convert to print_function, and start adding unicode_literals future as well

diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py
index 9fe33e866f1911fb132a51898887bec2e775098f..29352d5a4d6ad561b3148a39310c8ec580ff956b 100644 (file)
--- a/encode_submission/encode3.py
+++ b/encode_submission/encode3.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 """Create a track hub
 """
+from __future__ import print_function, unicode_literals
+
 from ConfigParser import SafeConfigParser
 import fnmatch
 from glob import glob
@@ -135,7 +137,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         writer = get_serializer()
-        print writer.serialize_model_to_string(model)
+        print(writer.serialize_model_to_string(model))
 
 
 def make_manifest(mapper, results, filename=None):

diff --git a/encode_submission/encode_find.py b/encode_submission/encode_find.py
index 60e0bee9b5700f8be2a58e7e45480dddf0bd0c6f..8333ca61901ba9bdd1e68ec10872ca8ec97ae037 100644 (file)
--- a/encode_submission/encode_find.py
+++ b/encode_submission/encode_find.py
@@ -2,6 +2,7 @@
 """
 Gather information about our submissions into a single RDF store
 """
+from __future__ import print_function, unicode_literals
 
 from datetime import datetime
 import hashlib
@@ -130,7 +131,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         serializer = get_serializer(name=opts.rdf_parser_name)
-        print serializer.serialize_model_to_string(model)
+        print(serializer.serialize_model_to_string(model))
 
 
 def make_parser():
@@ -261,11 +262,11 @@ def report_submissions_with_no_library(model):
     for row in results:
         subid = row['subid']
         name = row['name']
-        print "# {0}".format(name)
-        print "<{0}>".format(subid.uri)
-        print "  encodeSubmit:library_urn "\
-              "<http://jumpgate.caltech.edu/library/> ."
-        print ""
+        print("# {0}".format(name))
+        print("<{0}>".format(subid.uri))
+        print("  encodeSubmit:library_urn "\
+              "<http://jumpgate.caltech.edu/library/> .")
+        print("")
 
 def find_submissions_with_no_library(model):
     missing_lib_query_text = """

diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py
index 1aadb8398f92fec7a661e33cc9f219b4d656857a..53e2d4441663f8088ad9b96a248c1600abb01da0 100644 (file)
--- a/encode_submission/geo_gather.py
+++ b/encode_submission/geo_gather.py
@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function, unicode_literals
+
 from ConfigParser import SafeConfigParser
 import fnmatch
 from glob import glob
@@ -98,7 +100,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         writer = get_serializer()
-        print writer.serialize_model_to_string(model)
+        print(writer.serialize_model_to_string(model))
 
 
 def make_parser():

diff --git a/encode_submission/scan_extension.py b/encode_submission/scan_extension.py
index 39f19c6461c87e86d24f040a81d37f23dbaffd97..88d53f0653f9592d18f9f788044b81fb6db50f72 100644 (file)
--- a/encode_submission/scan_extension.py
+++ b/encode_submission/scan_extension.py
@@ -1,3 +1,5 @@
+from __future__ import print_function, unicode_literals
+
 from optparse import OptionParser
 import os
 import sys
@@ -13,7 +15,7 @@ def main(cmdline=None):
     if opts.rdf:
         print_rdf(common_extensions)
     else:
-        print common_extensions
+        print(common_extensions)
         
 def make_parser():
     parser = OptionParser("%prog: directory [directory...]")
@@ -70,7 +72,7 @@ def print_rdf(common_extensions):
         
     writer = rdfhelp.get_serializer()
     writer.set_namespace('thisSubmissionView', subView._prefix)
-    print writer.serialize_model_to_string(model)
+    print(writer.serialize_model_to_string(model))
 
 if __name__ == "__main__":
     main()

diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py
index bc3515b5c6511f101107d6a0dc94a6ac72c882f3..6961fa9bdf30818512f78815223fcc8a9137c6ce 100644 (file)
--- a/encode_submission/ucsc_gather.py
+++ b/encode_submission/ucsc_gather.py
@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function, unicode_literals
+
 from ConfigParser import SafeConfigParser
 import fnmatch
 from glob import glob
@@ -119,7 +121,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         writer = get_serializer()
-        print writer.serialize_model_to_string(model)
+        print(writer.serialize_model_to_string(model))
 
 
 def make_parser():

diff --git a/htsworkflow/pipelines/srf2fastq.py b/htsworkflow/pipelines/srf2fastq.py
index 0d895d9e4b18c8fbb968da470639df8808424339..0805879c2dad1b6a09b8090c3cc4b7661c93c094 100644 (file)
--- a/htsworkflow/pipelines/srf2fastq.py
+++ b/htsworkflow/pipelines/srf2fastq.py
@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function, unicode_literals
+
 import logging
 import mmap
 from optparse import OptionParser
@@ -27,7 +29,7 @@ def main(cmdline=None):
         logging.basicConfig(level=logging.WARN)
 
     if opts.version:
-        print version()
+        print(version())
         return 0
 
     if len(args) != 1:
@@ -241,7 +243,7 @@ def foo():
     target2_name = base + '_r2.fastq'
 
     for target_name in [target1_name, target2_name]:
-        print 'target name', target_name
+        print('target name', target_name)
         if os.path.exists(target_name):
             raise RuntimeError("%s exists" % (target_name,))
 

diff --git a/htsworkflow/pipelines/test/simulate_runfolder.py b/htsworkflow/pipelines/test/simulate_runfolder.py
index 759a13ee37f2f463771ac2429e64e9be49873031..0d48787abb25dfe8d6c77f4933e5ef6ce6c2706a 100644 (file)
--- a/htsworkflow/pipelines/test/simulate_runfolder.py
+++ b/htsworkflow/pipelines/test/simulate_runfolder.py
@@ -1,6 +1,8 @@
 """
 Create simulated solexa/illumina runfolders for testing
 """
+from __future__ import print_function, unicode_literals
+
 import gzip
 import os
 import shutil
@@ -653,12 +655,12 @@ class DemultiplexedPaths(object):
         return pathname
 
     def dump(self):
-        print ('index seq: {0}'.format(self.index_seq))
+        print('index seq: {0}'.format(self.index_seq))
 
-        print ('project dir: {0}'.format(self.project_dir))
-        print ('sample dir: {0}'.format(self.sample_dir))
-        print ('rootname: {0}'.format(self.rootname))
-        print ('path: {0}'.format(
+        print('project dir: {0}'.format(self.project_dir))
+        print('sample dir: {0}'.format(self.sample_dir))
+        print('rootname: {0}'.format(self.rootname))
+        print('path: {0}'.format(
             os.path.join(self.project_dir,
                          self.sample_dir,
                          self.rootname+'R1_001.fastq.gz')))
@@ -697,7 +699,7 @@ def print_ls_tree(root):
     """
     for dirpath, dirnames, filenames in os.walk(root):
         for filename in filenames:
-            print os.path.join(dirpath, filename)
+            print(os.path.join(dirpath, filename))
 
 
 class BaseCallInfo(object):

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index cc16f794ffa9392924880f566a7cbc243c444471..d9d38f8a708beac3a4636858ecddb280601b085b 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -1,5 +1,7 @@
 """Helper features for working with librdf
 """
+from __future__ import print_function, unicode_literals
+
 import collections
 from datetime import datetime
 from glob import glob
@@ -43,8 +45,8 @@ def display_query_results(results):
     """
     for row in results:
         for k, v in row.items()[::-1]:
-            print "{0}: {1}".format(k, v)
-        print
+            print("{0}: {1}".format(k, v))
+        print()
 
 def html_query_results(result_stream):
     from django.conf import settings
@@ -69,7 +71,7 @@ def html_query_results(result_stream):
             new_row[k] = Simplified(v)
         results.append(new_row)
     context = Context({'results': results,})
-    print template.render(context)
+    print(template.render(context))
 
 def blankOrUri(value=None):
     """Return a blank node for None or a resource node for strings.

diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py
index d11d98bb2642ed539f6da544c7057e40e0cfa935..e6bc5357cd919062e039f320e1eef33e806662e3 100644 (file)
--- a/htsworkflow/util/test/test_rdfhelp.py
+++ b/htsworkflow/util/test/test_rdfhelp.py
@@ -1,3 +1,5 @@
+from __future__ import print_function, unicode_literals
+
 import os
 import types
 from unittest import TestCase
@@ -262,7 +264,7 @@ _:a owl:imports "{loc}extra.turtle" .
 
 
 except ImportError as e:
-    print "Unable to test rdfhelp"
+    print("Unable to test rdfhelp")
 
 def suite():
     from unittest import TestSuite, defaultTestLoader

diff --git a/inventory/models.py b/inventory/models.py
index d41025ad2732953a2bd6091b536c1405791efdf4..1e8509600336bb38a8797fbf097e431b48f13ffc 100644 (file)
--- a/inventory/models.py
+++ b/inventory/models.py
@@ -28,7 +28,6 @@ def _assign_uuid(sender, instance, **kwargs):
     """
     Assigns a UUID to model on save
     """
-    #print 'Entered _assign_uuid'
     if instance.uuid is None or len(instance.uuid) != 32:
         instance.uuid = uuid.uuid1().hex
 

diff --git a/scripts/htsw-srf b/scripts/htsw-srf
index bcf835dbfa29c1d3707d0e9e602d5c5882093ce4..d933b800c9018384629817a32a2f3bce60a2eb25 100755 (executable)
--- a/scripts/htsw-srf
+++ b/scripts/htsw-srf
@@ -1,4 +1,5 @@
 #!/usr/bin/python
+from __future__ import print_function, unicode_literals
 
 import logging
 import optparse
@@ -116,9 +117,9 @@ def main(cmdline=None):
         run_commands(cwd, cmd_list, opts.jobs)
     else:
       for cwd, cmd_list in cmds.items():
-        print cwd
-        print cmd_list
-        print 'jobs: ', opts.jobs
+        print(cwd)
+        print(cmd_list)
+        print('jobs: ', opts.jobs)
 
     return 0