Merge pull request #682 from ICB-DCM/develop

Release 0.10.5

Author: dweindl

.travis.yml

@@ -92,7 +92,7 @@ matrix:
           branch: master
 
 install:
-    - export BASE_DIR=`pwd` 
+    - export BASE_DIR=`pwd`
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then mkdir -p ~/bin/ && ln -s /usr/bin/swig3.0 ~/bin/swig && export PATH=~/bin/:$PATH; fi # Python distutils only looks for `swig` and does not find `swig3.0`
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export PYTHON_EXECUTABLE=$(which python3); fi # cmake wont be able to find python3 on its own ...
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CI_MODE" == "test" ]]; then pip3 install --upgrade pip==9.0.3 setuptools wheel pkgconfig scipy; fi
@@ -113,6 +113,7 @@ script:
     - if [[ "$CI_MODE" == "test" ]]; then $FOLD notebooks "cd $BASE_DIR && scripts/runNotebook.sh python/examples/example_*/"; fi
     - if [[ "$TRAVIS_OS_NAME" != "linux" ]] && [[ "$CI_MODE" == "test" ]]; then $FOLD cpputest ./scripts/run-cpputest.sh; fi
     - if [[ "$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 $FOLD python-tests ./tests/testCMakeCompilation.sh; fi
     - if [[ "$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 valgrind ./scripts/run-valgrind.sh; fi
@@ -129,6 +130,6 @@ cache:
     - $HOME/Library/Caches/pip
     - $HOME/.cache/pip
   timeout: 1200
-    
+
 before_cache:
   - brew cleanup

CMakeLists.txt

@@ -2,6 +2,14 @@
 # Build AMICI library
 #
 cmake_minimum_required(VERSION 3.3)
+
+if(POLICY CMP0065)
+  cmake_policy(SET CMP0065 NEW)
+endif(POLICY CMP0065)
+if(POLICY CMP0077)
+  cmake_policy(SET CMP0077 NEW)
+endif(POLICY CMP0077)
+
 project(amici)
 
 set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
@@ -41,7 +49,7 @@ set(SUITESPARSE_LIBRARIES
     )
 
 set(SUNDIALS_LIB_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/lib")
-set(SUNDIALS_LIBRARIES 
+set(SUNDIALS_LIBRARIES
     ${SUNDIALS_LIB_DIR}/libsundials_nvecserial${CMAKE_STATIC_LIBRARY_SUFFIX}
     ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolband${CMAKE_STATIC_LIBRARY_SUFFIX}
     ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolklu${CMAKE_STATIC_LIBRARY_SUFFIX}
@@ -58,6 +66,8 @@ set(SUNDIALS_LIBRARIES
     )
 set(SUNDIALS_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/include")
 
+set(GSL_LITE_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/gsl")
+
 # AMICI requires BLAS, currently Intel MKL, CBLAS or MATLAB BLAS can be used.
 # The latter is not supported via CMake yet.
 set(BLAS "CBLAS" CACHE STRING "BLAS library to use")
@@ -113,6 +123,7 @@ target_include_directories(${PROJECT_NAME}
     $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
     PUBLIC $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>
     PUBLIC swig
+    PUBLIC ${GSL_LITE_INCLUDE_DIR}
     PUBLIC ${SUNDIALS_INCLUDE_DIRS}
     PUBLIC ${SUITESPARSE_INCLUDE_DIRS}
     PUBLIC ${HDF5_INCLUDE_DIRS}
@@ -134,12 +145,12 @@ add_custom_target(matlabInterface SOURCES src/interface_matlab.cpp src/returndat
 add_custom_target(
     fileTemplates
     SOURCES
-    src/CMakeLists.template.txt
+    src/CMakeLists.template.cmake
     src/main.template.cpp
     src/model_header.ODE_template.h
     src/wrapfunctions.ODE_template.h
     src/wrapfunctions.template.cpp
-    swig/CMakeLists_model.txt
+    swig/CMakeLists_model.cmake
     swig/modelname.template.i
     )
 

INSTALL.md

@@ -50,11 +50,11 @@ The python interface requires [SWIG](http://www.swig.org), which has to be insta
 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
-    
+
 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:
 
     mkdir -p ~/bin/ && ln -s $(which swig3.0) ~/bin/swig && export PATH=~/bin/:$PATH
@@ -87,7 +87,7 @@ Note that Microsoft Visual Studio compilers are currently not supported.
 To use AMICI from python, install the module and all other requirements using pip:
 
     pip3 install amici
-    
+
 You can now import it as python module:
 
     import amici
@@ -97,13 +97,13 @@ for use with Matlab or C++ and don't want to bothered with any unnecessary
 dependencies, you can run
 
     pip3 install --install-option --no-clibs amici
-    
+
 Note, however, that you will not be able to compile any model into a Python
 extension with this installation.
 
 #### Anaconda
 
-To use an Anaconda installation of python, proceed as follows:
+To use an Anaconda installation of python (https://www.anaconda.com/distribution/, Python>=3.6), proceed as follows:
 
 Since Anaconda provides own versions of some packages which might not work with amici (in particular the gcc compiler), create a minimal virtual environment via:
 
@@ -127,18 +127,50 @@ The option `--no-cache` may be helpful here to make sure the installation is don
 
 Now, you are ready to use AMICI in the virtual environment.
 
+#### Windows
+
+To install AMICI on Windows using python, you can proceed as follows:
+
+Some general remarks:
+
+* Install all libraries in a path not containing white spaces, e.g. directly under C:.
+* Replace the following paths according to your installation.
+* Slashes can be preferable to backslashes for some environment variables.
+* See also [#425](https://github.com/icb-dcm/amici/issues/425) for further discussion.
+
+Then, follow these steps:
+
+* A python environment for Windows is required. We recommend [Anaconda](https://www.anaconda.com/distribution/) with python >=3.6.
+* Install [mingw64](https://sourceforge.net/projects/mingw-w64/files/latest/download) (32bit will succeed to compile, but fail during linking). During installation, select Version=8.1.0, Architecture=x64_64. Add the following directory to `PATH`:
+    + `C:\mingw-w64\x86_64-8.1.0-posix-sjlj-rt_v6-rev0\mingw64\bin`
+* Make sure that this is the compiler that is found by the system (e.g. `where gcc` in a `cmd` should point to this installation).
+* Download CBLAS headers and libraries, e.g. [OpenBLAS](https://sourceforge.net/projects/openblas/files/v0.2.19/), binary distribution 0.2.19. Set the following environment variables:
+    + `BLAS_CFLAGS=-IC:/OpenBLAS-v0.2.19-Win64-int32/include`
+    + `BLAS_LIBS=-Wl,-Bstatic -LC:/OpenBLAS-v0.2.19-Win64-int32/lib -lopenblas -Wl,-Bdynamic`
+* Install [SWIG](http://www.swig.org/download.html) (version swigwin-3.0.12 worked) and add the following directory to `PATH`:
+    + `C:\swigwin-3.0.12`
+* Install AMICI using:
+
+    `pip install --global-option="build_clib" --global-option="--compiler=mingw32" --global-option="build_ext" --global-option="--compiler=mingw32" amici --no-cache-dir --verbose`
+
+Possible sources of errors:
+
+* On recent Windows versions, `anaconda3\Lib\distutils\cygwinccompiler.py` fails linking `msvcr140.dll` with `[...] x86_64-w64-mingw32/bin/ld.exe: cannot find -lmsvcr140`. This is not required for amici, so in `cygwinccompiler.py` `return ['msvcr140']` can be changed to `return []`.
+* If you use a python version where [python/cpython#880](https://github.com/python/cpython/pull/880) has not been fixed yet, you need to disable `define hypot _hypot in anaconda3\include/pyconfig.h` yourself.
+* `import amici` in python resulting in the very informative "ImportError: DLL load failed: The specified module could not be found." means that some amici module dependencies were not found (not the amici module itself). [DependencyWalker](http://www.dependencywalker.com/) will show you which ones.
+
 ### C++
 
-To use AMICI from C++, run the  
+To use AMICI from C++, run the
 
     ./scripts/buildSundials.sh
     ./scripts/buildSuitesparse.sh
     ./scripts/buildAmici.sh
-    
+
 script to compile amici libary. The static library file can then be linked from 
 
     ./build/libamici.a
- 
+
 In CMake-based packages, amici can be linked via
 
     find_package(Amici)