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AMICI-dev / AMICI

Advanced Multilanguage Interface to CVODES and IDAS
https://amici.readthedocs.io/
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sdist/install ignores changes in headers #1045

Closed FFroehlich closed 4 years ago

FFroehlich commented 4 years ago

major pain in the butt to debug any templated function ...

dweindl commented 4 years ago

I thought I always set force=True there. Happens for clib or extension?

FFroehlich commented 4 years ago

happens with scripts/installAmiciSource.sh. Would also be good if the amici library gets deleted since installation sometimes fails due to inconsistent (new, swig-generated) amici.py and old library object (which potentially misses new symbols).

dweindl commented 4 years ago

Can you show some verbose installation logs? Not sure why this would happen. Should recompile every time.

FFroehlich commented 4 years ago 
hdf5.h found in /usr/local/include
    libhdf5.a found in /usr/local/lib
    HDF5 library found. Building AMICI with HDF5 support.
    ENABLE_AMICI_DEBUGGING was set to TRUE. Building AMICI with debug symbols.
    running develop
    Testing SWIG executable swig4.0... FAILED.
    Testing SWIG executable swig3.0... FAILED.
    Testing SWIG executable swig... SUCCEEDED.
    Found SWIG version (4, 0, 1)
    Running SWIG: swig -doxygen -c++ -python -py3 -threads -Iamici/swig -Iamici/include -DAMICI_SWIG_WITHOUT_HDF5 -outdir /Users/ffroehlich/Documents/GitHub/AMICI/python/sdist/amici -o amici/amici_wrap_without_hdf5.cxx amici/swig/amici.i
    Running SWIG: swig -doxygen -c++ -python -py3 -threads -Iamici/swig -Iamici/include -outdir /Users/ffroehlich/Documents/GitHub/AMICI/python/sdist/amici -o amici/amici_wrap.cxx amici/swig/amici.i
    Changed cflags for amici with unix to ['-g', '-O0', '-Xpreprocessor', '-fopenmp', '-std=c++14']
    Changed cflags for sundials with unix to ['-g', '-O0', '-Xpreprocessor', '-fopenmp', '-Wno-misleading-indentation']
    Changed cflags for suitesparse with unix to ['-g', '-O0', '-Xpreprocessor', '-fopenmp', '-DDLONG', '-Wno-unused-but-set-variable']
    building 'amici' library
    ar rcs build/temp.macosx-10.14-x86_64-3.7/libamici.a build/temp.macosx-10.14-x86_64-3.7/amici/src/forwardproblem.o build/temp.macosx-10.14-x86_64-3.7/amici/src/symbolic_functions.o build/temp.macosx-10.14-x86_64-3.7/amici/src/cblas.o build/temp.macosx-10.14-x86_64-3.7/amici/src/rdata.o build/temp.macosx-10.14-x86_64-3.7/amici/src/exception.o build/temp.macosx-10.14-x86_64-3.7/amici/src/misc.o build/temp.macosx-10.14-x86_64-3.7/amici/src/solver_cvodes.o build/temp.macosx-10.14-x86_64-3.7/amici/src/sundials_linsol_wrapper.o build/temp.macosx-10.14-x86_64-3.7/amici/src/edata.o build/temp.macosx-10.14-x86_64-3.7/amici/src/model_ode.o build/temp.macosx-10.14-x86_64-3.7/amici/src/backwardproblem.o build/temp.macosx-10.14-x86_64-3.7/amici/src/hdf5.o build/temp.macosx-10.14-x86_64-3.7/amici/src/solver_idas.o build/temp.macosx-10.14-x86_64-3.7/amici/src/model_dae.o build/temp.macosx-10.14-x86_64-3.7/amici/src/vector.o build/temp.macosx-10.14-x86_64-3.7/amici/src/newton_solver.o build/temp.macosx-10.14-x86_64-3.7/amici/src/amici.o build/temp.macosx-10.14-x86_64-3.7/amici/src/abstract_model.o build/temp.macosx-10.14-x86_64-3.7/amici/src/model.o build/temp.macosx-10.14-x86_64-3.7/amici/src/steadystateproblem.o build/temp.macosx-10.14-x86_64-3.7/amici/src/solver.o build/temp.macosx-10.14-x86_64-3.7/amici/src/spline.o build/temp.macosx-10.14-x86_64-3.7/amici/src/sundials_matrix_wrapper.o
    ranlib build/temp.macosx-10.14-x86_64-3.7/libamici.a
    building 'sundials' library
    ar rcs build/temp.macosx-10.14-x86_64-3.7/libsundials.a build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunmatrix/dense/sunmatrix_dense.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunmatrix/band/sunmatrix_band.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunmatrix/sparse/sunmatrix_sparse.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/spgmr/sunlinsol_spgmr.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/sptfqmr/sunlinsol_sptfqmr.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/klu/sunlinsol_klu.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/dense/sunlinsol_dense.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/spfgmr/sunlinsol_spfgmr.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/pcg/sunlinsol_pcg.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/spbcgs/sunlinsol_spbcgs.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunlinsol/band/sunlinsol_band.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_direct.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idaa.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_ic.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_nls_stg.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_bbdpre.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_spils.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_nls.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_ls.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_io.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idas_nls_sim.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/idas/idaa_io.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_math.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_matrix.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_direct.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_nvector_senswrapper.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_dense.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_nvector.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_version.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_iterative.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_nonlinearsolver.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_linearsolver.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_band.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sundials/sundials_futils.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunnonlinsol/newton/sunnonlinsol_newton.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/sunnonlinsol/fixedpoint/sunnonlinsol_fixedpoint.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/nvector/serial/nvector_serial.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_spils.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_nls_stg.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_ls.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_nls_stg1.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_bbdpre.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_bandpre.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodea.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_nls_sim.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodea_io.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_nls.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_diag.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_io.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/sundials/src/cvodes/cvodes_direct.o
    ranlib build/temp.macosx-10.14-x86_64-3.7/libsundials.a
    building 'suitesparse' library
    ar rcs build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_analyze_given.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_analyze.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_defaults.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_diagnostics.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_dump.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_extract.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_factor.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_free_numeric.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_free_symbolic.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_kernel.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_memory.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_refactor.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_scale.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_sort.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_solve.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu_tsolve.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/KLU/Source/klu.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_1.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_2.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_aat.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_control.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_defaults.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_dump.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_global.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_info.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_order.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_post_tree.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_postorder.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_preprocess.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/AMD/Source/amd_valid.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/COLAMD/Source/colamd.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/BTF/Source/btf_maxtrans.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/BTF/Source/btf_order.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/BTF/Source/btf_strongcomp.o build/temp.macosx-10.14-x86_64-3.7/amici/ThirdParty/SuiteSparse/SuiteSparse_config/SuiteSparse_config.o
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a(klu_dump.o) has no symbols
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a(amd_dump.o) has no symbols
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a(amd_global.o) has no symbols
    ranlib build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a(klu_dump.o) has no symbols
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a(amd_dump.o) has no symbols
    /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a(amd_global.o) has no symbols
    running egg_info
    writing amici.egg-info/PKG-INFO
    writing dependency_links to amici.egg-info/dependency_links.txt
    writing entry points to amici.egg-info/entry_points.txt
    writing requirements to amici.egg-info/requires.txt
    writing top-level names to amici.egg-info/top_level.txt
    reading manifest file 'amici.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'amici.egg-info/SOURCES.txt'
    running build_ext
    copying build/temp.macosx-10.14-x86_64-3.7/libamici.a -> /Users/ffroehlich/Documents/GitHub/AMICI/python/sdist/amici/libs/libamici.a
    copying build/temp.macosx-10.14-x86_64-3.7/libsundials.a -> /Users/ffroehlich/Documents/GitHub/AMICI/python/sdist/amici/libs/libsundials.a
    copying build/temp.macosx-10.14-x86_64-3.7/libsuitesparse.a -> /Users/ffroehlich/Documents/GitHub/AMICI/python/sdist/amici/libs/libsuitesparse.a
    Changed extra_compile_args for unix to ['-g', '-O0', '-Xpreprocessor', '-fopenmp', '-std=c++14']
    building 'amici._amici' extension
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -Iamici/include -Iamici/ThirdParty/gsl/ -Iamici/ThirdParty/sundials/include -Iamici/ThirdParty/sundials/src -Iamici/ThirdParty/SuiteSparse/KLU/Include/ -Iamici/ThirdParty/SuiteSparse/AMD/Include/ -Iamici/ThirdParty/SuiteSparse/COLAMD/Include/ -Iamici/ThirdParty/SuiteSparse/BTF/Include/ -Iamici/ThirdParty/SuiteSparse/SuiteSparse_config -Iamici/ThirdParty/SuiteSparse/include -Iamici/ThirdParty/SuiteSparse/KLU/Include/ -Iamici/ThirdParty/SuiteSparse/AMD/Include/ -Iamici/ThirdParty/SuiteSparse/COLAMD/Include/ -Iamici/ThirdParty/SuiteSparse/BTF/Include/ -Iamici/ThirdParty/SuiteSparse/SuiteSparse_config -Iamici/ThirdParty/SuiteSparse/include -I/usr/local/include -I/Users/ffroehlich/Documents/GitHub/AMICI/build/venv/lib/python3.7/site-packages/numpy/core/include -I/Users/ffroehlich/Documents/GitHub/AMICI/build/venv/include -I/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c amici/amici_wrap.cxx -o build/temp.macosx-10.14-x86_64-3.7/amici/amici_wrap.o -g -O0 -Xpreprocessor -fopenmp -std=c++14
    clang++ -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk build/temp.macosx-10.14-x86_64-3.7/amici/amici_wrap.o -L/usr/local/lib -Lamici/libs -Lbuild/temp.macosx-10.14-x86_64-3.7 -lamici -lsundials -lsuitesparse -o build/lib.macosx-10.14-x86_64-3.7/amici/_amici.cpython-37m-darwin.so -lcblas -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 -g -Xpreprocessor -fopenmp -lomp
    copying build/lib.macosx-10.14-x86_64-3.7/amici/_amici.cpython-37m-darwin.so -> amici
    Creating /Users/ffroehlich/Documents/GitHub/AMICI/build/venv/lib/python3.7/site-packages/amici.egg-link (link to .)
    Adding amici 0.10.21 to easy-install.pth file
    Installing amici_import_petab script to /Users/ffroehlich/Documents/GitHub/AMICI/build/venv/bin
    Installing amici_import_petab.py script to /Users/ffroehlich/Documents/GitHub/AMICI/build/venv/bin

    Installed /Users/ffroehlich/Documents/GitHub/AMICI/python/sdist

Looks like its just relinking the static libraries and not rebuilding them.