Merge pull request #633 from ICB-DCM/develop

0.10.0 Release

Author: FFroehlich

.gitignore

@@ -1,193 +1,99 @@
-SuiteSparse/include/*
-
-SuiteSparse/lib/*
-
-SuiteSparse/share/*
-
-sundials/build/*
-
 CMakeFiles/*
 
 build/*
-
 build-debug/*
-
 build_xcode/*
-
 swig/python/build/*
-
 tests/cpputest/build/*
-
 tests/cpputest/build_xcode/*
-
 tests/cpputest/Testing/*
 
-ThirdParty/*
-
 doc/*
-
 fonts/*
-
-sed-ml/*
-
-stylesheets/*
-
-scripts/env.sh
-
 images/*
+stylesheets/*
 
-debug_amici/*
+sed-ml/*
 
 models/*
-
 !models/model_dirac
-
 models/model_dirac/build/*
-
 !models/model_steadystate
-
 models/model_steadystate/build/*
-
 !models/model_jakstat_adjoint
-
 models/model_jakstat_adjoint/build/*
-
 !models/model_jakstat_adjoint_o2
-
 models/model_jakstat_adjoint_o2/build/*
-
 !models/model_neuron
-
 models/model_neuron/build/*
-
 !models/model_neuron_o2
-
 models/model_neuron_o2/build/*
-
 !models/model_events
-
 models/model_events/build/*
-
 !models/model_nested_events
-
 models/model_nested_events/build/*
-
 !models/model_robertson
-
 models/model_robertson/build/*
 
 simulate_model_*_hdf.m
-
 simulate_model_*.m
 
-.DS_Store
-
 index.html
 
-Makefile
-
 AMICI.mlappinstall
 
+Makefile
 cmake_install.cmake
-
 CMakeCache.txt
-
 CMakeLists.txt.user
 
 .coveralls.yml
+.directory
+.project
+.pydevproject
+.settings/
+.idea/*
+.DS_Store
+.ipynb_checkpoints/
+python/.idea/*
 
 *.a
-
 *.info
-
 *.o
-
 *.obj
-
 *.eps
-
 *.mexmaci64
-
 *.mexa64
-
 *.mexw64
-
 *.mexmaci32
-
 *.mexa32
-
 *.mexw32
-
 *.eps
-
-*.js
-
 *.md5
-
 *.json
-
 *.mat
-
-*.js
-
-*.json
-
 *.m~
-
 *.plist
-
 *.make
-
 *.bin
-
 *.csv
-
 *.log
-
-tests/sbml-test-suite/
-
-tests/sedml-test-suite/
-
-tests/SBMLTestModels/
+*.pyc
+*.so
 
 matlab/mtoc/config/latexextras.sty-e
-
 matlab/mtoc/config/latexextras.sty
-
 matlab/mtoc/config/Doxyfile-e
 
-.directory
-
-.project
-
-.pydevproject
-
-.settings/
-
 cppcheck.txt
+coverage_py.xml
+testSuite.txt
 
 __pycache__
 
-tests/cpputest/writeResults.h5
-
-tests/cpputest/writeResults.h5.bak
-
-tests/sbml-test-suite/*
-
-python/.idea/misc.xml
-
-python/.idea/modules.xml
-
-python/.idea/python.iml
-
-python/.idea/workspace.xml
-
-.ipynb_checkpoints/
-
-*.pyc
+/misc.xml
 
 python/testSpeedy.py
-
 python/test.txt
 
 tests/test/*
@@ -212,28 +118,36 @@ tests/kinase_cascade_amici/*
 tests/hello_pysb_amici/*
 tests/fricker_2010_apoptosis_amici/*
 tests/explicit_amici/*
-
+tests/fixed_initial_amici/*
+tests/cpputest/writeResults.h5
+tests/cpputest/writeResults.h5.bak
+tests/sbml-test-suite/*
+tests/sbml-test-suite/
+tests/sedml-test-suite/
 */sbml-semantic-test-cases/*
+tests/SBMLTestModels/
 /python/test/amici-SBMLTest*/
-coverage_py.xml
-
-.idea/*
 
 python/examples/example_steadystate/model_steadystate_scaled/*
 python/examples/example_presimulation/model_presimulation/*
 python/examples/example_presimulation/model_presimulation_re/*
 
 python/sdist/amici.egg-info/*
-
 python/sdist/amici/version.txt
 python/sdist/amici/amici.py
 python/sdist/amici/amici_wrap.cxx
 python/sdist/amici/amici_without_hdf5.py
 python/sdist/amici/amici_wrap_without_hdf5.cxx
 
-testSuite.txt
-
 python/sdist/build/*
-*.so
 python/sdist/amici/git_version.txt
+
 AMICI_guide.pdf
+
+ThirdParty/bionetgen.tar.gz
+ThirdParty/BioNetGen-*
+ThirdParty/cpputest-master*
+ThirdParty/mtocpp-master*
+ThirdParty/sundials/build/*
+ThirdParty/SuiteSparse/lib/*
+ThirdParty/SuiteSparse/share/*

.travis.yml

@@ -84,8 +84,8 @@ install:
     - 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 git+https://github.com/pysb/pysb; fi
-    - if [[ "$TRAVIS_OS_NAME" != "linux" ]] && [[ "$CI_MODE" == "test" ]]; then pip3 install --user --upgrade pip==9.0.3 setuptools wheel pkgconfig scipy git+https://github.com/pysb/pysb; fi
+    - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CI_MODE" == "test" ]]; then pip3 install --upgrade pip==9.0.3 setuptools wheel pkgconfig scipy; fi
+    - if [[ "$TRAVIS_OS_NAME" != "linux" ]] && [[ "$CI_MODE" == "test" ]]; then pip3 install --user --upgrade pip==9.0.3 setuptools wheel pkgconfig scipy; fi
     - if [[ "$CI_MODE" == "deploy" ]]; then pip3 install --user --upgrade pip==9.0.3 doxypypy; fi # pinning pip because of https://github.com/pypa/pip/issues/5240
     - if [[ "$CI_MODE" == "test" ]]; then ./scripts/buildSuiteSparse.sh; fi
     - if [[ "$CI_MODE" == "test" ]]; then ./scripts/buildSundials.sh; fi
@@ -101,6 +101,8 @@ script:
     - export FOLD=$BASE_DIR/scripts/travis_wrap.sh
     - cd $BASE_DIR
     - if [[ "$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 $FOLD python-tests ./scripts/run-python-tests.sh; fi
     - if [[ "$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

CMakeLists.txt

@@ -41,11 +41,22 @@ set(SUITESPARSE_LIBRARIES
     )
 
 set(SUNDIALS_LIB_DIR "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/lib")
-set(SUNDIALS_LIBRARIES ${SUNDIALS_LIB_DIR}/libsundials_nvecserial${CMAKE_STATIC_LIBRARY_SUFFIX}
+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}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolpcg${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolspbcgs${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunlinsolspfgmr${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunmatrixband${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunmatrixdense${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunmatrixsparse${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunnonlinsolfixedpoint${CMAKE_STATIC_LIBRARY_SUFFIX}
+    ${SUNDIALS_LIB_DIR}/libsundials_sunnonlinsolnewton${CMAKE_STATIC_LIBRARY_SUFFIX}
     ${SUNDIALS_LIB_DIR}/libsundials_cvodes${CMAKE_STATIC_LIBRARY_SUFFIX}
     ${SUNDIALS_LIB_DIR}/libsundials_idas${CMAKE_STATIC_LIBRARY_SUFFIX}
     )
-set(SUNDIALS_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/include")
+set(SUNDIALS_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/ThirdParty/sundials/build/include")
 
 # AMICI requires BLAS, currently Intel MKL, CBLAS or MATLAB BLAS can be used.
 # The latter is not supported via CMake yet.
@@ -89,6 +100,7 @@ set(AMICI_SRC_LIST
     ${CMAKE_SOURCE_DIR}/src/steadystateproblem.cpp
     ${CMAKE_SOURCE_DIR}/src/backwardproblem.cpp
     ${CMAKE_SOURCE_DIR}/src/sundials_matrix_wrapper.cpp
+    ${CMAKE_SOURCE_DIR}/src/sundials_linsol_wrapper.cpp
     ${CMAKE_SOURCE_DIR}/src/abstract_model.cpp
     )
 

INSTALL.md

@@ -96,7 +96,7 @@ In case you only want to use the AMICI Python package for generating model code
 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
+    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.