Commit 1da356ff authored by Nicholas Breen's avatar Nicholas Breen

Merge branch 'debian-experimental' of...

Merge branch 'debian-experimental' of https://salsa.debian.org/debichem-team/gromacs into debian-experimental
parents 4f6137d2 2fef251b
gromacs (2019~beta1-1) experimental; urgency=medium
* New upstream beta release, upload to experimental.
- patches/reproducible-builds.patch and sphinx-version-detect.patch
removed, equivalent functionality integrated upstream.
- Other patches rebased.
* Rename libgromacs3 to libgromacs4 for SONAME increment.
-- Nicholas Breen <nbreen@debian.org> Sun, 28 Oct 2018 10:01:40 -0700
gromacs (2018.3-1) unstable; urgency=medium gromacs (2018.3-1) unstable; urgency=medium
* New upstream release. * New upstream release.
......
...@@ -29,7 +29,7 @@ Build-Depends-Indep: doxygen, ...@@ -29,7 +29,7 @@ Build-Depends-Indep: doxygen,
texlive-latex-base, texlive-latex-base,
texlive-latex-extra texlive-latex-extra
Rules-Requires-Root: no Rules-Requires-Root: no
Standards-Version: 4.2.0 Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs Vcs-Browser: https://salsa.debian.org/debichem-team/gromacs
Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git Vcs-Git: https://salsa.debian.org/debichem-team/gromacs.git
Homepage: http://www.gromacs.org/ Homepage: http://www.gromacs.org/
...@@ -73,7 +73,7 @@ Description: GROMACS molecular dynamics sim, data and documentation ...@@ -73,7 +73,7 @@ Description: GROMACS molecular dynamics sim, data and documentation
This package contains architecture-independent topology and force field This package contains architecture-independent topology and force field
data, documentation, man pages, and example files. data, documentation, man pages, and example files.
Package: libgromacs3 Package: libgromacs4
Architecture: any Architecture: any
Multi-Arch: same Multi-Arch: same
Section: libs Section: libs
...@@ -96,11 +96,11 @@ Package: libgromacs-dev ...@@ -96,11 +96,11 @@ Package: libgromacs-dev
Architecture: any Architecture: any
Section: libdevel Section: libdevel
Depends: fftw3-dev, Depends: fftw3-dev,
libgromacs3 (= ${binary:Version}), libgromacs4 (= ${binary:Version}),
${misc:Depends}, ${misc:Depends},
${shlibs:Depends} ${shlibs:Depends}
Recommends: gromacs-data Recommends: gromacs-data
Suggests: gromacs-mpich (= ${binary:Version}) | gromacs-openmpi (= ${binary:Version}) [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], Suggests: gromacs-mpich (= ${binary:Version}) | gromacs-openmpi (= ${binary:Version}),
libmpich-dev, libmpich-dev,
libx11-dev, libx11-dev,
zlib1g-dev zlib1g-dev
......
usr/share/doc/gromacs usr/share/doc/gromacs
usr/share/doc/gromacs-data usr/share/doc/gromacs-data
usr/share/doc/libgromacs-dev usr/share/doc/libgromacs-dev
usr/share/doc/libgromacs3 usr/share/doc/libgromacs4
usr/share/gromacs usr/share/gromacs
usr/share/gromacs/shell-specific usr/share/gromacs/shell-specific
...@@ -2,19 +2,22 @@ Description: Extend timeout for mdrun tests ...@@ -2,19 +2,22 @@ Description: Extend timeout for mdrun tests
Slower architectures, especially those without FPUs, may timeout on the Slower architectures, especially those without FPUs, may timeout on the
mdrun tests - extending the timeout modestly allows them to pass. mdrun tests - extending the timeout modestly allows them to pass.
Origin: vendor Origin: vendor
Last-Update: 2018-03-31 Last-Update: 2018-10-28
--- ---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs/src/testutils/TestMacros.cmake Index: gromacs/src/testutils/TestMacros.cmake
=================================================================== ===================================================================
--- gromacs.orig/src/testutils/TestMacros.cmake --- gromacs.orig/src/testutils/TestMacros.cmake
+++ gromacs/src/testutils/TestMacros.cmake +++ gromacs/src/testutils/TestMacros.cmake
@@ -103,7 +103,7 @@ function (gmx_register_gtest_test NAME E @@ -121,9 +121,9 @@ function (gmx_register_gtest_test NAME E
set(_timeout 30) if (GMX_USE_OPENCL)
if (ARG_INTEGRATION_TEST) set(_timeout 240)
list(APPEND _labels IntegrationTest) elseif (${CMAKE_BUILD_TYPE} STREQUAL TSAN)
- set(_timeout 120) - set(_timeout 300)
+ set(_timeout 600) + set(_timeout 1200)
else()
- set(_timeout 120)
+ set(_timeout 600)
endif()
gmx_get_test_prefix_cmd(_prefix_cmd IGNORE_LEAKS) gmx_get_test_prefix_cmd(_prefix_cmd IGNORE_LEAKS)
else() elseif (ARG_SLOW_TEST)
list(APPEND _labels UnitTest)
Description: Reproducible build modifications
By default, GROMACS embeds build time / host / username information. This
patch replaces those with values compatible with reproducible builds
(https://wiki.debian.org/ReproducibleBuilds).
Author: Nicholas Breen
Forwarded: not-needed
Last-Update: 2016-02-20
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/cmake/gmxSetBuildInformation.cmake
+++ b/cmake/gmxSetBuildInformation.cmake
@@ -53,6 +53,9 @@
include(gmxDetectCpu)
function(gmx_set_build_information)
+ set(BUILD_USER "buildd\@debian [CMAKE]" CACHE INTERNAL "Build user")
+ execute_process( COMMAND "dpkg-parsechangelog -S Date" WORKING_DIRECTORY ../.. OUTPUT_VARIABLE TMP_TIME OUTPUT_STRIP_TRAILING_WHITESPACE)
+ set(BUILD_TIME "${TMP_TIME}" CACHE INTERNAL "Build date & time")
if(NOT BUILD_USER)
if(CMAKE_HOST_UNIX)
execute_process( COMMAND whoami OUTPUT_VARIABLE TMP_USER OUTPUT_STRIP_TRAILING_WHITESPACE)
@@ -73,7 +76,7 @@ function(gmx_set_build_information)
if(NOT BUILD_HOST)
if(CMAKE_HOST_UNIX)
- execute_process( COMMAND uname -srm OUTPUT_VARIABLE TMP_HOST OUTPUT_STRIP_TRAILING_WHITESPACE)
+ execute_process( COMMAND uname -sm OUTPUT_VARIABLE TMP_HOST OUTPUT_STRIP_TRAILING_WHITESPACE)
else()
set(TMP_HOST "${CMAKE_HOST_SYSTEM} ${CMAKE_HOST_SYSTEM_PROCESSOR}")
endif()
readme.patch readme.patch
copyright-file.patch copyright-file.patch
reproducible-builds.patch
doxygen.patch doxygen.patch
disable-cpuinfotest.patch disable-cpuinfotest.patch
hurd-disable-numa-test.patch hurd-disable-numa-test.patch
mdrun-test-timeout.patch mdrun-test-timeout.patch
sphinx-version-detect.patch
Description: Identify newer python-sphinx versions
In recent versions, "sphinx-build --version" changed its output format
and moved from STDOUT to STDERR.
Author: Nicholas Breen <nbreen@debian.org>
Origin: vendor
Last-Update: 2018-04-27
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs/cmake/FindSphinx.cmake
===================================================================
--- gromacs.orig/cmake/FindSphinx.cmake
+++ gromacs/cmake/FindSphinx.cmake
@@ -44,12 +44,13 @@ mark_as_advanced(SPHINX_EXECUTABLE)
if (SPHINX_EXECUTABLE AND NOT DEFINED SPHINX_EXECUTABLE_VERSION)
execute_process(
COMMAND ${SPHINX_EXECUTABLE} --version
+ ERROR_VARIABLE SPHINX_VERSION_OUTPUT_VARIABLE
OUTPUT_VARIABLE SPHINX_VERSION_OUTPUT_VARIABLE
RESULT_VARIABLE SPHINX_VERSION_RESULT_VARIABLE
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE
)
- string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1" SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
+ string(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
set(SPHINX_EXECUTABLE_VERSION "${SPHINX_EXECUTABLE_VERSION}" CACHE INTERNAL "Version of ${SPHINX_EXECUTABLE}")
endif()
...@@ -217,15 +217,15 @@ install: build-arch install-basic install-mpich install-openmpi ...@@ -217,15 +217,15 @@ install: build-arch install-basic install-mpich install-openmpi
chmod 644 $(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific/* 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/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/libgromacs-dev/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs3/html dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs4/html
# this name is also given in documentation # this name is also given in documentation
dh_link -pgromacs-data usr/share/doc/gromacs-data/copyright usr/share/doc/gromacs-data/COPYING 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) # 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/demux.pl $(CURDIR)/debian/gromacs/usr/bin/demux
mv $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx.pl $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx mv $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx.pl $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx
mkdir -p $(CURDIR)/debian/libgromacs3/usr/lib/$(DEB_HOST_MULTIARCH) mkdir -p $(CURDIR)/debian/libgromacs4/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/*/*.so.* $(CURDIR)/debian/libgromacs3/usr/lib/$(DEB_HOST_MULTIARCH)/ mv $(CURDIR)/debian/gromacs/usr/lib/*/*.so.* $(CURDIR)/debian/libgromacs4/usr/lib/$(DEB_HOST_MULTIARCH)/
dh_installdirs -plibgromacs-dev dh_installdirs -plibgromacs-dev
mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/libgromacs-dev/usr/include mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/libgromacs-dev/usr/include
...@@ -241,7 +241,7 @@ install: build-arch install-basic install-mpich install-openmpi ...@@ -241,7 +241,7 @@ install: build-arch install-basic install-mpich install-openmpi
-rmdir $(CURDIR)/debian/gromacs/usr/share/gromacs -rmdir $(CURDIR)/debian/gromacs/usr/share/gromacs
# what are you doing here? # what are you doing here?
mv $(CURDIR)/debian/gromacs/usr/share/cmake $(CURDIR)/debian/libgromacs-dev/usr/share/gromacs/ mv $(CURDIR)/debian/gromacs/usr/share/cmake $(CURDIR)/debian/libgromacs-dev/usr/share/gromacs/
dh_lintian -pgromacs -pgromacs-data -plibgromacs3 dh_lintian -pgromacs -pgromacs-data -plibgromacs4
install-manual: build-manual install install-manual: build-manual install
dh_testdir dh_testdir
...@@ -312,8 +312,8 @@ binary-arch: build-arch install ...@@ -312,8 +312,8 @@ binary-arch: build-arch install
dh_compress -a dh_compress -a
dh_fixperms -a dh_fixperms -a
dh_makeshlibs -a dh_makeshlibs -a
dh_shlibdeps -plibgromacs3 -L libgromacs3 -l debian/libgromacs3/usr/lib dh_shlibdeps -plibgromacs4 -L libgromacs4 -l debian/libgromacs4/usr/lib
dh_shlibdeps -pgromacs -L libgromacs3 -l debian/libgromacs3/usr/lib:debian/gromacs/usr/lib dh_shlibdeps -pgromacs -L libgromacs4 -l debian/libgromacs4/usr/lib:debian/gromacs/usr/lib
dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib
dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib
dh_gencontrol -a dh_gencontrol -a
......
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