Merge pull request #780 from ICB-DCM/develop

Release 0.10.10

.gitignore

@@ -160,3 +160,4 @@ ThirdParty/SuiteSparse/lib/*
 ThirdParty/SuiteSparse/share/*
 ThirdParty/SuperLU_MT_3.1/
 ThirdParty/superlu_mt_3.1.tar.gz
+ThirdParty/swig-*

.travis.yml

@@ -9,7 +9,7 @@ matrix:
   fast_finish: true
   include:
     - os: linux
-      dist: xenial
+      dist: bionic
       language: python
       python: 3.7
       compiler: gcc
@@ -23,7 +23,6 @@ matrix:
             - libboost-serialization-dev
             - swig3.0
             - g++-5
-            - cppcheck
             - libc6-dbg
       env:
         - ENABLE_GCOV_COVERAGE=TRUE
@@ -44,7 +43,7 @@ matrix:
           tags: true
 
     - os: osx
-      osx_image: xcode10.1
+      osx_image: xcode11
       language: minimal
       compiler: clang
       env:
@@ -55,6 +54,7 @@ matrix:
             - hdf5
             - swig
             - gcc
+            - cppcheck
           update: true
       before_install:
         - travis_wait brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
@@ -64,7 +64,7 @@ matrix:
         - cd $BASE_DIR # cd to base dir for correct relative path in deploy
 
     - os: osx
-      osx_image: xcode10.1
+      osx_image: xcode11
       language: minimal
       compiler: clang
       env:
@@ -117,7 +117,7 @@ script:
     - if [[ "$TRAVIS_OS_NAME" != "linux" ]] && [[ "$CI_MODE" == "test" ]]; then $FOLD python-tests ./scripts/run-python-tests.sh; fi
     - if [[ "$TRAVIS_OS_NAME" != "linux" ]] && [[ "$CI_MODE" == "test" ]]; then $FOLD cmake ./tests/testCMakeCompilation.sh; fi
     - if [[ "$CI_MODE" == "deploy" ]]; then $FOLD doxygen ./scripts/run-doxygen.sh; fi
-    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CI_MODE" == "test" ]]; then $FOLD cppcheck ./scripts/run-cppcheck.sh; fi
+    - if [[ "$TRAVIS_OS_NAME" != "linux" ]] && [[ "$CI_MODE" == "test" ]]; then $FOLD cppcheck ./scripts/run-cppcheck.sh; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CI_MODE" == "test" ]]; then $FOLD valgrind ./scripts/run-valgrind.sh; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CI_MODE" == "test" ]]; then $FOLD codecov ./scripts/run-codecov.sh; fi
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$TRAVIS_EVENT_TYPE" == "cron" ]]; then $FOLD sbmltestsuite ./scripts/run-SBMLTestsuite.sh; fi

CMakeLists.txt

@@ -9,6 +9,10 @@ endif(POLICY CMP0065)
 if(POLICY CMP0077)
   cmake_policy(SET CMP0077 NEW)
 endif(POLICY CMP0077)
+if(POLICY CMP0074)
+  # Use package_ROOT environment variables
+  cmake_policy(SET CMP0074 NEW)
+endif(POLICY CMP0074)
 
 project(amici)
 
@@ -36,6 +40,7 @@ foreach(FLAG ${MY_CXX_FLAGS})
 endforeach(FLAG)
 
 # find dependencies
+include(GNUInstallDirs)
 find_package(HDF5 COMPONENTS C HL CXX REQUIRED)
 set(HDF5_LIBRARIES ${HDF5_HL_LIBRARIES} ${HDF5_C_LIBRARIES} ${HDF5_CXX_LIBRARIES})
 set(SUITESPARSE_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/SuiteSparse/")
@@ -48,7 +53,7 @@ set(SUITESPARSE_LIBRARIES
     ${SUITESPARSE_DIR}/SuiteSparse_config/libsuitesparseconfig${CMAKE_STATIC_LIBRARY_SUFFIX}
     )
 
-set(SUNDIALS_LIB_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/lib")
+set(SUNDIALS_LIB_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/${CMAKE_INSTALL_LIBDIR}")
 set(SUNDIALS_LIBRARIES
     ${SUNDIALS_LIB_DIR}/libsundials_nvecserial${CMAKE_STATIC_LIBRARY_SUFFIX}
     ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolband${CMAKE_STATIC_LIBRARY_SUFFIX}
@@ -83,14 +88,22 @@ set(GSL_LITE_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/gsl")
 # The latter is not supported via CMake yet.
 set(BLAS "CBLAS" CACHE STRING "BLAS library to use")
 set_property(CACHE BLAS PROPERTY STRINGS "CBLAS" "MKL" "ACCELERATE")
-add_definitions(-DAMICI_BLAS_${BLAS})
-if(${BLAS} STREQUAL "MKL")
-    set(BLAS_INCLUDE_DIRS "" CACHE STRING "")
-    set(BLAS_LIBRARIES -lmkl CACHE STRING "")
+if(${BLAS} STREQUAL "MKL" OR DEFINED ENV{MKLROOT})
+    if(DEFINED ENV{MKLROOT})
+        # This is set by Environment Modules
+        message(STATUS "Using MKL_INCDIR and MKL_LIB from environment module")
+        set(BLAS "MKL" CACHE STRING "BLAS library to use" FORCE)
+        set(BLAS_INCLUDE_DIRS "$ENV{MKL_INCDIR}" CACHE STRING "" FORCE)
+        set(BLAS_LIBRARIES "$ENV{MKL_LIB}" CACHE STRING "" FORCE)
+    else()
+        set(BLAS_INCLUDE_DIRS "" CACHE STRING "")
+        set(BLAS_LIBRARIES -lmkl CACHE STRING "")
+    endif()
 else()
     set(BLAS_INCLUDE_DIRS "" CACHE STRING "")
     set(BLAS_LIBRARIES -lcblas CACHE STRING "")
 endif()
+add_definitions(-DAMICI_BLAS_${BLAS})
 
 # Add target to create version file
 add_custom_target(
@@ -178,7 +191,6 @@ set(AUTHORS "Fabian Froehlich, Jan Hasenauer, Daniel Weindl and Paul Stapor")
 set(AUTHOR_EMAIL "[email protected]")
 
 # <Export cmake configuration>
-include(GNUInstallDirs)
 install(TARGETS ${PROJECT_NAME} EXPORT AmiciTargets
     ARCHIVE  DESTINATION ${CMAKE_INSTALL_LIBDIR}
     LIBRARY  DESTINATION ${CMAKE_INSTALL_LIBDIR}

INSTALL.md

@@ -47,6 +47,8 @@ You can now import it as python module:
 
     import amici
 
+For cases where this installation fails, check below for special setups
+and custom installations.
 For Python-AMICI usage see 
 [https://github.com/ICB-DCM/AMICI/blob/master/documentation/PYTHON.md](https://github.com/ICB-DCM/AMICI/blob/master/documentation/PYTHON.md).
 
@@ -181,6 +183,21 @@ Possible sources of errors:
   [DependencyWalker](http://www.dependencywalker.com/) will show you
   which ones.
 
+### Custom installation
+
+AMICI Python package installation can be customized using a number of
+environment variables:
+
+|Variable | Purpose | Example |
+|---|---|---|
+|`CC`| Setting the C(++) compiler | `CC=/usr/bin/g++`| 
+|`CFLAGS`| Extra compiler flags used in every compiler call | | 
+|`BLAS_CFLAGS`| Compiler flags for, e.g. BLAS include directories | | 
+|`BLAS_LIBS`| Flags for linking BLAS | | 
+|`ENABLE_GCOV_COVERAGE`| Set to build AMICI to provide code coverage information | `ENABLE_GCOV_COVERAGE=TRUE`| 
+|`ENABLE_AMICI_DEBUGGING`| Set to build AMICI with debugging symbols | `ENABLE_AMICI_DEBUGGING=TRUE`| 
+|`AMICI_PARALLEL_COMPILE`| Set to the number of parallel processes to be used for C(++) file compilation (defaults to 1)| `AMICI_PARALLEL_COMPILE=4`|
+
 
 <a name="matlab"></a>
 ## MATLAB
@@ -219,6 +236,11 @@ To use AMICI from C++, run the
 
 script to compile AMICI library.
 
+**NOTE**: On some systems, the CMake executable may be named something
+other than `cmake`. In this case, set the `CMAKE` environment variable
+to the correct name (e.g. `export CMAKE=cmake3`, in case you have CMake
+available as `cmake3`).
+
 The static library file can then be linked from
 
     ./build/libamici.a
@@ -311,21 +333,33 @@ or
 #### SWIG
 
 The python interface requires [SWIG](http://www.swig.org), which has to
-be installed by the user. Swig can be installed using package managers
-such as [brew](https://brew.sh) or [apt](https://wiki.debian.org/Apt):
+be installed by the user. As root user, SWIG can be installed using
+package managers such as [brew](https://brew.sh) or
+[apt](https://wiki.debian.org/Apt):
 
     brew install swig
 
 or
 
     apt-get install swig3.0
 
+Or by non-root users, using `scripts/downloadAndBuildSwig.sh` from the
+AMICI repository (not included in the PyPI package). The binary
+directory has to be added to the `PATH` environment variable, or `SWIG`
+has to be set as described in the following section.
+
+
+##### Using a non-default SWIG executable
+
 We note here that some linux package managers may provide swig
 executables as `swig3.0`, but installation as `swig` is required. This
-can be fixed using, e.g., symbolic links:
+can be fixed as root user using, e.g., symbolic links:
 
     mkdir -p ~/bin/ && ln -s $(which swig3.0) ~/bin/swig && export PATH=~/bin/:$PATH
 
+Non-root users can set the `SWIG` environment variable to the full
+path of the desired SWIG executable. This variable has be set during
+AMICI package installation as well as during model compilation.
 
 ### Matlab
 

cmake/version.cmake

@@ -6,7 +6,11 @@ if(Git_FOUND)
         )
 endif()
 
+# get project root directory
+get_filename_component(CMAKE_PARENT_LIST_DIR ${CMAKE_PARENT_LIST_FILE} DIRECTORY)
+get_filename_component(CMAKE_PARENT_LIST_DIR ${CMAKE_PARENT_LIST_DIR} DIRECTORY)
+
 execute_process(COMMAND sh -c "cat version.txt | tr -d '\n'"
-    WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+    WORKING_DIRECTORY "${CMAKE_PARENT_LIST_DIR}"
     OUTPUT_VARIABLE PROJECT_VERSION
     )

documentation/PYTHON.md

@@ -25,10 +25,10 @@ parameters that should be considered constants can be specified in a list of str
 
 ### Observables
 
-assignment rules that should be considered as observables can extracted using the `amici.assignmentRules2observables` function
+Assignment rules that should be considered as observables can extracted using the `amici.assignmentRules2observables` function.
 
-    observables = amici.assignmentRules2observables(sbml, filter=lambda variableId: 
-                                                    variableId.startswith('observable_') and not variableId.endswith('_sigma'))
+    observables = amici.assignmentRules2observables(sbml, filter_function=lambda variable: 
+                                                    variable.getId().startswith('observable_') and not variable.getId().endswith('_sigma'))
 
 ### Standard Deviations
 
@@ -44,7 +44,7 @@ to compile the sbml as python module, the user has to call the method `amici.sbm
     sbmlImporter.sbml2amici('test', 'test', 
                             observables=observables,
                             constantParameters=constantParameters,
-                            sigmas=sigma)
+                            sigmas=sigmas)
 
 Note: To build AMICI with OpenMP support, which allows to parallelize model simulations of multiple
 experimental conditions, set the environment variables `AMICI_CXXFLAGS` and `AMICI_LDFLAGS` to the