Commit 3665f428 authored by Nicholas Breen's avatar Nicholas Breen

Upstream beta release 2019-beta1, rebase patches

parent 1af49e64
gromacs (2019~beta1-1) experimental; urgency=medium gromacs (2019~beta1-1) experimental; urgency=medium
* New upstream beta release, upload to experimental. * New upstream beta release, upload to experimental.
- patches/reproducible-builds.patch and sphinx-version-detect.patch
removed, equivalent functionality integrated upstream.
- Other patches rebased.
-- Nicholas Breen <nbreen@debian.org> Sun, 28 Oct 2018 10:01:40 -0700 -- Nicholas Breen <nbreen@debian.org> Sun, 28 Oct 2018 10:01:40 -0700
......
...@@ -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()
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