diff --git a/documentation/python_installation.rst b/documentation/python_installation.rst index 6cc3402e61..dee9bfd4fc 100644 --- a/documentation/python_installation.rst +++ b/documentation/python_installation.rst @@ -79,6 +79,13 @@ Install the AMICI dependencies via ``pacman`` sudo pacman -S python swig openblas gcc hdf5 boost-libs +Export the bash variables ``BLAS_CFLAGS`` and ``BLAS_LIBS`` to point to where BLAS was installed, e.g.: + +.. code-block:: bash + + export BLAS_CFLAGS="-I/usr/include/openblas/" + export BLAS_LIBS="-lopenblas" + Install AMICI: .. code-block:: bash @@ -99,7 +106,14 @@ Alternatively: sudo pacman -Su python swig openblas gcc hdf5 boost-libs -3. Install AMICI: +3. Export the bash variables ``BLAS_CFLAGS`` and ``BLAS_LIBS`` to point to where BLAS was installed, e.g.: + +.. code-block:: bash + + export BLAS_CFLAGS="-I/usr/include/openblas/" + export BLAS_LIBS="-lopenblas" + +4. Install AMICI: .. code-block:: bash diff --git a/include/amici/defines.h b/include/amici/defines.h index 068b8a9d54..f5ed1e62bb 100644 --- a/include/amici/defines.h +++ b/include/amici/defines.h @@ -6,7 +6,6 @@ #endif #include -#include /* Math constants in case _USE_MATH_DEFINES is not supported */ #if defined(_USE_MATH_DEFINES) diff --git a/include/amici/misc.h b/include/amici/misc.h index c18606e3e9..81543b399d 100644 --- a/include/amici/misc.h +++ b/include/amici/misc.h @@ -9,7 +9,6 @@ #include #include #include -#include #include #include @@ -291,7 +290,7 @@ class CpuTimer { return d_milliseconds(clock::now() - start_).count(); } - static const bool uses_thread_clock = true; + static bool const uses_thread_clock = true; private: /** Start time */ @@ -330,7 +329,7 @@ class CpuTimer { / CLOCKS_PER_SEC; } - static const bool uses_thread_clock = false; + static bool const uses_thread_clock = false; private: /** Start time */ diff --git a/include/amici/model_dae.h b/include/amici/model_dae.h index dd16e74666..375ac018fd 100644 --- a/include/amici/model_dae.h +++ b/include/amici/model_dae.h @@ -10,7 +10,6 @@ #include #include -#include #include namespace amici { diff --git a/include/amici/model_ode.h b/include/amici/model_ode.h index 91e0c9cd45..6567ee5c95 100644 --- a/include/amici/model_ode.h +++ b/include/amici/model_ode.h @@ -10,7 +10,6 @@ #include #include -#include #include namespace amici { diff --git a/include/amici/serialization.h b/include/amici/serialization.h index 7d0428f71f..501b56618a 100644 --- a/include/amici/serialization.h +++ b/include/amici/serialization.h @@ -6,10 +6,7 @@ #include "amici/solver.h" #include "amici/solver_cvodes.h" -#include #include -#include -#include #include #include @@ -35,7 +32,7 @@ template void archiveVector(Archive& ar, T** p, int size) { if (Archive::is_loading::value) { if (*p != nullptr) - delete[] * p; + delete[] *p; ar& size; *p = size ? new T[size] : nullptr; } else { diff --git a/include/amici/spline.h b/include/amici/spline.h index 07a436e380..d6f6b24b01 100644 --- a/include/amici/spline.h +++ b/include/amici/spline.h @@ -1,6 +1,5 @@ #ifndef amici_spline_h #define amici_spline_h -#include namespace amici { diff --git a/include/amici/steadystateproblem.h b/include/amici/steadystateproblem.h index dc19c014c4..55c9aaca77 100644 --- a/include/amici/steadystateproblem.h +++ b/include/amici/steadystateproblem.h @@ -8,7 +8,6 @@ #include -#include #include namespace amici { diff --git a/src/amici.cpp b/src/amici.cpp index ee3949b0bf..6e85dde857 100644 --- a/src/amici.cpp +++ b/src/amici.cpp @@ -13,11 +13,6 @@ #include //return codes #include //realtype -#include -#include -#include -#include -#include #include #include #include diff --git a/src/backwardproblem.cpp b/src/backwardproblem.cpp index d1b89967db..c3a859ca85 100644 --- a/src/backwardproblem.cpp +++ b/src/backwardproblem.cpp @@ -8,9 +8,6 @@ #include "amici/solver.h" #include "amici/steadystateproblem.h" -#include -#include - namespace amici { BackwardProblem::BackwardProblem( diff --git a/src/edata.cpp b/src/edata.cpp index ddc3b65992..b9f95fca97 100644 --- a/src/edata.cpp +++ b/src/edata.cpp @@ -5,7 +5,6 @@ #include "amici/symbolic_functions.h" // getNaN #include -#include #include #include diff --git a/src/exception.cpp b/src/exception.cpp index 3a5811e4f5..0e031ccca0 100644 --- a/src/exception.cpp +++ b/src/exception.cpp @@ -3,7 +3,6 @@ #include #include -#include namespace amici { diff --git a/src/forwardproblem.cpp b/src/forwardproblem.cpp index c70a9074b1..72fd87c979 100644 --- a/src/forwardproblem.cpp +++ b/src/forwardproblem.cpp @@ -9,7 +9,6 @@ #include #include -#include namespace amici { diff --git a/src/hdf5.cpp b/src/hdf5.cpp index e0cdde88cd..d9d875cdf7 100644 --- a/src/hdf5.cpp +++ b/src/hdf5.cpp @@ -16,7 +16,6 @@ #include - namespace amici { namespace hdf5 { @@ -1161,8 +1160,8 @@ void readModelDataFromHDF5( model.setSteadyStateComputationMode( static_cast(getIntScalarAttribute( file, datasetPath, "steadyStateComputationMode" - )) - ); + )) + ); } if (attributeExists(file, datasetPath, "steadyStateSensitivityMode")) { diff --git a/src/model.cpp b/src/model.cpp index 017b9cf871..c50fcc60bf 100644 --- a/src/model.cpp +++ b/src/model.cpp @@ -6,7 +6,7 @@ #include #include -#include +#include #include #include #include diff --git a/src/newton_solver.cpp b/src/newton_solver.cpp index b8cbe8f34d..8c3fcca5f4 100644 --- a/src/newton_solver.cpp +++ b/src/newton_solver.cpp @@ -8,10 +8,6 @@ #include // dense solver #include // sparse solver -#include -#include -#include - namespace amici { NewtonSolver::NewtonSolver(Model const& model) diff --git a/src/rdata.cpp b/src/rdata.cpp index 56fc0023c0..e96f295d23 100644 --- a/src/rdata.cpp +++ b/src/rdata.cpp @@ -10,7 +10,6 @@ #include "amici/symbolic_functions.h" #include -#include namespace amici { diff --git a/src/solver.cpp b/src/solver.cpp index 56bed2a1a3..c114623050 100644 --- a/src/solver.cpp +++ b/src/solver.cpp @@ -5,8 +5,6 @@ #include "amici/symbolic_functions.h" #include -#include -#include #include namespace amici { diff --git a/src/splinefunctions.cpp b/src/splinefunctions.cpp index ba9865a729..8c888b450a 100644 --- a/src/splinefunctions.cpp +++ b/src/splinefunctions.cpp @@ -2,9 +2,9 @@ #include "amici/amici.h" #include "amici/defines.h" #include "amici/exception.h" -#include "amici/vector.h" #include // std::min +#include #include #include diff --git a/src/steadystateproblem.cpp b/src/steadystateproblem.cpp index c655b9b386..4576b43363 100644 --- a/src/steadystateproblem.cpp +++ b/src/steadystateproblem.cpp @@ -8,7 +8,6 @@ #include "amici/solver.h" #include -#include #include #include #include diff --git a/src/sundials_linsol_wrapper.cpp b/src/sundials_linsol_wrapper.cpp index de5d4f1d61..765f2a1f91 100644 --- a/src/sundials_linsol_wrapper.cpp +++ b/src/sundials_linsol_wrapper.cpp @@ -2,7 +2,6 @@ #include -#include // bad_alloc #include namespace amici { diff --git a/src/symbolic_functions.cpp b/src/symbolic_functions.cpp index 6c18d851b7..37e10fde62 100644 --- a/src/symbolic_functions.cpp +++ b/src/symbolic_functions.cpp @@ -12,7 +12,6 @@ #include #include #include -#include #if _MSC_VER && !__INTEL_COMPILER #include #define alloca _alloca diff --git a/tests/cpp/unittests/testSerialization.cpp b/tests/cpp/unittests/testSerialization.cpp index 5b4fb1ed2a..a516de0880 100644 --- a/tests/cpp/unittests/testSerialization.cpp +++ b/tests/cpp/unittests/testSerialization.cpp @@ -5,7 +5,7 @@ #include "testfunctions.h" #include - +#include #include void