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CHANGELOG.md
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			# Changelog

			All notable changes to this project will be documented in this file.

			The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) for final versions and [PEP440](https://www.python.org/dev/peps/pep-0440/) in case intermediate versions need to be released (e.g. development version `2.2.3.dev1` or release candidates `2.2.3rc1`), or individual commits are packaged.

			## Unrelease

			### Added

			- Added `tamaas.utils.publications` to print a list of publications relevant to
			the parts of Tamaas used in a script. Call at the end of a script for an
			exhaustive list.
			- Added `tamaas.mpi.gather` and `tamaas.mpi.scatter` to help handling of 2D data
			in MPI contexts.
			- Added `getBoundaryFields()/boundary_fields` function/property to `Model`.
			- Added constructor to `Model`, which is an alias to `ModelFactory.createModel`.
			- Added convenience `tamaas.dumpers._helper.netCDFtoParaview` function to
			convert model sequence to Paraview data file.
			- Added dump of surface fields as `FieldData` in VTK files
			- Added `scipy.sparse.linalg.LinearOperator` interface to `Westergaard`. A
			`LinearOperator` can be created by calling
			`scipy.sparse.linalg.aslinearoperator` on the operator object.

			## Changed

			- Filter for boundary fields in dumper should be smarter.
			- `read` functions in dumpers are now `@classmethod`
			- Changed sign of plastic correction in KatoSaturated solver to match the
			EPICSolver sign.
			- Plastic correction of KatoSaturated is registered in the model as
			"KatoSaturated::residual_displacement".
			- Changed to modern Python packaging (PEP517) with `setup.cfg` and
			`pyproject.toml`. A `setup.py` script is still provided for editable
			installations, see [gh#7953](https://github.com/pypa/pip/issues/7953). Once
			setuptools has stable support for
			[PEP621](https://peps.python.org/pep-0621/), `setup.cfg` will be merged into
			`pyproject.toml`. Note that source distributions that can be built with
			[`build`](https://pypi.org/project/build/) are not true source distributions,
			since they contain the compiled Python module of Tamaas.

			## Fixed

			- Fixed `tamaas.dumpers.NetCDFDumper` to dump in MPI context.

			## v2.4.0 -- 2022-03-22

			### Added

			- Added a `tamaas.utils` module.
			- Added `tamaas.utils.load_path` generator, which yields model objects for a
			sequence of applied loads.
			- Added `tamaas.utils.seeded_surfaces` generator, which yields surfaces for a
			sequence of random seeds.
			- Added `tamaas.utils.hertz_surface` which generates a parabolic (Hertzian)
			surface.
			- Added `tamaas.utils.log_context` context manager which locally sets the log
			level for Tamaas' logger.
			- Added `tamaas.compute.from_voigt` to convert Voigt/Mendel fields to dense
			tensor fields.
			- Added a deep-copy function to `ModelFactory` to copy `Model` objects. Use
			`model_copy = copy.deepcopy(model)` in Python to make a copy. Currently only
			copies registered fields, same as dumpers/readers.
			- Added a `read_sequence` method for dumpers to read model frames.
			- Automatic draft release on Zenodo.

			### Changed

			- `*_ROOT` variables for vendored dependencies GoogleTest and pybind11 now
			default to empty strings, so that the vendored trees in `third-party/` are not
			selected by default. This is so system packages are given priority. Vendored
			dependency submodules will eventually be deprecated.

			### Fixed

			- Fixed an issue with `scons -c` when GTest was missing.

			## v2.3.1 -- 2021-11-08

			### Added

			- Now using `clang-format`, `clang-tidy` and `flake8` for linting
			- Pre-built Tamaas images can be pulled with `docker pull
			registry.gitlab.com/tamaas/tamaas`
			- Added a `--version` flag to the `tamaas` command

			### Changed

			- The root `Dockerfile` now compiles Tamaas, so using Tamaas in Docker is easier.
			- The model attributes dumped to Numpy files are now written in a JSON-formatted
			string to avoid unsafe loading/unpickling of objects.
			- Removed the `build_doc` build option: now the doc targets are automatically
			added if the dependencies are met, and built if `scons doc` is called.
			- Removed the `use_googletest` build option: if tests are built and gtest is
			present, the corresponding tests will be built

			### Fixed

			- The command `tamaas plot` gracefully fails if Matplotlib is missing
			- Better heuristic to guess which fields are defined on boundary in dumpers
			(still not perfect and may give false negatives)

			## v2.3.0 -- 2021-06-15

			### Added

			- Added `read()` method to dumpers to create a model from a dump file
			- `getClusters()` can be called in MPI contact with partial contact maps
			- Added a JSON encoder class for models and a JSON dumper
			- CUDA compatibility is re-established, but has not been tested
			- Docstrings in the Python bindings for many classes/methods

			### Changed

			- Tamaas version numbers are now managed by
			[versioneer](https://github.com/python-versioneer/python-versioneer). This
			means that Git tags prefixed with `v` (e.g. `v2.2.3`) carry meaning and
			determine the version. When no tag is set, versioneer uses the last tag,
			specifies the commit short hash and the distance to the last tag (e.g.
			`2.2.2+33.ge314b0e`). This version string is used in the compiled library, the
			`setup.py` script and the `__version__` variable in the python module.
			- Tamaas migrated to [GitLab](https://gitlab.com/tamaas/tamaas)
			- Continuous delivery has been implemented:

			- the `master` branch will now automatically build and publish Python wheels
			to `https://gitlab.com/api/v4/projects/19913787/packages/pypi/simple`. These
			"nightly" builds can be installed with:

			pip install \
			--extra-index-url https://gitlab.com/api/v4/projects/19913787/packages/pypi/simple \
			tamaas

			- version tags pushed to `master` will automatically publish the wheels to
			[PyPI](https://pypi.org/project/tamaas/)

			### Deprecated

			- The `finalize()` function is now deprecated, since it is automatically called
			when the process terminates
			- Python versions 3.5 and below are not supported anymore

			### Fixed

			- Fixed a host of dump read/write issues when model type was not `volume_*d`.
			Dumper tests are now streamlined and systematic.
			- Fixed a bug where `Model::solveDirichlet` would not compute correctly
			- Fixed a bug where `Statistics::contact` would not normalize by the global
			number of surface points

			## v2.2.2 -- 2021-04-02

			### Added

			- Entry-point `tamaas` defines a grouped CLI for `examples/pipe_tools`. Try
			executing `tamaas surface -h` from the command-line!

			### Changed

			- `CXXFLAGS` are now passed to the linker
			- Added this changelog
			- Using absolute paths for environmental variables when running `scons test`
			- Reorganized documentation layout
			- Gave the build system a facelift (docs are now generated directly with SCons
			instead of a Makefile)

			### Deprecated

			- Python 2 support is discontinued. Version `v2.2.1` is the last PyPi build with
			a Python 2 wheel.
			- The scripts in `examples/pipe_tools` have been replaced by the `tamaas` command

			### Fixed

			- `UVWDumper` no longer imports `mpi4py` in sequential
			- Compiling with different Thrust/FFTW backends


			## v2.2.1 -- 2021-03-02

			### Added

			- Output registered fields and dumpers in `print(model)`
			- Added `operator[]` to the C++ model class (for fields)
			- Added `traction` and `displacement` properties to Python model bindings
			- Added `operators` property to Python model bindings, which provides a
			dict-like access to registered operators
			- Added `shape` and `spectrum` to properties to Python surface generator
			bindings
			- Surface generator constructor accepts surface global shape as argument
			- Choice of FFTW thread model

			### Changed

			- Tests use `/tmp` for temporary files
			- Updated dependency versions (Thrust, Pybind11)

			### Deprecated

			- Most `get___()` and `set___()` in Python bindings have been deprecated. They
			will generate a `DeprecationWarning`.

			### Removed

			- All legacy code


			## v2.2.0 -- 2020-12-31

			### Added

			- More accurate function for computation of contact area
			- Function to compute deviatoric of tensor fields
			- MPI implementation
			- Convenience `hdf5toVTK` function
			- Readonly properties `shape`, `global_shape`, `boundary_shape` on model to give
			shape information

			### Changed

			- Preprocessor defined macros are prefixed with `TAMAAS_`
			- Moved `tamaas.to_voigt` to `tamaas.compute.to_voigt`

			### Fixed

			- Warning about deprecated constructors with recent GCC versions
			- Wrong computation of grid strides
			- Wrong computation of grid sizes in views


			## v2.1.4 -- 2020-08-07

			### Added

			- Possibility to generate a static `libTamaas`
			- C++ implementation of DFSANE solver
			- Allowing compilation without OpenMP

			### Changed

			- NetCDF dumper writes frames to a single file

			### Fixed

			- Compatibility with SCons+Python 3

			## v2.1.3 -- 2020-07-27

			### Added

			- Version number to `TamaasInfo`

			### Changed

			- Prepending root directory when generating archive


			## v2.1.2 -- 2020-07-24

			This release changes some core internals related to discrete Fourier transforms
			for future MPI support.

			### Added

			- Caching `CXXFLAGS` in SCons build
			- SCons shortcut to create code archive
			- Test of the elastic-plastic contact solver
			- Paraview data dumper (`.pvd` files)
			- Compression for UVW dumper
			- `__contains__` and `__iter__` Python bindings of model
			- Warning message of possible overflow in Kelvin

			### Changed

			- Simplified `tamaas_info.cpp`, particularly the diff part
			- Using a new class `FFTEngine` to manage discrete Fourier transforms. Plans are
			re-used as much as possible with different data with the same shape. This is
			in view of future MPI developments
			- Redirecting I/O streams in solve functions so they can be used from Python
			(e.g. in Jupyter notebooks)
			- Calling `initialize()` and `finalize()` is no longer necessary

			### Fixed

			- Convergence issue with non-linear solvers
			- Memory error in volume potentials


			## v2.1.1 -- 2020-04-22

			### Added

			- SCons shortcut to run tests

			### Fixed

			- Correct `RPATH` for shared libraries
			- Issues with SCons commands introduced in v2.1.0
			- Tests with Python 2.7


			## v2.1.0 -- 2020-04-17

			### Added

			- SCons shortcuts to build/install Tamaas and its components
			- Selection of integration method for Kelvin operator
			- Compilation option to remove the legacy part of Tamaas
			- NetCDF dumper

			### Fixed

			- Link bug with clang
			- NaNs in Kato saturated solver

			## v2.0.0 -- 2019-11-11

			First public release. Contains relatively mature elastic-plastic contact code.

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