fixed travis.yml

evanfeinberg · evanfeinberg · commit a4e27de6c350 · 2016-02-14T17:39:57.000-08:00
diff --git a/.travis.yml b/.travis.yml
@@ -20,7 +20,7 @@ install:
 - conda install -c omnia keras
 - conda install seaborn
 - conda install six
-- conda install -c https://conda.anaconda.org/groakat pathos
+- pip install --user git+https://github.com/uqfoundation/pathos
 - python setup.py install
 script:
 - nosetests -v deepchem
diff --git a/datasets/construct_pdbbind_df.py b/datasets/construct_pdbbind_df.py
@@ -8,6 +8,7 @@
 from rdkit import Chem
 from glob import glob
 import re
+from sklearn.externals import joblib
 
 
 def extract_labels(pdbbind_label_file):
@@ -26,7 +27,7 @@ def extract_labels(pdbbind_label_file):
       labels[line[0]] = line[3]
   return labels
 
-def construct_df(pdb_stem_directory, pdbbind_label_file, pdbbind_df_pkl):
+def construct_df(pdb_stem_directory, pdbbind_label_file, pdbbind_df_joblib):
   """
   Takes as input a stem directory containing subdirectories with ligand
     and protein pdb/mol2 files, a pdbbind_label_file containing binding
@@ -89,5 +90,4 @@ def construct_df(pdb_stem_directory, pdbbind_label_file, pdbbind_df_pkl):
                                               'protein_pdb', 'ligand_pdb',
                                               'ligand_mol2', 'label'))
 
-  with open(pdbbind_df_pkl, "wb") as f:
-    pickle.dump(pdbbind_df, f)
+  joblib.dump(pdbbind_df, pdbbind_df_joblib)
