Add backwards-compatible Python 3 support

.travis.yml

@@ -1,6 +1,5 @@
 language: python
 python:
-  - "2.6"
   - "2.7"
   - "3.2"
   - "3.3"

docs/source/guide/install.rst

@@ -3,18 +3,25 @@
 Installation
 ============
 
+PubChemPy supports Python versions 2.7, 3.2, 3.3 and 3.4. There are no other dependencies.
+
 There are a variety of ways to download and install PubChemPy.
 
 Option 1: Use pip (recommended)
 -------------------------------
 
-The easiest and recommended way to install is using pip [#f1]_::
+The easiest and recommended way to install is using pip::
 
     pip install pubchempy
 
 This will download the latest version of PubChemPy, and place it in your `site-packages` folder so it is automatically
 available to all your python scripts.
 
+If you don't already have pip installed, you can `install it using get-pip.py`_::
+
+       curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
+       python get-pip.py
+
 Option 2: Download the latest release
 -------------------------------------
 
@@ -38,15 +45,6 @@ stable, but may include new features that have not yet been released. Simply clo
     cd PubChemPy
     python setup.py install
 
-.. rubric:: Footnotes
-
-.. [#f1] You can `install pip`_ using get-pip.py:
-   ::
-
-       curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
-       python get-pip.py
-
-
-.. _`install pip`: http://www.pip-installer.org/en/latest/installing.html
+.. _`install it using get-pip.py`: http://www.pip-installer.org/en/latest/installing.html
 .. _`download the latest release`: https://github.com/mcs07/PubChemPy/releases/
 .. _`available on GitHub`: https://github.com/mcs07/PubChemPy

docs/source/index.rst

@@ -37,6 +37,7 @@ Features
 - Download compound records as XML, ASNT/B, JSON, SDF and depiction as a PNG image.
 - Construct property tables using *pandas* DataFrames.
 - A complete Python wrapper around the `PubChem PUG REST web service`_.
+- Supports Python versions 2.7 – 3.4.
 
 User guide
 ----------

pubchempy.py

@@ -10,9 +10,16 @@
 import json
 import logging
 import os
+import sys
 import time
-import urllib
-import urllib2
+
+try:
+    from urllib.error import HTTPError
+    from urllib.parse import quote, urlencode
+    from urllib.request import urlopen
+except ImportError:
+    from urllib import urlencode
+    from urllib2 import quote, urlopen, HTTPError
 
 
 __author__ = 'Matt Swain'
@@ -26,57 +33,59 @@
 log.addHandler(logging.NullHandler())
 
 
+if sys.version_info[0] == 3:
+    text_types = str, bytes
+else:
+    text_types = basestring,
+
+
 def request(identifier, namespace='cid', domain='compound', operation=None, output='JSON', searchtype=None, **kwargs):
     """
     Construct API request from parameters and return the response.
 
     Full specification at http://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html
     """
-
     # If identifier is a list, join with commas into string
     if isinstance(identifier, int):
         identifier = str(identifier)
-    if not isinstance(identifier, basestring):
+    if not isinstance(identifier, text_types):
         identifier = ','.join(str(x) for x in identifier)
-
     # Filter None values from kwargs
-    kwargs = dict((k, v) for k, v in kwargs.iteritems() if v is not None)
-
+    kwargs = dict((k, v) for k, v in kwargs.items() if v is not None)
     # Build API URL
     urlid, postdata = None, None
     if namespace == 'sourceid':
         identifier = identifier.replace('/', '.')
     if namespace in ['listkey', 'formula', 'sourceid'] or (searchtype and namespace == 'cid') or domain == 'sources':
-        urlid = urllib2.quote(identifier.encode('utf8'))
+        urlid = quote(identifier.encode('utf8'))
     else:
-        postdata = '%s=%s' % (namespace, urllib2.quote(identifier.encode('utf8')))
+        postdata = urlencode([(namespace, identifier)]).encode('utf8')
     comps = filter(None, [API_BASE, domain, searchtype, namespace, urlid, operation, output])
     apiurl = '/'.join(comps)
     if kwargs:
-        apiurl += '?%s' % urllib.urlencode(kwargs)
-
+        apiurl += '?%s' % urlencode(kwargs)
     # Make request
     try:
         log.debug('Request URL: %s', apiurl)
         log.debug('Request data: %s', postdata)
-        response = urllib2.urlopen(apiurl, postdata).read()
+        response = urlopen(apiurl, postdata).read()
         return response
-    except urllib2.HTTPError as e:
+    except HTTPError as e:
         raise PubChemHTTPError(e)
 
 
 def get(identifier, namespace='cid', domain='compound', operation=None, output='JSON', searchtype=None, **kwargs):
     """Request wrapper that automatically handles async requests."""
     if searchtype or namespace in ['formula']:
         response = request(identifier, namespace, domain, None, 'JSON', searchtype, **kwargs)
-        status = json.loads(response)
+        status = json.loads(response.decode())
         if 'Waiting' in status and 'ListKey' in status['Waiting']:
             identifier = status['Waiting']['ListKey']
             namespace = 'listkey'
             while 'Waiting' in status and 'ListKey' in status['Waiting']:
                 time.sleep(2)
                 response = request(identifier, namespace, domain, operation, 'JSON', **kwargs)
-                status = json.loads(response)
+                status = json.loads(response.decode())
             if not output == 'JSON':
                 response = request(identifier, namespace, domain, operation, output, searchtype, **kwargs)
     else:
@@ -87,7 +96,7 @@ def get(identifier, namespace='cid', domain='compound', operation=None, output='
 def get_json(identifier, namespace='cid', domain='compound', operation=None, searchtype=None, **kwargs):
     """Request wrapper that automatically parses JSON response and supresses NotFoundError."""
     try:
-        return json.loads(get(identifier, namespace, domain, operation, 'JSON', searchtype, **kwargs))
+        return json.loads(get(identifier, namespace, domain, operation, 'JSON', searchtype, **kwargs).decode())
     except NotFoundError as e:
         log.info(e)
         return None
@@ -180,7 +189,7 @@ def get_assays(identifier, namespace='aid', **kwargs):
 
 
 def get_properties(properties, identifier, namespace='cid', searchtype=None, as_dataframe=False, **kwargs):
-    if isinstance(properties, basestring):
+    if isinstance(properties, text_types):
         properties = properties.split(',')
     properties = ','.join([PROPERTY_MAP.get(p, p) for p in properties])
     properties = 'property/%s' % properties
@@ -229,7 +238,7 @@ def get_aids(identifier, namespace='cid', domain='compound', searchtype=None, **
 
 def get_all_sources(domain='substance'):
     """Return a list of all current depositors of substances or assays."""
-    results = json.loads(get(domain, None, 'sources'))
+    results = json.loads(get(domain, None, 'sources').decode())
     return results['InformationList']['SourceName']
 
 
@@ -275,7 +284,7 @@ def from_cid(cls, cid, **kwargs):
 
         :param cid: The PubChem Compound Identifier (CID).
         """
-        record = json.loads(request(cid, **kwargs))['PC_Compounds'][0]
+        record = json.loads(request(cid, **kwargs).decode())['PC_Compounds'][0]
         return cls(record)
 
     def __repr__(self):
@@ -330,15 +339,15 @@ def atoms(self):
         }
         if 'z' in self.record['coords'][0]['conformers'][0]:
             a['z'] = self.record['coords'][0]['conformers'][0]['z']
-        atomlist = map(dict, zip(*[[(k, v) for v in value] for k, value in a.items()]))
+        atomlist = list(map(dict, list(zip(*[[(k, v) for v in value] for k, value in a.items()]))))
         if 'charge' in self.record['atoms']:
             for charge in self.record['atoms']['charge']:
                 atomlist[charge['aid']]['charge'] = charge['value']
         return atomlist
 
     @property
     def bonds(self):
-        blist = map(dict, zip(*[[(k, v) for v in value] for k, value in self.record['bonds'].items()]))
+        blist = list(map(dict, list(zip(*[[(k, v) for v in value] for k, value in self.record['bonds'].items()]))))
         if 'style' in self.record['coords'][0]['conformers'][0]:
             style = self.record['coords'][0]['conformers'][0]['style']
             for i, annotation in enumerate(style['annotation']):
@@ -557,7 +566,7 @@ def _parse_prop(search, proplist):
     """Extract property value from record using the given urn search filter."""
     props = [i for i in proplist if all(item in i['urn'].items() for item in search.items())]
     if len(props) > 0:
-        return props[0]['value'][props[0]['value'].keys()[0]]
+        return props[0]['value'][list(props[0]['value'].keys())[0]]
 
 
 class Substance(object):
@@ -578,7 +587,7 @@ def from_sid(cls, sid):
 
         :param sid: The PubChem Substance Identifier (SID).
         """
-        record = json.loads(request(sid, 'sid', 'substance'))['PC_Substances'][0]
+        record = json.loads(request(sid, 'sid', 'substance').decode())['PC_Substances'][0]
         return cls(record)
 
     def __init__(self, record):
@@ -689,7 +698,7 @@ def __init__(self, record):
 
     @classmethod
     def from_aid(cls, aid):
-        record = json.loads(request(aid, 'aid', 'assay'))['PC_AssayContainer'][0]
+        record = json.loads(request(aid, 'aid', 'assay').decode())['PC_AssayContainer'][0]
         return cls(record)
 
     @property
@@ -794,4 +803,4 @@ def __init__(self, msg='Some problem on the server side'):
 
 
 if __name__ == '__main__':
-    print __version__
+    print(__version__)

pubchempy_test.py

@@ -26,82 +26,82 @@ def setUp(self):
 
     def test_requests(self):
         """Test basic raw requests."""
-        print request('coumarin', 'name', record_type='3d')
-        print request('CCN(C1=N/C(=C/2\SC(=NC2=N)N(CC)CC)/C(=N/Nc2ccc(cc2)S(=O)(=O)C(F)(F)F)/S1)CC', 'smiles')
-        print request('DTP/NCI', 'sourceid', 'substance', '747285', 'SDF')
-        print request('coumarin', 'name', output='PNG', image_size='50x50')
+        print(request('coumarin', 'name', record_type='3d'))
+        print(request('CCN(C1=N/C(=C/2\SC(=NC2=N)N(CC)CC)/C(=N/Nc2ccc(cc2)S(=O)(=O)C(F)(F)F)/S1)CC', 'smiles'))
+        print(request('DTP/NCI', 'sourceid', 'substance', '747285', 'SDF'))
+        print(request('coumarin', 'name', output='PNG', image_size='50x50'))
 
     def test_listkeys(self):
         """Test asynchronous listkey requests."""
-        print get('CC', 'smiles', operation='cids', searchtype='superstructure')
-        print get(self.molform, 'formula', listkey_count=3)
+        print(get('CC', 'smiles', operation='cids', searchtype='superstructure'))
+        print(get(self.molform, 'formula', listkey_count=3))
 
     def test_properties(self):
-        print get_properties('IsomericSMILES', self.rucomplex, 'name')
+        print(get_properties('IsomericSMILES', self.rucomplex, 'name'))
 
     def test_synonyms(self):
-        print get_synonyms(self.phenanthrolinesmiles, 'smiles')
+        print(get_synonyms(self.phenanthrolinesmiles, 'smiles'))
 
     def test_compounds(self):
         c = Compound.from_cid(1)
-        print c.cid
-        print c.record
-        print c.atoms
-        print c.bonds
-        print c.charge
-        print c.molecular_formula
-        print c.molecular_weight
-        print c.canonical_smiles
-        print c.isomeric_smiles
-        print c.inchi
-        print c.inchikey
-        print c.iupac_name
-        print c.xlogp
-        print c.exact_mass
-        print c.monoisotopic_mass
-        print c.tpsa
-        print c.complexity
-        print c.h_bond_donor_count
-        print c.h_bond_acceptor_count
-        print c.rotatable_bond_count
-        print c.fingerprint
-        print c.heavy_atom_count
-        print c.isotope_atom_count
-        print c.atom_stereo_count
-        print c.defined_atom_stereo_count
-        print c.undefined_atom_stereo_count
-        print c.bond_stereo_count
-        print c.defined_bond_stereo_count
-        print c.undefined_bond_stereo_count
-        print c.covalent_unit_count
-        print c.coordinate_type
+        print(c.cid)
+        print(c.record)
+        print(c.atoms)
+        print(c.bonds)
+        print(c.charge)
+        print(c.molecular_formula)
+        print(c.molecular_weight)
+        print(c.canonical_smiles)
+        print(c.isomeric_smiles)
+        print(c.inchi)
+        print(c.inchikey)
+        print(c.iupac_name)
+        print(c.xlogp)
+        print(c.exact_mass)
+        print(c.monoisotopic_mass)
+        print(c.tpsa)
+        print(c.complexity)
+        print(c.h_bond_donor_count)
+        print(c.h_bond_acceptor_count)
+        print(c.rotatable_bond_count)
+        print(c.fingerprint)
+        print(c.heavy_atom_count)
+        print(c.isotope_atom_count)
+        print(c.atom_stereo_count)
+        print(c.defined_atom_stereo_count)
+        print(c.undefined_atom_stereo_count)
+        print(c.bond_stereo_count)
+        print(c.defined_bond_stereo_count)
+        print(c.undefined_bond_stereo_count)
+        print(c.covalent_unit_count)
+        print(c.coordinate_type)
 
         c = Compound.from_cid(1, record_type='3d')
-        print c.volume_3d
-        print c.multipoles_3d
-        print c.conformer_rmsd_3d
-        print c.effective_rotor_count_3d
-        print c.pharmacophore_features_3d
-        print c.mmff94_partial_charges_3d
-        print c.mmff94_energy_3d
-        print c.conformer_id_3d
-        print c.shape_selfoverlap_3d
-        print c.feature_selfoverlap_3d
-        print c.shape_fingerprint_3d
-        print c.coordinate_type
+        print(c.volume_3d)
+        print(c.multipoles_3d)
+        print(c.conformer_rmsd_3d)
+        print(c.effective_rotor_count_3d)
+        print(c.pharmacophore_features_3d)
+        print(c.mmff94_partial_charges_3d)
+        print(c.mmff94_energy_3d)
+        print(c.conformer_id_3d)
+        print(c.shape_selfoverlap_3d)
+        print(c.feature_selfoverlap_3d)
+        print(c.shape_fingerprint_3d)
+        print(c.coordinate_type)
 
     def test_csaids(self):
-        print get_cids('Aspirin', 'name', 'substance')
-        print get_cids('Aspirin', 'name', 'compound')
-        print get_sids('Aspirin', 'name', 'substance')
-        print get_aids('Aspirin', 'name', 'substance')
-        print get_aids('Aspirin', 'name', 'compound')
+        print(get_cids('Aspirin', 'name', 'substance'))
+        print(get_cids('Aspirin', 'name', 'compound'))
+        print(get_sids('Aspirin', 'name', 'substance'))
+        print(get_aids('Aspirin', 'name', 'substance'))
+        print(get_aids('Aspirin', 'name', 'compound'))
 
     def test_assays(self):
-        print get_assays(1, sid='67107,67121,67122')
+        print(get_assays(1, sid='67107,67121,67122'))
 
     def test_substructure(self):
-        print get_compounds('C1=CC2=C(C3=C(C=CC=N3)C=C2)N=C1', 'smiles', searchtype='substructure', listkey_count=3)
+        print(get_compounds('C1=CC2=C(C3=C(C=CC=N3)C=C2)N=C1', 'smiles', searchtype='substructure', listkey_count=3))
 
     def test_equality(self):
         self.assertEqual(Compound.from_cid(241), Compound.from_cid(241))