configure location of the test data with env

Author: chrisgorgo

circle.yml

@@ -32,6 +32,7 @@ test:
         environment:
           SPMMCRCMD: "$HOME/spm12/run_spm12.sh $HOME/mcr/v85/ script"
           FORCE_SPMMCR: 1
+          FSL_COURSE_DATA: "$HOME/examples/fsl_course_data"
         timeout: 1600
     - set -o pipefail && cd doc && make html 2>&1 | tee ~/log.txt
     - cat ~/log.txt && if grep -q "ERROR" ~/log.txt; then false; else true; fi

nipype/interfaces/fsl/base.py

@@ -263,4 +263,4 @@ def no_fsl():
 
 def no_fsl_course_data():
     """check if fsl_course data is present"""
-    return not (os.path.isdir(os.path.abspath('fsl_course_data')))
+    return not ('FSL_COURSE_DATA' in os.environ and os.path.isdir(os.path.abspath(os.environ['FSL_COURSE_DATA'])))

nipype/workflows/dmri/fsl/tests/test_dti.py

@@ -16,7 +16,7 @@
 @skipif(no_fsl)
 @skipif(no_fsl_course_data)
 def test_create_bedpostx_pipeline():
-    fsl_course_dir = os.path.abspath('fsl_course_data')
+    fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA'])
 
     mask_file = os.path.join(fsl_course_dir, "fdt/subj1.bedpostX/nodif_brain_mask.nii.gz")
     bvecs_file = os.path.join(fsl_course_dir, "fdt/subj1/bvecs")

nipype/workflows/dmri/fsl/tests/test_epi.py

@@ -13,10 +13,10 @@
 from nipype.workflows.dmri.fsl.epi import create_eddy_correct_pipeline
 
 
-#@skipif(no_fsl)
-#@skipif(no_fsl_course_data)
+@skipif(no_fsl)
+@skipif(no_fsl_course_data)
 def test_create_eddy_correct_pipeline():
-    fsl_course_dir = os.path.abspath('fsl_course_data')
+    fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA'])
 
     dwi_file = os.path.join(fsl_course_dir, "fdt/subj1/data.nii.gz")
 

nipype/workflows/dmri/fsl/tests/test_tbss.py

@@ -15,7 +15,7 @@
 
 
 def _tbss_test_helper(estimate_skeleton):
-    fsl_course_dir = os.path.abspath('fsl_course_data')
+    fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA'])
     fsl.FSLCommand.set_default_output_type('NIFTI_GZ')
     test_dir = tempfile.mkdtemp(prefix="nipype_test_tbss_")
     tbss_orig_dir = os.path.join(test_dir, "tbss_all_original")
@@ -121,13 +121,13 @@ def _tbss_test_helper(estimate_skeleton):
     shutil.rmtree(test_dir)
 
 
-@skipif(no_fsl)
+#@skipif(no_fsl)
 @skipif(no_fsl_course_data)
 def test_tbss_est_skeleton():
     _tbss_test_helper(True)
 
 
-@skipif(no_fsl)
+#@skipif(no_fsl)
 @skipif(no_fsl_course_data)
 def test_tbss_est_skeleton_use_precomputed_skeleton():
     _tbss_test_helper(False)