maint(ci): mechanism to run eddy only w/tag in commit message

Author: oesteban

.circleci/config.yml

@@ -300,6 +300,10 @@ jobs:
           name: Run full diffusion workflow on ds000206
           no_output_timeout: 4h
           command: |
+            eddy="--ignore eddy"
+            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[run[ _]?eddy\]' )" != "" ]]; then
+              eddy=""
+            fi
             mkdir -p /tmp/ds000206/work /tmp/ds000206/derivatives
             docker run -e FS_LICENSE=$FS_LICENSE --rm \
                 -v /tmp/data/ds000206:/data \
@@ -309,7 +313,7 @@ jobs:
                 -v /tmp/templateflow:/home/dmriprep/.cache/templateflow \
                 -v /tmp/ds000206/work:/work \
                 --user $(id -u):$(id -g) \
-                nipreps/dmriprep:latest /data /out participant -vv \
+                nipreps/dmriprep:latest /data /out participant -vv $eddy \
                 --fs-subjects-dir /data/derivatives/freesurfer-6.0.1 --sloppy \
                 --notrack --skip-bids-validation -w /work --omp-nthreads 2 --nprocs 2
       - store_artifacts:
@@ -381,6 +385,10 @@ jobs:
           name: Run full diffusion workflow on ds001771
           no_output_timeout: 4h
           command: |
+            eddy="--ignore eddy"
+            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[run[ _]?eddy\]' )" != "" ]]; then
+              eddy=""
+            fi
             mkdir -p /tmp/ds001771/work /tmp/ds001771/derivatives
             docker run -e FS_LICENSE=$FS_LICENSE --rm \
                 -v /tmp/data/ds001771:/data \
@@ -390,7 +398,7 @@ jobs:
                 -v /tmp/config/nipype.cfg:/home/dmriprep/.nipype/nipype.cfg \
                 -v /tmp/ds001771/work:/work \
                 --user $(id -u):$(id -g) \
-                nipreps/dmriprep:latest /data /out participant -vv \
+                nipreps/dmriprep:latest /data /out participant -vv $eddy \
                 -w /work --omp-nthreads 2 --nprocs 2 \
                 --notrack --skip-bids-validation --sloppy \
                 --fs-subjects-dir /data/derivatives/freesurfer-6.0.1 \

dmriprep/cli/parser.py

@@ -191,7 +191,7 @@ def _bids_filter(value):
         action="store",
         nargs="+",
         default=[],
-        choices=["fieldmaps", "sbref"],
+        choices=["fieldmaps", "sbref", "eddy"],
         help="ignore selected aspects of the input dataset to disable corresponding "
         "parts of the workflow (a space delimited list)",
     )

dmriprep/workflows/dwi/base.py

@@ -203,42 +203,43 @@ def _bold_reg_suffix(fallback):
         ])
         # fmt: on
 
-    # Eddy distortion correction
-    eddy_wf = init_eddy_wf(debug=config.execution.debug)
-    eddy_wf.inputs.inputnode.metadata = layout.get_metadata(str(dwi_file))
-
-    ds_report_eddy = pe.Node(
-        DerivativesDataSink(
-            base_directory=str(config.execution.output_dir),
-            desc="eddy",
-            datatype="figures",
-        ),
-        name="ds_report_eddy",
-        run_without_submitting=True,
-    )
+    if "eddy" not in config.workflow.ignore:
+        # Eddy distortion correction
+        eddy_wf = init_eddy_wf(debug=config.execution.debug)
+        eddy_wf.inputs.inputnode.metadata = layout.get_metadata(str(dwi_file))
 
-    eddy_report = pe.Node(
-        SimpleBeforeAfter(before_label="Distorted", after_label="Eddy Corrected",),
-        name="eddy_report",
-        mem_gb=0.1,
-    )
+        ds_report_eddy = pe.Node(
+            DerivativesDataSink(
+                base_directory=str(config.execution.output_dir),
+                desc="eddy",
+                datatype="figures",
+            ),
+            name="ds_report_eddy",
+            run_without_submitting=True,
+        )
 
-    # fmt:off
-    workflow.connect([
-        (dwi_reference_wf, eddy_wf, [
-            ("outputnode.dwi_file", "inputnode.dwi_file"),
-            ("outputnode.dwi_mask", "inputnode.dwi_mask"),
-        ]),
-        (inputnode, eddy_wf, [
-            ("in_bvec", "inputnode.in_bvec"),
-            ("in_bval", "inputnode.in_bval")
-        ]),
-        (dwi_reference_wf, eddy_report, [("outputnode.ref_image", "before")]),
-        (eddy_wf, eddy_report, [('outputnode.eddy_ref_image', 'after')]),
-        (dwi_reference_wf, ds_report_eddy, [("outputnode.dwi_file", "source_file")]),
-        (eddy_report, ds_report_eddy, [("out_report", "in_file")]),
-    ])
-    # fmt:on
+        eddy_report = pe.Node(
+            SimpleBeforeAfter(before_label="Distorted", after_label="Eddy Corrected",),
+            name="eddy_report",
+            mem_gb=0.1,
+        )
+
+        # fmt:off
+        workflow.connect([
+            (dwi_reference_wf, eddy_wf, [
+                ("outputnode.dwi_file", "inputnode.dwi_file"),
+                ("outputnode.dwi_mask", "inputnode.dwi_mask"),
+            ]),
+            (inputnode, eddy_wf, [
+                ("in_bvec", "inputnode.in_bvec"),
+                ("in_bval", "inputnode.in_bval")
+            ]),
+            (dwi_reference_wf, eddy_report, [("outputnode.ref_image", "before")]),
+            (eddy_wf, eddy_report, [('outputnode.eddy_ref_image', 'after')]),
+            (dwi_reference_wf, ds_report_eddy, [("outputnode.dwi_file", "source_file")]),
+            (eddy_report, ds_report_eddy, [("out_report", "in_file")]),
+        ])
+        # fmt:on
 
     # REPORTING ############################################################
     reportlets_wf = init_reportlets_wf(