Adding std printing to test reporting to help with errors

.travis.yml

@@ -33,6 +33,7 @@ install:
     - pip install --user keras_applications==1.0.6
     - pip install --user keras_preprocessing==1.0.5
     - pip install --user keras==2.2.4
+    - pip install --user coveralls
 
 #only test on master and tests branches
 branches:
@@ -49,7 +50,7 @@ before_script:
 #Run Unittests
 script:
     - python numpyversion.py
-    - py.test --pyargs speedcom --cov-report term-missing --cov=speedcom --cov-config .coveragerc
+    - py.test -s --pyargs speedcom --cov-report term-missing --cov=speedcom --cov-config .coveragerc
 
 #Print coverage reports
 after_success:

runtests.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
-py.test --pyargs speedcom --cov-report term-missing --cov=speedcom --cov-config .coveragerc
+py.test -s --pyargs speedcom --cov-report term-missing --cov=speedcom --cov-config .coveragerc
 rm speedcom/tests/__pycache__/*

speedcom/core.py

@@ -5,7 +5,7 @@
 
 #import speedcom
 
-def initiate_molecules(data_dir):
+def initiate_molecules(data_dir, test=False):
     """
     Takes in the directory containing all of the data files and returns a list
     of populated molecule objects.
@@ -28,6 +28,10 @@ def initiate_molecules(data_dir):
             my_molecules.append(Molecule(absorp, cid, columb, emiss, \
                 smiles, weight, file_name))
             my_added_molecules.append(cid)
+            if test:
+                print("ems cid: ", cid)
+            else:
+                pass
         else:
            pass
        #For all applicable absorption spectra put properties into molecule 
@@ -39,6 +43,10 @@ def initiate_molecules(data_dir):
             #it does, does it already have valid absorption peaks:
             if pubchem_molecule:
                 cid = pubchem_molecule.cid
+                if test:
+                    print("abs cid: ", cid)
+                else:
+                    pass
                 if cid in my_added_molecules:
                     found = 1
                     mol_index = my_added_molecules.index(cid)

speedcom/tests/test_speedcom.py

@@ -13,7 +13,8 @@ def test_proper_size(self):
         Ensure the appropriate number of molecule objects are returned
         upon initialization.
         """
-        mol_list_len = len(context.core.initiate_molecules(testing_dir))
+        mol_list_len = len(context.core.initiate_molecules(testing_dir, \
+            test=True))
         assert mol_list_len == 5, "initiate_molecules unable to find all \
             molecules, len = %f" %(mol_list_len)
         return