Merge pull request #84 from jchodera/test-data

Reorganize tests; simplify doctests.

pdbfixer/pdbfixer.py

@@ -45,6 +45,8 @@ import os
 import os.path
 import os.path
 import math
 import math
 
 
+from pkg_resources import resource_filename
+
 # Imports for urlopen
 # Imports for urlopen
 if sys.version_info >= (3,0):
 if sys.version_info >= (3,0):
     from urllib.request import urlopen
     from urllib.request import urlopen
@@ -156,29 +158,23 @@ class PDBFixer(object):
         Examples
         Examples
         --------
         --------
         
         
-        Start from a file object.
-
-        >>> pdbid = '1VII'
-        >>> url = 'http://www.rcsb.org/pdb/files/%s.pdb' % pdbid
-        >>> file = urlopen(url)
-        >>> fixer = PDBFixer(pdbfile=file)
-
         Start from a filename.
         Start from a filename.
         
         
-        >>> filename = 'test.pdb'
-        >>> file = urlopen(url)
-        >>> outfile = open(filename, 'w')
-        >>> outfile.write(file.read())
-        >>> outfile.close()
+        >>> filename = resource_filename('pdbfixer', 'tests/data/test.pdb')
         >>> fixer = PDBFixer(filename=filename)
         >>> fixer = PDBFixer(filename=filename)
 
 
+        Start from a file object.
+
+        >>> with open(filename) as f:
+        ...     fixer = PDBFixer(pdbfile=f)
+
         Start from a URL.
         Start from a URL.
 
 
-        >>> fixer = PDBFixer(url=url)
+        >>> fixer = PDBFixer(url='http://www.rcsb.org/pdb/files/1VII.pdb')
 
 
         Start from a PDB code.
         Start from a PDB code.
         
         
-        >>> fixer = PDBFixer(pdbid=pdbid)
+        >>> fixer = PDBFixer(pdbid='1VII')
 
 
         """
         """
 
 

tests/test_removechains.py → pdbfixer/tests/test_removechains.py

-from nose.tools import ok_, eq_, raises, assert_items_equal
+from nose.tools import ok_, eq_, raises, assert_list_equal
 import simtk.openmm.app as app
 import simtk.openmm.app as app
 import pdbfixer
 import pdbfixer
 import tempfile
 import tempfile
@@ -10,7 +10,7 @@ def remove_chain_ids_and_verify(pdbid, chain_ids_to_remove, expected_chain_ids_r
     fixer.removeChains(chainIds=chain_ids_to_remove)
     fixer.removeChains(chainIds=chain_ids_to_remove)
     # Check to make sure asserted chains remain.
     # Check to make sure asserted chains remain.
     chain_ids_remaining = [c.id for c in fixer.topology.chains()]
     chain_ids_remaining = [c.id for c in fixer.topology.chains()]
-    assert_items_equal(chain_ids_remaining, expected_chain_ids_remaining)
+    assert_list_equal(chain_ids_remaining, expected_chain_ids_remaining)
 
 
 def test_removechain_ids():
 def test_removechain_ids():
     remove_chain_ids_and_verify('4JSV', [], ['B', 'D', 'A', 'C', 'B', 'A'])
     remove_chain_ids_and_verify('4JSV', [], ['B', 'D', 'A', 'C', 'B', 'A'])
@@ -26,7 +26,7 @@ def remove_chain_indices_and_verify(pdbid, chain_indices_to_remove, expected_cha
     fixer.removeChains(chainIndices=chain_indices_to_remove)
     fixer.removeChains(chainIndices=chain_indices_to_remove)
     # Check to make sure asserted chains remain.
     # Check to make sure asserted chains remain.
     chain_ids_remaining = [c.id for c in fixer.topology.chains()]
     chain_ids_remaining = [c.id for c in fixer.topology.chains()]
-    assert_items_equal(chain_ids_remaining, expected_chain_ids_remaining)
+    assert_list_equal(chain_ids_remaining, expected_chain_ids_remaining)
 
 
 def test_removechain_indices():
 def test_removechain_indices():
     remove_chain_indices_and_verify('4JSV', [], ['B', 'D', 'A', 'C', 'B', 'A'])
     remove_chain_indices_and_verify('4JSV', [], ['B', 'D', 'A', 'C', 'B', 'A'])