warning when setting generator seed < 1

[doc] typo in README

[doc] silencing all remaining breathe warnings

[doc] silencing sphinx warnings about duplicate targets for links

[doc] cleaned up API auto documentation

[doc] silencing a lot of breathe warnings

simplified member functions in nonlinear_solvers

added deep-copy functionality for Model objects

[doc] added documentation for utils module

updated with an example of load_path use

started work on declarative simulation definition

linting

[doc] docstrings in __main__.py

added a from_voigt compute function

added tamaas.utils which contains some QOL functions

updated email

updated copyright

correcting some type conversion warnings

corrections from clang-tidy

added -pthread flag to test linking

[doc] adding favicon

fixed issue with scons -c

regenerating tamaas_info.cpp on changes in version

ignoring modules in ~/.local in the Docker/Singularty container

[ci] skip wheels upload if they already exist

Updated CHANGELOG

Merge branch 'master' of gitlab.com:tamaas/tamaas

[ci] using the "latest" tag with master branch

added libopenmpi-dev as explicit dependency in Dockerfile

[ci] activating MPI for deployed docker images

[doc] added documentation for gitlab docker image

[ci] added generation of docker images in CI

gracefully fail 'plot' if matplotlib is missing

stripped useless dependencies in the docker image

cleaned up definition of docker image

more robust testing if field is a boundary field

distutils is deprecated

[doc] correct copyright string

[joss] added ref to plastic contact paper

[joss] drafted an initial paragraph

[ci] updated bear call for bullseye

python linting

corrected fragmentation example to use "cohesive contact" energy

added python bindings for energies list functions in SMM + Material

Merge branch 'master' into features/materials

Merge branch 'master' into features/netcdf-mpi

added a `--version` flag to the tamaas command

[doc] added documentation on getEnergy

[doc] added dissipated energy doc for relevant materials

[doc] added energy explaination for plastic materials

silenced override warnings on HeatTransferModel dump() overloads

fixing copyright year and homepage url

[doc] fixed documentation metadata

[doc] added material parameters description and updated some figures

Merge branch 'features/sphinx'

[doc] integrating sphinx user manual with cmake-built doc

[doc] using existing doxygen index for namespace akantu

[user manual] added feengine chapter with isoparametric elements

added sphinx doc

fixed warning [-Wempty-body] in Mesh::read

added parser for junit in harbormaster ci scripts

protected pybind tests if python interface is not activated

Merge branch 'master' of ssh://c4science.ch/diffusion/AKAPRIV/akantu-private

Fixed compile error in user guide

setting rpath for python extension

modernizing InternalField

default values for InternalField members

added physical names selector to python interface

added restore history to InternalField

removed import mpi4py from python module

added previous state restore on Material

Merge branch 'features/dofs-separation-rewrote' of ssh://c4science.

Merge branch 'features/dofs-separation-rewrote' of ssh://c4science.

fixed shell elements

assembling residual in structural model

more flexible ElementTypeMapArray initializers

Merge branch 'features/dofs-separation-rewrote' of ssh://c4science.

fixing broken structural tests because of shape derivatives change

modified structural shape derivatives pipeline for shell elements

made block argument constant

implemented dkt shape derivatives + precompute dkt test

Merge branch 'features/dofs-separation-rewrote' of ssh://c4science.

cleanup of embedded

added patch test for DKT18 element

added rotation matrices for DKT18 + tangent modulus

Merge branch 'features/embedded-rewrote' into features/dofs-separation-rewrote

fixed computation of embedded gradient

removing useless stress_embedded

removed overload of insert function for ElementTypeMap

passing tests without pre-stress + memory savings in directing cosines

made new embedded compile

running test w/o error, but stiffness is wrong

small cleanup

Merge branch 'features/dofs-separation-rewrote' of ssh://c4science.

added allocating functor for material reinforcement

removed for_each_element plural

making embedded compile + remove pollution of K symbol with CGAL

compiling test with -frounding-math activated

added interface BtD... for ShapeStructural. To be implemented

modified material thermal test for google test