Merge pull request #111 from ramprasadn/oserror-fix

set abstract_sockets_supported to False

Author: ramprasadn

CHANGELOG.md

@@ -8,6 +8,11 @@ Please add a new candidate release at the top after changing the latest one. Fee
 
 Try to use the following format:
 
+## [3.7.4]
+
+### Fixed
+- OSError crashes due to socket address conflicts when using containers
+
 ## [x.x.x]
 
 ### Changed

genmod/commands/annotate_models.py

@@ -21,7 +21,7 @@
 import shutil
 import itertools
 
-from multiprocessing import JoinableQueue, Manager, cpu_count
+from multiprocessing import JoinableQueue, Manager, cpu_count, util
 from codecs import open
 from datetime import datetime
 from tempfile import NamedTemporaryFile
@@ -39,6 +39,7 @@
                     family_file, family_type, get_file_handle)
 
 logger = logging.getLogger(__name__)
+util.abstract_sockets_supported = False
 
 @click.command('models', short_help="Annotate inheritance")
 @variant_file

genmod/commands/score_compounds.py

@@ -17,7 +17,7 @@
 import logging
 import itertools
 
-from multiprocessing import JoinableQueue, Manager, cpu_count
+from multiprocessing import JoinableQueue, Manager, cpu_count, util
 from codecs import open
 from datetime import datetime
 from tempfile import NamedTemporaryFile
@@ -33,6 +33,7 @@
                     get_file_handle)
 
 logger = logging.getLogger(__name__)
+util.abstract_sockets_supported = False
 
 @click.command('compound', short_help="Score compounds")
 @variant_file

setup.py

@@ -20,7 +20,7 @@
     long_description = 'Tool for annotating patterns of genetic inheritance in Variant Call Format (VCF) files.'
 
 setup(name='genmod',
-    version='3.7.3',
+    version='3.7.4',
     description='Annotate genetic inheritance models in variant files',
     author = 'Mans Magnusson',
     author_email = 'mans.magnusson@scilifelab.se',

tests/utils/test_variant_printer.py

@@ -1,13 +1,13 @@
 from codecs import open
 from tempfile import NamedTemporaryFile
-from multiprocessing import Manager
+from multiprocessing import Manager, util
 from collections import OrderedDict
 
 from genmod.utils import VariantPrinter
 from genmod.vcf_tools import (get_variant_dict, get_info_dict, 
 get_variant_id, HeaderParser)
 
-
+util.abstract_sockets_supported = False
 
 def setup_vcf_file():
     """