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Co-authored-by: Chris Markiewicz <[email protected]>
nipreps · Dec 5, 2023 · a682abe · a682abe
1 parent bde2175
commit a682abe
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Showing 3 changed files with 9 additions and 19 deletions.
diff --git a/sdcflows/cli/main.py b/sdcflows/cli/main.py
@@ -95,7 +95,6 @@ def main(argv=None):
     if config.nipype.plugin in ("MultiProc", "LegacyMultiProc"):
         from contextlib import suppress
         import multiprocessing as mp
-        import multiprocessing.forkserver
         from concurrent.futures import ProcessPoolExecutor
 
         os.environ["OMP_NUM_THREADS"] = "1"

diff --git a/sdcflows/cli/parser.py b/sdcflows/cli/parser.py
@@ -137,17 +137,13 @@ def _bids_filter(value):
     g_bids = parser.add_argument_group("Options related to BIDS")
     g_bids.add_argument(
         "--participant-label",
-        "--participant_label",
-        "--participant-labels",
-        "--participant_labels",
-        dest="participant_label",
         action=ParticipantLabelAction,
         nargs="+",
         help="A space delimited list of participant identifiers or a single "
         "identifier (the sub- prefix can be removed).",
     )
     g_bids.add_argument(
-        "--session",
+        "--session-label",
         action="store",
         nargs="*",
         type=str,
@@ -180,9 +176,6 @@ def _bids_filter(value):
     g_perfm = parser.add_argument_group("Options to handle performance")
     g_perfm.add_argument(
         "--nprocs",
-        "--n_procs",
-        "--n_cpus",
-        "-n-cpus",
         action="store",
         type=PositiveInt,
         help="""\
@@ -200,7 +193,6 @@ def _bids_filter(value):
     )
     g_perfm.add_argument(
         "--omp-nthreads",
-        "--ants-nthreads",
         action="store",
         type=PositiveInt,
         help="""\
@@ -210,8 +202,6 @@ def _bids_filter(value):
 not be what you want in, e.g., shared systems like a HPC cluster.""",
     )
     g_perfm.add_argument(
-        "--mem",
-        "--mem_gb",
         "--mem-gb",
         dest="memory_gb",
         action="store",
@@ -222,7 +212,7 @@ def _bids_filter(value):
         "--debug",
         action="store_true",
         default=False,
-        help="Initiate in debug mode",
+        help="Enable changes to processing to aid in debugging",
     )
     g_perfm.add_argument(
         "--pdb",
@@ -256,8 +246,9 @@ def _bids_filter(value):
         help="only find estimable fieldmaps (that is, estimation is not triggered)",
     )
     g_outputs.add_argument(
-        "--fmapless",
-        action="store_true",
+        "--no-fmapless",
+        action="store_false",
+        dest="fieldmapless",
         default=False,
         help="Allow fieldmap-less estimation",
     )
@@ -271,9 +262,9 @@ def _bids_filter(value):
     g_outputs.add_argument(
         "--notrack",
         action="store_true",
-        help="Opt-out of sending tracking information of this run to the NiPreps developers. This"
-        " information helps to improve SDCFlows and provides an indicator of real world usage "
-        " crucial for obtaining funding.",
+        help="Opt-out of sending tracking information of this run to the NiPreps developers. "
+        "This information helps to improve SDCFlows and provides an indicator of "
+        "real world usage for obtaining funding.",
     )
 
     return parser

diff --git a/sdcflows/config.py b/sdcflows/config.py
@@ -400,7 +400,7 @@ class execution(_Config):
     """Drop into PDB when exceptions are encountered."""
     run_uuid = "{}_{}".format(strftime("%Y%m%d-%H%M%S"), uuid4())
     """Unique identifier of this particular run."""
-    session = None
+    session_label = None
     """Filter input dataset by session identifier."""
     sloppy = False
     """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""