refactored tests

lewisacidic · Jul 29, 2015 · 67f4e4e · 67f4e4e
1 parent 8c19b55
commit 67f4e4e
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Showing 13 changed files with 75 additions and 35 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -0,0 +1,5 @@
+[nosetests]
+verbosity=3
+with-doctest=1
+with-yanc=1
+with-coverage=1
diff --git a/skchem/descriptors/fingerprints.py b/skchem/descriptors/fingerprints.py
@@ -21,26 +21,58 @@ def skchemize(func, columns=None, *args, **kwargs):
     transform an RDKit fingerprinting function to work well with pandas
 
     >>> from rdkit import Chem
-    >>> from skchem import *
+    >>> import skchem
+    >>> from skchem.descriptors import skchemize
+    >>> from skchem.core import Mol
     >>> f = skchemize(Chem.RDKFingerprint)
     >>> m = Mol.from_smiles('c1ccccc1')
     >>> f(m)
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@@ -56,22 +88,22 @@ def skchemize(func, columns=None, *args, **kwargs):
     2045    0
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-    Length: 2048, dtype: int64
-
-    >>> df = skchem.read_sdf('skchem/tests/test_resources/hydrocarbons.sdf')
+    dtype: int64
+    >>> from skchem.data import resource
+    >>> df = skchem.read_sdf(resource('test_sdf', 'multi_molecule-simple.sdf'))
     >>> df.structure.apply(f)
-         0     1     2     3     4     5     6     7     8     9     ...   2038  \
-    Name                                                              ...
-    297      0     0     0     0     0     0     0     0     0     0  ...      0
-    6324     0     0     0     0     0     0     0     0     0     0  ...      0
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+          0     1     2     3     4     5     6     7     8     9     ...   2038  \\
+    name                                                              ...          
+    297      0     0     0     0     0     0     0     0     0     0  ...      0   
+    6324     0     0     0     0     0     0     0     0     0     0  ...      0   
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+    <BLANKLINE>
+          2039  2040  2041  2042  2043  2044  2045  2046  2047  
+    name                                                        
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+    <BLANKLINE>
     [3 rows x 2048 columns]
 
     """
@@ -109,12 +141,15 @@ def calculate(self, obj):
 
         """ calculate the fingerprint for the given object. """
 
-        if obj.__class__ is skc.core.Mol:
+        if isinstance(obj, skc.core.Mol):
             return self._calculate_m(obj)
 
-        elif obj.__class__ in [pd.DataFrame, pd.Series]:
+        elif isinstance(obj, pd.DataFrame) or isinstance(obj, pd.Series):
             return self._calculate_df(obj)
 
+        else:
+            raise NotImplementedError
+
     def _calculate_m(self, m):
 
         """ calculate the fingerprint for a molecule. """

diff --git a/skchem/io/smiles.py b/skchem/io/smiles.py
@@ -81,7 +81,7 @@ def parse(smiles):
                 """
                 return skchem.Mol.from_smiles(smiles)
 
-        df['structure'] = df['structure'].apply(parse)
+        df['structure'] = df['structure'].apply(str).apply(parse) #make sure is a string
 
         if force:
             df = df[df['structure'].notnull()]

diff --git a/skchem/tests/__init__.py → skchem/test/__init__.py b/skchem/tests/__init__.py → skchem/test/__init__.py
diff --git a/skchem/tests/test_core/test_atom.py → skchem/test/test_core/test_atom.py b/skchem/tests/test_core/test_atom.py → skchem/test/test_core/test_atom.py
diff --git a/skchem/tests/test_core/test_bond.py → skchem/test/test_core/test_bond.py b/skchem/tests/test_core/test_bond.py → skchem/test/test_core/test_bond.py
diff --git a/skchem/tests/test_core/test_conformer.py → skchem/test/test_core/test_conformer.py b/skchem/tests/test_core/test_conformer.py → skchem/test/test_core/test_conformer.py
diff --git a/skchem/tests/test_core/test_mol.py → skchem/test/test_core/test_mol.py b/skchem/tests/test_core/test_mol.py → skchem/test/test_core/test_mol.py
diff --git a/skchem/tests/test_data/__init__.py → skchem/test/test_data/__init__.py b/skchem/tests/test_data/__init__.py → skchem/test/test_data/__init__.py
diff --git a/skchem/tests/test_data/test_data.py → skchem/test/test_data/test_data.py b/skchem/tests/test_data/test_data.py → skchem/test/test_data/test_data.py
diff --git a/skchem/tests/test_io/test_sdf.py → skchem/test/test_io/test_sdf.py b/skchem/tests/test_io/test_sdf.py → skchem/test/test_io/test_sdf.py
diff --git a/skchem/tests/test_io/test_smiles.py → skchem/test/test_io/test_smiles.py b/skchem/tests/test_io/test_smiles.py → skchem/test/test_io/test_smiles.py
diff --git a/skchem/tests/test_skchemize.py → skchem/test/test_skchemize.py b/skchem/tests/test_skchemize.py → skchem/test/test_skchemize.py