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CNES / aviso-lagrangian

Finite Size Lyapunov Exponent (FSLE) is a local lagrangian diagnostics that is widely used for the study of transport and mixing processes of oceanographic tracers (Sea surface temperature, Ocean color ...). Its computation is derived from the definition of Finite-Time Lyapunov Exponent that allows the identification of Lagrangian Coherent Structures.
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Hi, I has had this problem when run the test (python setup.py test) #1

Open sebacornnejo opened 1 year ago

sebacornnejo commented 1 year ago

running test running egg_info writing src/lagrangian.egg-info/PKG-INFO writing dependency_links to src/lagrangian.egg-info/dependency_links.txt writing entry points to src/lagrangian.egg-info/entry_points.txt writing top-level names to src/lagrangian.egg-info/top_level.txt reading manifest file 'src/lagrangian.egg-info/SOURCES.txt' adding license file 'COPYING' writing manifest file 'src/lagrangian.egg-info/SOURCES.txt' running build_ext cmake /home/sebacornnejo/Software/aviso-lagrangian-main -DCMAKE_BUILD_TYPE=Release -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/sebacornnejo/Software/aviso-lagrangian-main/build/lib.linux-x86_64-3.7/lagrangian -DPYTHON_EXECUTABLE=/home/sebacornnejo/anaconda3/envs/env_FSLE/bin/python -DBoost_NO_SYSTEM_PATHS=TRUE -DBoost_NO_BOOST_CMAKE=TRUE -DBOOST_ROOT=/home/sebacornnejo/anaconda3/envs/env_FSLE -DUDUNITS2_ROOT=/home/sebacornnejo/anaconda3/envs/env_FSLE -DNETCDF_DIR=/home/sebacornnejo/anaconda3/envs/env_FSLE -DCMAKE_PREFIX_PATH=/home/sebacornnejo/anaconda3/envs/env_FSLE -DCMAKE_BUILD_TYPE=Release Re-run cmake no build system arguments -- pybind11 v2.11.0 dev1 -- Configuring done -- Generating done -- Build files have been written to: /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 cmake --build . --target core --config Release -- -j12 /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -S/home/sebacornnejo/Software/aviso-lagrangian-main -B/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/gmake -f CMakeFiles/Makefile2 core gmake[1]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -S/home/sebacornnejo/Software/aviso-lagrangian-main -B/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 --check-build-system CMakeFiles/Makefile.cmake 0 /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_progress_start /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles 54 /usr/bin/gmake -f CMakeFiles/Makefile2 CMakeFiles/core.dir/all gmake[2]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' /usr/bin/gmake -f CMakeFiles/lagrangian.dir/build.make CMakeFiles/lagrangian.dir/depend /usr/bin/gmake -f CMakeFiles/ncxx4.dir/build.make CMakeFiles/ncxx4.dir/depend gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' cd /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 && /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_depends "Unix Makefiles" /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/DependInfo.cmake --color= gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' cd /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 && /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_depends "Unix Makefiles" /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37 /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/ncxx4.dir/DependInfo.cmake --color= Dependencies file "CMakeFiles/lagrangian.dir/src/lib/axis.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal". Dependencies file "CMakeFiles/ncxx4.dir/third_party/netcdf-cxx4/cxx4/ncAtt.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/ncxx4.dir/compiler_depend.internal". Dependencies file "CMakeFiles/ncxx4.dir/third_party/netcdf-cxx4/cxx4/ncByte.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/ncxx4.dir/compiler_depend.internal". Dependencies file "CMakeFiles/lagrangian.dir/src/lib/datetime.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/lagrangian.dir/compiler_depend.internal". Dependencies file "CMakeFiles/ncxx4.dir/third_party/netcdf-cxx4/cxx4/ncChar.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/ncxx4.dir/compiler_depend.internal". 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Dependencies file "CMakeFiles/core.dir/src/core/map.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/core.dir/compiler_depend.internal". Dependencies file "CMakeFiles/core.dir/src/core/reader.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/core.dir/compiler_depend.internal". Dependencies file "CMakeFiles/core.dir/src/core/unit.cpp.o.d" is newer than depends file "/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles/core.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target core gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' /usr/bin/gmake -f CMakeFiles/core.dir/build.make CMakeFiles/core.dir/build gmake[3]: se entra en el directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' gmake[3]: No se hace nada para 'CMakeFiles/core.dir/build'. gmake[3]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' [100%] Built target core gmake[2]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' /home/sebacornnejo/anaconda3/envs/env_FSLE/bin/cmake -E cmake_progress_start /home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37/CMakeFiles 0 gmake[1]: se sale del directorio '/home/sebacornnejo/Software/aviso-lagrangian-main/build/temp.linux-x86_64-cpython-37' ============================= test session starts ============================== platform linux -- Python 3.7.12, pytest-6.2.3, py-1.10.0, pluggy-0.13.1 rootdir: /home/sebacornnejo/Software/aviso-lagrangian-main collected 2 items / 5 errors

==================================== ERRORS ==================================== _ ERROR collecting tests/test_datetime.py __ ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_datetime.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_datetime.py:17: in import lagrangian src/lagrangian/init.py:15: in from .core import ( E ImportError: dynamic module does not define module export function (PyInitcore) ____ ERROR collecting tests/testfield.py ____ ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_field.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_field.py:18: in import lagrangian src/lagrangian/init.py:15: in from .core import ( E ImportError: dynamic module does not define module export function (PyInit_core) __ ERROR collecting tests/test_integration.py __ ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_integration.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_integration.py:17: in import lagrangian src/lagrangian/init.py:15: in from .core import ( E ImportError: dynamic module does not define module export function (PyInit_core) __ ERROR collecting tests/test_map.py __ ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_map.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_map.py:18: in import lagrangian src/lagrangian/init.py:15: in from .core import ( E ImportError: dynamic module does not define module export function (PyInit_core) ____ ERROR collecting tests/testreader.py ____ ImportError while importing test module '/home/sebacornnejo/Software/aviso-lagrangian-main/tests/test_reader.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../anaconda3/envs/env_FSLE/lib/python3.7/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_reader.py:19: in import lagrangian src/lagrangian/init.py:15: in from .core import ( E ImportError: dynamic module does not define module export function (PyInit_core) =========================== short test summary info ============================ ERROR tests/test_datetime.py ERROR tests/test_field.py ERROR tests/test_integration.py ERROR tests/test_map.py ERROR tests/test_reader.py !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!! ============================== 5 errors in 0.46s ===============================

Regards!!!

albertotb commented 1 year ago

I've also had this problem when building from source. Installing from conda is an alternative that seems to work:

conda install -c fbriol lagrangian