niwrap-afni 0.5.0__tar.gz → 0.5.2__tar.gz

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: niwrap_afni
-Version: 0.5.0
+Version: 0.5.2
 Summary: NiWrap wrappers for AFNI.
 Author-email: CMI DAIR <dair@childmind.org>
 License-Expression: LGPL-2.1

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "niwrap_afni"
-version = "0.5.0"
+version = "0.5.2"
 description = "NiWrap wrappers for AFNI."
 license = "LGPL-2.1"
 authors = [{ name = "CMI DAIR", email = "dair@childmind.org" }]

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/src/niwrap_afni/afni/abids_json_tool_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ABIDS_JSON_TOOL_PY_METADATA = Metadata(
-    id="9cd5d1cbe0772f0f1c51d0bd811ef0336e43437f.boutiques",
+    id="e329338100a8b98497d00dd658e2d105dfa05630.boutiques",
     name="abids_json_tool.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,7 +17,16 @@ AbidsJsonToolPyParameters = typing.TypedDict('AbidsJsonToolPyParameters', {
     "__STYX_TYPE__": typing.Literal["abids_json_tool.py"],
     "input_file": InputPathType,
     "prefix": str,
+    "txt2json": bool,
+    "json2txt": bool,
+    "add_json": typing.NotRequired[list[str] | None],
     "del_json": typing.NotRequired[str | None],
+    "force_add": bool,
+    "overwrite": bool,
+    "help": bool,
+    "delimiter_major": typing.NotRequired[str | None],
+    "delimiter_minor": typing.NotRequired[str | None],
+    "literal_keys": bool,
     "values_stay_str": bool,
 })
 
@@ -64,7 +73,16 @@ class AbidsJsonToolPyOutputs(typing.NamedTuple):
 def abids_json_tool_py_params(
     input_file: InputPathType,
     prefix: str,
+    txt2json: bool = False,
+    json2txt: bool = False,
+    add_json: list[str] | None = None,
     del_json: str | None = None,
+    force_add: bool = False,
+    overwrite: bool = False,
+    help_: bool = False,
+    delimiter_major: str | None = None,
+    delimiter_minor: str | None = None,
+    literal_keys: bool = False,
     values_stay_str: bool = False,
 ) -> AbidsJsonToolPyParameters:
     """
@@ -74,7 +92,21 @@ def abids_json_tool_py_params(
         input_file: One file to convert. Enter NULL with -add_json to create\
             new json file.
         prefix: Output file name.
+        txt2json: Convert from ':' separated text file to json formatted file.
+        json2txt: Convert from json formatted file to ':' separated text file.
+        add_json: Add an attribute to the end of the specified json file.
         del_json: Remove attribute (KEY) from the -input json file.
+        force_add: Use with -add_json to overwrite an existing attribute in the\
+            specified json file.
+        overwrite: Use caution as this will overwrite the -prefix file if it\
+            exists!!.
+        help_: Show this help and exit.
+        delimiter_major: Specify the new (major) delimiter to separate keys and\
+            values when using '-txt2json' opt.
+        delimiter_minor: Specify the new (minor) delimiter to separate value\
+            items when using '-txt2json' opt.
+        literal_keys: Do not replace spaces with '_', nor parentheses and\
+            brackets with ''.
         values_stay_str: Each numeric or str item gets saved as a str;\
             otherwise, guess at int and float.
     Returns:
@@ -84,10 +116,22 @@ def abids_json_tool_py_params(
         "__STYXTYPE__": "abids_json_tool.py",
         "input_file": input_file,
         "prefix": prefix,
+        "txt2json": txt2json,
+        "json2txt": json2txt,
+        "force_add": force_add,
+        "overwrite": overwrite,
+        "help": help_,
+        "literal_keys": literal_keys,
         "values_stay_str": values_stay_str,
     }
+    if add_json is not None:
+        params["add_json"] = add_json
     if del_json is not None:
         params["del_json"] = del_json
+    if delimiter_major is not None:
+        params["delimiter_major"] = delimiter_major
+    if delimiter_minor is not None:
+        params["delimiter_minor"] = delimiter_minor
     return params
 
 
@@ -114,11 +158,38 @@ def abids_json_tool_py_cargs(
         "-prefix",
         params.get("prefix")
     ])
+    if params.get("txt2json"):
+        cargs.append("-txt2json")
+    if params.get("json2txt"):
+        cargs.append("-json2txt")
+    if params.get("add_json") is not None:
+        cargs.extend([
+            "-add_json",
+            *params.get("add_json")
+        ])
     if params.get("del_json") is not None:
         cargs.extend([
             "-del_json",
             params.get("del_json")
         ])
+    if params.get("force_add"):
+        cargs.append("-f")
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("delimiter_major") is not None:
+        cargs.extend([
+            "-delimiter_major",
+            params.get("delimiter_major")
+        ])
+    if params.get("delimiter_minor") is not None:
+        cargs.extend([
+            "-delimiter_minor",
+            params.get("delimiter_minor")
+        ])
+    if params.get("literal_keys"):
+        cargs.append("-literal_keys")
     if params.get("values_stay_str"):
         cargs.append("-values_stay_str")
     return cargs
@@ -170,7 +241,16 @@ def abids_json_tool_py_execute(
 def abids_json_tool_py(
     input_file: InputPathType,
     prefix: str,
+    txt2json: bool = False,
+    json2txt: bool = False,
+    add_json: list[str] | None = None,
     del_json: str | None = None,
+    force_add: bool = False,
+    overwrite: bool = False,
+    help_: bool = False,
+    delimiter_major: str | None = None,
+    delimiter_minor: str | None = None,
+    literal_keys: bool = False,
     values_stay_str: bool = False,
     runner: Runner | None = None,
 ) -> AbidsJsonToolPyOutputs:
@@ -185,7 +265,21 @@ def abids_json_tool_py(
         input_file: One file to convert. Enter NULL with -add_json to create\
             new json file.
         prefix: Output file name.
+        txt2json: Convert from ':' separated text file to json formatted file.
+        json2txt: Convert from json formatted file to ':' separated text file.
+        add_json: Add an attribute to the end of the specified json file.
         del_json: Remove attribute (KEY) from the -input json file.
+        force_add: Use with -add_json to overwrite an existing attribute in the\
+            specified json file.
+        overwrite: Use caution as this will overwrite the -prefix file if it\
+            exists!!.
+        help_: Show this help and exit.
+        delimiter_major: Specify the new (major) delimiter to separate keys and\
+            values when using '-txt2json' opt.
+        delimiter_minor: Specify the new (minor) delimiter to separate value\
+            items when using '-txt2json' opt.
+        literal_keys: Do not replace spaces with '_', nor parentheses and\
+            brackets with ''.
         values_stay_str: Each numeric or str item gets saved as a str;\
             otherwise, guess at int and float.
         runner: Command runner.
@@ -197,7 +291,16 @@ def abids_json_tool_py(
     params = abids_json_tool_py_params(
         input_file=input_file,
         prefix=prefix,
+        txt2json=txt2json,
+        json2txt=json2txt,
+        add_json=add_json,
         del_json=del_json,
+        force_add=force_add,
+        overwrite=overwrite,
+        help_=help_,
+        delimiter_major=delimiter_major,
+        delimiter_minor=delimiter_minor,
+        literal_keys=literal_keys,
         values_stay_str=values_stay_str,
     )
     return abids_json_tool_py_execute(params, execution)

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/src/niwrap_afni/afni/abids_tool.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ABIDS_TOOL_METADATA = Metadata(
-    id="ecdd7e187a3a330cd02d094f809fb0b75a51fe76.boutiques",
+    id="44f26320aab699eef15ef4c3c6fdea66a995e467.boutiques",
     name="abids_tool",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,7 +16,11 @@ ABIDS_TOOL_METADATA = Metadata(
 AbidsToolParameters = typing.TypedDict('AbidsToolParameters', {
     "__STYX_TYPE__": typing.Literal["abids_tool"],
     "input_files": list[InputPathType],
+    "tr_match": bool,
+    "add_tr": bool,
+    "add_slice_times": bool,
     "copy_prefix": typing.NotRequired[list[str] | None],
+    "help_flag": bool,
 })
 
 
@@ -61,21 +65,36 @@ class AbidsToolOutputs(typing.NamedTuple):
 
 def abids_tool_params(
     input_files: list[InputPathType],
+    tr_match: bool = False,
+    add_tr: bool = False,
+    add_slice_times: bool = False,
     copy_prefix: list[str] | None = None,
+    help_flag: bool = False,
 ) -> AbidsToolParameters:
     """
     Build parameters.
     
     Args:
         input_files: At least one 3d+time dataset in NIFTI format.
+        tr_match: Check if the TR in the json file matches the TR from input\
+            dataset header. (Returns 1 if match).
+        add_tr: Add the TR from the BIDS json file to the input dataset using\
+            3drefit.
+        add_slice_times: Add the slice times from the BIDS json file to the\
+            input dataset using 3drefit.
         copy_prefix: Copy both the NIFTI dataset(s) and matching .json file(s)\
             to PREFIX. Must have the same number of prefixes as datasets.
+        help_flag: Show help information and exit.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "abids_tool",
         "input_files": input_files,
+        "tr_match": tr_match,
+        "add_tr": add_tr,
+        "add_slice_times": add_slice_times,
+        "help_flag": help_flag,
     }
     if copy_prefix is not None:
         params["copy_prefix"] = copy_prefix
@@ -98,11 +117,19 @@ def abids_tool_cargs(
     cargs = []
     cargs.append("abids_tool.py")
     cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("tr_match"):
+        cargs.append("-TR_match")
+    if params.get("add_tr"):
+        cargs.append("-add_TR")
+    if params.get("add_slice_times"):
+        cargs.append("-add_slice_times")
     if params.get("copy_prefix") is not None:
         cargs.extend([
             "-copy",
             *params.get("copy_prefix")
         ])
+    if params.get("help_flag"):
+        cargs.append("-help")
     return cargs
 
 
@@ -153,7 +180,11 @@ def abids_tool_execute(
 
 def abids_tool(
     input_files: list[InputPathType],
+    tr_match: bool = False,
+    add_tr: bool = False,
+    add_slice_times: bool = False,
     copy_prefix: list[str] | None = None,
+    help_flag: bool = False,
     runner: Runner | None = None,
 ) -> AbidsToolOutputs:
     """
@@ -167,8 +198,15 @@ def abids_tool(
     
     Args:
         input_files: At least one 3d+time dataset in NIFTI format.
+        tr_match: Check if the TR in the json file matches the TR from input\
+            dataset header. (Returns 1 if match).
+        add_tr: Add the TR from the BIDS json file to the input dataset using\
+            3drefit.
+        add_slice_times: Add the slice times from the BIDS json file to the\
+            input dataset using 3drefit.
         copy_prefix: Copy both the NIFTI dataset(s) and matching .json file(s)\
             to PREFIX. Must have the same number of prefixes as datasets.
+        help_flag: Show help information and exit.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AbidsToolOutputs`).
@@ -177,7 +215,11 @@ def abids_tool(
     execution = runner.start_execution(ABIDS_TOOL_METADATA)
     params = abids_tool_params(
         input_files=input_files,
+        tr_match=tr_match,
+        add_tr=add_tr,
+        add_slice_times=add_slice_times,
         copy_prefix=copy_prefix,
+        help_flag=help_flag,
     )
     return abids_tool_execute(params, execution)
 

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/src/niwrap_afni/afni/adjunct_make_script_and_rst_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ADJUNCT_MAKE_SCRIPT_AND_RST_PY_METADATA = Metadata(
-    id="b713438ba08e71d534cca42445c2bcd23acbc3af.boutiques",
+    id="5cd9b08bee37168399c0b35d303c4cdeaaeeffeb.boutiques",
     name="adjunct_make_script_and_rst.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -120,7 +120,7 @@ def adjunct_make_script_and_rst_py_cargs(
     cargs.append("adjunct_make_script_and_rst.py")
     cargs.extend([
         "-input",
-        "-" + execution.input_file(params.get("input_script"))
+        execution.input_file(params.get("input_script"))
     ])
     cargs.extend([
         "--prefix_rst",

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/src/niwrap_afni/afni/afni_batch_r.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AFNI_BATCH_R_METADATA = Metadata(
-    id="78789aab686dc723a7f6543875033396e8a4b97c.boutiques",
+    id="8f19b113f220df5c4c707c9f78252bd08a223bb3.boutiques",
     name="AFNI_Batch_R",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -119,7 +119,6 @@ def afni_batch_r_cargs(
         cargs.append("--no-readline")
     if params.get("vanilla_mode"):
         cargs.append("--vanilla")
-    cargs.append("--args")
     if params.get("help"):
         cargs.append("-help")
     return cargs

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/src/niwrap_afni/afni/balloon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BALLOON_METADATA = Metadata(
-    id="d38a0b74f4c93d5365bdded27c362f4ddc6e6b5f.boutiques",
+    id="efa704edebd4da856d63213685c5a8439a31d101.boutiques",
     name="balloon",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,7 +18,9 @@ BalloonParameters = typing.TypedDict('BalloonParameters', {
     "tr": float,
     "num_scans": int,
     "event_times": InputPathType,
+    "t_rise": typing.NotRequired[list[float] | None],
     "t_fall": typing.NotRequired[list[float] | None],
+    "t_sustain": typing.NotRequired[list[float] | None],
 })
 
 
@@ -65,7 +67,9 @@ def balloon_params(
     tr: float,
     num_scans: int,
     event_times: InputPathType,
+    t_rise: list[float] | None = None,
     t_fall: list[float] | None = None,
+    t_sustain: list[float] | None = None,
 ) -> BalloonParameters:
     """
     Build parameters.
@@ -78,8 +82,12 @@ def balloon_params(
         event_times: The name of a file containing the event timings, in\
             seconds, as ASCII strings separated by white space, with time 0 being\
             the time at which the initial scan occurred.
+        t_rise: Haemodynamic rise time in seconds (typically between 4s and\
+            6s).
         t_fall: Haemodynamic fall time in seconds (typically between 4s and\
             6s).
+        t_sustain: Haemodynamic sustain time in seconds (typically between 0s\
+            and 4s).
     Returns:
         Parameter dictionary
     """
@@ -89,8 +97,12 @@ def balloon_params(
         "num_scans": num_scans,
         "event_times": event_times,
     }
+    if t_rise is not None:
+        params["t_rise"] = t_rise
     if t_fall is not None:
         params["t_fall"] = t_fall
+    if t_sustain is not None:
+        params["t_sustain"] = t_sustain
     return params
 
 
@@ -112,8 +124,12 @@ def balloon_cargs(
     cargs.append(str(params.get("tr")))
     cargs.append(str(params.get("num_scans")))
     cargs.append(execution.input_file(params.get("event_times")))
+    if params.get("t_rise") is not None:
+        cargs.extend(map(str, params.get("t_rise")))
     if params.get("t_fall") is not None:
         cargs.extend(map(str, params.get("t_fall")))
+    if params.get("t_sustain") is not None:
+        cargs.extend(map(str, params.get("t_sustain")))
     return cargs
 
 
@@ -165,7 +181,9 @@ def balloon(
     tr: float,
     num_scans: int,
     event_times: InputPathType,
+    t_rise: list[float] | None = None,
     t_fall: list[float] | None = None,
+    t_sustain: list[float] | None = None,
     runner: Runner | None = None,
 ) -> BalloonOutputs:
     """
@@ -184,8 +202,12 @@ def balloon(
         event_times: The name of a file containing the event timings, in\
             seconds, as ASCII strings separated by white space, with time 0 being\
             the time at which the initial scan occurred.
+        t_rise: Haemodynamic rise time in seconds (typically between 4s and\
+            6s).
         t_fall: Haemodynamic fall time in seconds (typically between 4s and\
             6s).
+        t_sustain: Haemodynamic sustain time in seconds (typically between 0s\
+            and 4s).
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BalloonOutputs`).
@@ -196,7 +218,9 @@ def balloon(
         tr=tr,
         num_scans=num_scans,
         event_times=event_times,
+        t_rise=t_rise,
         t_fall=t_fall,
+        t_sustain=t_sustain,
     )
     return balloon_execute(params, execution)
 

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/src/niwrap_afni/afni/brain_skin.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BRAIN_SKIN_METADATA = Metadata(
-    id="4f110568466cb173a0801348ecaabe46ca587148.boutiques",
+    id="b29116757bd00299a9e042bed62f178844c81d0f.boutiques",
     name="BrainSkin",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -24,6 +24,7 @@ BrainSkinParameters = typing.TypedDict('BrainSkinParameters', {
     "voxelize": typing.NotRequired[str | None],
     "infill": typing.NotRequired[str | None],
     "out_file": typing.NotRequired[InputPathType | None],
+    "vol_skin": typing.NotRequired[InputPathType | None],
     "vol_hull": typing.NotRequired[InputPathType | None],
     "no_zero_attraction": bool,
     "node_dbg": typing.NotRequired[float | None],
@@ -103,6 +104,7 @@ def brain_skin_params(
     voxelize: str | None = None,
     infill: str | None = None,
     out_file: InputPathType | None = None,
+    vol_skin: InputPathType | None = None,
     vol_hull: InputPathType | None = None,
     no_zero_attraction: bool = False,
     node_dbg: float | None = None,
@@ -124,6 +126,8 @@ def brain_skin_params(
         infill: Infill method. Choose from: slow: proper infill, but not\
             needed, fast: brutish infill, all we need (default).
         out_file: Output intermediary results from skin forming step.
+        vol_skin: Deform an Icosahedron to match the outer boundary of a mask\
+            volume.
         vol_hull: Deform an Icosahedron to match the convex hull of a mask\
             volume.
         no_zero_attraction: With vol_skin, the surface will try to shrink\
@@ -152,6 +156,8 @@ def brain_skin_params(
         params["infill"] = infill
     if out_file is not None:
         params["out_file"] = out_file
+    if vol_skin is not None:
+        params["vol_skin"] = vol_skin
     if vol_hull is not None:
         params["vol_hull"] = vol_hull
     if node_dbg is not None:
@@ -213,6 +219,11 @@ def brain_skin_cargs(
             "-out",
             execution.input_file(params.get("out_file"))
         ])
+    if params.get("vol_skin") is not None:
+        cargs.extend([
+            "-vol_skin",
+            execution.input_file(params.get("vol_skin"))
+        ])
     if params.get("vol_hull") is not None:
         cargs.extend([
             "-vol_hull",
@@ -293,6 +304,7 @@ def brain_skin(
     voxelize: str | None = None,
     infill: str | None = None,
     out_file: InputPathType | None = None,
+    vol_skin: InputPathType | None = None,
     vol_hull: InputPathType | None = None,
     no_zero_attraction: bool = False,
     node_dbg: float | None = None,
@@ -320,6 +332,8 @@ def brain_skin(
         infill: Infill method. Choose from: slow: proper infill, but not\
             needed, fast: brutish infill, all we need (default).
         out_file: Output intermediary results from skin forming step.
+        vol_skin: Deform an Icosahedron to match the outer boundary of a mask\
+            volume.
         vol_hull: Deform an Icosahedron to match the convex hull of a mask\
             volume.
         no_zero_attraction: With vol_skin, the surface will try to shrink\
@@ -342,6 +356,7 @@ def brain_skin(
         voxelize=voxelize,
         infill=infill,
         out_file=out_file,
+        vol_skin=vol_skin,
         vol_hull=vol_hull,
         no_zero_attraction=no_zero_attraction,
         node_dbg=node_dbg,

{niwrap_afni-0.5.0 → niwrap_afni-0.5.2}/src/niwrap_afni/afni/build_afni_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BUILD_AFNI_PY_METADATA = Metadata(
-    id="8b01bbfc26acb4a73b16110f6849bc381629f972.boutiques",
+    id="e6c59cd0d5e67711746b75a7e41644183586e675.boutiques",
     name="build_afni.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -27,6 +27,9 @@ BuildAfniPyParameters = typing.TypedDict('BuildAfniPyParameters', {
     "run_cmake": typing.NotRequired[str | None],
     "run_make": typing.NotRequired[str | None],
     "verbose_level": typing.NotRequired[float | None],
+    "help": bool,
+    "history": bool,
+    "show_valid_opts": bool,
     "version": bool,
 })
 
@@ -88,6 +91,9 @@ def build_afni_py_params(
     run_cmake: str | None = None,
     run_make: str | None = None,
     verbose_level: float | None = None,
+    help_: bool = False,
+    history: bool = False,
+    show_valid_opts: bool = False,
     version: bool = False,
 ) -> BuildAfniPyParameters:
     """
@@ -106,6 +112,9 @@ def build_afni_py_params(
         run_cmake: Choose whether to run a cmake build. Default is no.
         run_make: Choose whether to run a make build. Default is yes.
         verbose_level: Set the verbosity level. Default is 1.
+        help_: Show help message.
+        history: Show module history.
+        show_valid_opts: List valid options.
         version: Show the current version.
     Returns:
         Parameter dictionary
@@ -114,6 +123,9 @@ def build_afni_py_params(
         "__STYXTYPE__": "build_afni.py",
         "build_root": build_root,
         "prep_only": prep_only,
+        "help": help_,
+        "history": history,
+        "show_valid_opts": show_valid_opts,
         "version": version,
     }
     if clean_root is not None:
@@ -210,6 +222,12 @@ def build_afni_py_cargs(
             "-verb",
             str(params.get("verbose_level"))
         ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("history"):
+        cargs.append("-hist")
+    if params.get("show_valid_opts"):
+        cargs.append("-show_valid_opts")
     if params.get("version"):
         cargs.append("-ver")
     return cargs
@@ -273,6 +291,9 @@ def build_afni_py(
     run_cmake: str | None = None,
     run_make: str | None = None,
     verbose_level: float | None = None,
+    help_: bool = False,
+    history: bool = False,
+    show_valid_opts: bool = False,
     version: bool = False,
     runner: Runner | None = None,
 ) -> BuildAfniPyOutputs:
@@ -296,6 +317,9 @@ def build_afni_py(
         run_cmake: Choose whether to run a cmake build. Default is no.
         run_make: Choose whether to run a make build. Default is yes.
         verbose_level: Set the verbosity level. Default is 1.
+        help_: Show help message.
+        history: Show module history.
+        show_valid_opts: List valid options.
         version: Show the current version.
         runner: Command runner.
     Returns:
@@ -316,6 +340,9 @@ def build_afni_py(
         run_cmake=run_cmake,
         run_make=run_make,
         verbose_level=verbose_level,
+        help_=help_,
+        history=history,
+        show_valid_opts=show_valid_opts,
         version=version,
     )
     return build_afni_py_execute(params, execution)