fixes for python 3 support

CONTRIBUTING.rst

@@ -114,7 +114,7 @@ features or changes that you can implement yourself.
     (sbmlutils)$ pip install -e .
 
 9. When you are done making changes, check that your changes pass pep8
-    and the tests with tox for your local Python version::
+   and the tests with tox for your local Python version::
 
      (sbmlutils)$ tox -e pep8
 

sbmlutils/annotation.py

@@ -395,11 +395,11 @@ def annotations_from_file(file_path, delimiter='\t'):
     def annotations_from_csv(csvfile, delimiter='\t'):
         """ Read annotations from csv in annotation data structure. """
         res = []
-        f = open(csvfile, 'rb')
+        f = open(csvfile, 'rt')
         reader = csv.reader(f, delimiter=delimiter, quoting=csv.QUOTE_NONE)
 
         # first line is headers line
-        headers = reader.next()
+        headers = next(reader)
         logger.info('Headers: {}'.format(headers))
 
         # read entries

sbmlutils/formating.py

@@ -16,7 +16,7 @@ def annotation_to_html(cls, item):
         :param item: SBO item
         """
         items = []
-        for kcv in xrange(item.getNumCVTerms()):
+        for kcv in range(item.getNumCVTerms()):
             cv = item.getCVTerm(kcv)
             q_type = cv.getQualifierType()
             if q_type == 0:
@@ -25,7 +25,7 @@ def annotation_to_html(cls, item):
                 qualifier = annotation.BiologicalQualifierType[cv.getBiologicalQualifierType()]
             items.append(''.join(['<b>', qualifier, '</b>']))
 
-            for k in xrange(cv.getNumResources()):
+            for k in range(cv.getNumResources()):
                 uri = cv.getResourceURI(k)
                 tokens = uri.split('/')
                 resource_id = tokens[-1]
@@ -86,7 +86,7 @@ def modelHistoryToString(mhistory):
         return ""
     items = []
     items.append('<b>Creator</b>')
-    for kc in xrange(mhistory.getNumCreators()):
+    for kc in range(mhistory.getNumCreators()):
         cdata = []
         c = mhistory.getCreator(kc)
         if c.isSetGivenName():
@@ -100,7 +100,7 @@ def modelHistoryToString(mhistory):
         items.append(", ".join(cdata))
     if mhistory.isSetCreatedDate():
         items.append('<b>Created:</b> ' + dateToString(mhistory.getCreatedDate()))
-    for km in xrange(mhistory.getNumModifiedDates()):
+    for km in range(mhistory.getNumModifiedDates()):
         items.append('<b>Modified:</b> ' + dateToString(mhistory.getModifiedDate(km)))
     items.append('<br />')
     return "<br />".join(items)

sbmlutils/manipulation.py

@@ -4,6 +4,7 @@
 
 """
 from __future__ import print_function, division
+from six import iteritems
 import os
 import logging
 import warnings
@@ -32,7 +33,7 @@ def create_merged_doc(model_paths):
     comp_doc = doc.getPlugin("comp")
     comp_model = model.getPlugin("comp")
 
-    for emd_id, path in model_paths.iteritems():        
+    for emd_id, path in iteritems(model_paths):
         # create ExternalModelDefinitions
         emd = comp.create_ExternalModelDefinition(comp_doc, emd_id, source=path)
         # add submodel which references the external model definitions
@@ -50,7 +51,7 @@ def merge_models(model_paths, validate=True):
     """
     # necessary to convert models to SBML L3V1, unfortunately many biomodels/models
     # only L2V?, so additional step necessary
-    for mid, path in model_paths.iteritems():
+    for mid, path in iteritems(model_paths):
         if not os.path.exists(path):
             logging.error('Path for SBML file does not exist: {}'.format(path))
 

sbmlutils/report/templates/macros_helpers.html

@@ -4,7 +4,7 @@
 
 {% macro notes(item) %}
     {% if item.isSetNotes() %}
-        {{ item.notes_string.decode('utf-8') }}
+        {{ item.getNotesString }}
     {% endif %}
 {% endmacro %}
 

tox.ini

@@ -1,13 +1,16 @@
-# Test with
-
 [tox]
-envlist = py27, py35, py36
+envlist = pep8, py27, py35, py36
 
 [testenv]
 deps=
     pytest
     pytest-benchmark
 commands=
     pytest
-    # nosetests
-    # avoids import errors of 'nosetests' in virtualenv
+
+[testenv:pep8]
+skip_install = True
+deps =
+    pep8
+commands =
+    pep8 --show-source sbmlutils