Fix up documentation (PennLINC#1209)

docs/outputs.rst

@@ -58,8 +58,11 @@ The atlases currently used in *XCP-D* can be separated into three groups: subcor
 and combined cortical/subcortical.
 The two subcortical atlases are the Tian atlas :footcite:p:`tian2020topographic` and the
 CIFTI subcortical parcellation :footcite:p:`glasser2013minimal`.
-The cortical atlases are the Glasser :footcite:p:`Glasser_2016` and the
-Gordon :footcite:p:`Gordon_2014`.
+The cortical atlases are the Glasser :footcite:p:`Glasser_2016`, the
+Gordon :footcite:p:`Gordon_2014`,
+the MIDB precision brain atlas derived from ABCD data and thresholded at 75% probability
+:footcite:p:`hermosillo2022precision`,
+and the Myers-Labonte infant atlas thresholded at 50% probability :footcite:`myers2023functional`.
 The combined cortical/subcortical atlases are 10 different resolutions of the
 4S (Schaefer Supplemented with Subcortical Structures) atlas.
 

docs/usage.rst

@@ -51,6 +51,7 @@ Command-Line Arguments
 .. argparse::
    :ref: xcp_d.cli.parser._build_parser
    :prog: xcp_d
+   :func: _build_parser
 
    --band-stop-min : @after
       For the "notch" filter option, we recommend the following values.

xcp_d/cli/parser.py

@@ -65,7 +65,6 @@ def _build_parser():
     )
 
     # Required "mode" argument
-    optional = parser._action_groups.pop()
     required = parser.add_argument_group("required arguments")
     required.add_argument(
         "--mode",
@@ -82,9 +81,9 @@ def _build_parser():
     )
 
     # optional arguments
-    optional.add_argument("--version", action="version", version=verstr)
+    parser.add_argument("--version", action="version", version=verstr)
 
-    g_bids = optional.add_argument_group("Options for filtering BIDS queries")
+    g_bids = parser.add_argument_group("Options for filtering BIDS queries")
     g_bids.add_argument(
         "--participant-label",
         "--participant_label",
@@ -137,7 +136,7 @@ def _build_parser():
         ),
     )
 
-    g_perfm = optional.add_argument_group("Options for resource management")
+    g_perfm = parser.add_argument_group("Options for resource management")
     g_perfm.add_argument(
         "--nprocs",
         "--nthreads",
@@ -195,7 +194,7 @@ def _build_parser():
         help="Increases log verbosity for each occurence. Debug level is '-vvv'.",
     )
 
-    g_outputoption = optional.add_argument_group("Input flags")
+    g_outputoption = parser.add_argument_group("Input flags")
     g_outputoption.add_argument(
         "--input-type",
         "--input_type",
@@ -224,7 +223,7 @@ def _build_parser():
         ),
     )
 
-    g_param = optional.add_argument_group("Postprocessing parameters")
+    g_param = parser.add_argument_group("Postprocessing parameters")
     g_param.add_argument(
         "--dummy-scans",
         "--dummy_scans",
@@ -320,7 +319,7 @@ def _build_parser():
         help="After denoising, concatenate each derivative from each task across runs.",
     )
 
-    g_motion_filter = optional.add_argument_group(
+    g_motion_filter = parser.add_argument_group(
         title="Motion filtering parameters",
         description=(
             "These parameters enable and control a filter that will be applied to motion "
@@ -388,7 +387,7 @@ def _build_parser():
         help="Number of filter coeffecients for the motion parameter filter.",
     )
 
-    g_censor = optional.add_argument_group("Censoring and scrubbing options")
+    g_censor = parser.add_argument_group("Censoring and scrubbing options")
     g_censor.add_argument(
         "-r",
         "--head-radius",
@@ -437,7 +436,7 @@ def _build_parser():
 """,
     )
 
-    g_temporal_filter = optional.add_argument_group(
+    g_temporal_filter = parser.add_argument_group(
         title="Data filtering parameters",
         description=(
             "These parameters determine whether a bandpass filter will be applied to the BOLD "
@@ -491,7 +490,7 @@ def _build_parser():
         help="Number of filter coefficients for the Butterworth bandpass filter.",
     )
 
-    g_parcellation = optional.add_argument_group("Parcellation options")
+    g_parcellation = parser.add_argument_group("Parcellation options")
 
     g_atlases = g_parcellation.add_mutually_exclusive_group(required=False)
     all_atlases = select_atlases(atlases=None, subset="all")
@@ -529,7 +528,7 @@ def _build_parser():
         ),
     )
 
-    g_dcan = optional.add_argument_group("abcd/hbcd mode options")
+    g_dcan = parser.add_argument_group("abcd/hbcd mode options")
     g_dcan.add_argument(
         "--create-matrices",
         "--create_matrices",
@@ -571,7 +570,7 @@ def _build_parser():
 """,
     )
 
-    g_linc = optional.add_argument_group("linc mode options")
+    g_linc = parser.add_argument_group("linc mode options")
     g_linc.add_argument(
         "--abcc-qc",
         "--abcc_qc",
@@ -586,7 +585,7 @@ def _build_parser():
 """,
     )
 
-    g_other = optional.add_argument_group("Other options")
+    g_other = parser.add_argument_group("Other options")
     g_other.add_argument(
         "--aggregate-session-reports",
         dest="aggr_ses_reports",
@@ -703,7 +702,7 @@ def _build_parser():
         ),
     )
 
-    g_experimental = optional.add_argument_group("Experimental options")
+    g_experimental = parser.add_argument_group("Experimental options")
 
     g_experimental.add_argument(
         "--warp-surfaces-native2std",
@@ -723,8 +722,6 @@ def _build_parser():
 **IMPORTANT**: This parameter can only be run if the --file-format flag is set to cifti.
 """,
     )
-    # Add the optional parameters back in
-    parser._action_groups.append(optional)
 
     latest = check_latest()
     if latest is not None and currentv < latest:

xcp_d/utils/boilerplate.py

@@ -261,7 +261,10 @@ def describe_atlases(atlases):
         "Gordon": "the Gordon atlas [@Gordon_2014]",
         "Tian": "the Tian subcortical atlas [@tian2020topographic]",
         "HCP": "the HCP CIFTI subcortical atlas [@glasser2013minimal]",
-        "MIDB": "the MIDB precision brain atlas [@hermosillo2022precision]",
+        "MIDB": (
+            "the MIDB precision brain atlas derived from ABCD data and thresholded at 75% "
+            "probability [@hermosillo2022precision]"
+        ),
         "MyersLabonte": (
             "the Myers-Labonte infant atlas thresholded at 50% probability [@myers2023functional]"
         ),