Merge branch 'dev172_local'

Author: sgiavasis

.circleci/config.yml

@@ -141,11 +141,17 @@ jobs:
               VERSION=$(python -c "from info import __version__; print(__version__)")
               cd ..
               if ! [[ $CIRCLE_BRANCH = 'master' ]]
-                then if [[ $CIRCLE_BRANCH = 'develop' || ${CIRCLE_BRANCH:0:7} = 'hotfix/' ]]
-                  then REBASE_BASE_BRANCH=master
-                  else REBASE_BASE_BRANCH=develop
-                fi
-                GIT_SEQUENCE_EDITOR=dev/circleci_data/drop_version_bump_commits git rebase -X ours -i origin/$REBASE_BASE_BRANCH --empty drop
+                then
+                  git fetch --all
+                  if [[ -n ${CIRCLE_PR_NUMBER} && -n ${GITHUB_PR_BASE_TOKEN} ]]
+                    then
+                      curl -L "https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64" -o jq
+                      chmod +x jq
+                      REBASE_BASE=origin/$(curl -u shnizzedy:$GITHUB_PR_BASE_TOKEN "https://api.github.com/repos/$CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME/pulls/$CIRCLE_PR_NUMBER" | jq '.base.ref' | tr -d '"')
+                  else
+                    REBASE_BASE=$(git rev-parse --short HEAD~30)
+                  fi
+                GIT_SEQUENCE_EDITOR=dev/circleci_data/drop_version_bump_commits git rebase -X ours -i $REBASE_BASE --empty drop
               fi
               echo "v${VERSION}" > version
               sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" dev/docker_data/default_pipeline.yml

CPAC/distortion_correction/distortion_correction.py

@@ -465,7 +465,8 @@ def connect_distortion_correction(workflow, strat_list, c, diff, blip,
                 node, node_out = strat[epi_param_rp_key]
                 workflow.connect(node, node_out,
                                  match_epi_fmaps_node, 'epi_fmap_params_one')
-                if len(epi_rp_key) > 1:
+
+                if len(fmap_rp_list) > 1:
                     epi_rp_key = fmap_rp_list[1]
                     epi_param_rp_key = "{0}_scan_params".format(epi_rp_key)
                     node, node_out = strat[epi_rp_key]

CPAC/func_preproc/func_ingress.py

@@ -53,8 +53,10 @@ def connect_func_ingress(workflow, strat_list, c, sub_dict, subject_id,
         blip = False
         fmap_rp_list = []
         fmap_TE_list = []
+
         if "fmap" in sub_dict:
             for key in sub_dict["fmap"]:
+
                 gather_fmap = create_fmap_datasource(sub_dict["fmap"],
                                                      "fmap_gather_"
                                                      "{0}".format(key))
@@ -101,7 +103,7 @@ def connect_func_ingress(workflow, strat_list, c, sub_dict, subject_id,
                     })
                     fmap_TE_list.append("{}_TE".format(key))
 
-                if key == "epi_AP" or key == "epi_PA":
+                if "epi_" in key:
                     blip = True
 
             if diff:
@@ -164,19 +166,6 @@ def connect_func_ingress(workflow, strat_list, c, sub_dict, subject_id,
                 as_module=True
             ), name=workflow_name)
 
-        if "Selected Functional Volume" in c.func_reg_input:
-            get_func_volume = pe.Node(interface=afni.Calc(),
-                                      name='get_func_volume_{0}'.format(
-                                          num_strat))
-
-            get_func_volume.inputs.set(
-                expr='a',
-                single_idx=c.func_reg_input_volume,
-                outputtype='NIFTI_GZ'
-            )
-            workflow.connect(func_wf, 'outputspec.rest',
-                             get_func_volume, 'in_file_a')
-
         # wire in the scan parameter workflow
         workflow.connect(func_wf, 'outputspec.scan_params',
                          scan_params, 'data_config_scan_params')
@@ -205,9 +194,4 @@ def connect_func_ingress(workflow, strat_list, c, sub_dict, subject_id,
 
         strat.set_leaf_properties(func_wf, 'outputspec.rest')
 
-        if "Selected Functional Volume" in c.func_reg_input:
-            strat.update_resource_pool({
-                'selected_func_volume': (get_func_volume, 'out_file')
-            })
-
     return (workflow, diff, blip, fmap_rp_list)