[adios] 144/207: refresh patches for 1.7.0
Alastair McKinstry
mckinstry at moszumanska.debian.org
Fri Jun 12 06:04:51 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 1a6372b9370e6900179fe5d1f10269f97398d101
Author: Alastair McKinstry <mckinstry at debian.org>
Date: Sat Jun 14 15:04:18 2014 +0100
refresh patches for 1.7.0
---
debian/patches/mpi4py_fix.patch | 16 +-
debian/patches/netcdf-fix.patch | 10 +-
debian/patches/pkgconfig.patch | 24 +--
debian/patches/python3.patch | 337 ++++++++++++++++++++++++++--------------
debian/patches/security.patch | 52 +------
5 files changed, 252 insertions(+), 187 deletions(-)
diff --git a/debian/patches/mpi4py_fix.patch b/debian/patches/mpi4py_fix.patch
index 58a5663..16794fd 100644
--- a/debian/patches/mpi4py_fix.patch
+++ b/debian/patches/mpi4py_fix.patch
@@ -3,23 +3,23 @@ Description: Fix for missing MPI_Message in MPI < 3
Last-Updated: 2014-05-19
Forwarded: no
-Index: adios-1.6.0/wrappers/numpy/adios.pyx
+Index: adios-1.7.0/wrappers/numpy/adios.pyx
===================================================================
---- adios-1.6.0.orig/wrappers/numpy/adios.pyx
-+++ adios-1.6.0/wrappers/numpy/adios.pyx
-@@ -11,6 +11,8 @@ cimport numpy as np
- import mpi4py.MPI as MPI
- cimport mpi4py.MPI as MPI
+--- adios-1.7.0.orig/wrappers/numpy/adios.pyx
++++ adios-1.7.0/wrappers/numpy/adios.pyx
+@@ -17,6 +17,8 @@ cimport numpy as np
+ ##import mpi4py.MPI as MPI
+ ##cimport mpi4py.MPI as MPI
+cdef extern from '../compat.h': pass
+
import cython
cimport cython
-Index: adios-1.6.0/wrappers/numpy/compat.h
+Index: adios-1.7.0/wrappers/numpy/compat.h
===================================================================
--- /dev/null
-+++ adios-1.6.0/wrappers/numpy/compat.h
++++ adios-1.7.0/wrappers/numpy/compat.h
@@ -0,0 +1,9 @@
+/* Added to fix missing MPI_Message in older openmpi on Debian, etc
+ * Added mckinstry at debian.org, 2014-05-19
diff --git a/debian/patches/netcdf-fix.patch b/debian/patches/netcdf-fix.patch
index 0c079a0..60f1082 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-1.6.0/utils/bp2ncd/Makefile.in
+Index: adios-1.7.0/utils/bp2ncd/Makefile.in
===================================================================
---- 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 @@
+--- adios-1.7.0.orig/utils/bp2ncd/Makefile.in
++++ adios-1.7.0/utils/bp2ncd/Makefile.in
+@@ -109,12 +109,12 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCE
ACLOCAL = @ACLOCAL@
ADIOSLIB_CFLAGS = @ADIOSLIB_CFLAGS@
ADIOSLIB_CPPFLAGS = @ADIOSLIB_CPPFLAGS@
@@ -23,7 +23,7 @@ Index: adios-1.6.0/utils/bp2ncd/Makefile.in
ADIOSLIB_LDFLAGS = @ADIOSLIB_LDFLAGS@
ADIOSLIB_SEQ_CFLAGS = @ADIOSLIB_SEQ_CFLAGS@
ADIOSLIB_SEQ_CPPFLAGS = @ADIOSLIB_SEQ_CPPFLAGS@
-@@ -354,7 +354,7 @@
+@@ -367,7 +367,7 @@ bp2ncd_SOURCES = bp2ncd.c
@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/pkgconfig.patch b/debian/patches/pkgconfig.patch
index 0040668..97a8c3e 100644
--- a/debian/patches/pkgconfig.patch
+++ b/debian/patches/pkgconfig.patch
@@ -1,7 +1,7 @@
-Index: adios-1.6.0/adios.pc.in
+Index: adios-1.7.0/adios.pc.in
===================================================================
--- /dev/null
-+++ adios-1.6.0/adios.pc.in
++++ adios-1.7.0/adios.pc.in
@@ -0,0 +1,56 @@
+# Standard defines for pkg-config
+prefix=@prefix@
@@ -59,11 +59,11 @@ Index: adios-1.6.0/adios.pc.in
+Cflags: -pthread
+
+
-Index: adios-1.6.0/configure.ac
+Index: adios-1.7.0/configure.ac
===================================================================
---- adios-1.6.0.orig/configure.ac
-+++ adios-1.6.0/configure.ac
-@@ -694,6 +694,7 @@ AC_CONFIG_FILES([Makefile
+--- adios-1.7.0.orig/configure.ac
++++ adios-1.7.0/configure.ac
+@@ -747,6 +747,7 @@ AC_CONFIG_FILES([Makefile
examples/Fortran/global-array/Makefile
examples/Fortran/global-array-time/Makefile
adios_config.flags
@@ -71,11 +71,11 @@ Index: adios-1.6.0/configure.ac
])
AC_OUTPUT
-Index: adios-1.6.0/Makefile.in
+Index: adios-1.7.0/Makefile.in
===================================================================
---- adios-1.6.0.orig/Makefile.in
-+++ adios-1.6.0/Makefile.in
-@@ -83,7 +83,7 @@ am__CONFIG_DISTCLEAN_FILES = config.stat
+--- adios-1.7.0.orig/Makefile.in
++++ adios-1.7.0/Makefile.in
+@@ -87,7 +87,7 @@ am__CONFIG_DISTCLEAN_FILES = config.stat
mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES = utils/skel/lib/skel_have_adios_timing.py \
@@ -84,11 +84,11 @@ Index: adios-1.6.0/Makefile.in
CONFIG_CLEAN_VPATH_FILES =
am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
am__vpath_adj = case $$p in \
-@@ -404,6 +404,7 @@ SUBDIRS = src utils tests examples
+@@ -419,6 +419,7 @@ SUBDIRS = src utils tests examples
EXTRA_DIST = runconf \
KNOWN_BUGS \
adios_config \
+ adios.pc \
scripts/create.nssi.config.sh \
scripts/kill.nssi.staging.sh \
- scripts/start.nssi.staging.sh
+ scripts/start.nssi.staging.sh \
diff --git a/debian/patches/python3.patch b/debian/patches/python3.patch
index 22866db..b863456 100644
--- a/debian/patches/python3.patch
+++ b/debian/patches/python3.patch
@@ -1,12 +1,12 @@
Author: Alastair McKinstry <mckinstry at debian.org>
Description: Make the python code python2-3 agnostic.
-Last-Updated:2013-12-09
+Last-Updated:2014-06-14
Forwarded: no
-Index: adios-1.6.0/utils/skel/bin/skel
+Index: adios-1.7.0/utils/skel/bin/skel
===================================================================
---- adios-1.6.0.orig/utils/skel/bin/skel
-+++ adios-1.6.0/utils/skel/bin/skel
+--- adios-1.7.0.orig/utils/skel/bin/skel
++++ adios-1.7.0/utils/skel/bin/skel
@@ -1,5 +1,7 @@
#!/usr/bin/env python
@@ -15,16 +15,7 @@ Index: adios-1.6.0/utils/skel/bin/skel
import sys
import os.path
-@@ -81,7 +83,7 @@ def main(argv=None):
- try:
- config = adios.adiosConfig (args.project + '_skel.xml')
- except (IOError):
-- print "Error reading " + args.project + "_skel.xml. Try running skel xml " + args.project + " first."
-+ print( "Error reading " + args.project + "_skel.xml. Try running skel xml " + args.project + " first.")/
- return 1
-
- if args.subcommand == 'params':
-@@ -114,7 +116,7 @@ def main(argv=None):
+@@ -154,7 +156,7 @@ def main(argv=None):
skel_submit.generate_submit_scripts_with_args (parser)
return 0
@@ -33,10 +24,10 @@ Index: adios-1.6.0/utils/skel/bin/skel
if __name__ == "__main__":
-Index: adios-1.6.0/utils/skel/bin/skel_extract.py
+Index: adios-1.7.0/utils/skel/bin/skel_extract.py
===================================================================
---- adios-1.6.0.orig/utils/skel/bin/skel_extract.py
-+++ adios-1.6.0/utils/skel/bin/skel_extract.py
+--- adios-1.7.0.orig/utils/skel/bin/skel_extract.py
++++ adios-1.7.0/utils/skel/bin/skel_extract.py
@@ -1,5 +1,6 @@
#!/usr/bin/env python
@@ -69,10 +60,10 @@ Index: adios-1.6.0/utils/skel/bin/skel_extract.py
return iteration
-Index: adios-1.6.0/utils/skel/lib/skelconf.py
+Index: adios-1.7.0/utils/skel/lib/skelconf.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skelconf.py
-+++ adios-1.6.0/utils/skel/lib/skelconf.py
+--- adios-1.7.0.orig/utils/skel/lib/skelconf.py
++++ adios-1.7.0/utils/skel/lib/skelconf.py
@@ -1,5 +1,5 @@
+from __future__ import absolute_import, division, print_function, unicode_literals
import xml.dom.minidom
@@ -89,10 +80,10 @@ Index: adios-1.6.0/utils/skel/lib/skelconf.py
raise SystemExit
self.config_node = nodes[0]
-Index: adios-1.6.0/utils/gpp/ad_config.py
+Index: adios-1.7.0/utils/gpp/ad_config.py
===================================================================
---- adios-1.6.0.orig/utils/gpp/ad_config.py
-+++ adios-1.6.0/utils/gpp/ad_config.py
+--- adios-1.7.0.orig/utils/gpp/ad_config.py
++++ adios-1.7.0/utils/gpp/ad_config.py
@@ -1,3 +1,4 @@
+from __future__ import absolute_import, division, print_function, unicode_literals
import xml.dom.minidom
@@ -125,10 +116,10 @@ Index: adios-1.6.0/utils/gpp/ad_config.py
cleandims = []
#print ' get_dimensions of var '+self.get_fullpath()
for d in dims:
-Index: adios-1.6.0/utils/gpp/gpp.py
+Index: adios-1.7.0/utils/gpp/gpp.py
===================================================================
---- adios-1.6.0.orig/utils/gpp/gpp.py
-+++ adios-1.6.0/utils/gpp/gpp.py
+--- adios-1.7.0.orig/utils/gpp/gpp.py
++++ adios-1.7.0/utils/gpp/gpp.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -167,10 +158,10 @@ Index: adios-1.6.0/utils/gpp/gpp.py
raise SystemExit
-Index: adios-1.6.0/utils/skel/lib/adios.py
+Index: adios-1.7.0/utils/skel/lib/adios.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/adios.py
-+++ adios-1.6.0/utils/skel/lib/adios.py
+--- adios-1.7.0.orig/utils/skel/lib/adios.py
++++ adios-1.7.0/utils/skel/lib/adios.py
@@ -1,5 +1,5 @@
+from __future__ import print_function
import xml.dom.minidom
@@ -205,10 +196,10 @@ Index: adios-1.6.0/utils/skel/lib/adios.py
cleandims = []
for d in dims:
-Index: adios-1.6.0/utils/skel/lib/argparse.py
+Index: adios-1.7.0/utils/skel/lib/argparse.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/argparse.py
-+++ adios-1.6.0/utils/skel/lib/argparse.py
+--- adios-1.7.0.orig/utils/skel/lib/argparse.py
++++ adios-1.7.0/utils/skel/lib/argparse.py
@@ -81,7 +81,6 @@ __all__ = [
'ZERO_OR_MORE',
]
@@ -217,10 +208,10 @@ Index: adios-1.6.0/utils/skel/lib/argparse.py
import copy as _copy
import os as _os
import re as _re
-Index: adios-1.6.0/utils/skel/lib/skel_install.py
+Index: adios-1.7.0/utils/skel/lib/skel_install.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skel_install.py
-+++ adios-1.6.0/utils/skel/lib/skel_install.py
+--- adios-1.7.0.orig/utils/skel/lib/skel_install.py
++++ adios-1.7.0/utils/skel/lib/skel_install.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -228,10 +219,10 @@ Index: adios-1.6.0/utils/skel/lib/skel_install.py
import skel_settings
def main(argv=None):
-Index: adios-1.6.0/utils/skel/lib/skel_makefile.py
+Index: adios-1.7.0/utils/skel/lib/skel_makefile.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skel_makefile.py
-+++ adios-1.6.0/utils/skel/lib/skel_makefile.py
+--- adios-1.7.0.orig/utils/skel/lib/skel_makefile.py
++++ adios-1.7.0/utils/skel/lib/skel_makefile.py
@@ -1,5 +1,7 @@
#!/usr/bin/env python
@@ -240,7 +231,7 @@ Index: adios-1.6.0/utils/skel/lib/skel_makefile.py
import argparse
import os
import sys
-@@ -190,10 +192,10 @@ def main(argv=None):
+@@ -201,10 +203,10 @@ def main(argv=None):
lang = config.get_host_language ()
if 'c' == lang or 'C' == lang:
@@ -253,17 +244,17 @@ Index: adios-1.6.0/utils/skel/lib/skel_makefile.py
generate_makefiles_fortran (params)
-Index: adios-1.6.0/utils/skel/lib/skel_params.py
+Index: adios-1.7.0/utils/skel/lib/skel_params.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skel_params.py
-+++ adios-1.6.0/utils/skel/lib/skel_params.py
+--- adios-1.7.0.orig/utils/skel/lib/skel_params.py
++++ adios-1.7.0/utils/skel/lib/skel_params.py
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
import sys
import os
import argparse
-@@ -35,7 +36,7 @@ def generate_param_file_with_args (confi
+@@ -43,7 +44,7 @@ def generate_param_file_with_args (paren
# Only proceed if outfilename does not already exist, or if -f was used
if os.path.exists (outfilename) and not args.force:
@@ -271,8 +262,8 @@ Index: adios-1.6.0/utils/skel/lib/skel_params.py
+ print( "%s exists, aborting. Delete the file or use -f to overwrite." % outfilename)
return 999
- generate_param_file (args.project, outfilename, config, args.group, args.bpls)
-@@ -46,7 +47,7 @@ def generate_param_file (app, outfile, c
+ try:
+@@ -60,7 +61,7 @@ def generate_param_file (app, outfile, c
param_file = open (outfile, 'w')
if bplsfile is not None:
@@ -281,7 +272,7 @@ Index: adios-1.6.0/utils/skel/lib/skel_params.py
bpdata = skel_bpls.bpls (open (bplsfile, 'r') )
#Write the file header
-@@ -148,7 +149,7 @@ def main(argv=None):
+@@ -164,7 +165,7 @@ def main(argv=None):
# Only proceed if outfilename does not already exist.
if os.path.exists (outfilename):
@@ -290,10 +281,10 @@ Index: adios-1.6.0/utils/skel/lib/skel_params.py
return 999
generate_param_file (args.project, outfilename, config, args.group)
-Index: adios-1.6.0/utils/skel/lib/skel_settings.py
+Index: adios-1.7.0/utils/skel/lib/skel_settings.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skel_settings.py
-+++ adios-1.6.0/utils/skel/lib/skel_settings.py
+--- adios-1.7.0.orig/utils/skel/lib/skel_settings.py
++++ adios-1.7.0/utils/skel/lib/skel_settings.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -321,10 +312,10 @@ Index: adios-1.6.0/utils/skel/lib/skel_settings.py
def main(argv=None):
-Index: adios-1.6.0/utils/skel/lib/skel_source.py
+Index: adios-1.7.0/utils/skel/lib/skel_source.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skel_source.py
-+++ adios-1.6.0/utils/skel/lib/skel_source.py
+--- adios-1.7.0.orig/utils/skel/lib/skel_source.py
++++ adios-1.7.0/utils/skel/lib/skel_source.py
@@ -1,4 +1,5 @@
#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, unicode_literals
@@ -440,10 +431,10 @@ Index: adios-1.6.0/utils/skel/lib/skel_source.py
frees.add ('\nfree (' + v.get_gwrite() + ');')
for f in frees:
-Index: adios-1.6.0/utils/skel/lib/skel_submit.py
+Index: adios-1.7.0/utils/skel/lib/skel_submit.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skel_submit.py
-+++ adios-1.6.0/utils/skel/lib/skel_submit.py
+--- adios-1.7.0.orig/utils/skel/lib/skel_submit.py
++++ adios-1.7.0/utils/skel/lib/skel_submit.py
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-
@@ -460,7 +451,7 @@ Index: adios-1.6.0/utils/skel/lib/skel_submit.py
return 999
skel_file = open (outfilename, 'w')
-@@ -157,8 +157,8 @@ def generate_submit_scripts_with_args (p
+@@ -164,8 +164,8 @@ def generate_submit_scripts_with_args (p
try:
params = skelconf.skelConfig (args.project + '_params.xml')
except (IOError):
@@ -471,10 +462,10 @@ Index: adios-1.6.0/utils/skel/lib/skel_submit.py
return 1
generate_submit_scripts_from_xml (params)
-Index: adios-1.6.0/utils/skel/lib/skel_xml.py
+Index: adios-1.7.0/utils/skel/lib/skel_xml.py
===================================================================
---- adios-1.6.0.orig/utils/skel/lib/skel_xml.py
-+++ adios-1.6.0/utils/skel/lib/skel_xml.py
+--- adios-1.7.0.orig/utils/skel/lib/skel_xml.py
++++ adios-1.7.0/utils/skel/lib/skel_xml.py
@@ -1,5 +1,6 @@
#!/usr/bin/env python
@@ -482,7 +473,7 @@ Index: adios-1.6.0/utils/skel/lib/skel_xml.py
import argparse
import os
import xml.dom.minidom
-@@ -67,7 +68,7 @@ def create_from_yaml (project,args):
+@@ -68,7 +69,7 @@ def create_from_yaml (project,args):
# Only proceed if outfilename does not already exist, or if -f was used
if os.path.exists (outfilename) and not args.force:
@@ -491,7 +482,7 @@ Index: adios-1.6.0/utils/skel/lib/skel_xml.py
return 999
skel_file = open (outfilename, 'w')
-@@ -90,7 +91,7 @@ def create_from_xml (project, args):
+@@ -91,7 +92,7 @@ def create_from_xml (project, args):
# Only proceed if outfilename does not already exist, or if -f was used
if os.path.exists (outfilename) and not args.force:
@@ -500,69 +491,183 @@ Index: adios-1.6.0/utils/skel/lib/skel_xml.py
return 999
skel_file = open (outfilename, 'w')
-Index: adios-1.6.0/wrappers/numpy/example/ncdf2bp.py
-===================================================================
---- adios-1.6.0.orig/wrappers/numpy/example/ncdf2bp.py
-+++ adios-1.6.0/wrappers/numpy/example/ncdf2bp.py
-@@ -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-1.6.0/wrappers/numpy/test/adios_noxml_test.py
+Index: adios-1.7.0/wrappers/numpy/tests/test_adios.py
===================================================================
---- adios-1.6.0.orig/wrappers/numpy/test/adios_noxml_test.py
-+++ adios-1.6.0/wrappers/numpy/test/adios_noxml_test.py
-@@ -1,4 +1,5 @@
- #!/usr/bin/env python
-+from __future__ import absolute_import, division, print_function, unicode_literals
- from adios import *
- import numpy as np
+--- adios-1.7.0.orig/wrappers/numpy/tests/test_adios.py
++++ adios-1.7.0/wrappers/numpy/tests/test_adios.py
+@@ -5,11 +5,12 @@ Example:
+ $ python ./test_adios.py
+ """
-@@ -17,7 +18,7 @@ NX = 10
- size = 1
- rank = 0
- groupsize = 4 + 4 + 4 + 8 * 1 * NX
--t = np.array(range(NX), dtype=np.float64)
-+t = np.array(list(range(NX)), dtype=np.float64)
- set_group_size(fd, groupsize)
- write_int(fd, "NX", NX)
- write_int(fd, "size", size)
-Index: adios-1.6.0/wrappers/numpy/test/adios_read_test.py
-===================================================================
---- adios-1.6.0.orig/wrappers/numpy/test/adios_read_test.py
-+++ adios-1.6.0/wrappers/numpy/test/adios_read_test.py
-@@ -1,4 +1,5 @@
- #!/usr/bin/env python
-+
- from adios import *
++from __future__ import print_function
+ import adios as ad
import numpy as np
-@@ -9,6 +10,6 @@ g.printself()
- v = g.var["/temperature"]
+ ## Writing
+-print "\n>>> Writing ...\n"
++print( "\n>>> Writing ...\n")
+
+ ad.init("config.xml")
+ fd = ad.open("temperature", "adios_test.bp", "w")
+@@ -17,7 +18,7 @@ fd = ad.open("temperature", "adios_test.
+ NX = 10
+ size = 2
+ groupsize = 4 + 4 + 8 * size * NX
+-t = np.array(range(NX*size), dtype=np.float64)
++t = np.array(list(range(NX*size)), dtype=np.float64)
+ tt = t.reshape((size, NX))
+ ad.set_group_size(fd, groupsize)
+ ad.write_int(fd, "NX", NX)
+@@ -28,7 +29,7 @@ ad.close(fd)
+ ad.finalize()
+
+ ## Reading
+-print "\n>>> Reading ...\n"
++print( "\n>>> Reading ...\n")
+
+ f = ad.file("adios_test.bp")
+ f.printself()
+@@ -37,15 +38,15 @@ v = f.var['temperature']
v.printself()
--print v.read()
-+print(v.read())
-
+ val = v.read()
+-print val
++print(val)
+ assert ((tt == val).all())
f.close()
-Index: adios-1.6.0/wrappers/numpy/test/adios_write_test.py
+
+ ## Testing
+-print "\n>>> Test utility functions ...\n"
++print("\n>>> Test utility functions ...\n")
+
+-print "bpls:\n", ad.bpls('adios_test.bp')
+-print "readvar:\n", ad.readvar("adios_test.bp", "temperature")
++print ("bpls:\n", ad.bpls('adios_test.bp'))
++print("readvar:\n", ad.readvar("adios_test.bp", "temperature"))
+
+-print "\n>>> Done.\n"
++print("\n>>> Done.\n")
+
+Index: adios-1.7.0/wrappers/numpy/tests/test_adios_mpi.py
===================================================================
---- adios-1.6.0.orig/wrappers/numpy/test/adios_write_test.py
-+++ adios-1.6.0/wrappers/numpy/test/adios_write_test.py
-@@ -1,4 +1,5 @@
- #!/usr/bin/env python
-+from __future__ import absolute_import, division, print_function, unicode_literals
- import adios
+--- adios-1.7.0.orig/wrappers/numpy/tests/test_adios_mpi.py
++++ adios-1.7.0/wrappers/numpy/tests/test_adios_mpi.py
+@@ -4,7 +4,7 @@ Example:
+
+ $ mpiexec -n 4 python ./test_adios_mpi.py
+ """
+-
++from __future__ import print_function
+ import adios_mpi as ad
import numpy as np
+ from mpi4py import MPI
+@@ -15,14 +15,14 @@ rank = comm.Get_rank()
+ size = comm.Get_size()
-@@ -9,7 +10,7 @@ NX = 10
- size = 1
- rank = 0
+ ## Writing
+-print "\n>>> Writing ... (rank = %d)\n" % rank
++print ("\n>>> Writing ... (rank = %d)\n" % rank)
+
+ ad.init("config_mpi.xml", comm)
+ fd = ad.open("temperature", "adios_test_mpi.bp", "w", comm)
+
+ NX = 10
groupsize = 4 + 4 + 4 + 8 * 1 * NX
--t = np.array(range(NX), dtype=np.float64)
-+t = np.array(list(range(NXi)), dtype=np.float64)
- adios.set_group_size(fd, groupsize)
- adios.write_int(fd, "NX", NX)
- adios.write_int(fd, "size", size)
+-t = np.array(range(NX), dtype=np.float64) + rank*NX
++t = np.array(list(range(NX)), dtype=np.float64) + rank*NX
+ ad.set_group_size(fd, groupsize)
+ ad.write_int(fd, "NX", NX)
+ ad.write_int(fd, "rank", rank)
+@@ -34,7 +34,7 @@ ad.finalize()
+
+ ## Reading
+ if rank == 0:
+- print "\n>>> Reading ...\n"
++ print( "\n>>> Reading ...\n")
+
+ f = ad.file("adios_test_mpi.bp", comm=MPI.COMM_SELF)
+ f.printself()
+@@ -43,17 +43,17 @@ if rank == 0:
+ v.printself()
+
+ val = v.read()
+- print val
++ print( val)
+ assert (int(sum(sum(val))) == (size*NX-1)*(size*NX)/2)
+ f.close()
+
+-print "\n>>> Done.\n"
++print( "\n>>> Done.\n")
+
+ ## Testing
+ if rank == 0:
+- print "\n>>> Test utility functions ...\n"
++ print( "\n>>> Test utility functions ...\n")
+
+- print "bpls:\n", ad.bpls('adios_test_mpi.bp')
+- print "readvar:\n", ad.readvar("adios_test_mpi.bp", "temperature")
++ print( "bpls:\n", ad.bpls('adios_test_mpi.bp'))
++ print( "readvar:\n", ad.readvar("adios_test_mpi.bp", "temperature"))
+
+- print "\n>>> Done.\n"
++ print( "\n>>> Done.\n")
+Index: adios-1.7.0/wrappers/numpy/tests/test_adios_timestep.py
+===================================================================
+--- adios-1.7.0.orig/wrappers/numpy/tests/test_adios_timestep.py
++++ adios-1.7.0/wrappers/numpy/tests/test_adios_timestep.py
+@@ -4,12 +4,12 @@ Example:
+
+ $ python ./test_adios.py
+ """
+-
++from __future__ import print_function
+ import adios as ad
+ import numpy as np
+
+ ## Writing
+-print "\n>>> Writing ...\n"
++print ("\n>>> Writing ...\n")
+
+ ad.init("config.xml")
+
+@@ -22,7 +22,7 @@ for i in range(10):
+ NX = 10
+ size = 2
+ groupsize = 4 + 4 + 8 * size * NX
+- t = np.array(range(NX*size), dtype=np.float64) + i*NX*size
++ t = np.array(list(range(NX*size)), dtype=np.float64) + i*NX*size
+ tt = t.reshape((size, NX))
+ ad.set_group_size(fd, groupsize)
+ ad.write_int(fd, "NX", NX)
+@@ -33,7 +33,7 @@ for i in range(10):
+ ad.finalize()
+
+ ## Reading
+-print "\n>>> Reading step-by-step ...\n"
++print( "\n>>> Reading step-by-step ...\n")
+
+ f = ad.file("adios_test.bp")
+ f.printself()
+@@ -43,16 +43,16 @@ v.printself()
+
+ for i in range(10):
+ val = v.read(from_steps=i)
+- print "step =", i
+- print val
++ print ("step =", i)
++ print( val)
+
+ assert ((tt == val).all())
+
+ ## Testing
+-print "\n>>> Test utility functions ...\n"
++print( "\n>>> Test utility functions ...\n")
+
+-print "bpls:\n", ad.bpls('adios_test.bp')
+-print "readvar:\n", ad.readvar("adios_test.bp", "temperature")
++print("bpls:\n", ad.bpls('adios_test.bp'))
++print("readvar:\n", ad.readvar("adios_test.bp", "temperature"))
+
+-print "\n>>> Done.\n"
++print("\n>>> Done.\n")
+
diff --git a/debian/patches/security.patch b/debian/patches/security.patch
index 69c1db1..5d47f7b 100644
--- a/debian/patches/security.patch
+++ b/debian/patches/security.patch
@@ -1,48 +1,8 @@
-Index: adios-1.6.0/utils/bpls/bpls.c
+Index: adios-1.7.0/utils/skeldump/skeldump.c
===================================================================
---- adios-1.6.0.orig/utils/bpls/bpls.c 2014-02-17 09:42:30.000000000 +0000
-+++ adios-1.6.0/utils/bpls/bpls.c 2014-02-17 09:42:33.000000000 +0000
-@@ -388,7 +388,7 @@
-
-
- #define PRINT_DIMS(str, v, n, loopvar) printf("%s = { ", str); \
-- for (loopvar=0; loopvar<n;loopvar++) printf("%lld ", v[loopvar]); \
-+ for (loopvar=0; loopvar<n;loopvar++) printf("%lld ",(long long int) v[loopvar]); \
- printf("}")
-
- void printSettings(void) {
-@@ -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");
-- fprintf(out_plot, xtics);
-+ fprintf(out_plot, "%s", xtics); /* do it this way to silence false warning from error-security in gcc. sigh. */
- fprintf(out_plot, "plot '%s' using 3 smooth frequency w boxes\n", hist_file);
- fprintf(out_plot, "pause -1 'Press Enter to quit'\n");
- }
-@@ -1605,7 +1605,7 @@
-
- case adios_long_double:
- //fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
-- fprintf(outf,(f ? format : "????????"));
-+ fprintf(outf,"%s",(f ? format : "????????"));
- break;
-
- // TO DO
-@@ -1673,7 +1673,7 @@
-
- case adios_long_double:
- //fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
-- fprintf(outf,(f ? format : "????????"));
-+ fprintf(outf,"%s",(f ? format : "????????"));
- break;
-
-
-Index: adios-1.6.0/utils/skeldump/skeldump.c
-===================================================================
---- adios-1.6.0.orig/utils/skeldump/skeldump.c 2014-02-17 09:42:30.000000000 +0000
-+++ adios-1.6.0/utils/skeldump/skeldump.c 2014-02-17 09:49:39.247429839 +0000
-@@ -919,7 +919,7 @@
+--- adios-1.7.0.orig/utils/skeldump/skeldump.c
++++ adios-1.7.0/utils/skeldump/skeldump.c
+@@ -919,7 +919,7 @@ int print_data_hist(ADIOS_VARINFO * vi,
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");
@@ -51,7 +11,7 @@ Index: adios-1.6.0/utils/skeldump/skeldump.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");
}
-@@ -1498,7 +1498,7 @@
+@@ -1498,7 +1498,7 @@ int print_data_characteristics(void * mi
case adios_long_double:
//fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
@@ -60,7 +20,7 @@ Index: adios-1.6.0/utils/skeldump/skeldump.c
break;
// TO DO
-@@ -1566,7 +1566,7 @@
+@@ -1566,7 +1566,7 @@ int print_data(void *data, int item, enu
case adios_long_double:
//fprintf(outf,(f ? format : "%g "), ((double *) data)[item]);
--
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