#8: Python3 testing

.pydevproject

@@ -3,6 +3,6 @@
 <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
 <path>/${PROJECT_DIR_NAME}</path>
 </pydev_pathproperty>
-<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 3.0</pydev_property>
+<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python interpreter</pydev_property>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
 </pydev_project>

pyreference/reference.py

@@ -1,7 +1,8 @@
 from __future__ import print_function, absolute_import
 
 import HTSeq
-from deprecated import deprecated
+from functools import reduce
+from deprecation import deprecated
 import gzip
 import json
 from lazy import lazy
@@ -88,7 +89,7 @@ def __init__(self, build=None, config=None, **kwargs):
             params = load_params_from_config(build=build, config=config)
         except OSError as e:
             config_exception = e
-            params = {}
+            params = {"build" : build}
 
         # Set / Overwrite with non-null kwargs
         params.update({k : v for (k,v) in kwargs.items() if v is not None})
@@ -191,11 +192,11 @@ def get_gene_by_name(self, gene_name):
         return self.get_gene_by_id(gene_id)
 
 
-    #@deprecated(reason="Use get_gene_by_id")
+    #@deprecated(details="Use get_gene_by_id")
     def get_gene(self, gene_id):
         return self.get_gene_by_id(gene_id)
 
-    #@deprecated(reason="Use get_transcript_by_id")
+    #@deprecated(details="Use get_transcript_by_id")
     def get_transcript(self, transcript_id):
         return self.get_transcript_by_id(transcript_id)
 
@@ -349,7 +350,7 @@ def get_best_region(self, iv):
                 break
         return region
 
-    @deprecated(reason="Use get_best_region()")
+    @deprecated(details="Use get_best_region()")
     def get_region(self, iv):
         return self.get_best_region(iv)
 

pyreference/tests/test_reference.py

@@ -65,7 +65,7 @@ def test_genes(self):
                                      "3p_utr"          : "CGCCGCCCGC" },
         }
 
-        for test in test_cases.itervalues():
+        for test in six.itervalues(test_cases):
             transcript = self.reference.transcripts[test["transcript_id"]]
 
             utr = str(transcript.get_3putr_sequence()).upper()

pyreference/transcript.py

@@ -1,7 +1,7 @@
 from __future__ import print_function, absolute_import
 
 import HTSeq
-#from deprecated import deprecated
+#from from deprecation import deprecated
 from lazy import lazy
 
 from pyreference.genomic_region import GenomicRegion
@@ -37,7 +37,7 @@ def get_features_length(self, feature_type):
             length += feature[END] - feature[START] 
         return length
 
-    #@deprecated(reason="Use get_features_in_stranded_order")
+    #@deprecated(details="Use get_features_in_stranded_order")
     def get_features(self, feature_type):
         ''' returns list of HTSeq.GenomicFeature '''
         genomic_features = []
@@ -76,7 +76,7 @@ def get_features_in_stranded_order(self, feature_type):
     def length(self):
         return self.get_features_length("exon")
 
-    #@deprecated(reason="Use Transcript.length")
+    #@deprecated(details="Use Transcript.length")
     def get_transcript_length(self):
         return self.length
 

pyreference/utils/file_utils.py

@@ -3,14 +3,15 @@
 
 @author: dlawrence
 '''
-from md5 import md5
+from hashlib import md5
 import os
+import six
 
 
 try:
-    from pathlib import Path
+    from pathlib import Path #@UnresolvedImport
 except (ImportError,AttributeError):
-    from pathlib2 import Path
+    from pathlib2 import Path #@UnresolvedImport
 
 def name_from_file_name(file_name):
     return Path(file_name).name
@@ -26,12 +27,12 @@ def mk_path_for_file(f):
     mk_path(os.path.dirname(f))
 
 def file_or_file_name(f, mode='r'):
-    if isinstance(f, basestring): # Works on unicode
+    if isinstance(f, six.string_types):
         if 'w' in mode: # Create path if writing
             mk_path_for_file(f)
 
         return open(f, mode)
-    elif isinstance(f, file):
+    elif hasattr(f, 'read'):
         return f # Already a File object
     else:
         raise ValueError("'%s' (%s) not a file or string" % (f, type(f)))

pyreference/utils/genomics_utils.py

@@ -6,6 +6,11 @@
 from Bio import SeqIO
 import HTSeq
 
+try:
+    from sys import intern
+except (ImportError,AttributeError):
+    pass
+
 from pyreference.settings import CHROM, START, END, STRAND
 
 

requirements.txt

@@ -1,6 +1,6 @@
 biopython
 configargparse
-deprecated
+deprecation
 HTSeq
 lazy
 pyfasta

setup.py

@@ -4,7 +4,7 @@
 
 setup(name = 'pyreference',
       packages = find_packages(),
-      version = '0.3',
+      version = '0.4',
       description = 'Library for working with reference genomes',
       author = 'David Lawrence',
       author_email = '[email protected]',
@@ -14,7 +14,7 @@
       install_requires=[
         'biopython',
         'configargparse',
-        'deprecated',
+        'deprecation',
         'HTSeq',
         'lazy',
         'pyfasta',