Commit a68b7745 authored by Nicholas Breen's avatar Nicholas Breen

fix experimental->unstable merge issues

parent 44dc8ae3
......@@ -11,15 +11,17 @@ Build-Depends: cmake,
liblapack-dev,
libmpich-dev (>= 3.0.4-6),
libopenmpi-dev (>= 1.10.2-7),
libtinyxml-dev,
libx11-dev,
libxml2-dev,
zlib1g-dev
Build-Depends-Indep: doxygen,
ghostscript,
graphviz,
imagemagick,
mscgen,
python-sphinx,
python-sphinx (>= 1.4),
rdfind,
symlinks,
texlive-fonts-recommended,
texlive-latex-base,
texlive-latex-extra
......@@ -66,7 +68,7 @@ Description: GROMACS molecular dynamics sim, data and documentation
This package contains architecture-independent topology and force field
data, documentation, man pages, and example files.
Package: libgromacs1
Package: libgromacs2
Architecture: any
Section: libs
Depends: ${misc:Depends}, ${shlibs:Depends}
......@@ -88,7 +90,7 @@ Package: libgromacs-dev
Architecture: any
Section: libdevel
Depends: fftw3-dev,
libgromacs1 (= ${binary:Version}),
libgromacs2 (= ${binary:Version}),
${misc:Depends},
${shlibs:Depends}
Recommends: gromacs-data
......
usr/share/doc/gromacs
usr/share/doc/gromacs-data
usr/share/doc/libgromacs-dev
usr/share/doc/libgromacs1
usr/share/doc/libgromacs2
usr/share/gromacs
usr/share/gromacs/shell-specific
......@@ -11,4 +11,4 @@ Index: /usr/share/doc/gromacs/html/index.html
Files: /usr/share/doc/gromacs/html/*.html /usr/share/doc/gromacs/html/user-guide/*.html
Format: PDF
Files: /usr/share/doc/gromacs/html/manual-5.1.3.pdf
Files: /usr/share/doc/gromacs/html/manual*.pdf
no-symbols-control-file
# Adaptive Resolution Molecular Dynamics Simulation
spelling-error-in-binary usr/lib/*/libgromacs.so.* AdResS Address
spelling-error-in-binary usr/lib/*/libgromacs_d.so.* AdResS Address
......@@ -6,11 +6,11 @@ Origin: vendor
Forwarded: not-needed
Last-Update: 2015-09-26
---
Index: gromacs-5.1.3/CMakeLists.txt
Index: gromacs-2016~rc1/CMakeLists.txt
===================================================================
--- gromacs-5.1.3.orig/CMakeLists.txt
+++ gromacs-5.1.3/CMakeLists.txt
@@ -89,6 +89,9 @@ set(build_types_with_explicit_flags RELE
--- gromacs-2016~rc1.orig/CMakeLists.txt
+++ gromacs-2016~rc1/CMakeLists.txt
@@ -90,6 +90,9 @@ set(build_types_with_explicit_flags RELE
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
......@@ -20,12 +20,12 @@ Index: gromacs-5.1.3/CMakeLists.txt
# Set a default valgrind suppression file.
# This unfortunately needs to duplicate information from CTest to work as
# expected...
@@ -847,7 +850,7 @@ endif()
@@ -868,7 +871,7 @@ endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
-install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
+install(FILES DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
if(GMX_EXTERNAL_BOOST)
include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
if (GMX_BUILD_FOR_COVERAGE)
# Code heavy with asserts makes conditional coverage close to useless metric,
Description: Fix documentation FTBFS with doxygen >= 1.8.11
Author: Nicholas Breen
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=815678
Last-Update: Sun, 28 Feb 2016 10:54:59 -0800
Last-Update: Mon, 06 Jun 2016 08:22:42 -0700
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-5.1.2/docs/doxygen/gmxtree.py
Index: gromacs-2016~beta2/docs/doxygen/gmxtree.py
===================================================================
--- gromacs-5.1.2.orig/docs/doxygen/gmxtree.py
+++ gromacs-5.1.2/docs/doxygen/gmxtree.py
@@ -863,7 +863,7 @@ class GromacsTree(object):
"""Load Doxygen XML directory information for a single directory."""
path = dirdoc.get_path().rstrip('/')
if not os.path.isabs(path):
- self._reporter.xml_assert(dirdoc.get_xml_path(),
+ self._reporter.xml_assert(dirdoc._get_xml_path(),
"expected absolute path in Doxygen-produced XML file")
return
relpath = self._get_rel_path(path)
@@ -898,7 +898,7 @@ class GromacsTree(object):
# the path information is not set for unloaded files.
continue
if not os.path.isabs(path):
- self._reporter.xml_assert(filedoc.get_xml_path(),
+ self._reporter.xml_assert(filedoc._get_xml_path(),
"expected absolute path in Doxygen-produced XML file")
continue
extension = os.path.splitext(path)[1]
@@ -908,7 +908,7 @@ class GromacsTree(object):
--- gromacs-2016~beta2.orig/docs/doxygen/gmxtree.py
+++ gromacs-2016~beta2/docs/doxygen/gmxtree.py
@@ -912,7 +912,7 @@ class GromacsTree(object):
continue
dirdoc = filedoc.get_directory()
if not dirdoc:
......
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