Merge pull request #2240 from effigies/enh/reuse-config

ENH: Reuse config

Author: effigies

.circleci/config.yml

@@ -653,10 +653,10 @@ jobs:
       - run:
           name: Generate report with one artificial error
           command: |
+            set -x
             sudo mv /tmp/${DATASET}/derivatives/fmriprep/sub-100185.html \
                     /tmp/${DATASET}/derivatives/fmriprep/sub-100185_noerror.html
-            UUID="$(date '+%Y%m%d-%H%M%S_')$(uuidgen)"
-            mkdir -p /tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
+            UUID=$(grep uuid /tmp/${DATASET}/work/*/config.toml | cut -d\" -f 2)
             cp /tmp/src/fmriprep/fmriprep/data/tests/crash_files/*.txt \
                 /tmp/${DATASET}/derivatives/fmriprep/sub-100185/log/$UUID/
             set +e
@@ -666,7 +666,7 @@ jobs:
                 /tmp/data/${DATASET} /tmp/${DATASET}/derivatives participant \
                 --fs-no-reconall --sloppy --write-graph \
                 --output-spaces MNI152NLin2009cAsym:res-2 anat func \
-                --reports-only --run-uuid $UUID
+                --reports-only --config-file /tmp/${DATASET}/work/${UUID}/config.toml -vv
             RET=$?
             set -e
             [[ "$RET" -eq "1" ]]

fmriprep/cli/parser.py

@@ -318,6 +318,7 @@ def _bids_filter(value):
     )
     g_conf.add_argument(
         "--random-seed",
+        dest="_random_seed",
         action="store",
         type=int,
         default=None,
@@ -505,12 +506,11 @@ def _bids_filter(value):
         "aggregation, not reportlet generation for specific nodes.",
     )
     g_other.add_argument(
-        "--run-uuid",
+        "--config-file",
         action="store",
-        default=None,
-        help="Specify UUID of previous run, to include error logs in report. "
-        "No effect without --reports-only.",
-    )
+        metavar="FILE",
+        help="Use pre-generated configuration file. Values in file will be overridden "
+             "by command-line arguments.")
     g_other.add_argument(
         "--write-graph",
         action="store_true",
@@ -575,6 +575,12 @@ def parse_args(args=None, namespace=None):
 
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
+
+    if opts.config_file:
+        skip = {} if opts.reports_only else {"execution": ("run_uuid",)}
+        config.load(opts.config_file, skip=skip)
+        config.loggers.cli.info(f"Loaded previous configuration file {opts.config_file}")
+
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts))