag: Do not download and run new @uab script.
+        proto: Access afni host via specified PROTOCOL.
+        quick_flag: Quick mode, no fancies.
+        show_obsoletes_flag: List any obsolete packages.
+        show_obsoletes_grep_flag: List any obsolete packages (easy to grep).
+        show_system_progs_flag: Show system programs that do not belong in\
+            abin.
+        sys_ok_flag: OK to update, even if system progs found.
+        test_flag: Just attempt the download and quit.
+        test_protos_flag: Test download protocols and exit.
+        revert_flag: Revert binaries to previous version.
+        local_package: Install local PACKAGE.tgz package.
+        prog_list: Install given programs, not whole PACKAGE.
+        package: Install distribution package PACKAGE.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@update.afni.binaries",
+        "defaults_flag": defaults_flag,
+        "help_flag": help_flag,
+        "help_sys_progs_flag": help_sys_progs_flag,
+        "curl_flag": curl_flag,
+        "do_dotfiles_flag": do_dotfiles_flag,
+        "do_extras_flag": do_extras_flag,
+        "echo_flag": echo_flag,
+        "no_cert_verify_flag": no_cert_verify_flag,
+        "no_recur_flag": no_recur_flag,
+        "quick_flag": quick_flag,
+        "show_obsoletes_flag": show_obsoletes_flag,
+        "show_obsoletes_grep_flag": show_obsoletes_grep_flag,
+        "show_system_progs_flag": show_system_progs_flag,
+        "sys_ok_flag": sys_ok_flag,
+        "test_flag": test_flag,
+        "test_protos_flag": test_protos_flag,
+        "revert_flag": revert_flag,
+    }
+    if apsearch is not None:
+        params["apsearch"] = apsearch
+    if bindir is not None:
+        params["bindir"] = bindir
+    if make_backup is not None:
+        params["make_backup"] = make_backup
+    if proto is not None:
+        params["proto"] = proto
+    if local_package is not None:
+        params["local_package"] = local_package
+    if prog_list is not None:
+        params["prog_list"] = prog_list
+    if package is not None:
+        params["package"] = package
+    return params
+
+
+def v__update_afni_binaries_cargs(
+    params: VUpdateAfniBinariesParameters,
+    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("@update.afni.binaries")
+    if params.get("defaults_flag"):
+        cargs.append("-defaults")
+    if params.get("help_flag"):
+        cargs.append("-help")
+    if params.get("help_sys_progs_flag"):
+        cargs.append("-help_sys_progs")
+    if params.get("apsearch") is not None:
+        cargs.extend([
+            "-apsearch",
+            params.get("apsearch")
+        ])
+    if params.get("bindir") is not None:
+        cargs.extend([
+            "-bindir",
+            params.get("bindir")
+        ])
+    if params.get("curl_flag"):
+        cargs.append("-curl")
+    if params.get("do_dotfiles_flag"):
+        cargs.append("-do_dotfiles")
+    if params.get("do_extras_flag"):
+        cargs.append("-do_extras")
+    if params.get("echo_flag"):
+        cargs.append("-echo")
+    if params.get("make_backup") is not None:
+        cargs.extend([
+            "-make_backup",
+            params.get("make_backup")
+        ])
+    if params.get("no_cert_verify_flag"):
+        cargs.append("-no_cert_verify")
+    if params.get("no_recur_flag"):
+        cargs.append("-no_recur")
+    if params.get("proto") is not None:
+        cargs.extend([
+            "-proto",
+            params.get("proto")
+        ])
+    if params.get("quick_flag"):
+        cargs.append("-quick")
+    if params.get("show_obsoletes_flag"):
+        cargs.append("-show_obsoletes")
+    if params.get("show_obsoletes_grep_flag"):
+        cargs.append("-show_obsoletes_grep")
+    if params.get("show_system_progs_flag"):
+        cargs.append("-show_system_progs")
+    if params.get("sys_ok_flag"):
+        cargs.append("-sys_ok")
+    if params.get("test_flag"):
+        cargs.append("-test")
+    if params.get("test_protos_flag"):
+        cargs.append("-test_protos")
+    if params.get("revert_flag"):
+        cargs.append("-revert")
+    if params.get("local_package") is not None:
+        cargs.extend([
+            "-local_package",
+            params.get("local_package")
+        ])
+    if params.get("prog_list") is not None:
+        cargs.extend([
+            "-prog_list",
+            *params.get("prog_list")
+        ])
+    if params.get("package") is not None:
+        cargs.extend([
+            "-package",
+            params.get("package")
+        ])
+    return cargs
+
+
+def v__update_afni_binaries_outputs(
+    params: VUpdateAfniBinariesParameters,
+    execution: Execution,
+) -> VUpdateAfniBinariesOutputs:
+    """
+    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 = VUpdateAfniBinariesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__update_afni_binaries_execute(
+    params: VUpdateAfniBinariesParameters,
+    execution: Execution,
+) -> VUpdateAfniBinariesOutputs:
+    """
+    Install or update AFNI binaries.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VUpdateAfniBinariesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__update_afni_binaries_cargs(params, execution)
+    ret = v__update_afni_binaries_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__update_afni_binaries(
+    defaults_flag: bool = False,
+    help_flag: bool = False,
+    help_sys_progs_flag: bool = False,
+    apsearch: str | None = None,
+    bindir: str | None = None,
+    curl_flag: bool = False,
+    do_dotfiles_flag: bool = False,
+    do_extras_flag: bool = False,
+    echo_flag: bool = False,
+    make_backup: str | None = None,
+    no_cert_verify_flag: bool = False,
+    no_recur_flag: bool = False,
+    proto: str | None = None,
+    quick_flag: bool = False,
+    show_obsoletes_flag: bool = False,
+    show_obsoletes_grep_flag: bool = False,
+    show_system_progs_flag: bool = False,
+    sys_ok_flag: bool = False,
+    test_flag: bool = False,
+    test_protos_flag: bool = False,
+    revert_flag: bool = False,
+    local_package: str | None = None,
+    prog_list: list[str] | None = None,
+    package: str | None = None,
+    runner: Runner | None = None,
+) -> VUpdateAfniBinariesOutputs:
+    """
+    Install or update AFNI binaries.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        defaults_flag: Install current package into abin.
+        help_flag: Show this help.
+        help_sys_progs_flag: List system programs that block update.
+        apsearch: Specify getting apsearch updates.
+        bindir: Set AFNI binary directory to ABIN.
+        curl_flag: Default to curl instead of wget.
+        do_dotfiles_flag: Try to initialize dot files if needed.
+        do_extras_flag: Do extra niceties (beyond simple install).
+        echo_flag: Turn on shell command echo.
+        make_backup: Make a backup of binaries before replacing.
+        no_cert_verify_flag: Do not verify the server CA certificate.
+        no_recur_flag: Do not download and run new @uab script.
+        proto: Access afni host via specified PROTOCOL.
+        quick_flag: Quick mode, no fancies.
+        show_obsoletes_flag: List any obsolete packages.
+        show_obsoletes_grep_flag: List any obsolete packages (easy to grep).
+        show_system_progs_flag: Show system programs that do not belong in\
+            abin.
+        sys_ok_flag: OK to update, even if system progs found.
+        test_flag: Just attempt the download and quit.
+        test_protos_flag: Test download protocols and exit.
+        revert_flag: Revert binaries to previous version.
+        local_package: Install local PACKAGE.tgz package.
+        prog_list: Install given programs, not whole PACKAGE.
+        package: Install distribution package PACKAGE.
+        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 = v__update_afni_binaries_params(
+        defaults_flag=defaults_flag,
+        help_flag=help_flag,
+        help_sys_progs_flag=help_sys_progs_flag,
+        apsearch=apsearch,
+        bindir=bindir,
+        curl_flag=curl_flag,
+        do_dotfiles_flag=do_dotfiles_flag,
+        do_extras_flag=do_extras_flag,
+        echo_flag=echo_flag,
+        make_backup=make_backup,
+        no_cert_verify_flag=no_cert_verify_flag,
+        no_recur_flag=no_recur_flag,
+        proto=proto,
+        quick_flag=quick_flag,
+        show_obsoletes_flag=show_obsoletes_flag,
+        show_obsoletes_grep_flag=show_obsoletes_grep_flag,
+        show_system_progs_flag=show_system_progs_flag,
+        sys_ok_flag=sys_ok_flag,
+        test_flag=test_flag,
+        test_protos_flag=test_protos_flag,
+        revert_flag=revert_flag,
+        local_package=local_package,
+        prog_list=prog_list,
+        package=package,
+    )
+    return v__update_afni_binaries_execute(params, execution)
+
+
+__all__ = [
+    "VUpdateAfniBinariesOutputs",
+    "VUpdateAfniBinariesParameters",
+    "V__UPDATE_AFNI_BINARIES_METADATA",
+    "v__update_afni_binaries",
+    "v__update_afni_binaries_params",
+]

niwrap_afni/afni/v__vol_center.py

@@ -0,0 +1,188 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__VOL_CENTER_METADATA = Metadata(
+    id="4ce13662130110b3fd50b4a405a5d296faf47380.boutiques",
+    name="@VolCenter",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VVolCenterParameters = typing.TypedDict('VVolCenterParameters', {
+    "__STYX_TYPE__": typing.Literal["@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(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__vol_center_params(
+    dset: InputPathType,
+    orient: str | None = None,
+) -> VVolCenterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: Input volume dataset.
+        orient: Output coordinate system orientation (e.g., RAI).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@VolCenter",
+        "dset": dset,
+    }
+    if orient is not None:
+        params["orient"] = orient
+    return params
+
+
+def v__vol_center_cargs(
+    params: VVolCenterParameters,
+    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("@VolCenter")
+    cargs.extend([
+        "-dset",
+        execution.input_file(params.get("dset"))
+    ])
+    if params.get("orient") is not None:
+        cargs.extend([
+            "-or",
+            params.get("orient")
+        ])
+    return cargs
+
+
+def v__vol_center_outputs(
+    params: VVolCenterParameters,
+    execution: Execution,
+) -> VVolCenterOutputs:
+    """
+    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 = VVolCenterOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__vol_center_execute(
+    params: VVolCenterParameters,
+    execution: Execution,
+) -> VVolCenterOutputs:
+    """
+    Tool to return the center of volume for a given dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VVolCenterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__vol_center_cargs(params, execution)
+    ret = v__vol_center_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__vol_center(
+    dset: InputPathType,
+    orient: str | None = None,
+    runner: Runner | None = None,
+) -> VVolCenterOutputs:
+    """
+    Tool to return the center of volume for a given dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: Input volume dataset.
+        orient: Output coordinate system orientation (e.g., RAI).
+        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 = v__vol_center_params(
+        dset=dset,
+        orient=orient,
+    )
+    return v__vol_center_execute(params, execution)
+
+
+__all__ = [
+    "VVolCenterOutputs",
+    "VVolCenterParameters",
+    "V__VOL_CENTER_METADATA",
+    "v__vol_center",
+    "v__vol_center_params",
+]