Merge pull request #25 from abradle/master

Fixes for testing without network / locally.

Author: abradle

.travis.yml

@@ -4,7 +4,6 @@ language: python
 python:
   - "2.6"
   - "2.7"
-  - "3.2"
   - "3.3"
   - "3.4"
   - "3.5"

MANIFEST.in

@@ -1,2 +1,3 @@
 include README.md CHANGELOG.md LICENSE.txt
 include setup.py
+include mmtf/tests/testdatastore/4CUP.mmtf.gz mmtf/tests/testdatastore/4CUP.mmtf

mmtf/api/default_api.py

@@ -12,6 +12,18 @@
 from .mmtf_writer import MMTFEncoder,TemplateEncoder
 
 
+def _internet_on(address):
+    """
+    Check to see if the internet is on by pinging a set address.
+    :param address: the IP or address to hit
+    :return: a boolean - true if can be reached, false if not.
+    """
+    try:
+        urllib2.urlopen(address, timeout=1)
+        return True
+    except urllib2.URLError as err:
+        return False
+
 def write_mmtf(file_path, input_data, input_function):
     """API function to write data as MMTF to a file
 

mmtf/tests/codec_tests.py

@@ -3,13 +3,15 @@
 import msgpack
 import numpy
 
-from mmtf import codecs,fetch,parse,parse_gzip, converters
-from mmtf.api.default_api import ungzip_data,write_mmtf,MMTFEncoder,MMTFDecoder
+from mmtf import fetch,parse,parse_gzip, converters
+from mmtf.api.default_api import ungzip_data,write_mmtf,MMTFDecoder,_internet_on
 from mmtf.codecs import encoders
 from mmtf.utils.codec_utils import parse_header
+from mmtf.utils.constants import BASE_URL
 from mmtf.codecs.default_codec import codec_dict
 from mmtf.codecs.decoders import numpy_decoders as decoders
 
+
 def run_all(unit_test, encoded_data, decoded_data, param, codec_id):
     """Test that a given codec can work in the forward backward and round trip both ways."""
     try:
@@ -191,7 +193,10 @@ def test_gzip_open(self):
         ungzip_data(open("mmtf/tests/testdatastore/4CUP.mmtf.gz","rb").read())
 
     def test_fetch(self):
-        decoded = fetch("4CUP")
+        if _internet_on(BASE_URL):
+            decoded = fetch("4CUP")
+        else:
+            print("Warning - cannot connect to "+BASE_URL)
 
 
     def array_eq(self,array_one, array_two):
@@ -297,10 +302,13 @@ def test_round_trip(self):
         self.check_equal(data_in, data_rt)
 
     def round_trip(self,pdb_id):
-        data_in = fetch(pdb_id)
-        write_mmtf(pdb_id+".mmtf", data_in, MMTFDecoder.pass_data_on)
-        data_rt = parse(pdb_id+".mmtf")
-        self.check_equal(data_in, data_rt)
+        if _internet_on(BASE_URL):
+            data_in = fetch(pdb_id)
+            write_mmtf(pdb_id+".mmtf", data_in, MMTFDecoder.pass_data_on)
+            data_rt = parse(pdb_id+".mmtf")
+            self.check_equal(data_in, data_rt)
+        else:
+            print("Warning - cannot connect to "+BASE_URL)
 
     def test_round_trip_list(self):
         id_list = [

mmtf/utils/codec_utils.py

@@ -3,6 +3,7 @@
 import mmtf
 import mmtf.utils.constants
 
+
 def parse_header(input_array):
     """Parse the header and return it along with the input array minus the header.
     :param input_array the array to parse

requirements.txt

@@ -1,4 +1,4 @@
-ipython
+ipython==5.4.1
 numpy
 nose
 msgpack-python

setup.py

@@ -19,7 +19,7 @@
     # Versions should comply with PEP440.  For a discussion on single-sourcing
     # the version across setup.py and the project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='1.0.5',
+    version='1.0.6',
 
     description='A decoding libary for the PDB mmtf format',
     long_description=long_description,