Merge branch 'master' into features/materials
e0a01ad22e7e
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Authored by frerot on May 9 2022, 15:47.

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Merge branch 'master' into features/materials

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frerot

May 9 2022, 15:47

Pushed

frerot

May 9 2022, 15:49

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rTAMAAS93fa1380f6bd: flake8 formating
rTAMAAS26424b111ba5: Merge branch 'master' into features/materials

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frerot committed rTAMAASe0a01ad22e7e: Merge branch 'master' into features/materials (authored by frerot).May 9 2022, 15:47

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
93fa1380f6bd	frerot	flake8 formating	May 9 2022
d19c6d819ecd	frerot	correctly handling dump mpi compatibility	May 6 2022
6c36659917ba	frerot	added test for publications	May 6 2022
94fe16d9801f	frerot	using local and global variables for publications	May 6 2022
3c46870d9e1a	frerot	added emojis to readme	May 6 2022
0eb41bf3cc68	frerot	refreshed README	May 6 2022
b6681ec70d25	frerot	handling test when nc-config is missing	May 5 2022
2eedc50cbe2c	frerot	added tests for netcdf mpi IO	May 5 2022
5a6df2de8725	frerot	fixed test error when uvw not installed	May 5 2022
f5cabe2f7b85	frerot	correctly setting PYTHONPATH for scons test	May 5 2022
c41c37254b85	frerot	ensuring consistent compiler flags in configure	May 2 2022
41d64abe7e11	frerot	added __all__ definition in utils.py	May 2 2022
18ccd214e887	frerot	added CITATION.cff	Apr 27 2022
1825edb7098a	frerot	adding Tamaas information to dump files	Apr 25 2022
1ff450e7eb80	frerot	logging last iteration in contact solvers	Apr 22 2022
02dde1d5fb78	frerot	added functional accessor for contact solvers	Apr 22 2022
aa6cca2b4d5f	frerot	[doc] added mentions of NetCDFDumper with MPI	Apr 14 2022
fdd25350ee5b	frerot	NetCDFDumper can now dump in MPI	Apr 14 2022
808f4ef5312b	frerot	defining boundary field predicate in C++	Apr 14 2022
9f4af773627d	frerot	building wheels for CPython 3.10	Apr 13 2022
161c4a472b3a	frerot	[doc] using python 3.9 in RTD	Apr 13 2022
065559880bba	frerot	[doc] added inkscape for better svg renders	Apr 13 2022
a554b1529b91	frerot	[doc] not setting python.version for RTD	Apr 13 2022
9e7bd7be633a	frerot	[doc] adjusting RTD config	Apr 13 2022
35573d1ad029	frerot	[doc] specified tools.python for RTD	Apr 13 2022
155db27422cb	frerot	[doc] setting RTD image to ubuntu 20.04	Apr 13 2022
7b96a49f1c3e	frerot	[doc] using system imagemagick in RTD	Apr 13 2022
c3fd65b80bf5	frerot	[doc] added some documentation on how to use MPI	Apr 13 2022
9e8d3742735c	frerot	better render of scaling plot in doc	Apr 13 2022
6973f0ebe85c	frerot	added python3-h5py-mpi to Docker image	Apr 13 2022
4278fed63fde	frerot	installing imagemagick in ReadTheDocs	Apr 7 2022
95e0fd5ce8a9	frerot	Merge branch 'master' of gitlab.com:tamaas/tamaas	Apr 7 2022
f9607922e458	frerot	added python constructor for Model	Apr 7 2022
d66fc61e74f0	Lucas Frérot	defining return types for scatter and gather	Apr 6 2022
68395442fa89	frerot	fixed return policy for scatter and gather bindings	Apr 6 2022
c99a4cb9feb3	Lucas Frérot	Merge branch 'features/distribute' into 'master'	Apr 6 2022
f6c88495cce5	frerot	added tamaas.mpi.scatter and tamaas.mpi.gather	Apr 6 2022
3901c186d1d1	frerot	added tamaas.utils.publications to print relevant publications	Apr 5 2022
9a13073aadb7	frerot	fixing warnings in examples	Apr 5 2022
1ec57adb4a77	frerot	removed stray print in zenodo.py	Mar 22 2022
9a0b47c737c0	frerot	updated changelog with version 2.4.0	Mar 22 2022
071fecd8cb41	frerot	[ci] using debian stable image for zenodo step	Mar 22 2022
3967641eb149	frerot	[ci] added stage to draft new zenodo release	Mar 21 2022
3ac1070eb4fc	frerot	deleting old files in zenodo draft	Mar 21 2022
0d26241b3a23	frerot	added zenodo script to create new zenodo releases	Mar 21 2022
9c468c5ff329	frerot	can execute INFOS.py to get version	Mar 21 2022
67c3aba76431	frerot	setting strip_info=True by default	Mar 21 2022
932a5e9b9558	frerot	added a read_sequence method to read data frames	Mar 21 2022
d3bb19ec4c8d	frerot	prioritizing system packages instead of vendored dependencies	Mar 17 2022
e0d715877c62	frerot	uniformized behavior of PYBIND11_ROOT compared to *_ROOT variables	Mar 17 2022

Changes (230)
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				Path
	M			.clang-tidy
	M			.gitlab-ci.yml
	M			.readthedocs.yml
	A			.style.yapf
	M			CHANGELOG.md
	A			CITATION.cff
	M			Dockerfile
	M			INFOS.py
	M			README.md
	M			SConstruct
	M			doc/SConscript
	M			doc/doxygen/Doxyfile.in
	A			doc/icon.ico
	M			doc/sphinx/source/api_reference.rst
	M			doc/sphinx/source/conf.py
	M			doc/sphinx/source/contact.rst
	M			doc/sphinx/source/figures/complexity.svg
	M			doc/sphinx/source/index.rst
	M			doc/sphinx/source/model.rst
	A			doc/sphinx/source/mpi.rst
	M			doc/sphinx/source/overview.rst
	M			doc/sphinx/source/performance.rst
	M			doc/sphinx/source/quickstart.rst
	M			doc/sphinx/source/rough_surfaces.rst
	M			examples/adhesion.py
	M			examples/pipe_tools/contact
	M			examples/pipe_tools/plot
	M			examples/pipe_tools/surface
	M			examples/plasticity.py
	M			examples/rough_contact.py
	M			examples/saturated.py
	M			examples/statistics.py
	M			examples/stresses.py
	M			python/SConscript
	M			python/cast.hh
	M			python/numpy.hh
	M			python/setup.py.in
	M			python/tamaas/__init__.py.in
	M			python/tamaas/__main__.py
	M			python/tamaas/compute.py
	M			python/tamaas/dumpers/__init__.py
	M			python/tamaas/dumpers/_helper.py
	M			python/tamaas/nonlinear_solvers/__init__.py
	A			python/tamaas/utils.py
	M			python/tamaas_module.cpp
	M			python/wrap.hh
	M			python/wrap/compute.cpp
	M			python/wrap/core.cpp
	M			python/wrap/model.cpp
	M			python/wrap/model_extensions.hh
	M			python/wrap/mpi.cpp
	M			python/wrap/percolation.cpp
	M			python/wrap/solvers.cpp
	M			python/wrap/surface.cpp
	M			python/wrap/test_features.cpp
	M			site_scons/detect.py
	M			site_scons/site_init.py
	M			site_scons/site_tools/doxygen.py
	M			site_scons/site_tools/nvcc.py
	M			site_scons/site_tools/sphinx.py
	M			site_scons/site_tools/tamaas.py
	M			site_scons/version.py
	M			src/SConscript
	M			src/core/array.hh
	M			src/core/computes.cpp
	M			src/core/computes.hh
	M			src/core/cuda/cufft_engine.cpp
	M			src/core/cuda/cufft_engine.hh
	M			src/core/cuda/unified_allocator.hh
	M			src/core/fft_engine.cpp
	M			src/core/fft_engine.hh
	M			src/core/fftw/fftw_allocator.hh
	M			src/core/fftw/fftw_engine.cpp
	M			src/core/fftw/fftw_engine.hh
	M			src/core/fftw/interface.hh
	M			src/core/fftw/interface_impl.hh
	M			src/core/fftw/mpi/fftw_mpi_engine.cpp
	M			src/core/fftw/mpi/fftw_mpi_engine.hh
	M			src/core/fftw/mpi/interface.hh
	M			src/core/grid.cpp
	M			src/core/grid.hh
	M			src/core/grid_base.hh
	M			src/core/grid_hermitian.cpp
	M			src/core/grid_hermitian.hh
	M			src/core/grid_tmpl.hh
	M			src/core/grid_view.hh
	M			src/core/iterator.hh
	M			src/core/logger.cpp
	M			src/core/logger.hh
	M			src/core/loop.cpp
	M			src/core/loop.hh
	M			src/core/loops/apply.hh
	M			src/core/loops/loop_utils.hh
	M			src/core/mpi_interface.cpp
	M			src/core/mpi_interface.hh
	M			src/core/partitioner.hh
	M			src/core/ranges.hh
	M			src/core/static_types.hh
	M			src/core/statistics.cpp
	M			src/core/statistics.hh
	M			src/core/tamaas.cpp
	M			src/core/tamaas.hh
	M			src/model/adhesion_functional.cpp
	M			src/model/adhesion_functional.hh
	M			src/model/be_engine.cpp
	M			src/model/be_engine.hh
	M			src/model/boussinesq.cpp
	M			src/model/boussinesq.hh
	M			src/model/boussinesq_helper.hh
	M			src/model/elastic_functional.cpp
	M			src/model/elastic_functional.hh
	M			src/model/elasto_plastic/isotropic_hardening.cpp
	M			src/model/functional.hh
	M			src/model/hooke.cpp
	M			src/model/hooke.hh
	M			src/model/influence.hh
	M			src/model/integral_operator.cpp
	M			src/model/integral_operator.hh
	M			src/model/integration/accumulator.hh
	M			src/model/integration/element.cpp
	M			src/model/integration/element.hh
	M			src/model/integration/integrator.hh
	M			src/model/kelvin.cpp
	M			src/model/kelvin.hh
	M			src/model/kelvin_helper.hh
	M			src/model/materials/internal.hh
	M			src/model/materials/isotropic_hardening.cpp
	M			src/model/materials/isotropic_hardening.hh
	M			src/model/materials/material.hh
	M			src/model/meta_functional.cpp
	M			src/model/meta_functional.hh
	M			src/model/mindlin.cpp
	M			src/model/mindlin.hh
	M			src/model/model.cpp
	M			src/model/model.hh
	M			src/model/model_dumper.hh
	M			src/model/model_factory.cpp
	M			src/model/model_factory.hh
	M			src/model/model_template.cpp
	M			src/model/model_template.hh
	M			src/model/model_type.cpp
	M			src/model/model_type.hh
	M			src/model/residual.cpp
	M			src/model/residual.hh
	M			src/model/volume_potential.cpp
	M			src/model/volume_potential.hh
	M			src/model/westergaard.cpp
	M			src/model/westergaard.hh
	M			src/percolation/flood_fill.cpp
	M			src/percolation/flood_fill.hh
	M			src/solvers/beck_teboulle.cpp
	M			src/solvers/beck_teboulle.hh
	M			src/solvers/condat.cpp
	M			src/solvers/condat.hh
	M			src/solvers/contact_solver.cpp
	M			src/solvers/contact_solver.hh
	M			src/solvers/dfsane_solver.cpp
	M			src/solvers/dfsane_solver.hh
	M			src/solvers/ep_solver.cpp
	M			src/solvers/ep_solver.hh
	M			src/solvers/epic.cpp
	M			src/solvers/epic.hh
	M			src/solvers/kato.cpp
	M			src/solvers/kato.hh
	M			src/solvers/kato_saturated.cpp
	M			src/solvers/kato_saturated.hh
	M			src/solvers/polonsky_keer_rey.cpp
	M			src/solvers/polonsky_keer_rey.hh
	M			src/solvers/polonsky_keer_tan.cpp
	M			src/solvers/polonsky_keer_tan.hh
	M			src/surface/filter.hh
	M			src/surface/isopowerlaw.cpp
	M			src/surface/isopowerlaw.hh
	M			src/surface/regularized_powerlaw.cpp
	M			src/surface/regularized_powerlaw.hh
	M			src/surface/surface_generator.cpp
	M			src/surface/surface_generator.hh
	M			src/surface/surface_generator_filter.cpp
	M			src/surface/surface_generator_filter.hh
	M			src/surface/surface_generator_random_phase.cpp
	M			src/surface/surface_generator_random_phase.hh
	M			src/tamaas_info.hh
	M			tests/SConscript
	M			tests/ci/build_wheels.sh
	M			tests/ci/docker/debian.mpi
	M			tests/ci/docker/manylinux
	M			tests/ci/docker/ubuntu_lts.cuda
	A			tests/ci/zenodo.py
	M			tests/conftest.py
	M			tests/fftfreq.py
	M			tests/mpi_routines.py
	M			tests/tamaas_gtest_main.cc
	M			tests/test.hh
	M			tests/test_boussinesq_surface.py
	P			tests/test_copy.py Copied from tests/test_voigt.py
	M			tests/test_dumper.py
	M			tests/test_epic.py
	M			tests/test_fftfreq.cpp
	M			tests/test_fftw.cpp
	M			tests/test_flood_fill.py
	M			tests/test_grid.cpp
	M			tests/test_gtest.py
	M			tests/test_hertz.py
	M			tests/test_hertz_disp.py
	M			tests/test_hertz_kato.py
	M			tests/test_integral_operators.py
	M			tests/test_integration.cpp
	M			tests/test_loop.cpp
	M			tests/test_memory.py
	M			tests/test_model.cpp
	M			tests/test_mpi.cpp
	M			tests/test_mpi_routines.py
	M			tests/test_patch_westergaard.py
	P			tests/test_publications.py Copied from tests/test_voigt.py
	M			tests/test_rough_surface.cpp
	M			tests/test_saturated_pressure.py
	M			tests/test_static_types.cpp
	M			tests/test_surface.py
	M			tests/test_tangential.py
	P			tests/test_voigt.py Copied to multiple locations: tests/test_copy.py tests/test_publications.py
	M			tests/test_westergaard.py
	M			third-party/expolit/include/expolit/differentiation.hh
	M			third-party/expolit/include/expolit/expolit
	M			third-party/expolit/include/expolit/exponential.hh
	M			third-party/expolit/include/expolit/integration.hh
	M			third-party/expolit/include/expolit/litteral.hh
	M			third-party/expolit/include/expolit/operations.hh
	M			third-party/expolit/include/expolit/polynomial.hh
	M			third-party/expolit/include/expolit/types.hh
	M			third-party/expolit/tests/tests_gtest.cc