[deal.ii] 01/02: Update copyright/patches/rules/control for version 8.4.1

Matthias Maier tamiko-guest at moszumanska.debian.org
Sat Jul 16 00:42:13 UTC 2016 

This is an automated email from the git hooks/post-receive script.

tamiko-guest pushed a commit to branch master
in repository deal.ii.

commit 3d60c5221ed92605d2eefe24652cb5dd7aa926d3
Author: Matthias Maier <tamiko+DEBIAN at kyomu.43-1.org>
Date:   Fri Jul 15 10:48:40 2016 +0000

    Update copyright/patches/rules/control for version 8.4.1
---
 debian/changelog                                   |  5 +--
 debian/control                                     | 22 ++++++++----
 debian/copyright                                   | 18 +++-------
 ...l.ii-8.1.0.install => libdeal.ii-8.4.1.install} |  0
 debian/patches/allow_boost_1.58.patch              | 20 +++++++++++
 .../allow_different_slepc_petsc_versions.patch     | 42 ++++++++++++++++++++++
 debian/patches/fix_parameter_handler_cxx11.patch   | 18 ----------
 debian/patches/fix_suitesparse.patch               | 38 --------------------
 debian/patches/series                              |  5 ++-
 debian/patches/use_fPIC_instead_of_fpic.patch      | 12 +++----
 debian/patches/use_local_deal_ico.patch            | 31 ----------------
 debian/rules                                       | 33 +++++++++--------
 12 files changed, 112 insertions(+), 132 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 01da72e..a42e7b2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,9 @@
-deal.ii (8.1.0-7) UNRELEASED; urgency=medium
+deal.ii (8.4.1-1) UNRELEASED; urgency=medium
 
   * Use -fPIC instead of -fpic to fix FTBFS on arm64, thanks Matthias Klose
+  * Enable MPI and a number of other external dependencies
 
- -- Graham Inggs <ginggs at debian.org>  Fri, 01 Apr 2016 12:26:46 +0200
+ -- Matthias Maier <tamiko+DEBIAN at kyomu.43-1.org>  Fri, 15 Jul 2016 12:55:45 +0000
 
 deal.ii (8.1.0-6) unstable; urgency=medium
 
diff --git a/debian/control b/debian/control
index 908dc3a..f42ed70 100644
--- a/debian/control
+++ b/debian/control
@@ -8,15 +8,25 @@ Vcs-Browser: https://anonscm.debian.org/cgit/debian-science/packages/deal.ii.git
 Vcs-Git: https://anonscm.debian.org/git/debian-science/packages/deal.ii.git
 Homepage: http://www.dealii.org/
 Build-Depends: debhelper (>= 9.20150628), cmake, doxygen, graphviz,
- liblapack-dev, libsuitesparse-dev, libtbb-dev, libboost-iostreams-dev,
- libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, zlib1g-dev
+ libarpack2-dev, libboost-iostreams-dev, libboost-serialization-dev,
+ libboost-system-dev, libboost-thread-dev, libbz2-dev, libgsl-dev, libhdf5-dev,
+ libhdf5-mpi-dev, liblapack-dev, libmuparser-dev, libnetcdf-dev,
+ libnetcdf-cxx-legacy-dev, liboce-foundation-dev, liboce-modeling-dev,
+ liboce-ocaf-dev, liboce-visualization-dev, libp4est-dev, libsuitesparse-dev,
+ libtbb-dev, mpi-default-dev, petsc-dev, slepc-dev, trilinos-all-dev,
+ zlib1g-dev
 
 Package: libdeal.ii-dev
 Section: libdevel
 Architecture: any
-Depends: ${misc:Depends}, libdeal.ii-8.1.0 (= ${binary:Version}),
- liblapack-dev, libsuitesparse-dev, libtbb-dev, libboost-iostreams-dev,
- libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, zlib1g-dev
+Depends: ${misc:Depends}, libdeal.ii-8.4.1 (= ${binary:Version}),
+ libarpack2-dev, libboost-iostreams-dev, libboost-serialization-dev,
+ libboost-system-dev, libboost-thread-dev, libbz2-dev, libgsl-dev, libhdf5-dev,
+ libhdf5-mpi-dev, liblapack-dev, libmuparser-dev, libnetcdf-dev,
+ libnetcdf-cxx-legacy-dev, liboce-foundation-dev, liboce-modeling-dev,
+ liboce-ocaf-dev, liboce-visualization-dev, libp4est-dev, libsuitesparse-dev,
+ libtbb-dev, mpi-default-dev, petsc-dev, slepc-dev, trilinos-all-dev,
+ zlib1g-dev
 Recommends: cmake
 Description: Differential Equations Analysis Library - development files
  deal.II is a C++ program library targeted at the computational solution of
@@ -26,7 +36,7 @@ Description: Differential Equations Analysis Library - development files
  .
  This package contains the development files.
 
-Package: libdeal.ii-8.1.0
+Package: libdeal.ii-8.4.1
 Architecture: any
 Multi-Arch: same
 Depends: ${misc:Depends}, ${shlibs:Depends}
diff --git a/debian/copyright b/debian/copyright
index d653a56..64d7c4c 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -5,27 +5,18 @@ Source: https://www.dealii.org/
 Files: *
 Copyright:
  Wolfgang Bangerth
+ Denis Davydov
  Timo Heister
- Guido Kanschat
  Luca Heltai
+ Guido Kanschat
  Martin Kronbichler
  Matthias Maier
  Bruno Turcksin
+ David Wells
  Toby Young
- et al. (see doc/authors.html)
+ et al. (see AUTHORS)
 License: LGPL-2.1+
 
-Files: contrib/mesh_conversion/*
-Copyright:
- Jean-Paul Pelteret
- Timo Heister
-License: GPL-2.0
- This program is distributed under the GNU GPL v2.0 copyright. Details can
- be found at: http://www.gnu.org/licenses/gpl-2.0.html
- .
- On Debian systems, the full text of the GNU General Public License
- version 2 can be found in the file `/usr/share/common-licenses/GPL-2'.
-
 Files: contrib/parameter_gui/*
 Copyright:
  Martin Steigemann
@@ -34,6 +25,7 @@ License: LGPL-2.1+
 
 Files: debian/*
 Copyright:
+ Graham Inggs
  Matthias Maier
 License: LGPL-2.1+
 
diff --git a/debian/libdeal.ii-8.1.0.install b/debian/libdeal.ii-8.4.1.install
similarity index 100%
rename from debian/libdeal.ii-8.1.0.install
rename to debian/libdeal.ii-8.4.1.install
diff --git a/debian/patches/allow_boost_1.58.patch b/debian/patches/allow_boost_1.58.patch
new file mode 100644
index 0000000..3819850
--- /dev/null
+++ b/debian/patches/allow_boost_1.58.patch
@@ -0,0 +1,20 @@
+diff --git a/cmake/configure/configure_boost.cmake b/cmake/configure/configure_boost.cmake
+index a097da7..81dab37 100644
+--- a/cmake/configure/configure_boost.cmake
++++ b/cmake/configure/configure_boost.cmake
+@@ -52,15 +52,6 @@ MACRO(FEATURE_BOOST_FIND_EXTERNAL var)
+ 
+   IF(BOOST_FOUND)
+     SET(${var} TRUE)
+-
+-    #
+-    # Blacklist version 1.58 because we get serialization errors with it. At
+-    # least version 1.56 and 1.59 are known to work.
+-    #
+-    IF("${BOOST_VERSION_MAJOR}" STREQUAL "1" AND "${BOOST_VERSION_MINOR}" STREQUAL "58")
+-      MESSAGE(STATUS "Boost version 1.58 is not compatible with deal.II!")
+-      SET(${var} FALSE)
+-    ENDIF()
+   ENDIF()
+ ENDMACRO()
+ 
diff --git a/debian/patches/allow_different_slepc_petsc_versions.patch b/debian/patches/allow_different_slepc_petsc_versions.patch
new file mode 100644
index 0000000..7c71c00
--- /dev/null
+++ b/debian/patches/allow_different_slepc_petsc_versions.patch
@@ -0,0 +1,42 @@
+diff --git a/cmake/configure/configure_slepc.cmake b/cmake/configure/configure_slepc.cmake
+index 35d139e..e27fb83 100644
+--- a/cmake/configure/configure_slepc.cmake
++++ b/cmake/configure/configure_slepc.cmake
+@@ -24,36 +24,7 @@ MACRO(FEATURE_SLEPC_FIND_EXTERNAL var)
+   FIND_PACKAGE(SLEPC)
+ 
+   IF(SLEPC_FOUND)
+-    #
+-    # Check whether SLEPc and PETSc are compatible according to
+-    # SLEPc's rules: This is equivalent to asking if the VERSION_MAJOR
+-    # and VERSION_MINOR of PETSc and SLEPc are
+-    # equivalent; and where VERSION_SUBMINORs are allowed to differ.
+-    #
+-    IF( ("${SLEPC_VERSION_MAJOR}" STREQUAL "${PETSC_VERSION_MAJOR}")
+-       AND
+-       ("${SLEPC_VERSION_MINOR}" STREQUAL "${PETSC_VERSION_MINOR}"))
+-      SET(${var} TRUE)
+-    ELSE()
+-
+-      MESSAGE(STATUS "Could not find a sufficient SLEPc installation: "
+-        "The SLEPc library must have the same version as the PETSc library."
+-        )
+-      SET(SLEPC_ADDITIONAL_ERROR_STRING
+-        "Could not find a sufficient SLEPc installation: "
+-        "The SLEPc library must have the same version as the PETSc library.\n"
+-        )
+-
+-      UNSET(SLEPC_INCLUDE_DIR_ARCH CACHE)
+-      UNSET(SLEPC_INCLUDE_DIR_COMMON CACHE)
+-      UNSET(SLEPC_LIBRARY CACHE)
+-      SET(SLEPC_DIR "" CACHE PATH
+-        "An optional hint to a SLEPc directory"
+-        )
+-      MARK_AS_ADVANCED(CLEAR SLEPC_DIR)
+-
+-      SET(${var} FALSE)
+-    ENDIF()
++    SET(${var} TRUE)
+   ENDIF()
+ ENDMACRO()
+ 
diff --git a/debian/patches/fix_parameter_handler_cxx11.patch b/debian/patches/fix_parameter_handler_cxx11.patch
deleted file mode 100644
index cbaba75..0000000
--- a/debian/patches/fix_parameter_handler_cxx11.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-Description: Use an explicit cast when need a bool from optional<...>
- The implicit cast was previously allowed, but newer versions of BOOST
- together with C++11 mark the cast as 'explicit',
- and it fails in the current context.
-Origin: upstream, https://github.com/dealii/dealii/commit/57d975bc4c9c3d76bce59ee7462a6e94487c7e82#diff-68feb64779ad59c9cb61e300a1ab2917
-Author: Wolfgang Bangerth <bangerth at math.tamu.edu>
-Last-Update: 2014-08-21
---- a/source/base/parameter_handler.cc
-+++ b/source/base/parameter_handler.cc
-@@ -1275,7 +1275,7 @@
- bool
- ParameterHandler::is_parameter_node (const boost::property_tree::ptree &p)
- {
--  return (p.get_optional<std::string>("value"));
-+  return static_cast<bool>(p.get_optional<std::string>("value"));
- }
- 
- 
diff --git a/debian/patches/fix_suitesparse.patch b/debian/patches/fix_suitesparse.patch
deleted file mode 100644
index 8f88181..0000000
--- a/debian/patches/fix_suitesparse.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Description: Remove libsuitesparseconfig.a from link interface
-Author: Matthias Maier <tamiko+DEBIAN at kyomu.43-1.org>
-
---- deal.ii-8.1.0.orig/cmake/modules/FindUMFPACK.cmake
-+++ deal.ii-8.1.0/cmake/modules/FindUMFPACK.cmake
-@@ -103,7 +103,6 @@ FIND_UMFPACK_LIBRARY(CHOLMOD cholmod)
- FIND_UMFPACK_LIBRARY(COLAMD colamd)
- FIND_UMFPACK_LIBRARY(CCOLAMD ccolamd)
- FIND_UMFPACK_LIBRARY(CAMD camd)
--FIND_UMFPACK_LIBRARY(SuiteSparse_config suitesparseconfig)
- 
- IF(EXISTS ${UMFPACK_INCLUDE_DIR}/umfpack.h)
-   FILE(STRINGS "${UMFPACK_INCLUDE_DIR}/umfpack.h" UMFPACK_VERSION_MAJOR_STRING
-@@ -126,7 +125,7 @@ IF(EXISTS ${UMFPACK_INCLUDE_DIR}/umfpack
-     )
- ENDIF()
- 
--SET(_output ${UMFPACK_LIBRARY} ${CHOLMOD_LIBRARY} ${CCOLAMD_LIBRARY} ${COLAMD_LIBRARY} ${CAMD_LIBRARY} ${AMD_LIBRARY} ${SuiteSparse_config_LIBRARY})
-+SET(_output ${UMFPACK_LIBRARY} ${CHOLMOD_LIBRARY} ${CCOLAMD_LIBRARY} ${COLAMD_LIBRARY} ${CAMD_LIBRARY} ${AMD_LIBRARY})
- FIND_PACKAGE_HANDLE_STANDARD_ARGS(UMFPACK DEFAULT_MSG
-   _output # Cosmetic: Gives nice output
-   UMFPACK_LIBRARY
-@@ -147,7 +146,6 @@ MARK_AS_ADVANCED(
-   CCOLAMD_LIBRARY
-   COLAMD_LIBRARY
-   SuiteSparse_config_INCLUDE_DIR
--  SuiteSparse_config_LIBRARY
-   UMFPACK_INCLUDE_DIR
-   UMFPACK_LIBRARY
-   )
-@@ -161,7 +159,6 @@ IF(UMFPACK_FOUND)
-     ${COLAMD_LIBRARY}
-     ${CAMD_LIBRARY}
-     ${AMD_LIBRARY}
--    ${SuiteSparse_config_LIBRARY}
-     )
- 
-   #
diff --git a/debian/patches/series b/debian/patches/series
index 4b191ac..c81ccaa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-fix_suitesparse.patch
-use_local_deal_ico.patch
-fix_parameter_handler_cxx11.patch
+allow_boost_1.58.patch
+allow_different_slepc_petsc_versions.patch
 use_fPIC_instead_of_fpic.patch
diff --git a/debian/patches/use_fPIC_instead_of_fpic.patch b/debian/patches/use_fPIC_instead_of_fpic.patch
index deac897..efd6e7a 100644
--- a/debian/patches/use_fPIC_instead_of_fpic.patch
+++ b/debian/patches/use_fPIC_instead_of_fpic.patch
@@ -1,15 +1,13 @@
-Description: Use -fPIC instead of -fpic
- This avoids 'Too many GOT entries' on arm64.
-Author: Graham Inggs <ginggs at debian.org>
-Last-Update: 2016-03-31
+diff --git a/cmake/setup_compiler_flags_gnu.cmake b/cmake/setup_compiler_flags_gnu.cmake
+index 4cccd53..cc75241 100644
 --- a/cmake/setup_compiler_flags_gnu.cmake
 +++ b/cmake/setup_compiler_flags_gnu.cmake
-@@ -47,7 +47,7 @@
+@@ -46,7 +46,7 @@ ENDIF()
  #
  # Set the pic flag.
  #
--ENABLE_IF_SUPPORTED(CMAKE_CXX_FLAGS "-fpic")
-+ENABLE_IF_SUPPORTED(CMAKE_CXX_FLAGS "-fPIC")
+-ENABLE_IF_SUPPORTED(DEAL_II_CXX_FLAGS "-fpic")
++ENABLE_IF_SUPPORTED(DEAL_II_CXX_FLAGS "-fPIC")
  
  #
  # Check whether the -as-needed flag is available. If so set it to link
diff --git a/debian/patches/use_local_deal_ico.patch b/debian/patches/use_local_deal_ico.patch
deleted file mode 100644
index 69d4e6d..0000000
--- a/debian/patches/use_local_deal_ico.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-Description: Use local (offline) icon instead of an external one
- This patch replaces all external links to http://www.dealii.org/deal.ico
- by local ones.
-Author: Matthias Maier <tamiko+DEBIAN at kyomu.43-1.org>
-
---- deal.ii-8.1.0.orig/doc/doxygen/CMakeLists.txt
-+++ deal.ii-8.1.0/doc/doxygen/CMakeLists.txt
-@@ -149,6 +149,12 @@ INSTALL(FILES
-   COMPONENT documentation
-   )
- 
-+INSTALL(FILES
-+  ${CMAKE_SOURCE_DIR}/doc/deal.ico
-+  DESTINATION ${DEAL_II_DOCHTML_RELDIR}/doxygen/deal.II
-+  COMPONENT documentation
-+  )
-+
- INSTALL(DIRECTORY
-   ${CMAKE_CURRENT_BINARY_DIR}/deal.II
-   DESTINATION ${DEAL_II_DOCHTML_RELDIR}/doxygen
---- deal.ii-8.1.0.orig/doc/doxygen/scripts/mod_header.pl.in
-+++ deal.ii-8.1.0/doc/doxygen/scripts/mod_header.pl.in
-@@ -6,7 +6,7 @@ $year += 1900;
- 
- if (m'</head>')
- {
--    print '<link rel="SHORTCUT ICON" href="http://www.dealii.org/deal.ico"></link>', "\n";
-+    print '<link rel="SHORTCUT ICON" href="deal.ico"></link>', "\n";
-     print '<meta name="author" content="The deal.II Authors <authors at dealii.org>"></meta>', "\n";
-     print '<meta name="copyright" content="Copyright (C) 1998 - ', $year, ' by the deal.II authors"></meta>', "\n";
-     print '<meta name="deal.II-version" content="@DEAL_II_PACKAGE_VERSION@"></meta>', "\n";
diff --git a/debian/rules b/debian/rules
index 81e9b20..3a4a947 100755
--- a/debian/rules
+++ b/debian/rules
@@ -7,25 +7,37 @@ DEB_HOST_MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
 
 override_dh_auto_configure:
 	dh_auto_configure -- \
+	-DCMAKE_PREFIX_PATH="/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/openmpi;/usr/include/hdf5/openmpi" \
 	-DCMAKE_BUILD_TYPE=DebugRelease \
 	-DDEAL_II_ALLOW_AUTODETECTION=OFF \
 	-DDEAL_II_ALLOW_BUNDLED=OFF \
 	-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF \
 	-DDEAL_II_COMPONENT_DOCUMENTATION=ON \
-	-DDEAL_II_COMPONENT_MESH_CONVERTER=OFF \
-	-DDEAL_II_COMPONENT_COMPAT_FILES=OFF \
+	-DDEAL_II_WITH_ARPACK=ON \
+	-DDEAL_II_WITH_BOOST=ON \
+	-DDEAL_II_WITH_BZIP2=ON \
+	-DDEAL_II_WITH_GSL=ON \
+	-DDEAL_II_WITH_HDF5=ON \
 	-DDEAL_II_WITH_LAPACK=ON \
+	-DDEAL_II_WITH_MPI=ON \
+	-DDEAL_II_WITH_MUPARSER=ON \
+	-DDEAL_II_WITH_NETCDF=ON \
+	-DDEAL_II_WITH_OPENCASCADE=ON \
+	-DDEAL_II_WITH_P4EST=ON \
+	-DDEAL_II_WITH_PETSC=ON \
+	-DDEAL_II_WITH_SLEPC=ON \
 	-DDEAL_II_WITH_THREADS=ON \
+	-DDEAL_II_WITH_TRILINOS=ON \
 	-DDEAL_II_WITH_UMFPACK=ON \
 	-DDEAL_II_WITH_ZLIB=ON \
 	-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=OFF \
 	-DDEAL_II_BASE_NAME="deal.ii" \
-	-DDEAL_II_CMAKE_MACROS_RELDIR=share/deal.ii/cmake/macros \
 	-DDEAL_II_DOCHTML_RELDIR=share/doc/libdeal.ii-doc/html \
 	-DDEAL_II_DOCREADME_RELDIR=share/doc/libdeal.ii-doc \
 	-DDEAL_II_EXAMPLES_RELDIR=share/doc/libdeal.ii-doc/examples \
+	-DDEAL_II_LIBRARY_RELDIR=lib/$(DEB_HOST_MULTIARCH) \
 	-DDEAL_II_PROJECT_CONFIG_RELDIR=share/cmake/deal.II \
-	-DDEAL_II_LIBRARY_RELDIR=lib/$(DEB_HOST_MULTIARCH)
+	-DDEAL_II_SHARE_RELDIR=share/deal.ii/
 
 TMP_DOC := debian/tmp/usr/share/doc/libdeal.ii-doc
 override_dh_auto_install:
@@ -38,15 +50,8 @@ override_dh_auto_install:
 	# Remove external links to the W3C validator icon:
 	find $(TMP_DOC)/html \
 		-type f -name '*.html' -exec sed -i 's#\(<img.*w3.org.*\)</a>#</a>#' {} \;
-	# Remove a java script embedding to google groups:
-	sed -i  -e 's#.*getElementById.*forum_embed.*##g' \
-		-e 's#.*groups\.google\.com/forum/embed.*##g' \
-		$(TMP_DOC)/html/mail.html
 	# Remove superfluous license file
 	rm $(TMP_DOC)/LICENSE
-	# Remove empty directories
-	rm -r $(TMP_DOC)/examples/step-35/lib
-	rmdir $(TMP_DOC)/html/glossary
 
 override_dh_compress:
 	# Do not compress example source code, and icons:
@@ -56,10 +61,10 @@ override_dh_strip:
 	dh_strip --ddeb-migration='libdeal.ii-dbg (<< 8.1.0-6~)'
 
 
-VERSION := 8.1.0
+VERSION := 8.4.1
 get-orig-source:
-	wget --no-clobber -O deal.ii-$(VERSION).tar.gz https://dealii.googlecode.com/files/deal.II-$(VERSION).tar.gz
-	wget --no-clobber -O deal.ii-doc-$(VERSION).tar.gz https://dealii.googlecode.com/files/deal.offlinedoc-$(VERSION).tar.gz
+	wget --no-clobber -O deal.ii-$(VERSION).tar.gz https://github.com/dealii/dealii/releases/download/v$(VERSION)/dealii-$(VERSION).tar.gz
+	wget --no-clobber -O deal.ii-doc-$(VERSION).tar.gz https://github.com/dealii/dealii/releases/download/v$(VERSION)/dealii-$(VERSION)-offline_documentation.tar.gz
 	mkdir deal.ii-$(VERSION)
 	tar --strip-components=1 -C deal.ii-$(VERSION) -xzf deal.ii-$(VERSION).tar.gz
 	mkdir -p deal.ii-$(VERSION)/doc/doxygen/deal.II

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/deal.ii.git

More information about the debian-science-commits mailing list