Merge pull request #989 from natefoo/smash_eggs

Add a script for creating binary-compatibility.cfg and run it from common_startup.sh

lib/galaxy/dependencies/__init__.py

@@ -62,7 +62,7 @@ class ConditionalDependencies( object ):
         return asbool( self.config["fluent_log"] )
 
     def check_raven( self ):
-        return asbool( self.config["sentry_dsn"] )
+        return self.config.get("sentry_dsn", None) is not None
 
     def check_weberror( self ):
         return ( asbool( self.config["debug"] ) and

scripts/binary_compatibility.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+"""
+Creates a Python binary-compatibility.cfg as described here:
+
+    https://mail.python.org/pipermail/distutils-sig/2015-July/026617.html
+"""
+from __future__ import print_function
+
+# Vaguely Python 2.6 compatibile ArgumentParser import
+try:
+    from argparse import ArgumentParser
+except ImportError:
+    from optparse import OptionParser
+
+    class ArgumentParser(OptionParser):
+
+        def __init__(self, **kwargs):
+            self.delegate = OptionParser(**kwargs)
+
+        def add_argument(self, *args, **kwargs):
+            if "required" in kwargs:
+                del kwargs["required"]
+            return self.delegate.add_option(*args, **kwargs)
+
+        def parse_args(self, args=None):
+            (options, args) = self.delegate.parse_args(args)
+            return options
+
+import sys
+import json
+
+from pip.pep425tags import get_platform, get_supported
+from pip.platform import get_specific_platform
+
+
+compatible_platforms = {
+    'centos': 'rhel'
+}
+
+
+def install_compat():
+    this_plat = get_specific_platform()[0]
+    compat_plat = compatible_platforms.get(this_plat, None)
+    rval = {}
+    if compat_plat:
+        print('{} is binary compatible with {} (and can install {} wheels)'
+              .format(this_plat, compat_plat, compat_plat),
+              file=sys.stderr)
+        for py, abi, plat in get_supported():
+            if this_plat in plat:
+                rval[plat] = {'install': [plat.replace(this_plat, compat_plat)]}
+    return rval
+
+
+def main():
+    arg_parser = ArgumentParser()
+    arg_parser.add_argument('-o', '--output', default=None, help='Output to file')
+    args = arg_parser.parse_args()
+
+    compat = install_compat()
+
+    if compat:
+        if args.output is not None:
+            with open(args.output, 'w') as out:
+                json.dump(compat, out)
+        else:
+            print(json.dumps(install_compat()))
+
+
+if __name__ == '__main__':
+    main()

scripts/common_startup.sh

@@ -106,6 +106,8 @@ if [ $FETCH_WHEELS -eq 1 ]; then
     # venv (e.g. virtualenv-burrito's pip and six)
     unset PYTHONPATH
     pip install --pre --no-index --find-links ${GALAXY_WHEELS_INDEX_URL}/pip --upgrade pip
+    # binary-compatibility.cfg may need to be created (e.g. on CentOS)
+    [ ! -f ${VIRTUAL_ENV}/binary-compatibility.cfg ] && python ./scripts/binary_compatibility.py -o ${VIRTUAL_ENV}/binary-compatibility.cfg
     pip install -r requirements.txt --index-url ${GALAXY_WHEELS_INDEX_URL}
     GALAXY_CONDITIONAL_DEPENDENCIES=`PYTHONPATH=lib python -c "import galaxy.dependencies; print '\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE'))"`
     [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url ${GALAXY_WHEELS_INDEX_URL}