move nipype config file to entrypoint, fix test_spm #1538

Author: oesteban

Dockerfile

@@ -31,13 +31,6 @@ MAINTAINER Stanford Center for Reproducible Neuroscience <crn.poldracklab@gmail.
 
 # Preparations
 RUN ln -snf /bin/bash /bin/sh
-WORKDIR /root
-
-RUN mkdir -p .nipype && \
-    echo '[logging]' > .nipype/nipype.cfg && \
-    echo 'workflow_level = DEBUG' >> .nipype/nipype.cfg && \
-    echo 'interface_level = DEBUG' >> .nipype/nipype.cfg && \
-    echo 'filemanip_level = DEBUG' >> .nipype/nipype.cfg
 
 # Install this branch's code
 WORKDIR /root/src

docker/circleci/run_builddocs.sh

@@ -7,6 +7,6 @@ source activate nipypetests-2.7
 mkdir -p /scratch/docs
 set -o pipefail && cd /root/src/nipype/doc && make html 2>&1 | tee /scratch/builddoc.log
 cp -r /root/src/nipype/doc/_build/html/* /scratch/docs/
-chmod 755 -R /scratch/docs
-chmod 755 /scratch/builddoc.log
+chmod 775 -R /scratch/docs
+chmod 775 /scratch/builddoc.log
 cat /scratch/builddoc.log && if grep -q "ERROR" /scratch/builddoc.log; then false; else true; fi

docker/circleci/run_examples.sh

@@ -2,5 +2,12 @@
 for i in /etc/profile.d/*.sh; do
     source $i
 done
+
+mkdir -p /root/.nipype
+echo '[logging]' > /root/.nipype/nipype.cfg
+echo 'workflow_level = DEBUG' >> /root/.nipype/nipype.cfg
+echo 'interface_level = DEBUG' >> /root/.nipype/nipype.cfg
+echo 'filemanip_level = DEBUG' >> /root/.nipype/nipype.cfg
+
 source activate nipypetests-2.7
 python /root/src/nipype/tools/run_examples.py $@

examples/test_spm.py

@@ -9,6 +9,10 @@
 import os.path as op
 
 
+def _get_first(inlist):
+    if isinstance(inlist, (list, tuple)):
+        return inlist[0]
+    return inlist
 
 def test_spm(name='test_spm_3d'):
     """
@@ -18,8 +22,8 @@ def test_spm(name='test_spm_3d'):
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(niu.IdentityInterface(fields=['in_data']), name='inputnode')
-    dgr = pe.Node(nio.DataGrabber(template="feeds/data/fmri.nii.gz", outfields=['out_file']),
-                  name='datasource')
+    dgr = pe.Node(nio.DataGrabber(template="feeds/data/fmri.nii.gz", outfields=['out_file'],
+                                  sort_filelist=False), name='datasource')
 
     stc = pe.Node(spm.SliceTiming(
         num_slices=21, time_repetition=1.0, time_acquisition=2. - 2. / 32,
@@ -33,12 +37,12 @@ def test_spm(name='test_spm_3d'):
     if name == 'test_spm_3d':
         split = pe.Node(fsl.Split(dimension="t", output_type="NIFTI"), name="split")
         workflow.connect([
-            (dgr, split, [('out_file', 'in_file')]),
+            (dgr, split, [(('out_file', _get_first), 'in_file')]),
             (split, stc, [("out_files", "in_files")])])
     elif name == 'test_spm_4d':
         gunzip = pe.Node(Gunzip(), name="gunzip")
         workflow.connect([
-            (dgr, gunzip, [('out_file', 'in_file')]),
+            (dgr, gunzip, [(('out_file', _get_first), 'in_file')]),
             (gunzip, stc, [("out_file", "in_files")])
         ])
     else: