Commit 13450026 authored by Nicholas Breen's avatar Nicholas Breen

Roll back to r6294, last unstable upload; subsequent experimental changes already branched off

parent 3cfb3bfc
gromacs (2016~rc1-1) experimental; urgency=medium
* First upstream release candidate.
- Drop patches from beta2-2, incorporated or fixed upstream.
* Switch from building with libxml2 to libtinyxml.
* rules: Convert deprecated debhelper -s flags to -a.
-- Nicholas Breen <nbreen@debian.org> Mon, 11 Jul 2016 18:28:25 -0700
gromacs (2016~beta2-2) experimental; urgency=medium
* Two patches to address test suits failures:
- numerically-unstable-gaussian-test.patch: Backport a fix from git
master branch to address Gaussian test failures on all i386
platforms. (http://redmine.gromacs.org/issues/1986)
- disable-hardware-topology-tests.patch: Two CPU info tests cause hard
failures that should probably just be warnings, so disable those tests
for now. (http://redmine.gromacs.org/issues/1987)
-- Nicholas Breen <nbreen@debian.org> Fri, 17 Jun 2016 06:40:18 -0700
gromacs (2016~beta2-1) experimental; urgency=low
* Beta for major new upstream release. New date-based versioning system.
- SONAME bump: package rename, libgromacs1 -> libgromacs2
- spelling and empty-man7-directory patches incorporated upstream.
- Refresh other patches.
- Versioned Depends: on python-sphinx (>= 1.4) for new imgmath
extension.
* Update Standards-Version to 3.9.8, no changes required.
-- Nicholas Breen <nbreen@debian.org> Tue, 07 Jun 2016 14:20:10 -0700
gromacs (5.1.2-3) experimental; urgency=medium
* Add LD_LIBRARY_PATH overrides to unit tests.
-- Nicholas Breen <nbreen@debian.org> Thu, 21 Apr 2016 17:35:41 -0700
gromacs (5.1.2-2) experimental; urgency=medium
* Run upstream unit tests. Supports DEB_BUILD_OPTIONS=nocheck bypass.
* Use rdfind/symlinks to reduce internal duplication in doxygen output.
* Only build process changes in this upload - uploading to
experimental as a safety.
-- Nicholas Breen <nbreen@debian.org> Mon, 18 Apr 2016 21:04:31 -0700
gromacs (5.1.2-1) unstable; urgency=medium
* New upstream release.
......
......@@ -11,21 +11,19 @@ Build-Depends: cmake,
liblapack-dev,
libmpich-dev (>= 3.0.4-6),
libopenmpi-dev (>= 1.10.2-7) [alpha amd64 arm64 armel armhf hppa hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el s390x sparc sparc64 x32],
libtinyxml-dev,
libx11-dev,
libxml2-dev,
zlib1g-dev
Build-Depends-Indep: doxygen,
ghostscript,
graphviz,
imagemagick,
mscgen,
python-sphinx (>= 1.4),
rdfind,
symlinks,
python-sphinx,
texlive-fonts-recommended,
texlive-latex-base,
texlive-latex-extra
Standards-Version: 3.9.8
Standards-Version: 3.9.7
Homepage: http://www.gromacs.org/
Vcs-Browser: https://anonscm.debian.org/viewvc/debichem/
Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/gromacs/
......@@ -68,7 +66,7 @@ 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: libgromacs2
Package: libgromacs1
Architecture: any
Section: libs
Depends: ${misc:Depends}, ${shlibs:Depends}
......@@ -90,7 +88,7 @@ Package: libgromacs-dev
Architecture: any
Section: libdevel
Depends: fftw3-dev,
libgromacs2 (= ${binary:Version}),
libgromacs1 (= ${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/libgromacs2
usr/share/doc/libgromacs1
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*.pdf
Files: /usr/share/doc/gromacs/html/manual-5.1.2.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-2016~rc1/CMakeLists.txt
Index: gromacs-5.1/CMakeLists.txt
===================================================================
--- gromacs-2016~rc1.orig/CMakeLists.txt
+++ gromacs-2016~rc1/CMakeLists.txt
@@ -90,6 +90,9 @@ set(build_types_with_explicit_flags RELE
--- gromacs-5.1.orig/CMakeLists.txt
+++ gromacs-5.1/CMakeLists.txt
@@ -89,6 +89,9 @@ set(build_types_with_explicit_flags RELE
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
......@@ -20,12 +20,12 @@ Index: gromacs-2016~rc1/CMakeLists.txt
# Set a default valgrind suppression file.
# This unfortunately needs to duplicate information from CTest to work as
# expected...
@@ -868,7 +871,7 @@ endif()
@@ -844,7 +847,7 @@ 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_BUILD_FOR_COVERAGE)
# Code heavy with asserts makes conditional coverage close to useless metric,
if(GMX_EXTERNAL_BOOST)
include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
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: Mon, 06 Jun 2016 08:22:42 -0700
Last-Update: Sun, 28 Feb 2016 10:54:59 -0800
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-2016~beta2/docs/doxygen/gmxtree.py
Index: gromacs-5.1.2/docs/doxygen/gmxtree.py
===================================================================
--- gromacs-2016~beta2.orig/docs/doxygen/gmxtree.py
+++ gromacs-2016~beta2/docs/doxygen/gmxtree.py
@@ -912,7 +912,7 @@ class GromacsTree(object):
--- 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):
continue
dirdoc = filedoc.get_directory()
if not dirdoc:
......
Description: Do not create empty man/man7 directory
Author: Nicholas Breen
Origin: vendor
Last-Update: 2015-09-27
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-5.1/docs/CMakeLists.txt
===================================================================
--- gromacs-5.1.orig/docs/CMakeLists.txt
+++ gromacs-5.1/docs/CMakeLists.txt
@@ -268,10 +268,6 @@ if (MAN_PAGE_DIR)
DESTINATION ${MAN_INSTALL_DIR}/man1
COMPONENT man OPTIONAL
FILES_MATCHING PATTERN "*.1")
- install(DIRECTORY ${MAN_PAGE_DIR}/
- DESTINATION ${MAN_INSTALL_DIR}/man7
- COMPONENT man OPTIONAL
- FILES_MATCHING PATTERN "*.7")
endif()
gmx_cpack_add_generated_source_directory(man)
readme.patch
copyright-file.patch
spelling.patch
empty-man7-directory.patch
reproducible-builds.patch
doxygen.patch
This diff is collapsed.
......@@ -112,10 +112,6 @@ build-basic: configure-stamp
dh_testdir
$(MAKE) -C build/basic
$(MAKE) -C build/basic-dp
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
LD_LIBRARY_PATH=$(CURDIR)/build/basic/lib $(MAKE) -C build/basic check
LD_LIBRARY_PATH=$(CURDIR)/build/basic-dp/lib $(MAKE) -C build/basic-dp check
endif
touch $@
build-manual:
......@@ -128,9 +124,7 @@ build-manual:
# Generate PDF
$(MAKE) manual -C build/documentation
# Generate HTML
# This sometimes seems to work the *second* time? Still trying to trace it down.
$(MAKE) webpage -C build/documentation || \
(echo "===== Failed to build documentation, retrying." ; $(MAKE) webpage -C build/documentation )
$(MAKE) webpage -C build/documentation
build-mpich: configure-stamp
dh_testdir
......@@ -139,10 +133,6 @@ build-mpich: configure-stamp
sed -e 's/#MPIABBR#/mpich/g' -e 's/#MPIPROG#/MPICH2/g' \
< debian/gromacs-parallel.README.Debian.in \
> debian/gromacs-mpich.README.Debian
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
LD_LIBRARY_PATH=$(CURDIR)/build/mpich/lib $(MAKE) -C build/mpich check
LD_LIBRARY_PATH=$(CURDIR)/build/mpich-dp/lib $(MAKE) -C build/mpich-dp check
endif
touch $@
build-openmpi: configure-stamp
......@@ -153,10 +143,6 @@ ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
sed -e 's/#MPIABBR#/openmpi/g' -e 's/#MPIPROG#/OpenMPI/g' \
< debian/gromacs-parallel.README.Debian.in \
> debian/gromacs-openmpi.README.Debian
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
LD_LIBRARY_PATH=$(CURDIR)/build/openmpi/lib $(MAKE) -C build/openmpi check
LD_LIBRARY_PATH=$(CURDIR)/build/openmpi-dp/lib $(MAKE) -C build/openmpi-dp check
endif
endif
touch $@
......@@ -187,15 +173,15 @@ install: build-arch install-basic install-mpich install-openmpi
chmod 644 $(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific/*
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/gromacs-data/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs-dev/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs2/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs1/html
# this name is also given in documentation
dh_link -pgromacs-data usr/share/doc/gromacs-data/copyright usr/share/doc/gromacs-data/COPYING
# rename a pair of Perl scripts to drop the .pl extension (Policy 10.4)
mv $(CURDIR)/debian/gromacs/usr/bin/demux.pl $(CURDIR)/debian/gromacs/usr/bin/demux
mv $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx.pl $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx
mkdir -p $(CURDIR)/debian/libgromacs2/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/*/*.so.* $(CURDIR)/debian/libgromacs2/usr/lib/$(DEB_HOST_MULTIARCH)/
mkdir -p $(CURDIR)/debian/libgromacs1/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/*/*.so.* $(CURDIR)/debian/libgromacs1/usr/lib/$(DEB_HOST_MULTIARCH)/
dh_installdirs -plibgromacs-dev
mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/libgromacs-dev/usr/include
......@@ -211,14 +197,12 @@ install: build-arch install-basic install-mpich install-openmpi
-rmdir $(CURDIR)/debian/gromacs/usr/share/gromacs
# what are you doing here?
mv $(CURDIR)/debian/gromacs/usr/share/cmake $(CURDIR)/debian/libgromacs-dev/usr/share/gromacs/
dh_lintian -pgromacs -pgromacs-data -plibgromacs2
dh_lintian -pgromacs -pgromacs-data -plibgromacs1
install-manual: build-manual install
dh_testdir
dh_testroot
dh_install -pgromacs-data
rdfind -outputname /dev/null -makesymlinks true $(CURDIR)/debian/gromacs-data/usr/share/doc/
symlinks -r -s -c $(CURDIR)/debian/gromacs-data/usr/share/doc/
install-basic: build-arch
dh_testdir
......@@ -273,24 +257,24 @@ binary-indep: build-arch build-indep install install-manual
dh_builddeb -i
binary-arch: build-arch install
dh_testdir -a
dh_testroot -a
dh_installchangelogs -a
dh_installdocs -a
dh_testdir -s
dh_testroot -s
dh_installchangelogs -s
dh_installdocs -s
dh_strip -A
dh_compress -a
dh_fixperms -a
dh_makeshlibs -a
dh_shlibdeps -plibgromacs2 -L libgromacs2 -l debian/libgromacs2/usr/lib
dh_shlibdeps -pgromacs -L libgromacs2 -l debian/libgromacs2/usr/lib:debian/gromacs/usr/lib
dh_compress -s
dh_fixperms -s
dh_makeshlibs -s
dh_shlibdeps -plibgromacs1 -L libgromacs1 -l debian/libgromacs1/usr/lib
dh_shlibdeps -pgromacs -L libgromacs1 -l debian/libgromacs1/usr/lib:debian/gromacs/usr/lib
dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib
endif
dh_gencontrol -a
dh_installdeb -a
dh_md5sums -a
dh_builddeb -a
dh_gencontrol -s
dh_installdeb -s
dh_md5sums -s
dh_builddeb -s
binary: binary-indep binary-arch
......
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