GH-661 update notebooks to not fail

Author: nicain

.gitignore

@@ -12,6 +12,14 @@ eggs/
 test-reports/*
 doc_template/examples/nb/connectivity/experiment_*
 doc_template/examples/nb/Website_Inquiry_RT_45792 /experiment_*
+doc_template/examples_root/examples/nb/*.zip
+doc_template/examples_root/examples/nb/*.json
+doc_template/examples_root/examples/nb/*.swc
+doc_template/examples_root/examples/nb/*.nrrd
+doc_template/examples_root/examples/nb/*.csv
+doc_template/examples_root/examples/nb/brain_observatory
+doc_template/examples_root/examples/nb/modfiles
+doc_template/examples_root/examples/nb/*.nbconvert.ipynb
 *pyc
 .eggs/
 .pytest_cache/

Makefile

@@ -70,6 +70,10 @@ $(NOTEBOOKS):
 
 notebooks: $(NOTEBOOKS)
 
+notebooks-neuron:
+	jupyter-nbconvert --to notebook --execute --ExecutePreprocessor.timeout=$(timeout) --ExecutePreprocessor.kernel_name=$(python_kernel) ./doc_template/examples_root/examples/nb/neuron/pulse_stimulus.ipynb
+
+
 FORCE:
 
 clean:

allensdk/core/brain_observatory_nwb_data_set.py

@@ -900,6 +900,13 @@ def get_motion_correction(self):
         if motion_correction is None:
             raise KeyError("Could not find motion correction data.")
 
+        # Python3 compatibility:
+        rename_dict = {}
+        for c in motion_correction.columns:
+            if not isinstance(c, str):
+                rename_dict[c] = c.decode("utf-8")
+        motion_correction.rename(columns=rename_dict, inplace=True)
+
         return motion_correction
 
     def save_analysis_dataframes(self, *tables):