[adios] 79/207: refresh patches
Alastair McKinstry
mckinstry at moszumanska.debian.org
Fri Jun 12 06:04:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
mckinstry pushed a commit to branch master
in repository adios.
commit 534d643601cb4dfc54c8fa49f69a200dcd685a5c
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Mon Feb 17 09:42:30 2014 +0000
refresh patches
---
debian/changelog | 1 +
debian/patches/debian_paths.patch | 98 +++++++++++++++------
debian/patches/mpi_in_place.patch | 18 ++--
debian/patches/netcdf-fix.patch | 10 +--
debian/patches/python3.patch | 180 ++++++++++++++++----------------------
debian/patches/security.patch | 14 +--
6 files changed, 165 insertions(+), 156 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 29bd9be..1bb812a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
adios (1.6.0-1) UNRELEASED; urgency=medium
* New upstream. Closes: #732276, #727312.
+ * Ship in xz format.
-- Alastair McKinstry <mckinstry at debian.org> Sun, 22 Dec 2013 07:21:03 +0000
diff --git a/debian/patches/debian_paths.patch b/debian/patches/debian_paths.patch
index f5fb82c..cab6836 100644
--- a/debian/patches/debian_paths.patch
+++ b/debian/patches/debian_paths.patch
@@ -3,36 +3,43 @@ Description: Change paths to match Debian and FHS
Forwarded: no
Last-Updated: 2013-12-09
-Index: adios-1.5.0/utils/skel/lib/skel_makefile.py
+Index: adios-1.6.0/utils/skel/lib/skel_makefile.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_makefile.py 2013-12-09 20:26:51.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_makefile.py 2013-12-09 20:26:51.000000000 +0000
-@@ -34,7 +34,7 @@
- makefile_template_name = '~/.skel/templates/Makefile.default.tpl'
- makefile_template = open(os.path.expanduser(makefile_template_name), 'r')
-
-- include_statement = "" + os.path.dirname (sys.argv[0]) + '/../etc/skel/compiler_fragment.mk'
-+ include_statement = '/etc/adios/skel/compiler_fragment.mk'
+--- adios-1.6.0.orig/utils/skel/lib/skel_makefile.py 2014-02-17 09:37:11.833940953 +0000
++++ adios-1.6.0/utils/skel/lib/skel_makefile.py 2014-02-17 09:38:51.492140048 +0000
+@@ -41,8 +41,8 @@
+ try:
+ params = skelconf.skelConfig (args.project + '_params.xml')
+ except (IOError):
+- print "Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first,"
+- print "then check that " + args.project + "_params.xml exists."
++ print( "Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first,")
++ print("then check that " + args.project + "_params.xml exists.")
+ return
- for template_line in makefile_template:
+ generate_makefiles (params, config)
+@@ -57,7 +57,7 @@
-@@ -72,10 +72,10 @@
+ # Only proceed if outfilename does not already exist, or if -f was used
+ if os.path.exists (outfilename) and not args.force:
+- print "%s exists, aborting. Delete the file or use -f to overwrite." % outfilename
++ print( "%s exists, aborting. Delete the file or use -f to overwrite." % outfilename)
+ return 999
- # Makefile generation no longer depends on the target, just using default here.
- #makefile_template_name = os.path.dirname (sys.argv[0]) + '/../etc/skel/templates/Makefile.' + platform + '.tpl'
-- makefile_template_name = os.path.dirname (sys.argv[0]) + '/../etc/skel/templates/Makefile.default.tpl'
-+ makefile_template_name = '/etc/adios/skel/templates/Makefile.default.tpl'
+ skel_file = open (outfilename, 'w')
+@@ -97,7 +97,7 @@
+ makefile_template_name = '~/.skel/templates/Makefile.default.tpl'
makefile_template = open(os.path.expanduser(makefile_template_name), 'r')
- include_statement = "" + os.path.dirname (sys.argv[0]) + '/../etc/skel/compiler_fragment.mk'
-+ include_statement = "" + '/etc/adios/skel/compiler_fragment.mk'
++ include_statement = '/etc/adios/skel/compiler_fragment.mk'
- for template_line in makefile_template:
+ bindir = os.path.abspath(os.path.dirname(sys.argv[0]))
-Index: adios-1.5.0/utils/skel/lib/skel_settings.py
+Index: adios-1.6.0/utils/skel/lib/skel_settings.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_settings.py 2013-12-09 20:26:51.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_settings.py 2013-12-09 20:26:51.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_settings.py 2014-02-17 09:37:11.833940953 +0000
++++ adios-1.6.0/utils/skel/lib/skel_settings.py 2014-02-17 09:37:11.829942393 +0000
@@ -54,7 +54,7 @@
skel_settings_dir_name = os.path.expanduser ('~/.skel')
if not os.path.exists (skel_settings_dir_name):
@@ -42,29 +49,38 @@ Index: adios-1.5.0/utils/skel/lib/skel_settings.py
print('Created ' + skel_settings_dir_name)
-Index: adios-1.5.0/utils/gpp/ad_config.py
+Index: adios-1.6.0/utils/gpp/ad_config.py
===================================================================
---- adios-1.5.0.orig/utils/gpp/ad_config.py 2013-12-09 20:26:49.000000000 +0000
-+++ adios-1.5.0/utils/gpp/ad_config.py 2013-12-09 20:27:16.000000000 +0000
+--- adios-1.6.0.orig/utils/gpp/ad_config.py 2014-02-17 09:37:11.833940953 +0000
++++ adios-1.6.0/utils/gpp/ad_config.py 2014-02-17 09:42:05.467456558 +0000
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
from __future__ import absolute_import, division, print_function, unicode_literals
import xml.dom.minidom
import type_mapper
-Index: adios-1.5.0/utils/gpp/type_mapper.py
+@@ -104,7 +105,7 @@
+ # Returns the variable from this group with the specified name, or None
+ def get_var (self, varfullpath):
+ #print ' get_var('+varfullpath+')'
+- if self.vardict.has_key (varfullpath):
++ if varfullpath in self.vardict:
+ return self.vardict [varfullpath]
+
+ return None
+Index: adios-1.6.0/utils/gpp/type_mapper.py
===================================================================
---- adios-1.5.0.orig/utils/gpp/type_mapper.py 2013-12-09 20:02:59.000000000 +0000
-+++ adios-1.5.0/utils/gpp/type_mapper.py 2013-12-09 20:28:56.000000000 +0000
+--- adios-1.6.0.orig/utils/gpp/type_mapper.py 2014-02-17 09:37:11.833940953 +0000
++++ adios-1.6.0/utils/gpp/type_mapper.py 2014-02-17 09:37:11.829942393 +0000
@@ -1,4 +1,4 @@
-
+#!/usr/bin/env python
c_types = {
'string' : 'string',
-Index: adios-1.5.0/utils/skel/bin/skel_extract.py
+Index: adios-1.6.0/utils/skel/bin/skel_extract.py
===================================================================
---- adios-1.5.0.orig/utils/skel/bin/skel_extract.py 2013-12-09 20:26:49.000000000 +0000
-+++ adios-1.5.0/utils/skel/bin/skel_extract.py 2013-12-09 20:56:22.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/bin/skel_extract.py 2014-02-17 09:37:11.833940953 +0000
++++ adios-1.6.0/utils/skel/bin/skel_extract.py 2014-02-17 09:37:11.829942393 +0000
@@ -113,7 +113,7 @@
# check the selected fields
for field in selected_fields:
@@ -74,3 +90,27 @@ Index: adios-1.5.0/utils/skel/bin/skel_extract.py
return
#Print the header
+Index: adios-1.6.0/utils/skel/lib/skel_source.py
+===================================================================
+--- adios-1.6.0.orig/utils/skel/lib/skel_source.py 2014-02-17 09:37:08.575116968 +0000
++++ adios-1.6.0/utils/skel/lib/skel_source.py 2014-02-17 09:41:14.801181900 +0000
+@@ -681,7 +681,7 @@
+
+ # Only proceed if outfilename does not already exist, or if -f was used
+ if os.path.exists (outfilename) and not args.force:
+- print "%s exists, aborting. Delete the file or use -f to overwrite." % outfilename
++ print( "%s exists, aborting. Delete the file or use -f to overwrite." % outfilename)
+ return 999
+
+ skel_file = open (outfilename, 'w')
+@@ -712,8 +712,8 @@
+ try:
+ params = skelconf.skelConfig (args.project + '_params.xml')
+ except (IOError):
+- print "Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first,"
+- print "then check that " + args.project + "_params.xml exists."
++ print("Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first,")
++ print("then check that " + args.project + "_params.xml exists.")
+ return
+
+ # Determine the target language
diff --git a/debian/patches/mpi_in_place.patch b/debian/patches/mpi_in_place.patch
index 9ae27d7..71d1d87 100644
--- a/debian/patches/mpi_in_place.patch
+++ b/debian/patches/mpi_in_place.patch
@@ -3,12 +3,12 @@ Author: Alastair McKinstry <mckinstry at debian.org>
Last-Updated: 2013-04-10
Forwarded: no
-Index: adios.git/src/write/adios_mpi_lustre.c
+Index: adios-1.6.0/src/write/adios_mpi_lustre.c
===================================================================
---- adios.git.orig/src/write/adios_mpi_lustre.c 2013-12-09 18:44:57.000000000 +0000
-+++ adios.git/src/write/adios_mpi_lustre.c 2013-12-09 18:44:57.000000000 +0000
-@@ -744,7 +744,11 @@
- ,fd->group->name, md->old_pg_root
+--- adios-1.6.0.orig/src/write/adios_mpi_lustre.c 2014-02-17 09:36:58.002897426 +0000
++++ adios-1.6.0/src/write/adios_mpi_lustre.c 2014-02-17 09:36:57.998898475 +0000
+@@ -741,7 +741,11 @@
+ ,fd->group->name, md->index
);
MPI_Scatter (offsets, 3, MPI_LONG_LONG
+#ifdef MPI_IN_PLACE
@@ -19,7 +19,7 @@ Index: adios.git/src/write/adios_mpi_lustre.c
,0, md->group_comm
);
md->b.read_pg_offset = offsets [0];
-@@ -838,7 +842,11 @@
+@@ -835,7 +839,11 @@
else
offsets [0] = fd->write_size_bytes;
@@ -31,7 +31,7 @@ Index: adios.git/src/write/adios_mpi_lustre.c
,offsets, 1, MPI_LONG_LONG
,0, md->group_comm
);
-@@ -861,7 +869,11 @@
+@@ -858,7 +866,11 @@
md->b.pg_index_offset = offsets [md->size - 1]
+ last_offset;
MPI_Scatter (offsets, 1, MPI_LONG_LONG
@@ -43,7 +43,7 @@ Index: adios.git/src/write/adios_mpi_lustre.c
,0, md->group_comm
);
fd->base_offset = offsets [0];
-@@ -1140,7 +1152,11 @@
+@@ -1138,7 +1150,11 @@
else
offsets [0] = fd->write_size_bytes;
@@ -55,7 +55,7 @@ Index: adios.git/src/write/adios_mpi_lustre.c
,offsets, 1, MPI_LONG_LONG
,0, md->group_comm
);
-@@ -1156,7 +1172,11 @@
+@@ -1154,7 +1170,11 @@
md->b.pg_index_offset = offsets [md->size - 1]
+ last_offset;
MPI_Scatter (offsets, 1, MPI_LONG_LONG
diff --git a/debian/patches/netcdf-fix.patch b/debian/patches/netcdf-fix.patch
index c4b182d..0c079a0 100644
--- a/debian/patches/netcdf-fix.patch
+++ b/debian/patches/netcdf-fix.patch
@@ -4,11 +4,11 @@ Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=662995
Forwarded: no
Last-Updated: 2012-03-09
-Index: adios.git/utils/bp2ncd/Makefile.in
+Index: adios-1.6.0/utils/bp2ncd/Makefile.in
===================================================================
---- adios.git.orig/utils/bp2ncd/Makefile.in 2013-12-09 18:45:09.000000000 +0000
-+++ adios.git/utils/bp2ncd/Makefile.in 2013-12-09 18:45:08.000000000 +0000
-@@ -98,12 +98,12 @@
+--- adios-1.6.0.orig/utils/bp2ncd/Makefile.in 2014-02-17 09:37:05.732139370 +0000
++++ adios-1.6.0/utils/bp2ncd/Makefile.in 2014-02-17 09:37:05.728140789 +0000
+@@ -106,12 +106,12 @@
ACLOCAL = @ACLOCAL@
ADIOSLIB_CFLAGS = @ADIOSLIB_CFLAGS@
ADIOSLIB_CPPFLAGS = @ADIOSLIB_CPPFLAGS@
@@ -23,7 +23,7 @@ Index: adios.git/utils/bp2ncd/Makefile.in
ADIOSLIB_LDFLAGS = @ADIOSLIB_LDFLAGS@
ADIOSLIB_SEQ_CFLAGS = @ADIOSLIB_SEQ_CFLAGS@
ADIOSLIB_SEQ_CPPFLAGS = @ADIOSLIB_SEQ_CPPFLAGS@
-@@ -325,7 +325,7 @@
+@@ -354,7 +354,7 @@
@USE_PARALLEL_COMPILER_TRUE at bp2ncd_LDFLAGS = $(ADIOSLIB_LDFLAGS) -static-libtool-libs
@USE_PARALLEL_COMPILER_FALSE at bp2ncd_LDADD = $(top_builddir)/src/libadios_internal_nompi.a \
@USE_PARALLEL_COMPILER_FALSE@ $(ADIOSLIB_INT_LDADD)
diff --git a/debian/patches/python3.patch b/debian/patches/python3.patch
index f1fec3a..b27ed52 100644
--- a/debian/patches/python3.patch
+++ b/debian/patches/python3.patch
@@ -3,10 +3,10 @@ Description: Make the python code python2-3 agnostic.
Last-Updated:2013-12-09
Forwarded: no
-Index: adios-1.5.0/utils/skel/bin/skel
+Index: adios-1.6.0/utils/skel/bin/skel
===================================================================
---- adios-1.5.0.orig/utils/skel/bin/skel 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/bin/skel 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/bin/skel 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/bin/skel 2014-02-17 09:37:08.563121337 +0000
@@ -1,5 +1,7 @@
#!/usr/bin/env python
@@ -15,7 +15,7 @@ Index: adios-1.5.0/utils/skel/bin/skel
import sys
import os.path
-@@ -61,7 +63,7 @@
+@@ -81,7 +83,7 @@
try:
config = adios.adiosConfig (args.project + '_skel.xml')
except (IOError):
@@ -24,19 +24,8 @@ Index: adios-1.5.0/utils/skel/bin/skel
return 1
if args.subcommand == 'params':
-@@ -72,8 +74,8 @@
- try:
- params = skelconf.skelConfig (args.project + '_params.xml')
- except (IOError):
-- print "Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first,"
-- print "then copy the generated " + args.project + "_params.xml.default, and edit to suit your needs."
-+ print("Error reading " + args.project + "_params.xml. Try running skel params " + args.project + " first,")
-+ print("then copy the generated " + args.project + "_params.xml.default, and edit to suit your needs.")
- return 1
-
- if args.subcommand == 'makefile':
-@@ -92,7 +94,7 @@
- skel_submit.generate_submit_scripts (params)
+@@ -114,7 +116,7 @@
+ skel_submit.generate_submit_scripts_with_args (parser)
return 0
- print 'Unknown subcommand, exiting.'
@@ -44,10 +33,10 @@ Index: adios-1.5.0/utils/skel/bin/skel
if __name__ == "__main__":
-Index: adios-1.5.0/utils/skel/bin/skel_extract.py
+Index: adios-1.6.0/utils/skel/bin/skel_extract.py
===================================================================
---- adios-1.5.0.orig/utils/skel/bin/skel_extract.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/bin/skel_extract.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/bin/skel_extract.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/bin/skel_extract.py 2014-02-17 09:37:08.563121337 +0000
@@ -1,5 +1,6 @@
#!/usr/bin/env python
@@ -64,10 +53,10 @@ Index: adios-1.5.0/utils/skel/bin/skel_extract.py
return
#Print the header
-Index: adios-1.5.0/utils/skel/lib/skelconf.py
+Index: adios-1.6.0/utils/skel/lib/skelconf.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skelconf.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skelconf.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skelconf.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skelconf.py 2014-02-17 09:37:08.563121337 +0000
@@ -1,5 +1,5 @@
+from __future__ import absolute_import, division, print_function, unicode_literals
import xml.dom.minidom
@@ -84,10 +73,10 @@ Index: adios-1.5.0/utils/skel/lib/skelconf.py
raise SystemExit
self.config_node = nodes[0]
-Index: adios-1.5.0/utils/gpp/ad_config.py
+Index: adios-1.6.0/utils/gpp/ad_config.py
===================================================================
---- adios-1.5.0.orig/utils/gpp/ad_config.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/gpp/ad_config.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/gpp/ad_config.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/gpp/ad_config.py 2014-02-17 09:37:08.567119882 +0000
@@ -1,3 +1,4 @@
+from __future__ import absolute_import, division, print_function, unicode_literals
import xml.dom.minidom
@@ -111,28 +100,19 @@ Index: adios-1.5.0/utils/gpp/ad_config.py
def get_host_language (self):
return self.config_node.getAttribute ('host-language')
-@@ -100,7 +101,7 @@
-
- # Returns the variable from this group with the specified name, or None
- def get_var (self, varname):
-- if self.vardict.has_key (varname):
-+ if varname in self.vardict:
- return self.vardict [varname]
-
- return None
-@@ -164,7 +165,7 @@
+@@ -182,7 +183,7 @@
return None
else:
# place the dimensions in a list and remove the time-index if it is there.
- dims = filter (lambda x : x != self.time_index, self.var_node.getAttribute ('dimensions').split(',') )
+ dims = [x for x in self.var_node.getAttribute ('dimensions').split(',') if x != self.time_index]
cleandims = []
+ #print ' get_dimensions of var '+self.get_fullpath()
for d in dims:
-
-Index: adios-1.5.0/utils/gpp/gpp.py
+Index: adios-1.6.0/utils/gpp/gpp.py
===================================================================
---- adios-1.5.0.orig/utils/gpp/gpp.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/gpp/gpp.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/gpp/gpp.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/gpp/gpp.py 2014-02-17 09:37:08.567119882 +0000
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -140,7 +120,7 @@ Index: adios-1.5.0/utils/gpp/gpp.py
import sys
import os
-@@ -17,10 +17,10 @@
+@@ -22,10 +22,10 @@
if rv == 0:
return 'success'
elif rv == 32512: # System unable to find adios_lint command
@@ -153,7 +133,7 @@ Index: adios-1.5.0/utils/gpp/gpp.py
return 'failure'
-@@ -235,7 +235,7 @@
+@@ -244,7 +244,7 @@
# Must be called with one argument, the name of the xml file
if len (sys.argv) != 2:
@@ -162,7 +142,7 @@ Index: adios-1.5.0/utils/gpp/gpp.py
return 1
-@@ -256,7 +256,7 @@
+@@ -265,7 +265,7 @@
elif lang == 'c' or lang == 'cpp':
generate_c (config)
else:
@@ -171,10 +151,10 @@ Index: adios-1.5.0/utils/gpp/gpp.py
raise SystemExit
-Index: adios-1.5.0/utils/skel/lib/adios.py
+Index: adios-1.6.0/utils/skel/lib/adios.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/adios.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/adios.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/adios.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/adios.py 2014-02-17 09:37:08.567119882 +0000
@@ -1,5 +1,5 @@
+from __future__ import print_function
import xml.dom.minidom
@@ -200,7 +180,7 @@ Index: adios-1.5.0/utils/skel/lib/adios.py
def get_host_language (self):
return self.host_language
-@@ -141,7 +141,7 @@
+@@ -157,7 +157,7 @@
return None
else:
# place the dimensions in a list and remove the time-index if it is there.
@@ -209,10 +189,10 @@ Index: adios-1.5.0/utils/skel/lib/adios.py
cleandims = []
for d in dims:
-Index: adios-1.5.0/utils/skel/lib/argparse.py
+Index: adios-1.6.0/utils/skel/lib/argparse.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/argparse.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/argparse.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/argparse.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/argparse.py 2014-02-17 09:37:08.567119882 +0000
@@ -81,7 +81,6 @@
'ZERO_OR_MORE',
]
@@ -221,10 +201,10 @@ Index: adios-1.5.0/utils/skel/lib/argparse.py
import copy as _copy
import os as _os
import re as _re
-Index: adios-1.5.0/utils/skel/lib/skel_install.py
+Index: adios-1.6.0/utils/skel/lib/skel_install.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_install.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_install.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_install.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skel_install.py 2014-02-17 09:37:08.571118424 +0000
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -232,10 +212,10 @@ Index: adios-1.5.0/utils/skel/lib/skel_install.py
import skel_settings
def main(argv=None):
-Index: adios-1.5.0/utils/skel/lib/skel_makefile.py
+Index: adios-1.6.0/utils/skel/lib/skel_makefile.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_makefile.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_makefile.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_makefile.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skel_makefile.py 2014-02-17 09:37:08.571118424 +0000
@@ -1,5 +1,7 @@
#!/usr/bin/env python
@@ -244,7 +224,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_makefile.py
import argparse
import os
import sys
-@@ -121,10 +123,10 @@
+@@ -190,10 +192,10 @@
lang = config.get_host_language ()
if 'c' == lang or 'C' == lang:
@@ -257,20 +237,20 @@ Index: adios-1.5.0/utils/skel/lib/skel_makefile.py
generate_makefiles_fortran (params)
-Index: adios-1.5.0/utils/skel/lib/skel_params.py
+Index: adios-1.6.0/utils/skel/lib/skel_params.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_params.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_params.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_params.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skel_params.py 2014-02-17 09:37:08.571118424 +0000
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
import sys
import os
import argparse
-Index: adios-1.5.0/utils/skel/lib/skel_settings.py
+Index: adios-1.6.0/utils/skel/lib/skel_settings.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_settings.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_settings.py 2013-12-09 19:59:55.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_settings.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skel_settings.py 2014-02-17 09:37:08.571118424 +0000
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -298,17 +278,17 @@ Index: adios-1.5.0/utils/skel/lib/skel_settings.py
def main(argv=None):
-Index: adios-1.5.0/utils/skel/lib/skel_source.py
+Index: adios-1.6.0/utils/skel/lib/skel_source.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_source.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_source.py 2013-12-09 20:01:16.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_source.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skel_source.py 2014-02-17 09:37:08.575116968 +0000
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
import sys
import os
import argparse
-@@ -83,25 +84,25 @@
+@@ -84,25 +85,25 @@
# same program var (as is done by genarray)
c_file.write ('\n\n// Scalar declarations')
declarations = set()
@@ -338,19 +318,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
c_file.write (adios.cFormatter.get_initialization (v, params.get_group (g.get_name() ) ) )
if measure.use_sleep_before_open():
-@@ -197,9 +198,9 @@
-
-
- if measure.use_adios_timing():
-- print "Use adios timing"
-+ print("Use adios timing")
- else:
-- print "Don't use adios timing"
-+ print("Don't use adios timing")
-
-
- # Detailed reporting disabled, use adios timing instead.
-@@ -230,7 +231,7 @@
+@@ -220,7 +221,7 @@
# free the array memory
c_file.write ('\n\n// Free the arrays')
frees = set()
@@ -359,7 +327,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
frees.add ('\nfree (' + v.get_gwrite() + ');')
for f in frees:
-@@ -307,7 +308,7 @@
+@@ -297,7 +298,7 @@
# same program var (as is done by genarray)
f_file.write ('\n\n! Scalar declarations')
declarations = set()
@@ -368,7 +336,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
declarations.add (adios.fortranFormatter.get_declaration (v, params.get_group (g.get_name() ) ) )
for d in declarations:
-@@ -315,7 +316,7 @@
+@@ -305,7 +306,7 @@
f_file.write ('\n\n! Array declarations')
declarations = set()
@@ -377,7 +345,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
declarations.add (adios.fortranFormatter.get_declaration (v, params.get_group (g.get_name() ) ) )
for d in declarations:
-@@ -345,13 +346,13 @@
+@@ -335,13 +336,13 @@
# For now, just do the numerical values first, then come back and do the more
# complicated ones. This won't cover something like a depends on b, b depends on c,
# but it will work for the moment
@@ -393,7 +361,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
#split at the spaces, just print the ones where the third element is a number
init_str = adios.fortranFormatter.get_initialization (v, params.get_group (g.get_name() ) )
if not init_str.split (None, 2)[2].isdigit():
-@@ -360,7 +361,7 @@
+@@ -350,7 +351,7 @@
f_file.write ('\n\n! Initialize the arrays')
# And the vector initializations
@@ -402,7 +370,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
f_file.write (adios.fortranFormatter.get_initialization (v, params.get_group (g.get_name() ) ) )
-@@ -545,7 +546,7 @@
+@@ -535,7 +536,7 @@
# same program var (as is done by genarray)
c_file.write ('\n\n// Scalar declarations')
declarations = set()
@@ -411,7 +379,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
declarations.add (adios.cFormatter.get_declaration (v, params.get_group (g.get_name() ) ) )
for d in declarations:
-@@ -553,7 +554,7 @@
+@@ -543,7 +544,7 @@
c_file.write ('\n\n// Array declarations')
declarations = set()
@@ -420,7 +388,7 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
declarations.add (adios.cFormatter.get_declaration (v, params.get_group (g.get_name() ) ) )
for d in declarations:
-@@ -630,7 +631,7 @@
+@@ -620,7 +621,7 @@
# free the array memory
c_file.write ('\n\n// Free the arrays')
frees = set()
@@ -429,10 +397,10 @@ Index: adios-1.5.0/utils/skel/lib/skel_source.py
frees.add ('\nfree (' + v.get_gwrite() + ');')
for f in frees:
-Index: adios-1.5.0/utils/skel/lib/skel_submit.py
+Index: adios-1.6.0/utils/skel/lib/skel_submit.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_submit.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_submit.py 2013-12-09 19:59:56.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_submit.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skel_submit.py 2014-02-17 09:37:08.575116968 +0000
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -440,31 +408,31 @@ Index: adios-1.5.0/utils/skel/lib/skel_submit.py
import argparse
import os
-Index: adios-1.5.0/utils/skel/lib/skel_xml.py
+Index: adios-1.6.0/utils/skel/lib/skel_xml.py
===================================================================
---- adios-1.5.0.orig/utils/skel/lib/skel_xml.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/utils/skel/lib/skel_xml.py 2013-12-09 19:59:56.000000000 +0000
+--- adios-1.6.0.orig/utils/skel/lib/skel_xml.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/utils/skel/lib/skel_xml.py 2014-02-17 09:37:08.575116968 +0000
@@ -1,5 +1,6 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
import argparse
+ import os
import xml.dom.minidom
-
-Index: adios-1.5.0/wrappers/numpy/example/ncdf2bp.py
+Index: adios-1.6.0/wrappers/numpy/example/ncdf2bp.py
===================================================================
---- adios-1.5.0.orig/wrappers/numpy/example/ncdf2bp.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/wrappers/numpy/example/ncdf2bp.py 2013-12-09 19:59:56.000000000 +0000
+--- adios-1.6.0.orig/wrappers/numpy/example/ncdf2bp.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/wrappers/numpy/example/ncdf2bp.py 2014-02-17 09:37:08.575116968 +0000
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
from adios import *
from scipy.io import netcdf
import numpy as np
-Index: adios-1.5.0/wrappers/numpy/test/adios_noxml_test.py
+Index: adios-1.6.0/wrappers/numpy/test/adios_noxml_test.py
===================================================================
---- adios-1.5.0.orig/wrappers/numpy/test/adios_noxml_test.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/wrappers/numpy/test/adios_noxml_test.py 2013-12-09 19:59:57.000000000 +0000
+--- adios-1.6.0.orig/wrappers/numpy/test/adios_noxml_test.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/wrappers/numpy/test/adios_noxml_test.py 2014-02-17 09:37:08.579115520 +0000
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
@@ -480,10 +448,10 @@ Index: adios-1.5.0/wrappers/numpy/test/adios_noxml_test.py
set_group_size(fd, groupsize)
write_int(fd, "NX", NX)
write_int(fd, "size", size)
-Index: adios-1.5.0/wrappers/numpy/test/adios_read_test.py
+Index: adios-1.6.0/wrappers/numpy/test/adios_read_test.py
===================================================================
---- adios-1.5.0.orig/wrappers/numpy/test/adios_read_test.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/wrappers/numpy/test/adios_read_test.py 2013-12-09 19:59:57.000000000 +0000
+--- adios-1.6.0.orig/wrappers/numpy/test/adios_read_test.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/wrappers/numpy/test/adios_read_test.py 2014-02-17 09:37:08.579115520 +0000
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+
@@ -498,10 +466,10 @@ Index: adios-1.5.0/wrappers/numpy/test/adios_read_test.py
+print(v.read())
f.close()
-Index: adios-1.5.0/wrappers/numpy/test/adios_write_test.py
+Index: adios-1.6.0/wrappers/numpy/test/adios_write_test.py
===================================================================
---- adios-1.5.0.orig/wrappers/numpy/test/adios_write_test.py 2013-12-09 19:59:57.000000000 +0000
-+++ adios-1.5.0/wrappers/numpy/test/adios_write_test.py 2013-12-09 19:59:57.000000000 +0000
+--- adios-1.6.0.orig/wrappers/numpy/test/adios_write_test.py 2014-02-17 09:37:08.583114078 +0000
++++ adios-1.6.0/wrappers/numpy/test/adios_write_test.py 2014-02-17 09:37:08.579115520 +0000
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
diff --git a/debian/patches/security.patch b/debian/patches/security.patch
index df00613..198b032 100644
--- a/debian/patches/security.patch
+++ b/debian/patches/security.patch
@@ -1,8 +1,8 @@
-Index: adios.git/utils/bpls/bpls.c
+Index: adios-1.6.0/utils/bpls/bpls.c
===================================================================
---- adios.git.orig/utils/bpls/bpls.c 2013-12-09 18:45:05.000000000 +0000
-+++ adios.git/utils/bpls/bpls.c 2013-12-09 18:45:04.000000000 +0000
-@@ -374,7 +374,7 @@
+--- adios-1.6.0.orig/utils/bpls/bpls.c 2014-02-17 09:37:03.277019645 +0000
++++ adios-1.6.0/utils/bpls/bpls.c 2014-02-17 09:37:03.273021079 +0000
+@@ -388,7 +388,7 @@
#define PRINT_DIMS(str, v, n, loopvar) printf("%s = { ", str); \
@@ -11,7 +11,7 @@ Index: adios.git/utils/bpls/bpls.c
printf("}")
void printSettings(void) {
-@@ -850,7 +850,7 @@
+@@ -1026,7 +1026,7 @@
strcat(xtics, ")\n");
fprintf(out_plot, "start = -0.5\npos(x) = start + x * 1\nset boxwidth 1\nset style fill solid border 5#5lt6#6\n");
@@ -20,7 +20,7 @@ Index: adios.git/utils/bpls/bpls.c
fprintf(out_plot, "plot '%s' using 3 smooth frequency w boxes\n", hist_file);
fprintf(out_plot, "pause -1 'Press Enter to quit'\n");
}
-@@ -1425,7 +1425,7 @@
+@@ -1605,7 +1605,7 @@
case adios_long_double:
//fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
@@ -29,7 +29,7 @@ Index: adios.git/utils/bpls/bpls.c
break;
// TO DO
-@@ -1493,7 +1493,7 @@
+@@ -1673,7 +1673,7 @@
case adios_long_double:
//fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
--
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