Merge 717d1e8 into 2d86b54

.travis.yml

@@ -3,6 +3,7 @@ python:
   - "2.7"
   - "3.5"
   - "3.6"
+  - "3.7"
 
 install:
   - sudo apt-get update

CHANGELOG.rst

@@ -6,6 +6,7 @@ Changelog
 ------------
 Added
 ~~~~~
+- Support for Python 3.7
 - ``Cython`` added as dependency and ``SciPy`` removed
 - ``conkit.misc.deprecate`` decorator for easier tagging
 - ``ContactMap.match`` provides keyword to ``add_false_negatives`` found in the reference but not in contact map

conkit/core/contactmap.py

@@ -776,8 +776,8 @@ def match(self,
         # 3. Add false negatives
         # ================================================================
         if add_false_negatives:
-            for contact in contact_map2:
-                contactid = tuple([contact.res1_seq, contact.res2_seq])
+            for contactid in contact_map2.as_list():
+                contactid = tuple(contactid)
                 if contactid not in contact_map1:
                     contact = contact_map2[contactid].copy()
                     contact.false_negative = True
@@ -787,8 +787,8 @@ def match(self,
         # 4. Remove unmatched contacts
         # ================================================================
         if remove_unmatched:
-            for contact in contact_map1:
-                contactid = tuple([contact.res1_seq, contact.res2_seq])
+            for contactid in contact_map1.as_list():
+                contactid = tuple(contactid)
                 if contact_map1[contactid].status_unknown:
                     contact_map1.remove(contactid)
 

conkit/core/sequence.py

@@ -89,6 +89,10 @@ def __add__(self, other):
         seq = self.seq + other.seq
         return Sequence(id, seq)
 
+    def __len__(self):
+        """The sequence length"""
+        return len(self._seq)
+
     def __repr__(self):
         if self.seq_len > 12:
             seq_string = ''.join([self.seq[:5], '...', self.seq[-5:]])
@@ -156,7 +160,7 @@ def seq_encoded(self):
     @property
     def seq_len(self):
         """The protein sequence length"""
-        return len(self.seq)
+        return len(self)
 
     def align_global(self, other, id_chars=2, nonid_chars=1, gap_open_pen=-0.5, gap_ext_pen=-0.1, inplace=False):
         """Generate a global alignment between two :obj:`Sequence <conkit.core.sequence.Sequence>` instances

setup.py

@@ -161,6 +161,7 @@ def version():
     "Programming Language :: Python :: 2.7",
     "Programming Language :: Python :: 3.5",
     "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]