make the whole pipeline work

.gitignore

@@ -22,3 +22,10 @@ docs/site/
 # committed for packages, but should be committed for applications that require a static
 # environment.
 Manifest.toml
+
+#vim
+.*.swp
+
+#BinaryBuilder
+/build
+/products

LICENSE

-MIT License
-
-Copyright (c) 2021 Luxembourg Centre for Systems Biomedicine
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

LICENSE

+libsbml-cxxwrapjl/LICENSE
\ No newline at end of file

Project.toml

@@ -2,3 +2,7 @@ name = "SBML"
 uuid = "e5567a89-2604-4b09-9718-f5f78e97c3bb"
 authors = ["Mirek Kratochvil <exa.exa@gmail.com>"]
 version = "0.1.0"
+
+[deps]
+CxxWrap = "1f15a43c-97ca-5a2a-ae31-89f07a497df4"
+SBML_jll = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1"

README.md

 # SBML.jl
+
+This is a simple wrap of some of the libSBML functionality.
+
+Current status is "under development", something works, more wrapped stuff will
+be added by need.
+
+## How to use this
+
+First, build the C++ library and a wrapper and register it in your julia
+installation. You usually want to specify a single architecture to build, to
+avoid building all of them.
+```
+./build_tarballs.jl x86_64-linux-gnu --deploy=local 
+```
+
+After that, you should be able to load the SBML in Julia:
+```
+Pkg] dev --local .
+julia> using SBML
+julia> getLibSBMLDottedVersion()
+"5.19.0"
+```

build_tarballs.jl

 #!/usr/bin/env julia
 using BinaryBuilder, Pkg
 
-# This needs unprivileged containers:
-# sysctl kernel.unprivileged_userns_clone=1
+julia_version = v"1.5.3"
 
 name = "SBML"
 version = v"5.19.0"
@@ -14,25 +13,64 @@ sources = [
 ]
 
 script = raw"""
-find ${prefix}
-cd ${WORKSPACE}/srcdir/libsbml-5.19.0
+
+if [[ $target == i686-* ]] || [[ $target == arm-* ]]; then
+    export processor=pentium4
+else
+    export processor=x86-64
+fi
+
+# first install SBML to a temp location
+
+cd ${WORKSPACE}/srcdir
+SBMLNAME=libsbml-*
+
+cd ${WORKSPACE}/srcdir/${SBMLNAME}
 mkdir build
 cd build
-cmake -DCMAKE_INSTALL_PREFIX=${WORKSPACE}/srcdir/libsbml-install -DCMAKE_INCLUDE_PATH="${prefix}/include/libxml2;${prefix}/include" -DCMAKE_LIBRARY_PATH=${prefix}/lib ..
+cmake \
+  -DCMAKE_INSTALL_PREFIX=${prefix} \
+  -DCMAKE_LIBRARY_PATH=${prefix}/lib \
+  -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TARGET_TOOLCHAIN} \
+  -DCMAKE_INCLUDE_PATH="${prefix}/include/libxml2;${prefix}/include" \
+  ..
 make -j${nproc}
 make install
+
+# now the wrapper
+
 cd ${WORKSPACE}/srcdir/wrapper
 mkdir build
 cd build
-PKG_CONFIG_PATH=${WORKSPACE}/srcdir/libsbml-install/lib/pkgconfig cmake -DCMAKE_INSTALL_PREFIX=${prefix} ..
+
+SBML_PC_DIR="${prefix}/lib/pkgconfig"
+
+PKG_CONFIG_PATH=$SBML_PC_DIR pkg-config libsbml --cflags --libs
+
+PKG_CONFIG_PATH=${SBML_PC_DIR} cmake \
+  -DCMAKE_INSTALL_PREFIX=${prefix} \
+  -DCMAKE_LIBRARY_PATH=${prefix}/lib \
+  -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TARGET_TOOLCHAIN} \
+  -DJulia_PREFIX=${prefix} \
+  ..
+  
 make -j${nproc}
 make install
+
+# install licenses (note: using `cp` is not fine, but the build env lacks
+# `install` version that could do this correctly)
+
+LICENSEDIR=${prefix}/share/licenses/SBML
+mkdir -p $LICENSEDIR
+cp ${WORKSPACE}/srcdir/wrapper/LICENSE $LICENSEDIR/LICENSE-wrapper
+cp ${WORKSPACE}/srcdir/${SBMLNAME}/LICENSE.txt $LICENSEDIR/LICENSE-libSBML
+cp ${WORKSPACE}/srcdir/${SBMLNAME}/COPYING.txt $LICENSEDIR/COPYING-libSBML
 """
 
-#platforms = supported_platforms()
-platforms=[
-    Linux(:x86_64, libc=:glibc),
-]
+platforms = supported_platforms()
+#platforms = [ Linux(:x86_64, libc=:glibc) ]
+
+platforms = expand_cxxstring_abis(platforms)
 
 products = [
     LibraryProduct("libsbml-cxxwrapjl", :libsbml),
@@ -40,9 +78,12 @@ products = [
 
 dependencies = [
     Dependency("libcxxwrap_julia_jll"),
-    BuildDependency(PackageSpec(name="Julia_jll")), #see ygdrassil/SDPA
+    Dependency("CompilerSupportLibraries_jll"),
+    BuildDependency(PackageSpec(name="libjulia_jll", version=julia_version)),
     Dependency("XML2_jll"),
     Dependency("Zlib_jll"),
 ]
 
-build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies)
+build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies;
+    preferred_gcc_version=v"10",
+    julia_compat = "$(julia_version.major).$(julia_version.minor)")

libsbml-cxxwrapjl/CMakeLists.txt

@@ -3,26 +3,35 @@ project(sbml-cxxwrapjl)
 
 cmake_minimum_required(VERSION 3.10)
 
-set(CMAKE_MACOSX_RPATH 1)
-#TODO why? set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
+set(CMAKE_VERBOSE_MAKEFILE ON)
 
-find_package(JlCxx REQUIRED)
-get_target_property(JlCxx_location JlCxx::cxxwrap_julia LOCATION)
-get_filename_component(JlCxx_location ${JlCxx_location} DIRECTORY)
-set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${JlCxx_location}")
-message(STATUS "Found JlCxx at ${JlCxx_location}")
+set(CMAKE_MACOSX_RPATH 0)
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+find_package(JlCxx)
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${Julia_LIBRARY_DIR}")
+#get_target_property(JlCxx_location JlCxx::cxxwrap_julia LOCATION)
+#get_filename_component(JlCxx_location ${JlCxx_location} DIRECTORY)
+#set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${JlCxx_location}")
+#message(STATUS "Found JlCxx at ${JlCxx_location}")
+include_directories(${Julia_INCLUDE_DIRS})
+include_directories(${CMAKE_SOURCE_DIR}/include)
+include_directories(${INTERFACE_INCLUDE_DIRECTORIES})
 
 find_package(PkgConfig)
 
 pkg_check_modules(SBML libsbml REQUIRED)
+message(STATUS "SBML includedir: ${SBML_INCLUDEDIR}")
 
 add_library(sbml-cxxwrapjl SHARED
 	src/cxxwrap.cpp
 	src/versions.cpp
 )
 
-target_include_directories(sbml-cxxwrapjl PUBLIC ${SBML_INCLUDEDIR})
+target_include_directories(sbml-cxxwrapjl SYSTEM PUBLIC ${SBML_INCLUDEDIR})
 target_link_directories(sbml-cxxwrapjl PUBLIC ${SBML_LIBDIR})
 target_link_libraries(sbml-cxxwrapjl
 	${SBML_LIBRARIES}
 	JlCxx::cxxwrap_julia)
+
+install(TARGETS sbml-cxxwrapjl)

libsbml-cxxwrapjl/LICENSE

+MIT License
+
+Copyright (c) 2021 Luxembourg Centre for Systems Biomedicine
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

src/SBML.jl

 module SBML
 
 using CxxWrap
+using SBML_jll
 
-# TODO: load the libsbml project from the BinaryBuilder destination
-@wrapmodule("./libsbml-cxxwrapjl.so")
+@wrapmodule(libsbml)
+
+# version tools
+export getLibSBMLDependencyVersionOf,
+    getLibSBMLDottedVersion,
+    getLibSBMLVersion,
+    getLibSBMLVersionString,
+    isLibSBMLCompiledWith
 
 function __init__()
   @initcxx