Test collection on real data.

Author: tsalo

.github/workflows/build-test-publish.yml

@@ -184,6 +184,11 @@ jobs:
         datalad update -r --merge -d hcph-pilot_fieldmaps/
         datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/*
 
+        # ds005250
+        datalad install -r https://gin.g-node.org/tsalo/ds005250-sdcflows.git
+        datalad update -r --merge -d ds005250-sdcflows/
+        datalad get -r -J 2 -d ds005250-sdcflows/ ds005250-sdcflows/sub-04/ses-2/
+
     - name: Set FreeSurfer variables
       run: |
         echo "FREESURFER_HOME=$HOME/.cache/freesurfer" >> $GITHUB_ENV

sdcflows/utils/wrangler.py

@@ -321,6 +321,15 @@ def find_estimators(
     FieldmapEstimation(sources=<2 files>, method=<EstimatorType.ANAT: 5>,
                        bids_id='auto_...')]
 
+    >>> find_estimators(
+    ...     layout=layouts['ds005250-sdcflows'],
+    ...     subject='04',
+    ...     fmapless=False,
+    ...     force_fmapless=False,
+    ...     bids_filters={'session': '2'},
+    ... )  # doctest: +ELLIPSIS
+    [FieldmapEstimation(sources=<10 files>, method=<EstimatorType.MEDIC: 6>,
+                        bids_id='auto_...')]
     """
     from .misc import create_logger
     from bids.layout import Query

sdcflows/workflows/fit/medic.py

@@ -70,11 +70,17 @@ def init_medic_wf(name="medic_wf"):
     -----
     This workflow performs minimal preparation before running the MEDIC algorithm,
     as implemented in ``vandandrew/warpkit``.
+
+    Any downstream processing piplines that use this workflow should include
+    the following references in their boilerplate BibTeX file:
+
+    - medic: https://doi.org/10.1101/2023.11.28.568744
     """
     workflow = Workflow(name=name)
 
     workflow.__desc__ = """\
-A dynamic fieldmap was estimated from multi-echo EPI data using the MEDIC algorithm (@medic).
+Volume-wise *B<sub>0</sub>* nonuniformity maps (or *fieldmaps*) were estimated from
+complex-valued, multi-echo EPI data using the MEDIC algorithm (@medic).
 """
 
     inputnode = pe.Node(niu.IdentityInterface(fields=INPUT_FIELDS), name="inputnode")