Merge pull request #916 from sys-bio/develop

Merge latest updates for release.

.azurepipelines/getLLVM.py

@@ -0,0 +1,85 @@
+"""
+Get LLVM from url.
+
+Usage:
+
+    python getLLVM.py <llvm_download_link> <llvm_install_prefix?
+
+For example:
+
+    python getLLVM.py https://github.com/sys-bio/llvm-13.x/releases/download/llvmorg-13.0.0/llvm13-ubuntu-gcc10-rel.tar.gz /mnt/d/roadrunner/roadrunner/llvm-download-test/ubuntu
+
+"""
+
+
+import glob
+import argparse
+import os
+from os.path import join, splitext, isdir, isfile
+import zipfile
+import tarfile
+import requests
+import io
+import shutil
+
+# command line arguments
+parser = argparse.ArgumentParser()
+parser.add_argument("llvm_download_link", type=str, help="Url to compressed llvm-13.x link to download")
+parser.add_argument("llvm_install_prefix", type=str, help="Where to install llvm (directory that will contain bin, include, lib etc")
+args = parser.parse_args()
+
+# filename of downloaded zip, llvm-13.x-Darwin-Release.zip
+compressed_llvm_filename = args.llvm_download_link.split('/')[-1]
+
+# absolute path to compressed_llvm_filename
+abs_compressed_llvm_filename = join(args.llvm_install_prefix, compressed_llvm_filename)
+
+# e.g. ('llvm-13.x-Darwin-Release', '.zip')
+downloaded_llvm_folder, ext = splitext(compressed_llvm_filename)
+# when link is tar.gz, get rid of extra .tar
+if ".tar" in downloaded_llvm_folder:
+    downloaded_llvm_folder = downloaded_llvm_folder.replace(".tar", "")
+
+# make install prefix if not exists
+if not isdir(args.llvm_install_prefix):
+    os.makedirs(args.llvm_install_prefix)
+
+print("compressed_llvm_filename".ljust(20), compressed_llvm_filename)
+print("abs_compressed_llvm_filename".ljust(20), abs_compressed_llvm_filename)
+print("downloaded_llvm_folder".ljust(20), downloaded_llvm_folder)
+print("args.llvm_download_link".ljust(20), args.llvm_download_link)
+print("downloaded_llvm_folder, ext".ljust(20), downloaded_llvm_folder, ext)
+
+# we expect a folder called bin in
+abs_downloaded_llvm_folder = join(args.llvm_install_prefix, downloaded_llvm_folder)
+
+# Don't download if we already have it
+if not isdir(join(abs_downloaded_llvm_folder, "bin")):
+    print("downloading llvm-13.x from {}".format(args.llvm_download_link))
+    r = requests.get(args.llvm_download_link, stream=True)
+    if ext == ".zip":
+        z = zipfile.ZipFile(io.BytesIO(r.content))
+        z.extractall(args.llvm_install_prefix)
+    elif ext == ".gz":
+        z = tarfile.open(fileobj=r.raw, mode="r|gz")
+        z.extractall(args.llvm_install_prefix)
+    else:
+        raise ValueError("Unsupported extension")
+else :
+    print("Found existing llvm, not downloading llvm")
+
+# move from unzip dir to llvm_install_prefix
+folders = glob.glob(join(abs_downloaded_llvm_folder, "*"))
+print(folders)
+for f in folders:
+    shutil.move(f, args.llvm_install_prefix)
+
+
+if isfile(abs_compressed_llvm_filename):
+    os.remove(abs_compressed_llvm_filename)
+
+
+
+
+
+

.gitignore

@@ -53,11 +53,22 @@ cmake-*
 build
 out
 
+#test output file(s?)
+test/sbml-test-suite/stochastic/results.tsv
+
 install-release
 build-debug
 build-release
 install-debug
 roadrunner-install-*
 
 # temp.
-sundials
+sundials
+test/PerformanceTests/biomodels
+test/PerformanceTests/biomodels.zip
+test/PerformanceTests/simulations
+test/PerformanceTests/OldData
+build-msvc
+
+biomodels
+biomodels.zip

CMakeLists.txt

@@ -1,14 +1,15 @@
 cmake_minimum_required(VERSION 3.16)
 
+
 # libRoadRunner semantic versioning (http://semver.org/) - used to generate
 # source files expose library version information
 
 #########################################################################
 # Version information and include modules
 
 set(ROADRUNNER_VERSION_MAJOR 2)
-set(ROADRUNNER_VERSION_MINOR 1)
-set(ROADRUNNER_VERSION_PATCH 3)
+set(ROADRUNNER_VERSION_MINOR 2)
+set(ROADRUNNER_VERSION_PATCH 0)
 
 set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")
 project(
@@ -102,6 +103,9 @@ option(BUILD_LLVM "Build the LLVM back end" ON)
 # note I've tried using the C backend and it no longer compiles. Could be useful to keep though
 option(BUILD_LEGACY_C "Build the legacy C code generating backend (deprecated)" OFF)
 
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "../roadrunner-${CMAKE_GENERATOR_PLATFORM}-${CMAKE_BUILD_TYPE}" CACHE PATH "..." FORCE)
+endif()
 
 # should we build the swig python wrapper?
 option(BUILD_PYTHON "Build the SWIG generated python wrapper" OFF)
@@ -121,12 +125,12 @@ if (BUILD_PYTHON)
     # build directories
     set(PYTHON_PACKAGE_SITE_DIR_BUILD_TREE "${CMAKE_BINARY_DIR}/lib/site-packages" CACHE PATH "Path to Python site packages directory in the build tree")
     set(PYTHON_PACKAGE_BUILD_PREFIX "${PYTHON_PACKAGE_SITE_DIR_BUILD_TREE}/roadrunner")
-    set(RR_PYTHON_TESTING_BUILD_PREFIX "${PYTHON_PACKAGE_BUILD_PREFIX}/testing")
+    set(RR_PYTHON_TESTING_BUILD_PREFIX "${PYTHON_PACKAGE_BUILD_PREFIX}/tests")
 
     # install directories
     set(PYTHON_PACKAGE_SITE_DIR "${CMAKE_INSTALL_PREFIX}/site-packages" CACHE PATH "Path to Python site packages directory in the install tree")
     set(PYTHON_PACKAGE_INSTALL_PREFIX "${PYTHON_PACKAGE_SITE_DIR}/roadrunner")#CACHE PATH "Destination for roadrunner python bindings.")
-    set(RR_PYTHON_TESTING_INSTALL_PREFIX "${PYTHON_PACKAGE_INSTALL_PREFIX}/testing")
+    set(RR_PYTHON_TESTING_INSTALL_PREFIX "${PYTHON_PACKAGE_INSTALL_PREFIX}/tests")
 
 
     # plugin directories
@@ -174,6 +178,8 @@ if ("${CMAKE_BUILD_TYPE}" STREQUAL "Asan")
     # and they will only work if CMake can find address sanitizer
     # executable.
     #
+    # Only works on macos.
+    #
     # The Asan build is based on the Debug build, but with a few extra flags
     #
     get_property(isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
@@ -191,21 +197,25 @@ if ("${CMAKE_BUILD_TYPE}" STREQUAL "Asan")
         endif ()
     endif ()
 
+    set(WHICH_SANITIZER "address" CACHE STRING "which sanitizer to use. address, memory, thread, leak, undefined")
+    set(SANITIZER_OPTIONS "-fno-omit-frame-pointer" CACHE STRING "options to pass to command -fsanitize")
+
+    message(STATUS "WHICH_SANITIZER ${WHICH_SANITIZER}")
 
     set(CMAKE_C_FLAGS_ASAN
-            "${CMAKE_C_FLAGS_DEBUG} -fsanitize=address -fno-omit-frame-pointer" CACHE STRING
+            "${CMAKE_C_FLAGS_DEBUG} -fsanitize=${WHICH_SANITIZER} ${SANITIZER_OPTIONS}" CACHE STRING
             "Flags used by the C compiler for Asan build type or configuration." FORCE)
 
     set(CMAKE_CXX_FLAGS_ASAN
-            "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=address -fno-omit-frame-pointer" CACHE STRING
+            "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=${WHICH_SANITIZER} ${SANITIZER_OPTIONS}" CACHE STRING
             "Flags used by the C++ compiler for Asan build type or configuration." FORCE)
 
     set(CMAKE_EXE_LINKER_FLAGS_ASAN
-            "${CMAKE_SHARED_LINKER_FLAGS_DEBUG} -fsanitize=address" CACHE STRING
+            "${CMAKE_SHARED_LINKER_FLAGS_DEBUG} -fsanitize=${WHICH_SANITIZER}" CACHE STRING
             "Linker flags to be used to create executables for Asan build type." FORCE)
 
     set(CMAKE_SHARED_LINKER_FLAGS_ASAN
-            "${CMAKE_SHARED_LINKER_FLAGS_DEBUG} -fsanitize=address" CACHE STRING
+            "${CMAKE_SHARED_LINKER_FLAGS_DEBUG} -fsanitize=${WHICH_SANITIZER}" CACHE STRING
             "Linker lags to be used to create shared libraries for Asan build type." FORCE)
 endif ()
 
@@ -388,6 +398,7 @@ find_package(PocoFoundation CONFIG REQUIRED)
 find_package(PocoNet CONFIG REQUIRED)
 find_package(PocoXML CONFIG REQUIRED)
 find_package(LLVM REQUIRED)
+
 find_package(SUNDIALS CONFIG REQUIRED)
 
 # not for windows. So not required, but we throw error if not win and not found.
@@ -403,13 +414,15 @@ set(BUILD_STATIC_LIBS ON)
 
 # install dependencies so clients can use roadrunner from c++/cmake
 message(STATUS "CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_LIBDIR}")
-install(DIRECTORY ${RR_DEPENDENCIES_INSTALL_PREFIX}/lib DESTINATION ${CMAKE_INSTALL_PREFIX})
-install(DIRECTORY ${RR_DEPENDENCIES_INSTALL_PREFIX}/bin DESTINATION ${CMAKE_INSTALL_PREFIX})
-install(DIRECTORY ${RR_DEPENDENCIES_INSTALL_PREFIX}/include DESTINATION ${CMAKE_INSTALL_PREFIX})
-install(DIRECTORY ${RR_DEPENDENCIES_INSTALL_PREFIX}/share DESTINATION ${CMAKE_INSTALL_PREFIX})
-
+install(DIRECTORY "${RR_DEPENDENCIES_INSTALL_PREFIX}/lib" DESTINATION "${CMAKE_INSTALL_PREFIX}")
+install(DIRECTORY "${RR_DEPENDENCIES_INSTALL_PREFIX}/bin" DESTINATION "${CMAKE_INSTALL_PREFIX}")
+install(DIRECTORY "${RR_DEPENDENCIES_INSTALL_PREFIX}/include" DESTINATION "${CMAKE_INSTALL_PREFIX}")
+install(DIRECTORY "${RR_DEPENDENCIES_INSTALL_PREFIX}/share" DESTINATION "${CMAKE_INSTALL_PREFIX}")
+if (WIN32)
+    install(DIRECTORY "${RR_DEPENDENCIES_INSTALL_PREFIX}/cmake" DESTINATION "${CMAKE_INSTALL_PREFIX}")
+endif()
 # install a cmake script for consumer libraries to easily import roadrunner targets
-install(FILES cmake/ImportRoadrunnerAndDependencies.cmake DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake")
+install(FILES "cmake/ImportRoadrunnerAndDependencies.cmake" DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake")
 
 if (${MINGW})
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=gnu++0x")
@@ -495,7 +508,7 @@ if (BUILD_TESTS)
 
     message(STATUS "building tests")
 
-    file(GLOB PYTHON_TEST_FILES "wrappers/Python/roadrunner/testing/*.*")
+    file(GLOB PYTHON_TEST_FILES "test/python/*.*")
 
     file(GLOB PYTHON_TEST_DATA "${CMAKE_CURRENT_SOURCE_DIR}/test/rrtest_files/*.rrtest")
 
@@ -504,21 +517,21 @@ if (BUILD_TESTS)
     foreach (f ${PYTHON_TEST_FILES})
         if (NOT IS_DIRECTORY ${f})
             get_filename_component(FILE_NAME ${f} NAME)
-            configure_file(${f} lib/site-packages/roadrunner/testing/${FILE_NAME} COPYONLY)
+            configure_file(${f} lib/site-packages/roadrunner/tests/${FILE_NAME} COPYONLY)
         endif ()
     endforeach ()
 
     foreach (f ${PYTHON_TEST_DATA})
         if (NOT IS_DIRECTORY ${f})
             get_filename_component(FILE_NAME ${f} NAME)
-            configure_file(${f} lib/site-packages/roadrunner/testing/test_data/${FILE_NAME} COPYONLY)
+            configure_file(${f} lib/site-packages/roadrunner/tests/test_data/${FILE_NAME} COPYONLY)
         endif ()
     endforeach ()
 
     foreach (f ${TEST_DATA_XML})
         if (NOT IS_DIRECTORY ${f})
             get_filename_component(FILE_NAME ${f} NAME)
-            configure_file(${f} lib/site-packages/roadrunner/testing/test_data/${FILE_NAME} COPYONLY)
+            configure_file(${f} lib/site-packages/roadrunner/tests/test_data/${FILE_NAME} COPYONLY)
         endif ()
     endforeach ()
 

README.md

@@ -24,6 +24,8 @@ libroadrunner is a C/C++ library that supports simulation of SBML based models.
 
 We provide C/C++, Python and Julia bindings.
 
+Sometimes the link to the C API docs goes bad in the readthedocs. If this happens, here is a permanent link that should remain whatever happens:
+
 # Installation
 Python front end (stable):
 
@@ -37,7 +39,13 @@ Experimental front end:
 
 `pip install libroadrunner-experimental`
 
-# [Click here to get Documentation](http://sys-bio.github.io/roadrunner/)
+# Documentation
+
+[Python API Documentation](http://sys-bio.github.io/roadrunner/)
+
+[C API Documention](https://sys-bio.github.io/roadrunner/OriginalDoxygenStyleDocs/html/index.html)
+
+# Copyright
 
 Copyright 2013-2021
 
@@ -84,19 +92,21 @@ downloaded from http://sourceforge.net/projects/libroadrunner/files and can be i
 ready for use.
 
 ## Docker images
-Currently we have a manylinux2014 "base" and "build" docker images. The 
+Currently we have a manylinux2014 [build](https://hub.docker.com/repository/docker/ciaranwelsh/roadrunner-manylinux2014-base) docker image. The 
 base provides the environment you need to be able to build roadrunner 
-yourself on manylinux2014 (centos 7). The "build" image, in constrast
-is an image where roadrunner has already been built on top of the "base" 
-image. 
+yourself on manylinux2014 (centos 8).  
+
+There are two docker tags associated with roadrunner depending on which 
+version of llvm you want to build with. The options are llvm-13.x for newer 
+roadrunner versions (> v2.2.0) and llvm-6.x for older.
 
 To get the base image: 
 
-`docker pull ciaranwelsh/roadrunner-manylinux2014-base:latest`
+`docker pull ciaranwelsh/roadrunner-manylinux2014-base:llvm-13.x`
 
 and the build image:
 
-`docker pull ciaranwelsh/roadrunner-manylinux2014-build:latest`
+`docker pull ciaranwelsh/roadrunner-manylinux2014-build:llvm-13.x`
 
 Docker build scripts can be found under the `docker` directory from the roadrunner
 root directory.