[med-svn] [libroadrunner] 02/02: Add initial but not working packaging
Andreas Tille
tille at debian.org
Wed Feb 1 10:55:39 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libroadrunner.
commit 3a8d75af525b265776cf891e1d5fc212012a8519
Author: Andreas Tille <tille at debian.org>
Date: Wed Feb 1 11:53:39 2017 +0100
Add initial but not working packaging
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 73 ++++++++++++++++++++++++++++
debian/copyright | 45 +++++++++++++++++
debian/patches/debug_cmake.patch | 42 ++++++++++++++++
debian/patches/do_not_build_depend_git.patch | 43 ++++++++++++++++
debian/patches/series | 2 +
debian/rules | 15 ++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++
debian/watch | 3 ++
11 files changed, 242 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..533cfb7
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+libroadrunner (1.4.8-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 31 Jan 2017 09:50:22 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..3074808
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,73 @@
+Source: libroadrunner
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 10),
+ llvm-dev,
+ cmake,
+ libncurses5-dev,
+ zlib1g-dev,
+ libbz2-dev,
+ python-dev,
+ python-llvmlite,
+ python-numpy,
+ swig,
+ libsbml5-dev,
+ libxml2-dev,
+ libsundials-serial-dev,
+ libpoco-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libroadrunner.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libroadrunner.git
+Homepage: http://libroadrunner.org/
+
+Package: libroadrunner
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: simulation engine for systems and synthetic biology
+ LibRoadRunner is a high performance and portable simulation engine for
+ systems and synthetic biology. I can run on many platforms including
+ Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the
+ original C# roadRunner developed by Frank Bergmann and Herbert Sauro.
+ The same original functionality however remains, including the
+ original C API, the structural analysis code, sensitivity and steady
+ state analyses, but with significant improvements to performance, back-
+ end design, better event handling, new C++ API and stochastic
+ simulation support.
+
+Package: libroadrunner-dev
+Section: libdevel
+Architecture: any
+Depends: libroadrunner (= ${binary:Version})
+Description: simulation engine for systems and synthetic biology (development)
+ LibRoadRunner is a high performance and portable simulation engine for
+ systems and synthetic biology. I can run on many platforms including
+ Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the
+ original C# roadRunner developed by Frank Bergmann and Herbert Sauro.
+ The same original functionality however remains, including the
+ original C API, the structural analysis code, sensitivity and steady
+ state analyses, but with significant improvements to performance, back-
+ end design, better event handling, new C++ API and stochastic
+ simulation support.
+ .
+ This package contains the header files for libroadrunner.
+
+Package: python-roadrunner
+Section: python
+Architecture: any
+Depends: libroadrunner (= ${binary:Version}),
+ python-numpy
+Description: Python bindings for libroadrunner
+ LibRoadRunner is a high performance and portable simulation engine for
+ systems and synthetic biology. I can run on many platforms including
+ Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the
+ original C# roadRunner developed by Frank Bergmann and Herbert Sauro.
+ The same original functionality however remains, including the
+ original C API, the structural analysis code, sensitivity and steady
+ state analyses, but with significant improvements to performance, back-
+ end design, better event handling, new C++ API and stochastic
+ simulation support.
+ .
+ This package contains the Python bindings for libroadrunner.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5fbaf44
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,45 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: roadrunner
+Source: https://github.com/sys-bio/roadrunner
+Files-Excluded:
+
+Files: *
+Copyright: 2012-2016 University of Washington, Seattle, WA, USA
+License: Apache-2.0
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: Apache-2.0
+
+License: Apache-2.0
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * In plain english this means:
+ *
+ * You CAN freely download and use this software, in whole or in part, for personal,
+ * company internal, or commercial purposes;
+ *
+ * You CAN use the software in packages or distributions that you create.
+ *
+ * You SHOULD include a copy of the license in any redistribution you may make;
+ *
+ * You are NOT required include the source of software, or of any modifications you may
+ * have made to it, in any redistribution you may assemble that includes it.
+ *
+ * YOU CANNOT:
+ *
+ * redistribute any piece of this software without proper attribution;
+ .
+ On Debian systems you can find the full text of the Apache 2.0 license
+ at /usr/share/common-licenses/Apache-2.0
+
diff --git a/debian/patches/debug_cmake.patch b/debian/patches/debug_cmake.patch
new file mode 100644
index 0000000..3a810c3
--- /dev/null
+++ b/debian/patches/debug_cmake.patch
@@ -0,0 +1,42 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 31 Jan 2017 09:50:22 +0100
+Description: Fixes:
+ CMake Error at cmake/FindLLVM.cmake:159 (STRING):
+ string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
+ command.
+ Call Stack (most recent call first):
+ CMakeLists.txt:78 (find_package)
+FIXME: Output warning about empty ${LLVM_LIBRARIES} variable which probably is
+ not what we want ...
+
+--- a/cmake/FindLLVM.cmake
++++ b/cmake/FindLLVM.cmake
+@@ -146,6 +146,13 @@ if (LLVM_CONFIG_EXECUTABLE)
+
+ # link libraries, currently only need core, jit and native.
+ # TODO: in future, replace this with something like LLVM_CORE_LIBS, LLVM_JIT_LIBS...
++ if( DEFINED ${LLVM_CONFIG_EXECUTABLE} )
++ message( "LLVM_CONFIG_EXECUTABLE defined. Value is ${LLVM_CONFIG_EXECUTABLE}")
++ else()
++ message("FIXME: Variable LLVM_CONFIG_EXECUTABLE is empty!")
++ endif()
++
++ STRING(REGEX REPLACE "[\n\t\r ]+" ";" LLVM_LIBRARIES "${LLVM_LIBRARIES}")
+ execute_process(
+ COMMAND ${LLVM_CONFIG_EXECUTABLE} --libfiles core jit native
+ OUTPUT_VARIABLE LLVM_LIBRARIES
+@@ -156,7 +163,13 @@ if (LLVM_CONFIG_EXECUTABLE)
+ STRING(REGEX REPLACE "lib([^/\\]*)\\.a" "\\1.lib" LLVM_LIBRARIES ${LLVM_LIBRARIES})
+ endif()
+ # we get a space sep list from llvm-config, make it a cmake ; separated list.
+- STRING(REGEX REPLACE "[\n\t\r ]+" ";" LLVM_LIBRARIES ${LLVM_LIBRARIES})
++ if( DEFINED ${LLVM_LIBRARIES} )
++ message( "LLVM_LIBRARIES defined. Value is ${LLVM_LIBRARIES}")
++ else()
++ message("FIXME: Variable LLVM_LIBRARIES is empty!")
++ endif()
++
++ STRING(REGEX REPLACE "[\n\t\r ]+" ";" LLVM_LIBRARIES "${LLVM_LIBRARIES}")
+ message(STATUS "LLVM_LIBRARIES: ${LLVM_LIBRARIES}")
+
+ # starting with LLVM 3.4 (at least on Ubuntu) it requres functions in
diff --git a/debian/patches/do_not_build_depend_git.patch b/debian/patches/do_not_build_depend_git.patch
new file mode 100644
index 0000000..14f1afd
--- /dev/null
+++ b/debian/patches/do_not_build_depend_git.patch
@@ -0,0 +1,43 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 31 Jan 2017 09:50:22 +0100
+Description: Since we are not packaging specific Git commits there is no
+ point in checking what branch / commit
+
+--- a/source/CMakeLists.txt
++++ b/source/CMakeLists.txt
+@@ -9,34 +9,11 @@ install( FILES ${CMAKE_CURRENT_BINARY_DI
+
+ OPTION(USE_POCO_NET "Use poco net library" ON)
+
+-# pre-process the GitInfo.h.in file and insert the response from git about
+-# last commit and current branch.
+-# may not have git, set default replacement strings then.
+-find_program(GIT git)
+-
+-if(GIT)
+- message("found git: ${GIT}")
+- execute_process(
+- COMMAND ${GIT} symbolic-ref -q --short HEAD
+- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+- OUTPUT_VARIABLE ROADRUNNER_GIT_BRANCH
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- )
+-
+-
+- execute_process(
+- COMMAND ${GIT} log -1 --format=%H
+- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+- OUTPUT_VARIABLE ROADRUNNER_GIT_LAST_COMMIT
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- )
+-else()
+ # could not find GIT
+- message("could not find git")
++ message("git is not used in Debian package")
+
+ set(ROADRUNNER_GIT_BRANCH "git not found, unknown git branch")
+ set(ROADRUNNER_GIT_LAST_COMMIT "git not found, unknown git commit")
+-endif(GIT)
+
+ # Add semantic version info set in root-level CMake script
+ configure_file(rrVersionInfo.h.in rrVersionInfo.h @ONLY)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..edeedb6
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+do_not_build_depend_git.patch
+debug_cmake.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..a00d412
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+DEB_CMAKE_NORMAL_ARGS += -DLLVM_CONFIG_EXECUTABLE=/usr/bin/llvm-config \
+ -DBUILD_PYTHON=TRUE
+
+## -DTHIRD_PARTY_INSTALL_FOLDER=/home/user/devel/install/roadrunner-deps
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ dh_auto_configure -- $(DEB_CMAKE_NORMAL_ARGS)
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..c94558c
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Endre T. Somogyi and Jean-Marie Bouteiller and James A. Glazier and Matthias König and J. Kyle Medley and Maciej H. Swat and Herbert M. Sauro
+ Title: "libRoadRunner: a high performance SBML simulation and analysis library"
+ Journal: Bioinformatics
+ Year: 2015
+ Volume: 31
+ Number: 20
+ Pages: 3315-21
+ DOI: 10.1093/bioinformatics/btv363
+ PMID: 26085503
+ URL: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv363
+ eprint: https://academic.oup.com/bioinformatics/article-pdf/31/20/3315/5040907/btv363.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..10b5c16
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/sys-bio/roadrunner/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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